2BL2

The membrane rotor of the V-type ATPase from Enterococcus hirae

PDB DOI: https://doi.org/10.2210/pdb2BL2/pdb

Classification: HYDROLASE
Organism(s): Enterococcus hirae
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2005-02-25 Released: 2005-04-05
Deposition Author(s): Murata, T., Yamato, I., Kakinuma, Y., Leslie, A.G.W., Walker, J.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.200 (Depositor)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of the Rotor of the Vacuolar-Type Na- ATPase from Enterococcus Hirae

Murata, T., Yamato, I., Kakinuma, Y., Leslie, A.G.W., Walker, J.E.

(2005) Science 308: 654

PubMed: 15802565 Search on PubMed
DOI: https://doi.org/10.1126/science.1110064
Primary Citation of Related Structures:
2BL2

PubMed Abstract:
The membrane rotor ring from the vacuolar-type (V-type) sodium ion-pumping adenosine triphosphatase (Na+-ATPase) from Enterococcus hirae consists of 10 NtpK subunits, which are homologs of the 16-kilodalton and 8-kilodalton proteolipids found in other V-ATPases and in F1Fo- or F-ATPases, respectively. Each NtpK subunit has four transmembrane alpha helices, with a sodium ion bound between helices 2 and 4 at a site buried deeply in the membrane that includes the essential residue glutamate-139. This site is probably connected to the membrane surface by two half-channels in subunit NtpI, against which the ring rotates. Symmetry mismatch between the rotor and catalytic domains appears to be an intrinsic feature of both V- and F-ATPases.

Organizational Affiliation

Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK.

Macromolecule Content

Total Structure Weight: 207.74 kDa
Atom Count: 13,367
Modelled Residue Count: 1,560
Deposited Residue Count: 1,560
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-TYPE SODIUM ATP SYNTHASE SUBUNIT K	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	156	Enterococcus hirae	Mutation(s): 0 EC: 3.6.3.14 Membrane Entity: Yes
UniProt
Find proteins for P43457 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore P43457 Go to UniProtKB: P43457
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43457
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LHG Query on LHG Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain BC [auth I] SDF format, chain CA [auth B] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain DC [auth I] SDF format, chain EB [auth F] SDF format, chain EC [auth I] SDF format, chain FA [auth C] SDF format, chain FC [auth I] SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain IC [auth I] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain KB [auth F] SDF format, chain KC [auth J] SDF format, chain LC [auth J] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NB [auth G] SDF format, chain O [auth A] SDF format, chain OB [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain QB [auth G] SDF format, chain RA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain TB [auth H] SDF format, chain U [auth A] SDF format, chain UA [auth D] SDF format, chain UB [auth H] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain WB [auth H] SDF format, chain X [auth B] SDF format, chain XB [auth H] SDF format, chain Y [auth B] SDF format, chain CC [auth I] SDF format, chain FB [auth F] SDF format, chain HA [auth C] SDF format, chain LB [auth F] SDF format, chain N [auth A] SDF format, chain YA [auth E] SDF format, chain Z [auth B] MOL2 format, chain BB [auth F] MOL2 format, chain BC [auth I] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain DC [auth I] MOL2 format, chain EB [auth F] MOL2 format, chain EC [auth I] MOL2 format, chain FA [auth C] MOL2 format, chain FC [auth I] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain IC [auth I] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain KC [auth J] MOL2 format, chain LC [auth J] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NB [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain QB [auth G] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth H] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain UB [auth H] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain WB [auth H] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain CC [auth I] MOL2 format, chain FB [auth F] MOL2 format, chain HA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B] mmCIF format, chain BB [auth F] mmCIF format, chain BC [auth I] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain DC [auth I] mmCIF format, chain EB [auth F] mmCIF format, chain EC [auth I] mmCIF format, chain FA [auth C] mmCIF format, chain FC [auth I] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth F] mmCIF format, chain IC [auth I] mmCIF format, chain JB [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth F] mmCIF format, chain KC [auth J] mmCIF format, chain LC [auth J] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NB [auth G] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth G] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain QB [auth G] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain TB [auth H] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain UB [auth H] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain WB [auth H] mmCIF format, chain X [auth B] mmCIF format, chain XB [auth H] mmCIF format, chain Y [auth B] mmCIF format, chain CC [auth I] mmCIF format, chain FB [auth F] mmCIF format, chain HA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain N [auth A] mmCIF format, chain YA [auth E] mmCIF format, chain Z [auth B]	BB [auth F] BC [auth I] CA [auth B] CC [auth I] DA [auth C] BB [auth F], BC [auth I], CA [auth B], CC [auth I], DA [auth C], DB [auth F], DC [auth I], EB [auth F], EC [auth I], FA [auth C], FB [auth F], FC [auth I], GA [auth C], GB [auth F], HA [auth C], IC [auth I], JB [auth F], K [auth A], KA [auth C], KB [auth F], KC [auth J], LB [auth F], LC [auth J], M [auth A], MA [auth D], N [auth A], NB [auth G], O [auth A], OB [auth G], P [auth A], PA [auth D], QA [auth D], QB [auth G], RA [auth D], S [auth A], T [auth A], TA [auth D], TB [auth H], U [auth A], UA [auth D], UB [auth H], VA [auth D], W [auth B], WA [auth D], WB [auth H], X [auth B], XB [auth H], Y [auth B], YA [auth E], Z [auth B]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain BB [auth F] Focus chain BC [auth I] Focus chain CA [auth B] Focus chain CC [auth I] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain DC [auth I] Focus chain EB [auth F] Focus chain EC [auth I] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain FC [auth I] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain IC [auth I] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain KC [auth J] Focus chain LB [auth F] Focus chain LC [auth J] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain QB [auth G] Focus chain RA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth D] Focus chain TB [auth H] Focus chain U [auth A] Focus chain UA [auth D] Focus chain UB [auth H] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain WB [auth H] Focus chain X [auth B] Focus chain XB [auth H] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain BB [auth F] Focus chain BC [auth I] Focus chain CA [auth B] Focus chain CC [auth I] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain DC [auth I] Focus chain EB [auth F] Focus chain EC [auth I] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain FC [auth I] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain IC [auth I] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain KC [auth J] Focus chain LB [auth F] Focus chain LC [auth J] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain QB [auth G] Focus chain RA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth D] Focus chain TB [auth H] Focus chain U [auth A] Focus chain UA [auth D] Focus chain UB [auth H] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain WB [auth H] Focus chain X [auth B] Focus chain XB [auth H] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B]
UMQ Query on UMQ Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth E] SDF format, chain BA [auth B] SDF format, chain GC [auth I] SDF format, chain HB [auth F] SDF format, chain HC [auth I] SDF format, chain IA [auth C] SDF format, chain IB [auth F] SDF format, chain JA [auth C] SDF format, chain LA [auth C] SDF format, chain MB [auth F] SDF format, chain MC [auth J] SDF format, chain NA [auth D] SDF format, chain NC [auth J] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RB [auth G] SDF format, chain SA [auth D] SDF format, chain SB [auth G] SDF format, chain YB [auth H] SDF format, chain ZA [auth E] SDF format, chain ZB [auth H] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain GC [auth I] MOL2 format, chain HB [auth F] MOL2 format, chain HC [auth I] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MB [auth F] MOL2 format, chain MC [auth J] MOL2 format, chain NA [auth D] MOL2 format, chain NC [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth G] MOL2 format, chain SA [auth D] MOL2 format, chain SB [auth G] MOL2 format, chain YB [auth H] MOL2 format, chain ZA [auth E] MOL2 format, chain ZB [auth H] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain GC [auth I] mmCIF format, chain HB [auth F] mmCIF format, chain HC [auth I] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth F] mmCIF format, chain JA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MB [auth F] mmCIF format, chain MC [auth J] mmCIF format, chain NA [auth D] mmCIF format, chain NC [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth G] mmCIF format, chain SA [auth D] mmCIF format, chain SB [auth G] mmCIF format, chain YB [auth H] mmCIF format, chain ZA [auth E] mmCIF format, chain ZB [auth H]	AA [auth B] AB [auth E] BA [auth B] GC [auth I] HB [auth F] AA [auth B], AB [auth E], BA [auth B], GC [auth I], HB [auth F], HC [auth I], IA [auth C], IB [auth F], JA [auth C], LA [auth C], MB [auth F], MC [auth J], NA [auth D], NC [auth J], Q [auth A], R [auth A], RB [auth G], SA [auth D], SB [auth G], YB [auth H], ZA [auth E], ZB [auth H]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BA [auth B] Focus chain GC [auth I] Focus chain HB [auth F] Focus chain HC [auth I] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain JA [auth C] Focus chain LA [auth C] Focus chain MB [auth F] Focus chain MC [auth J] Focus chain NA [auth D] Focus chain NC [auth J] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RB [auth G] Focus chain SA [auth D] Focus chain SB [auth G] Focus chain YB [auth H] Focus chain ZA [auth E] Focus chain ZB [auth H] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BA [auth B] Focus chain GC [auth I] Focus chain HB [auth F] Focus chain HC [auth I] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain JA [auth C] Focus chain LA [auth C] Focus chain MB [auth F] Focus chain MC [auth J] Focus chain NA [auth D] Focus chain NC [auth J] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RB [auth G] Focus chain SA [auth D] Focus chain SB [auth G] Focus chain YB [auth H] Focus chain ZA [auth E] Focus chain ZB [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AC [auth I] SDF format, chain CB [auth F] SDF format, chain EA [auth C] SDF format, chain JC [auth J] SDF format, chain L [auth A] SDF format, chain OA [auth D] SDF format, chain PB [auth G] SDF format, chain V [auth B] SDF format, chain VB [auth H] SDF format, chain XA [auth E] MOL2 format, chain AC [auth I] MOL2 format, chain CB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain JC [auth J] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PB [auth G] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth H] MOL2 format, chain XA [auth E] mmCIF format, chain AC [auth I] mmCIF format, chain CB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain JC [auth J] mmCIF format, chain L [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain PB [auth G] mmCIF format, chain V [auth B] mmCIF format, chain VB [auth H] mmCIF format, chain XA [auth E]	AC [auth I] CB [auth F] EA [auth C] JC [auth J] L [auth A] AC [auth I], CB [auth F], EA [auth C], JC [auth J], L [auth A], OA [auth D], PB [auth G], V [auth B], VB [auth H], XA [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AC [auth I] Focus chain CB [auth F] Focus chain EA [auth C] Focus chain JC [auth J] Focus chain L [auth A] Focus chain OA [auth D] Focus chain PB [auth G] Focus chain V [auth B] Focus chain VB [auth H] Focus chain XA [auth E] Interactions & Density Focus chain AC [auth I] Focus chain CB [auth F] Focus chain EA [auth C] Focus chain JC [auth J] Focus chain L [auth A] Focus chain OA [auth D] Focus chain PB [auth G] Focus chain V [auth B] Focus chain VB [auth H] Focus chain XA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.200 (Depositor)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.136	α = 90
b = 125.604	β = 90
c = 210.866	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
SHELXD	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-04-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-04-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other