1N7F | pdb_00001n7f

Crystal structure of the sixth PDZ domain of GRIP1 in complex with liprin C-terminal peptide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1n7fb_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Glutamate receptor-interacting protein 1, GRIP1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1n7fa_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Glutamate receptor-interacting protein 1, GRIP1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PDZ domain-like	8036696	3000388	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PDZ domain-like	8036696	3000388	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PDZ_2	e1n7fB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: PDZ_2	ECOD (v294.1)
A	PDZ_2	e1n7fA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: PDZ_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	AMPA receptor interacting protein GRIP	protein binding binding signaling receptor binding PDZ domain binding protein domain specific binding ionotropic glutamate receptor binding glutamate receptor binding enzyme binding GTPase binding protein transporter activity transporter activity	cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor positive regulation of protein localization to plasma membrane regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor positive regulation of protein localization to plasma membrane regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process localization intracellular protein localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery regulation of biological process protein localization to cell periphery protein localization to plasma membrane biological regulation positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process regulation of protein localization to plasma membrane cellular response to stimulus response to ketone response to lipid response to alcohol response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to phorbol 13-acetate 12-myristate cellular response to alcohol response to chemical cellular response to phorbol 13-acetate 12-myristate cellular response to lipid cellular response to ketone transport establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development cerebral cortex development multicellular organism development central nervous system development anatomical structure development telencephalon development system development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process cellular developmental process regulation of neuron projection arborization cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis regulation of cell morphogenesis cellular component organization positive regulation of developmental process neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization cellular component organization or biogenesis regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization regulation of cell projection organization positive regulation of neuron projection arborization generation of neurons anatomical structure morphogenesis neuron projection arborization neuron development dendrite development dendrite arborization dendrite morphogenesis cell morphogenesis involved in neuron differentiation regulation of synaptic plasticity trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication regulation of synaptic scaling synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of biological quality cellular response to acid chemical cellular response to nitrogen compound cellular response to amino acid stimulus response to glycine response to nitrogen compound response to amino acid cellular response to glycine response to acid chemical negative regulation of signaling negative regulation of biological process negative regulation of synaptic transmission negative regulation of cell communication negative regulation of cellular process long-term synaptic depression positive regulation of cell communication long-term synaptic potentiation positive regulation of synaptic transmission positive regulation of signaling positive regulation of nervous system development regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of dendrite morphogenesis positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process regulation of neuron projection development regulation of nervous system development positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal process regulation of multicellular organismal development positive regulation of dendrite morphogenesis regulation of plasma membrane bounded cell projection organization establishment of protein localization protein localization to synapse neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to plasma membrane establishment of protein localization to postsynaptic membrane endocytic recycling neurotransmitter receptor transport to plasma membrane neurotransmitter receptor transport, endosome to plasma membrane intercellular transport establishment of localization in cell neurotransmitter receptor transport, endosome to postsynaptic membrane protein localization to postsynaptic membrane neurotransmitter receptor transport establishment of protein localization to membrane intracellular transport protein-containing complex localization endosomal transport vesicle-mediated transport to the plasma membrane endosome to plasma membrane protein transport regulation of postsynaptic membrane neurotransmitter receptor levels protein transport protein localization to postsynapse protein localization to cell junction receptor localization to synapse intracellular protein transport regulation of postsynaptic membrane potential system process positive regulation of signal transduction regulation of system process positive regulation of excitatory postsynaptic potential regulation of signal transduction chemical synaptic transmission, postsynaptic positive regulation of response to stimulus modulation of excitatory postsynaptic potential signal transduction mini excitatory postsynaptic potential cell surface receptor signaling pathway nervous system process regulation of nervous system process regulation of mini excitatory postsynaptic potential positive regulation of mini excitatory postsynaptic potential regulation of response to stimulus excitatory postsynaptic potential regulation of membrane potential	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane somatodendritic compartment cell body perikaryon neuronal cell body cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane somatodendritic compartment cell body perikaryon neuronal cell body presynapse presynaptic active zone cell projection proximal dendrite dendrite dendritic tree neuron projection plasma membrane bounded cell projection presynaptic membrane synaptic cleft extracellular region protein-containing complex cell cortex intracellular anatomical structure exocyst cytoplasm vesicle tethering complex glutamatergic synapse membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle recycling endosome endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle spine synapse neuron to neuron synapse asymmetric synapse dendritic shaft neuron spine dendritic spine perinuclear region of cytoplasm dendritic spine neck polymeric cytoskeletal fiber intracellular membraneless organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton axon axon terminus distal axon terminal bouton neuron projection terminus dendritic spine head membrane microdomain membrane raft GABA-ergic synapse organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane excitatory synapse postsynaptic density postsynaptic specialization
C, D	8-mer peptide from interacting protein (liprin)	-	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process regulation of postsynaptic membrane neurotransmitter receptor levels biological regulation regulation of biological quality regulation of localization cellular localization regulation of cellular process regulation of protein localization negative regulation of biological process negative regulation of protein localization to plasma membrane localization cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process regulation of postsynaptic membrane neurotransmitter receptor levels biological regulation regulation of biological quality regulation of localization cellular localization regulation of cellular process regulation of protein localization negative regulation of biological process negative regulation of protein localization to plasma membrane localization negative regulation of cellular process intracellular protein localization regulation of protein localization to membrane negative regulation of protein localization regulation of biological process protein localization to cell periphery protein localization to plasma membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane negative regulation of protein localization to membrane regulation of cellular localization macromolecule localization negative regulation of protein localization to cell periphery regulation of protein localization to plasma membrane cortical cytoskeleton organization microtubule cytoskeleton organization cytoplasmic microtubule organization cortical microtubule organization cellular component organization organelle organization microtubule-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process regulation of actin filament bundle assembly cellular component biogenesis cellular component assembly actin filament bundle organization actin filament-based process stress fiber assembly negative regulation of supramolecular fiber organization regulation of actin filament organization negative regulation of stress fiber assembly actin cytoskeleton organization actomyosin structure organization negative regulation of cellular component organization negative regulation of cytoskeleton organization actin filament organization regulation of cellular component biogenesis negative regulation of actin filament bundle assembly regulation of organelle organization regulation of stress fiber assembly negative regulation of organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization cell junction organization synapse organization cellular response to stimulus response to stimulus signaling signal transduction cell communication	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction presynapse synapse presynaptic active zone cell periphery cell cortex intracellular anatomical structure cytoplasm cytosol Schaffer collateral - CA1 synapse cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction presynapse synapse presynaptic active zone cell periphery cell cortex intracellular anatomical structure cytoplasm cytosol Schaffer collateral - CA1 synapse axon cell projection neuron projection plasma membrane bounded cell projection membrane-bounded organelle neuron spine endomembrane system dendritic spine somatodendritic compartment postsynapse spine apparatus organelle dendrite dendritic tree protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR043545	Glutamate receptor-interacting protein 1/2	Family
A, B	IPR041489	PDZ domain 6	Domain
A, B	IPR036034	PDZ superfamily	Homologous Superfamily
A, B	IPR001478	PDZ domain	Domain
C, D	IPR057892	Liprin-alpha, CC2 domain	Domain
C, D	IPR037620	Liprin-alpha, SAM domain 1	Domain
C, D	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
C, D	IPR029515	Liprin	Family
C, D	IPR037622	Liprin-alpha, SAM domain 3	Domain
C, D	IPR001660	Sterile alpha motif domain	Domain
C, D	IPR037621	Liprin-alpha, SAM domain 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q13136	rheumatoid arthritis astrocytic tumor gastric carcinoma large cell medulloblastoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer tuberculosis dermatomyositis Gaucher disease lung cancer non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis astrocytic tumor gastric carcinoma large cell medulloblastoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer tuberculosis dermatomyositis Gaucher disease lung cancer non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis exocrine pancreatic carcinoma glioblastoma malignant ependymoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Pick disease

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.