1YCE | pdb_00001yce

Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus

PDB DOI: https://doi.org/10.2210/pdb1YCE/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Ilyobacter tartaricus
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2004-12-22 Released: 2005-04-12
Deposition Author(s): Meier, T., Polzer, P., Diederichs, K., Welte, W., Dimroth, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the rotor ring of F-Type Na+-ATPase from Ilyobacter tartaricus.

Meier, T., Polzer, P., Diederichs, K., Welte, W., Dimroth, P.

(2005) Science 308: 659-662

PubMed: 15860619 Search on PubMed
DOI: https://doi.org/10.1126/science.1111199
Primary Citation of Related Structures:
1YCE

PubMed Abstract:
In the crystal structure of the membrane-embedded rotor ring of the sodium ion-translocating adenosine 5'-triphosphate (ATP) synthase of Ilyobacter tartaricus at 2.4 angstrom resolution, 11 c subunits are assembled into an hourglass-shaped cylinder with 11-fold symmetry. Sodium ions are bound in a locked conformation close to the outer surface of the cylinder near the middle of the membrane. The structure supports an ion-translocation mechanism in the intact ATP synthase in which the binding site converts from the locked conformation into one that opens toward subunit a as the rotor ring moves through the subunit a/c interface.

Organizational Affiliation

Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH), Zürich Hönggerberg, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 394.53 kDa
Atom Count: 28,101
Modelled Residue Count: 3,916
Deposited Residue Count: 3,916
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
subunit c	A AA [auth e] B BA [auth f] C A, AA [auth e], B, BA [auth f], C, CA [auth g], D, DA [auth h], E, EA [auth i], F, FA [auth j], G, GA [auth k], H, HA [auth l], I, IA [auth m], J, JA [auth n], K, KA [auth o], L, LA [auth p], M, MA [auth q], N, NA [auth r], O, OA [auth s], P, PA [auth t], Q, QA [auth u], R, RA [auth v], S, T, U, V, W [auth a], X [auth b], Y [auth c], Z [auth d]	89	Ilyobacter tartaricus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8KRV3 (Ilyobacter tartaricus) Explore Q8KRV3 Go to UniProtKB: Q8KRV3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KRV3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F09 Query on F09 Download Ideal Coordinates CCD File SDF format, chain BB [auth E] SDF format, chain BD [auth i] SDF format, chain FC [auth T] SDF format, chain HD [auth l] SDF format, chain JB [auth I] SDF format, chain JD [auth m] SDF format, chain LB [auth J] SDF format, chain LC [auth a] SDF format, chain LD [auth n] SDF format, chain NB [auth K] SDF format, chain NC [auth b] SDF format, chain ND [auth o] SDF format, chain PC [auth c] SDF format, chain RC [auth d] SDF format, chain TC [auth e] SDF format, chain TD [auth r] SDF format, chain VA [auth B] SDF format, chain VB [auth O] SDF format, chain VC [auth f] SDF format, chain VD [auth s] SDF format, chain XD [auth t] SDF format, chain ZA [auth D] SDF format, chain ZB [auth Q] SDF format, chain ZC [auth h] SDF format, chain ZD [auth u] SDF format, chain BC [auth R] SDF format, chain BE [auth v] SDF format, chain DB [auth F] SDF format, chain DC [auth S] SDF format, chain DD [auth j] SDF format, chain FB [auth G] SDF format, chain FD [auth k] SDF format, chain HB [auth H] SDF format, chain HC [auth U] SDF format, chain JC [auth V] SDF format, chain PB [auth L] SDF format, chain PD [auth p] SDF format, chain RB [auth M] SDF format, chain RD [auth q] SDF format, chain TA [auth A] SDF format, chain TB [auth N] SDF format, chain XA [auth C] SDF format, chain XB [auth P] SDF format, chain XC [auth g] MOL2 format, chain BB [auth E] MOL2 format, chain BD [auth i] MOL2 format, chain FC [auth T] MOL2 format, chain HD [auth l] MOL2 format, chain JB [auth I] MOL2 format, chain JD [auth m] MOL2 format, chain LB [auth J] MOL2 format, chain LC [auth a] MOL2 format, chain LD [auth n] MOL2 format, chain NB [auth K] MOL2 format, chain NC [auth b] MOL2 format, chain ND [auth o] MOL2 format, chain PC [auth c] MOL2 format, chain RC [auth d] MOL2 format, chain TC [auth e] MOL2 format, chain TD [auth r] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth O] MOL2 format, chain VC [auth f] MOL2 format, chain VD [auth s] MOL2 format, chain XD [auth t] MOL2 format, chain ZA [auth D] MOL2 format, chain ZB [auth Q] MOL2 format, chain ZC [auth h] MOL2 format, chain ZD [auth u] MOL2 format, chain BC [auth R] MOL2 format, chain BE [auth v] MOL2 format, chain DB [auth F] MOL2 format, chain DC [auth S] MOL2 format, chain DD [auth j] MOL2 format, chain FB [auth G] MOL2 format, chain FD [auth k] MOL2 format, chain HB [auth H] MOL2 format, chain HC [auth U] MOL2 format, chain JC [auth V] MOL2 format, chain PB [auth L] MOL2 format, chain PD [auth p] MOL2 format, chain RB [auth M] MOL2 format, chain RD [auth q] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth N] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth P] MOL2 format, chain XC [auth g] mmCIF format, chain BB [auth E] mmCIF format, chain BD [auth i] mmCIF format, chain FC [auth T] mmCIF format, chain HD [auth l] mmCIF format, chain JB [auth I] mmCIF format, chain JD [auth m] mmCIF format, chain LB [auth J] mmCIF format, chain LC [auth a] mmCIF format, chain LD [auth n] mmCIF format, chain NB [auth K] mmCIF format, chain NC [auth b] mmCIF format, chain ND [auth o] mmCIF format, chain PC [auth c] mmCIF format, chain RC [auth d] mmCIF format, chain TC [auth e] mmCIF format, chain TD [auth r] mmCIF format, chain VA [auth B] mmCIF format, chain VB [auth O] mmCIF format, chain VC [auth f] mmCIF format, chain VD [auth s] mmCIF format, chain XD [auth t] mmCIF format, chain ZA [auth D] mmCIF format, chain ZB [auth Q] mmCIF format, chain ZC [auth h] mmCIF format, chain ZD [auth u] mmCIF format, chain BC [auth R] mmCIF format, chain BE [auth v] mmCIF format, chain DB [auth F] mmCIF format, chain DC [auth S] mmCIF format, chain DD [auth j] mmCIF format, chain FB [auth G] mmCIF format, chain FD [auth k] mmCIF format, chain HB [auth H] mmCIF format, chain HC [auth U] mmCIF format, chain JC [auth V] mmCIF format, chain PB [auth L] mmCIF format, chain PD [auth p] mmCIF format, chain RB [auth M] mmCIF format, chain RD [auth q] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth N] mmCIF format, chain XA [auth C] mmCIF format, chain XB [auth P] mmCIF format, chain XC [auth g]	BB [auth E] BC [auth R] BD [auth i] BE [auth v] DB [auth F] BB [auth E], BC [auth R], BD [auth i], BE [auth v], DB [auth F], DC [auth S], DD [auth j], FB [auth G], FC [auth T], FD [auth k], HB [auth H], HC [auth U], HD [auth l], JB [auth I], JC [auth V], JD [auth m], LB [auth J], LC [auth a], LD [auth n], NB [auth K], NC [auth b], ND [auth o], PB [auth L], PC [auth c], PD [auth p], RB [auth M], RC [auth d], RD [auth q], TA [auth A], TB [auth N], TC [auth e], TD [auth r], VA [auth B], VB [auth O], VC [auth f], VD [auth s], XA [auth C], XB [auth P], XC [auth g], XD [auth t], ZA [auth D], ZB [auth Q], ZC [auth h], ZD [auth u]	NONAN-1-OL C₉ H₂₀ O ZWRUINPWMLAQRD-UHFFFAOYSA-N		Interactions Focus chain BB [auth E] Focus chain BC [auth R] Focus chain BD [auth i] Focus chain BE [auth v] Focus chain DB [auth F] Focus chain DC [auth S] Focus chain DD [auth j] Focus chain FB [auth G] Focus chain FC [auth T] Focus chain FD [auth k] Focus chain HB [auth H] Focus chain HC [auth U] Focus chain HD [auth l] Focus chain JB [auth I] Focus chain JC [auth V] Focus chain JD [auth m] Focus chain LB [auth J] Focus chain LC [auth a] Focus chain LD [auth n] Focus chain NB [auth K] Focus chain NC [auth b] Focus chain ND [auth o] Focus chain PB [auth L] Focus chain PC [auth c] Focus chain PD [auth p] Focus chain RB [auth M] Focus chain RC [auth d] Focus chain RD [auth q] Focus chain TA [auth A] Focus chain TB [auth N] Focus chain TC [auth e] Focus chain TD [auth r] Focus chain VA [auth B] Focus chain VB [auth O] Focus chain VC [auth f] Focus chain VD [auth s] Focus chain XA [auth C] Focus chain XB [auth P] Focus chain XC [auth g] Focus chain XD [auth t] Focus chain ZA [auth D] Focus chain ZB [auth Q] Focus chain ZC [auth h] Focus chain ZD [auth u] Interactions & Density Focus chain BB [auth E] Focus chain BC [auth R] Focus chain BD [auth i] Focus chain BE [auth v] Focus chain DB [auth F] Focus chain DC [auth S] Focus chain DD [auth j] Focus chain FB [auth G] Focus chain FC [auth T] Focus chain FD [auth k] Focus chain HB [auth H] Focus chain HC [auth U] Focus chain HD [auth l] Focus chain JB [auth I] Focus chain JC [auth V] Focus chain JD [auth m] Focus chain LB [auth J] Focus chain LC [auth a] Focus chain LD [auth n] Focus chain NB [auth K] Focus chain NC [auth b] Focus chain ND [auth o] Focus chain PB [auth L] Focus chain PC [auth c] Focus chain PD [auth p] Focus chain RB [auth M] Focus chain RC [auth d] Focus chain RD [auth q] Focus chain TA [auth A] Focus chain TB [auth N] Focus chain TC [auth e] Focus chain TD [auth r] Focus chain VA [auth B] Focus chain VB [auth O] Focus chain VC [auth f] Focus chain VD [auth s] Focus chain XA [auth C] Focus chain XB [auth P] Focus chain XC [auth g] Focus chain XD [auth t] Focus chain ZA [auth D] Focus chain ZB [auth Q] Focus chain ZC [auth h] Focus chain ZD [auth u]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain CD [auth j] SDF format, chain ED [auth k] SDF format, chain GD [auth l] SDF format, chain ID [auth m] SDF format, chain MB [auth K] SDF format, chain MD [auth o] SDF format, chain OB [auth L] SDF format, chain OC [auth c] SDF format, chain QB [auth M] SDF format, chain SA [auth A] SDF format, chain SB [auth N] SDF format, chain SC [auth e] SDF format, chain UA [auth B] SDF format, chain UB [auth O] SDF format, chain UC [auth f] SDF format, chain UD [auth s] SDF format, chain WB [auth P] SDF format, chain WD [auth t] SDF format, chain YB [auth Q] SDF format, chain YC [auth h] SDF format, chain AC [auth R] SDF format, chain AD [auth i] SDF format, chain AE [auth v] SDF format, chain CB [auth F] SDF format, chain CC [auth S] SDF format, chain EB [auth G] SDF format, chain EC [auth T] SDF format, chain GB [auth H] SDF format, chain GC [auth U] SDF format, chain IB [auth I] SDF format, chain IC [auth V] SDF format, chain KB [auth J] SDF format, chain KC [auth a] SDF format, chain KD [auth n] SDF format, chain MC [auth b] SDF format, chain OD [auth p] SDF format, chain QC [auth d] SDF format, chain QD [auth q] SDF format, chain SD [auth r] SDF format, chain WA [auth C] SDF format, chain WC [auth g] SDF format, chain YA [auth D] SDF format, chain YD [auth u] MOL2 format, chain AB [auth E] MOL2 format, chain CD [auth j] MOL2 format, chain ED [auth k] MOL2 format, chain GD [auth l] MOL2 format, chain ID [auth m] MOL2 format, chain MB [auth K] MOL2 format, chain MD [auth o] MOL2 format, chain OB [auth L] MOL2 format, chain OC [auth c] MOL2 format, chain QB [auth M] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth N] MOL2 format, chain SC [auth e] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth O] MOL2 format, chain UC [auth f] MOL2 format, chain UD [auth s] MOL2 format, chain WB [auth P] MOL2 format, chain WD [auth t] MOL2 format, chain YB [auth Q] MOL2 format, chain YC [auth h] MOL2 format, chain AC [auth R] MOL2 format, chain AD [auth i] MOL2 format, chain AE [auth v] MOL2 format, chain CB [auth F] MOL2 format, chain CC [auth S] MOL2 format, chain EB [auth G] MOL2 format, chain EC [auth T] MOL2 format, chain GB [auth H] MOL2 format, chain GC [auth U] MOL2 format, chain IB [auth I] MOL2 format, chain IC [auth V] MOL2 format, chain KB [auth J] MOL2 format, chain KC [auth a] MOL2 format, chain KD [auth n] MOL2 format, chain MC [auth b] MOL2 format, chain OD [auth p] MOL2 format, chain QC [auth d] MOL2 format, chain QD [auth q] MOL2 format, chain SD [auth r] MOL2 format, chain WA [auth C] MOL2 format, chain WC [auth g] MOL2 format, chain YA [auth D] MOL2 format, chain YD [auth u] mmCIF format, chain AB [auth E] mmCIF format, chain CD [auth j] mmCIF format, chain ED [auth k] mmCIF format, chain GD [auth l] mmCIF format, chain ID [auth m] mmCIF format, chain MB [auth K] mmCIF format, chain MD [auth o] mmCIF format, chain OB [auth L] mmCIF format, chain OC [auth c] mmCIF format, chain QB [auth M] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth N] mmCIF format, chain SC [auth e] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth O] mmCIF format, chain UC [auth f] mmCIF format, chain UD [auth s] mmCIF format, chain WB [auth P] mmCIF format, chain WD [auth t] mmCIF format, chain YB [auth Q] mmCIF format, chain YC [auth h] mmCIF format, chain AC [auth R] mmCIF format, chain AD [auth i] mmCIF format, chain AE [auth v] mmCIF format, chain CB [auth F] mmCIF format, chain CC [auth S] mmCIF format, chain EB [auth G] mmCIF format, chain EC [auth T] mmCIF format, chain GB [auth H] mmCIF format, chain GC [auth U] mmCIF format, chain IB [auth I] mmCIF format, chain IC [auth V] mmCIF format, chain KB [auth J] mmCIF format, chain KC [auth a] mmCIF format, chain KD [auth n] mmCIF format, chain MC [auth b] mmCIF format, chain OD [auth p] mmCIF format, chain QC [auth d] mmCIF format, chain QD [auth q] mmCIF format, chain SD [auth r] mmCIF format, chain WA [auth C] mmCIF format, chain WC [auth g] mmCIF format, chain YA [auth D] mmCIF format, chain YD [auth u]	AB [auth E] AC [auth R] AD [auth i] AE [auth v] CB [auth F] AB [auth E], AC [auth R], AD [auth i], AE [auth v], CB [auth F], CC [auth S], CD [auth j], EB [auth G], EC [auth T], ED [auth k], GB [auth H], GC [auth U], GD [auth l], IB [auth I], IC [auth V], ID [auth m], KB [auth J], KC [auth a], KD [auth n], MB [auth K], MC [auth b], MD [auth o], OB [auth L], OC [auth c], OD [auth p], QB [auth M], QC [auth d], QD [auth q], SA [auth A], SB [auth N], SC [auth e], SD [auth r], UA [auth B], UB [auth O], UC [auth f], UD [auth s], WA [auth C], WB [auth P], WC [auth g], WD [auth t], YA [auth D], YB [auth Q], YC [auth h], YD [auth u]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain AC [auth R] Focus chain AD [auth i] Focus chain AE [auth v] Focus chain CB [auth F] Focus chain CC [auth S] Focus chain CD [auth j] Focus chain EB [auth G] Focus chain EC [auth T] Focus chain ED [auth k] Focus chain GB [auth H] Focus chain GC [auth U] Focus chain GD [auth l] Focus chain IB [auth I] Focus chain IC [auth V] Focus chain ID [auth m] Focus chain KB [auth J] Focus chain KC [auth a] Focus chain KD [auth n] Focus chain MB [auth K] Focus chain MC [auth b] Focus chain MD [auth o] Focus chain OB [auth L] Focus chain OC [auth c] Focus chain OD [auth p] Focus chain QB [auth M] Focus chain QC [auth d] Focus chain QD [auth q] Focus chain SA [auth A] Focus chain SB [auth N] Focus chain SC [auth e] Focus chain SD [auth r] Focus chain UA [auth B] Focus chain UB [auth O] Focus chain UC [auth f] Focus chain UD [auth s] Focus chain WA [auth C] Focus chain WB [auth P] Focus chain WC [auth g] Focus chain WD [auth t] Focus chain YA [auth D] Focus chain YB [auth Q] Focus chain YC [auth h] Focus chain YD [auth u] Interactions & Density Focus chain AB [auth E] Focus chain AC [auth R] Focus chain AD [auth i] Focus chain AE [auth v] Focus chain CB [auth F] Focus chain CC [auth S] Focus chain CD [auth j] Focus chain EB [auth G] Focus chain EC [auth T] Focus chain ED [auth k] Focus chain GB [auth H] Focus chain GC [auth U] Focus chain GD [auth l] Focus chain IB [auth I] Focus chain IC [auth V] Focus chain ID [auth m] Focus chain KB [auth J] Focus chain KC [auth a] Focus chain KD [auth n] Focus chain MB [auth K] Focus chain MC [auth b] Focus chain MD [auth o] Focus chain OB [auth L] Focus chain OC [auth c] Focus chain OD [auth p] Focus chain QB [auth M] Focus chain QC [auth d] Focus chain QD [auth q] Focus chain SA [auth A] Focus chain SB [auth N] Focus chain SC [auth e] Focus chain SD [auth r] Focus chain UA [auth B] Focus chain UB [auth O] Focus chain UC [auth f] Focus chain UD [auth s] Focus chain WA [auth C] Focus chain WB [auth P] Focus chain WC [auth g] Focus chain WD [auth t] Focus chain YA [auth D] Focus chain YB [auth Q] Focus chain YC [auth h] Focus chain YD [auth u]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.246 (Depositor), 0.250 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.7	α = 90
b = 140	β = 118.4
c = 153	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-04-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-04-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description