6WM4

Human V-ATPase in state 3 with SidK and ADP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.

Wang, L.Wu, D.Robinson, C.V.Wu, H.Fu, T.M.

(2020) Mol Cell 80: 501

  • DOI: https://doi.org/10.1016/j.molcel.2020.09.029
  • Primary Citation of Related Structures:  
    6WLW, 6WLZ, 6WM2, 6WM3, 6WM4

  • PubMed Abstract: 

    Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V 1 complex for ATP hydrolysis and a membrane-embedded V o complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the V o complex. We define ATP6AP1 as a structural hub for V o complex assembly because it connects to multiple V o subunits and phospholipids in the c-ring. The glycolipids and the glycosylated V o subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA. Electronic address: wang@hkl.hms.harvard.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a isoform 1A [auth R]837Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q93050 (Homo sapiens)
Explore Q93050 
Go to UniProtKB:  Q93050
PHAROS:  Q93050
GTEx:  ENSG00000033627 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93050
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q93050-2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C 1B [auth O]382Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21283 (Homo sapiens)
Explore P21283 
Go to UniProtKB:  P21283
PHAROS:  P21283
GTEx:  ENSG00000155097 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21283
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1C [auth J],
E [auth I],
G [auth H]
226Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P36543 (Homo sapiens)
Explore P36543 
Go to UniProtKB:  P36543
PHAROS:  P36543
GTEx:  ENSG00000131100 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36543
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit G 1D [auth M],
F [auth L],
H [auth K]
118Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O75348 (Homo sapiens)
Explore O75348 
Go to UniProtKB:  O75348
PHAROS:  O75348
GTEx:  ENSG00000136888 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75348
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 1I [auth S]81Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O15342 (Homo sapiens)
Explore O15342 
Go to UniProtKB:  O15342
PHAROS:  O15342
GTEx:  ENSG00000113732 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15342
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease kappaJ [auth T]137Homo sapiensMutation(s): 0 
EC: 3.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P5S7 (Homo sapiens)
Explore Q6P5S7 
Go to UniProtKB:  Q6P5S7
GTEx:  ENSG00000219200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P5S7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase catalytic subunit AK [auth B],
L [auth C],
M [auth A]
617Homo sapiensMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P38606 (Homo sapiens)
Explore P38606 
Go to UniProtKB:  P38606
PHAROS:  P38606
GTEx:  ENSG00000114573 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38606
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit B, brain isoformN [auth E],
O [auth F],
P [auth D]
511Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21281 (Homo sapiens)
Explore P21281 
Go to UniProtKB:  P21281
PHAROS:  P21281
GTEx:  ENSG00000147416 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21281
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
SidKQ [auth Y],
R [auth Z],
S [auth X]
573Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZWW6 
Go to UniProtKB:  Q5ZWW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZWW6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit DT [auth G]247Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5K8 (Homo sapiens)
Explore Q9Y5K8 
Go to UniProtKB:  Q9Y5K8
PHAROS:  Q9Y5K8
GTEx:  ENSG00000100554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5K8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit FU [auth N]119Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16864 (Homo sapiens)
Explore Q16864 
Go to UniProtKB:  Q16864
PHAROS:  Q16864
GTEx:  ENSG00000128524 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16864
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1V [auth U]470Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15904 (Homo sapiens)
Explore Q15904 
Go to UniProtKB:  Q15904
PHAROS:  Q15904
GTEx:  ENSG00000071553 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15904
Glycosylation
Glycosylation Sites: 6Go to GlyGen: Q15904-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Renin receptorW [auth V]350Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O75787 (Homo sapiens)
Explore O75787 
Go to UniProtKB:  O75787
PHAROS:  O75787
GTEx:  ENSG00000182220 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75787
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 21 kDa proteolipid subunitX [auth 0]205Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99437 (Homo sapiens)
Explore Q99437 
Go to UniProtKB:  Q99437
PHAROS:  Q99437
GTEx:  ENSG00000117410 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99437
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunit155Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P27449 (Homo sapiens)
Explore P27449 
Go to UniProtKB:  P27449
GTEx:  ENSG00000185883 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27449
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit d 1HA [auth Q]351Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P61421 (Homo sapiens)
Explore P61421 
Go to UniProtKB:  P61421
PHAROS:  P61421
GTEx:  ENSG00000159720 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61421
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit HIA [auth P]483Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI12 (Homo sapiens)
Explore Q9UI12 
Go to UniProtKB:  Q9UI12
PHAROS:  Q9UI12
GTEx:  ENSG00000047249 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI12
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
LA [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
JA [auth R]
KA [auth R]
MA [auth U]
NA [auth U]
OA [auth U]
JA [auth R],
KA [auth R],
MA [auth U],
NA [auth U],
OA [auth U],
PA [auth U],
QA [auth U],
RA [auth U]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary