6L93 | pdb_00006l93

X-ray structure of the ligand-free human TRPV1 ankyrin repeat domain

PDB DOI: https://doi.org/10.2210/pdb6L93/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-08 Released: 2020-03-18
Deposition Author(s): Tanaka, M., Hayakawa, K., Unno, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.47 Å
R-Value Free:
0.270 (Depositor), 0.272 (DCC)
R-Value Work:
0.220 (Depositor), 0.225 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure determination of the human TRPV1 ankyrin-repeat domain under nonreducing conditions.

Tanaka, M., Hayakawa, K., Ogawa, N., Kurokawa, T., Kitanishi, K., Ite, K., Matsui, T., Mori, Y., Unno, M.

(2020) Acta Crystallogr F Struct Biol Commun 76: 130-137

PubMed: 32133998 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X20001533
Primary Citation Related Structures:
6L93

PubMed Abstract:
TRPV1, a member of the transient receptor potential (TRP) channels family, has been found to be involved in redox sensing. The crystal structure of the human TRPV1 ankyrin-repeat domain (TRPV1-ARD) was determined at 4.5 Å resolution under nonreducing conditions. This is the first report of the crystal structure of a ligand-free form of TRPV1-ARD and in particular of the human homologue. The structure showed a unique conformation in finger loop 3 near Cys258, which is most likely to be involved in inter-subunit disulfide-bond formation. Also, in human TRPV1-ARD it was possible for solvent to access Cys258. This structural feature might be related to the high sensitivity of human TRPV1 to oxidants. ESI-MS revealed that Cys258 did not form an S-OH functionality even under nonreducing conditions.

Organizational Affiliation

Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan.

Macromolecule Content

Total Structure Weight: 185 kDa
Atom Count: 11,813
Modeled Residue Count: 1,518
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 1	A, B, C, D, E A, B, C, D, E, F	280	Homo sapiens	Mutation(s): 0 Gene Names: TRPV1, VR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NER1 (Homo sapiens) Explore Q8NER1 Go to UniProtKB: Q8NER1
PHAROS: Q8NER1 GTEx: ENSG00000196689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NER1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.47 Å
R-Value Free: 0.270 (Depositor), 0.272 (DCC)
R-Value Work: 0.220 (Depositor), 0.225 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.228	α = 90
b = 167.414	β = 108.375
c = 112.632	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.