1yce

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

Method: X-RAY DIFFRACTION

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein homooligomer	Homooligomer	11 / 0 / 0 / 0	Consistent with protein count
2	Protein homooligomer	Homooligomer	11 / 0 / 0 / 0	Consistent with protein count
3	Protein homooligomer	Homooligomer	11 / 0 / 0 / 0	Consistent with protein count
4	Protein homooligomer	Homooligomer	11 / 0 / 0 / 0	Consistent with protein count

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1yce
Deposition date deposition_date	2004-12-22
Structure title title	Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus
Keywords keywords	ATP Synthase, Na binding site, membrane protein; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

1yce__assembly_3__model_1

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

Download this curve (.dat)

1yce__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yce__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	28.74 Å
Rg (electron density)	27.75 Å
Total Rg	28.71 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	`1yce__assembly_1__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yce__assembly_2__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yce__assembly_3__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1yce__assembly_4__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	subunit c
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	28101

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	513

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6. Fold Classification (SCOP + CATH) 44 domains

CATH v4.4 (44 domains)

Domain ID domain_id	1yceA01
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	1yceB01
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	1yceC01
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	1yceD01
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	1yceE01
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	1yceF01
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	1yceG01
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	1yceH01
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	1yceI01
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	1yceJ01
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	1yceK01
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	1yceL01
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	1yceM01
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	1yceN01
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	1yceO01
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	1yceP01
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	1yceQ01
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	1yceR01
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	1yceS01
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	1yceT01
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	1yceU01
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	1yceV01
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	1ycea01
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	1yceb01
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	1ycec01
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	1yced01
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	1ycee01
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	1ycef01
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	1yceg01
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	1yceh01
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	1ycei01
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	1ycej01
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	1ycek01
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	1ycel01
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	1ycem01
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	1ycen01
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	1yceo01
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	1ycep01
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	1yceq01
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	1ycer01
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	1yces01
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	1ycet01
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	1yceu01
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	1ycev01
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

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Unit-cell length a length_a	147.700 Å
Unit-cell length b length_b	140.000 Å
Unit-cell length c length_c	153.000 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	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2028
R_work r_work	0.2006
R_free r_free	0.2460