SAXSdb — 8ywt

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

V-type ATP synthase subunit I

Thermus thermophilus HB8

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） water × 8	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

Thermus thermophilus HB8

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） water × 8	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

Thermus thermophilus HB8

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） water × 8	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)

Thermus thermophilus HB8

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） water × 8	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

Thermus thermophilus HB8

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） water × 8	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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ywt
Deposition date deposition_date	2024-04-01
Last revision last_revision	2024-12-04
Structure title title	The isolated 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

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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.

8ywt__assembly_1__model_1

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

Download this curve (.dat)

8ywt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ywt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.22 Å
Rg (electron density)	38.12 Å
Total Rg	38.57 Å
Atom count	13916
Residues	1895
Excluded volume	252400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ywt__assembly_1__model_1`	hexadecameric （16）	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 (6)

Entity 1 Entity 1 polymer

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N
Atom count atom_count	13986

MIAPMEKLVLAGPKGRAKELLQSLQQAGVVHLETLRPEALSAYQLSPEERAELRRWEAVSAGAEHTLSLLGLEAEPARPFPEGLEAAEKALSPIQAHAEGLTRQKQELEEELALAQAYLEPLERLAALAHGLDKSPFLRVIPFLLTEKELPLVEEALRKALEDRYLLAHEAYAGGVAALVVVHRKEVDQAKAALSRAGVAELRLPGALGELPLSEAARRLKERAEAAPRELSEVRQHLAKLARESASTLQSLWTRAQDEVARLKALEELASGRFGFALLGYVPVKAKPKVEEALARHKESVVYAFEPVDEHHEADRIPVVLDNPPWAKPFELLVSFLNTPKYGTFDPTPVVPVFFPFWFGMIVGDIGYALLFYLVGRWLSGYVKRNEPLVIDLFALKLKPQVIGKLVHILNWMVFWTVVWGVIYGEFFGTFLEHLGVFGTPEHPGLIPILIHRIDTAKTANLLILLSVAFGVVLVFFGLALRAYLGLKHRHMAHFWEGVGYLGGLVGVLALAASYLGNLQAGWLQGLMYLGFGVFLLAVLMSRIWLMIPEIFTQAGHILSHIRIYAVGAAGGILAGLLTDVGFALAERLGLLGVLLGLLVAGVLHLLILLLTTLGHMLQPIRLLWVEFFTKFGFYEENGRPYRPFKSVREAQ

Source Source

Source organism organism	Thermus thermophilus HB8
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Thermus thermophilus HB8

Entity 2 Entity 2 polymer

Description description	V-type ATP synthase, subunit K
Molecular weight formula_weight	10256.2 kDa
Source method src_method	man
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

MKKLLVTVLLAVFGALAFAAEEAAASGGLDRGLIAVGMGLAVGLAALGTGVAQARIGAAGVGAIAEDRSNFGTALIFLLLPETLVIFGLLIAFILNGRLHHH

Source Source

Source organism organism	Thermus thermophilus HB8
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Thermus thermophilus HB8

Entity 3 Entity 3 polymer

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MADDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVCP

Source Source

Source organism organism	Thermus thermophilus HB8
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Thermus thermophilus HB8

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	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MTGGLVLNAISRAGGAMGGLGLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP

Source Source

Source organism organism	Thermus thermophilus HB8
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Thermus thermophilus HB8

Entity 5 Entity 5 polymer

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MSKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEALARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARLDRAWDALSSKVAQALWG

Source Source

Source organism organism	Thermus thermophilus HB8
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Thermus thermophilus HB8

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

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Resolution resolution	2.800 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	370215

The isolated 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

8ywt__assembly_1__model_1

8ywt__assembly_1__model_1 | I(q)

8ywt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 water

7. Citations (1)