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
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

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(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

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 CC [auth I] 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 FB [auth F] SDF format, chain FC [auth I] SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain HA [auth C] 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 LB [auth F] SDF format, chain LC [auth J] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] 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 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 YA [auth E] SDF format, chain Z [auth B] SDF format, chain IC [auth I] SDF format, chain UA [auth D] MOL2 format, chain BB [auth F] MOL2 format, chain BC [auth I] MOL2 format, chain CA [auth B] MOL2 format, chain CC [auth I] 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 FB [auth F] MOL2 format, chain FC [auth I] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain HA [auth C] 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 LB [auth F] MOL2 format, chain LC [auth J] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] 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 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 YA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain IC [auth I] MOL2 format, chain UA [auth D]	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 ZA [auth E] SDF format, chain ZB [auth H] SDF format, chain YB [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 ZA [auth E] MOL2 format, chain ZB [auth H] MOL2 format, chain YB [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]	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]