SAXSdb — 6ly9

▼

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

V-type ATP synthase subunit I

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type ATP synthase, subunit K × 12 （Q5SIT7） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase, subunit (VAPC-THERM) × 1 （Q5SIT5） V-type ATP synthase subunit E × 1 （P74901）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SIT6_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain N； PDBConstruct 1–652； UniProt 1–652

V-type ATP synthase, subunit K

OrganismNot specified

UniProt Q5SIT7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase, subunit (VAPC-THERM) × 1 （Q5SIT5） V-type ATP synthase subunit E × 1 （P74901）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SIT7_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain O； PDBConstruct 1–99； UniProt 1–99 Author chain P； PDBConstruct 1–99； UniProt 1–99 Author chain Q； PDBConstruct 1–99； UniProt 1–99 Author chain R； PDBConstruct 1–99； UniProt 1–99 Author chain S； PDBConstruct 1–99； UniProt 1–99 Author chain T； PDBConstruct 1–99； UniProt 1–99 Author chain U； PDBConstruct 1–99； UniProt 1–99 Author chain V； PDBConstruct 1–99； UniProt 1–99 Author chain W； PDBConstruct 1–99； UniProt 1–99 Author chain X； PDBConstruct 1–99； UniProt 1–99 Author chain Y； PDBConstruct 1–99； UniProt 1–99 Author chain Z； PDBConstruct 1–99； UniProt 1–99

V-type ATP synthase subunit C

OrganismNot specified

UniProt P74902

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） V-type ATP synthase, subunit (VAPC-THERM) × 1 （Q5SIT5） V-type ATP synthase subunit E × 1 （P74901）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATC_THET8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–323； UniProt 1–323

V-type ATP synthase, subunit (VAPC-THERM)

OrganismNot specified

UniProt Q5SIT5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase subunit E × 1 （P74901）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SIT5_THET8
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain K； PDBConstruct 1–120； UniProt 1–120

V-type ATP synthase subunit E

OrganismNot specified

UniProt P74901

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase, subunit (VAPC-THERM) × 1 （Q5SIT5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATE_THET8
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain L； PDBConstruct 1–188； UniProt 1–188

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	6ly9
Deposition date deposition_date	2020-02-13
Structure title title	The membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus
Keywords keywords	rotary ATPase, V/A-ATPase, molecular motor, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

6ly9__assembly_1__model_1

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

Download this curve (.dat)

6ly9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ly9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.33 Å
Rg (electron density)	37.25 Å
Total Rg	37.73 Å
Atom count	13888
Residues	1894
Excluded volume	251940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ly9__assembly_1__model_1`	hexadecameric （16）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	V-type ATP synthase subunit I
Molecular weight formula_weight	72204.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N
Atom count atom_count	13888

MIAPMEKLVLAGPKGRAKELLQSLQQAGVVHLETLRPEALSAYQLSPEERAELRRWEAVSAGAEHTLSLLGLEAEPARPFPEGLEAAEKALSPIQAHAEGLTRQKQELEEELALAQAYLEPLERLAALAHGLDKSPFLRVIPFLLTEKELPLVEEALRKALEDRYLLAHEAYAGGVAALVVVHRKEVDQAKAALSRAGVAELRLPGALGELPLSEAARRLKERAEAAPRELSEVRQHLAKLARESASTLQSLWTRAQDEVARLKALEELASGRFGFALLGYVPVKAKPKVEEALARHKESVVYAFEPVDEHHEADRIPVVLDNPPWAKPFELLVSFLNTPKYGTFDPTPVVPVFFPFWFGMIVGDIGYALLFYLVGRWLSGYVKRNEPLVIDLFALKLKPQVIGKLVHILNWMVFWTVVWGVIYGEFFGTFLEHLGVFGTPEHPGLIPILIHRIDTAKTANLLILLSVAFGVVLVFFGLALRAYLGLKHRHMAHFWEGVGYLGGLVGVLALAASYLGNLQAGWLQGLMYLGFGVFLLAVLMSRIWLMIPEIFTQAGHILSHIRIYAVGAAGGILAGLLTDVGFALAERLGLLGVLLGLLVAGVLHLLILLLTTLGHMLQPIRLLWVEFFTKFGFYEENGRPYRPFKSVREAQ

Entity 2 Entity 2 polymer

Description description	V-type ATP synthase, subunit K
Molecular weight formula_weight	9841.7 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,Q,R,S,T,U,V,W,X,Y,Z

MKKLLVTVLLAVFGALAFAAEEAAASGGLDRGLIAVGMGLAVGLAALGTGVAQARIGAAGVGAIAEDRSNFGTALIFLLLPETLVIFGLLIAFILNGRL

Entity 3 Entity 3 polymer

Description description	V-type ATP synthase subunit C
Molecular weight formula_weight	35968.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MADDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVCP

Entity 4 Entity 4 polymer

Description description	V-type ATP synthase, subunit (VAPC-THERM)
Molecular weight formula_weight	13166.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MTGGLVLNAISRAGGAMGGLGLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP

Entity 5 Entity 5 polymer

Description description	V-type ATP synthase subunit E
Molecular weight formula_weight	20645.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MSKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEALARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARLDRAWDALSSKVAQALWG

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.93 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	157618

The membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus

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

V-type ATP synthase subunit I

State in the Current Structure

Other States of the Same Protein in the Database

V-type ATP synthase, subunit K

State in the Current Structure

Other States of the Same Protein in the Database

V-type ATP synthase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

V-type ATP synthase, subunit (VAPC-THERM)

State in the Current Structure

Other States of the Same Protein in the Database

V-type ATP synthase subunit E

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

6ly9__assembly_1__model_1

6ly9__assembly_1__model_1 | I(q)

6ly9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

7. Citations (1)

The membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus

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

V-type ATP synthase subunit I

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase, subunit K

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase, subunit (VAPC-THERM)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase subunit E

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

6ly9__assembly_1__model_1

6ly9__assembly_1__model_1 | I(q)

6ly9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

7. Citations (1)