2wgm

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase

Method: X-RAY DIFFRACTION

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 11	SODIUM ION × 11 NONAN-1-OL × 11 water × 11	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 11	SODIUM ION × 11 NONAN-1-OL × 11 water × 11	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 11	SODIUM ION × 11 NONAN-1-OL × 11 water × 11	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 11	SODIUM ION × 11 NONAN-1-OL × 11 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPL_ILYTA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 1–89 Author chain B； PDBConstruct 1–89； UniProt 1–89 Author chain C； PDBConstruct 1–89； UniProt 1–89 Author chain D； PDBConstruct 1–89； UniProt 1–89 Author chain E； PDBConstruct 1–89； UniProt 1–89 Author chain F； PDBConstruct 1–89； UniProt 1–89 Author chain G； PDBConstruct 1–89； UniProt 1–89 Author chain H； PDBConstruct 1–89； UniProt 1–89 Author chain I； PDBConstruct 1–89； UniProt 1–89 Author chain J； PDBConstruct 1–89； UniProt 1–89 Author chain K； PDBConstruct 1–89； UniProt 1–89 Author chain L； PDBConstruct 1–89； UniProt 1–89 Author chain M； PDBConstruct 1–89； UniProt 1–89 Author chain N； PDBConstruct 1–89； UniProt 1–89 Author chain O； PDBConstruct 1–89； UniProt 1–89 Author chain P； PDBConstruct 1–89； UniProt 1–89 Author chain Q； PDBConstruct 1–89； UniProt 1–89 Author chain R； PDBConstruct 1–89； UniProt 1–89 Author chain S； PDBConstruct 1–89； UniProt 1–89 Author chain T； PDBConstruct 1–89； UniProt 1–89 Author chain U； PDBConstruct 1–89； UniProt 1–89 Author chain V； PDBConstruct 1–89； UniProt 1–89 Author chain a； PDBConstruct 1–89； UniProt 1–89 Author chain b； PDBConstruct 1–89； UniProt 1–89 Author chain c； PDBConstruct 1–89； UniProt 1–89 Author chain d； PDBConstruct 1–89； UniProt 1–89 Author chain e； PDBConstruct 1–89； UniProt 1–89 Author chain f； PDBConstruct 1–89； UniProt 1–89 Author chain g； PDBConstruct 1–89； UniProt 1–89 Author chain h； PDBConstruct 1–89； UniProt 1–89 Author chain i； PDBConstruct 1–89； UniProt 1–89 Author chain j； PDBConstruct 1–89； UniProt 1–89 Author chain k； PDBConstruct 1–89； UniProt 1–89 Author chain l； PDBConstruct 1–89； UniProt 1–89 Author chain m； PDBConstruct 1–89； UniProt 1–89 Author chain n； PDBConstruct 1–89； UniProt 1–89 Author chain o； PDBConstruct 1–89； UniProt 1–89 Author chain p； PDBConstruct 1–89； UniProt 1–89 Author chain q； PDBConstruct 1–89； UniProt 1–89 Author chain r； PDBConstruct 1–89； UniProt 1–89 Author chain s； PDBConstruct 1–89； UniProt 1–89 Author chain t； PDBConstruct 1–89； UniProt 1–89 Author chain u； PDBConstruct 1–89； UniProt 1–89 Author chain v； PDBConstruct 1–89； UniProt 1–89

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2wgm
Deposition date deposition_date	2009-04-21
Structure title title	Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase
Keywords keywords	;F1FO-ATP SYNTHASE ROTOR, SODIUM-MOTIVE FORCE, CELL INNER MEMBRANE CF(0), TRANSPORT, LIPID-BINDING, ION COORDINATION AND SELECTIVITY, MEMBRANE PROTEIN, HYDROGEN ION TRANSPORT, TRANSMEMBRANE, C-RING STRUCTURE, SODIUM TRANSPORT, CELL MEMBRANE, ATP SYNTHESIS ;; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2wgm__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2wgm__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wgm__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.57 Å
Rg (electron density)	27.59 Å
Total Rg	28.55 Å
Atom count	6897
Residues	979
Excluded volume	127400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wgm__assembly_1__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wgm__assembly_2__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2wgm__assembly_3__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2wgm__assembly_4__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
Molecular weight formula_weight	8799.3 kDa
Source method src_method	nat
Copy count entity_count	44

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v
Atom count atom_count	28001

MDMLFAKTVVLAASAVGAGTAMIAGIGPGVGQGYAAGKAVESVARQPEAKGDIISTMVLGQAVAESTGIYSLVIALILLYANPFVGLLG

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	44

Entity 3 Entity 3 non-polymer

Description description	NONAN-1-OL
Molecular weight formula_weight	144.3 kDa
Source method src_method	syn
Copy count entity_count	44

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	413

▼

6. Fold Classification (SCOP + CATH) 44 domains

CATH v4.4 (44 domains)

Domain ID domain_id	2wgmA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmH01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmI01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmJ01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmK01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmL01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmM01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmN01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmO01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmP01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmQ01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmR01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmS01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmT01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmU01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmV01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgma01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmb01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmc01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmd01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgme01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmf01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmg01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmh01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmi01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmj01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmk01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgml01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmm01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmn01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmo01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmp01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmq01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmr01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgms01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmt01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmu01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	2wgmv01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

▶

Unit-cell length a length_a	146.690 Å
Unit-cell length b length_b	139.280 Å
Unit-cell length c length_c	151.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	88

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	39.678 Å
R factor r_factor	0.2215
R_work r_work	0.2203
R_free r_free	0.2451

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2wgm__assembly_3__model_1

2wgm__assembly_3__model_1 | I(q)

2wgm__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 44 domains

CATH v4.4 (44 domains)

7. Citations (1)

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2wgm__assembly_3__model_1

2wgm__assembly_3__model_1 | I(q)

2wgm__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 44 domains

CATH v4.4 (44 domains)

7. Citations (1)