3k5b

Crystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase

Method: X-RAY DIFFRACTION

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

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

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	V-type ATP synthase subunit E × 1 （P74901）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	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	1
Chains and sequence ranges	Author chain B； PDBConstruct 2–104； UniProt 18–120 Author chain G； PDBConstruct 2–104； UniProt 18–120

V-type ATP synthase subunit E

Thermus thermophilus

UniProt P74901

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	V-type ATP synthase, subunit (VAPC-THERM) × 1 （Q5SIT5）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	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	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–188； UniProt 1–188 Author chain E； 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	3k5b
Deposition date deposition_date	2009-10-07
Structure title title	Crystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase
Keywords keywords	;right handed coiled coil, vacuolar ATPase/synthase, V-Type ATPase/synthase, A-Type ATPase/synthase, peripheral stator, peripheral stalk, ATP synthesis, Hydrogen ion transport, Ion transport, Transport, HYDROLASE ;; HYDROLASE
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.

3k5b__assembly_1__model_1

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

Download this curve (.dat)

3k5b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3k5b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.08 Å
Rg (electron density)	47.80 Å
Total Rg	47.01 Å
Atom count	1997
Residues	281
Excluded volume	34996 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3k5b__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3k5b__assembly_2__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	V-type ATP synthase, subunit (VAPC-THERM)
Molecular weight formula_weight	11668.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,B
Atom count atom_count	4056

GGGLGLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	V-type ATP synthase subunit E
Molecular weight formula_weight	20887.3 kDa
Mutation mutation	Emmm: L134M, L171M, L178M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A

MSKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEAMARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARMDRAWDAMSSKVAQALWG

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3k5ba1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.4 — V-type ATPase subunit E-like
Family Family family	d.81.4.1 — V-type ATPase subunit E C-terminal domain

Domain ID domain_id	d3k5ba2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.36 — V-type ATPase peripheral stalk subunit E coiled coil
Family Family family	h.1.36.1 — V-type ATPase peripheral stalk subunit E coiled coil

Domain ID domain_id	d3k5bb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.37 — V-type ATPase peripheral stalk subunit G coiled coil
Family Family family	h.1.37.1 — V-type ATPase peripheral stalk subunit G coiled coil

Domain ID domain_id	d3k5be1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.4 — V-type ATPase subunit E-like
Family Family family	d.81.4.1 — V-type ATPase subunit E C-terminal domain

Domain ID domain_id	d3k5be2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.36 — V-type ATPase peripheral stalk subunit E coiled coil
Family Family family	h.1.36.1 — V-type ATPase peripheral stalk subunit E coiled coil

Domain ID domain_id	d3k5bg_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.37 — V-type ATPase peripheral stalk subunit G coiled coil
Family Family family	h.1.37.1 — V-type ATPase peripheral stalk subunit G coiled coil

CATH v4.4 (6 domains)

Domain ID domain_id	3k5bA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	620 — F1F0 ATP synthase subunit B, membrane domain

Domain ID domain_id	3k5bA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	30 — ATP synthase, E subunit, C-terminal

Domain ID domain_id	3k5bB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2950 —

Domain ID domain_id	3k5bE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	620 — F1F0 ATP synthase subunit B, membrane domain

Domain ID domain_id	3k5bE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	30 — ATP synthase, E subunit, C-terminal

Domain ID domain_id	3k5bG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2950 —

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Unit-cell length a length_a	75.781 Å
Unit-cell length b length_b	79.755 Å
Unit-cell length c length_c	75.796 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	29.660 Å
R factor r_factor	0.2350
R_work r_work	0.2320
R_free r_free	0.2880

Crystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase

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

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

3k5b__assembly_1__model_1

3k5b__assembly_1__model_1 | I(q)

3k5b__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase

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

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

3k5b__assembly_1__model_1

3k5b__assembly_1__model_1 | I(q)

3k5b__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)