3a5c

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase

Method: X-RAY DIFFRACTION

▼

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

V-type ATP synthase alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATA_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–578； UniProt 1–578 Author chain B； PDBConstruct 1–578； UniProt 1–578 Author chain C； PDBConstruct 1–578； UniProt 1–578 Author chain I； PDBConstruct 1–578； UniProt 1–578 Author chain J； PDBConstruct 1–578； UniProt 1–578 Author chain K； PDBConstruct 1–578； UniProt 1–578

V-type ATP synthase beta chain

OrganismNot specified

UniProt Q56404

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATB_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–478； UniProt 1–478 Author chain E； PDBConstruct 1–478； UniProt 1–478 Author chain F； PDBConstruct 1–478； UniProt 1–478 Author chain L； PDBConstruct 1–478； UniProt 1–478 Author chain M； PDBConstruct 1–478； UniProt 1–478 Author chain N； PDBConstruct 1–478； UniProt 1–478

V-type ATP synthase subunit D

OrganismNot specified

UniProt O87880

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit F × 1 （P74903） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit F × 1 （P74903） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATD_THET8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–223； UniProt 1–223 Author chain O； PDBConstruct 1–223； UniProt 1–223

V-type ATP synthase subunit F

OrganismNot specified

UniProt P74903

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATF_THET8
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–104； UniProt 1–104 Author chain P； PDBConstruct 1–104； UniProt 1–104

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	3a5c
Deposition date deposition_date	2009-08-06
Structure title title	Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase
Keywords keywords	;V-ATPase, asymmetric, rotation, vacuolar type, HYDROLASE, ATP synthesis, ATP-binding, Hydrogen ion transport, Ion transport, Nucleotide-binding, Transport ;; HYDROLASE
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.

3a5c__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3a5c__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a5c__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	44.40 Å
Rg (electron density)	43.81 Å
Total Rg	44.16 Å
Atom count	16094
Residues	3266
Excluded volume	258190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a5c__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3a5c__assembly_2__model_1`	octameric （8）	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 alpha chain
Molecular weight formula_weight	63700.0 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,I,J,K
Atom count atom_count	32188

MIQGVIQKIAGPAVIAKGMLGARMYDICKVGEEGLVGEIIRLDGDTAFVQVYEDTSGLKVGEPVVSTGLPLAVELGPGMLNGIYDGIQRPLERIREKTGIYITRGVVVHALDREKKWAWTPMVKPGDEVRGGMVLGTVPEFGFTHKILVPPDVRGRVKEVKPAGEYTVEEPVVVLEDGTELKMYHTWPVRRARPVQRKLDPNTPFLTGMRILDVLFPVAMGGTAAIPGPFGSGKTVTQQSLAKWSNADVVVYVGCGERGNEMTDVLVEFPELTDPKTGGPLMHRTVLIANTSNMPVAAREASIYVGVTIAEYFRDQGFSVALMADSTSRWAEALREISSRLEEMPAEEGYPPYLAARLAAFYERAGKVITLGGEEGAVTIVGAVSPPGGDMSEPVTQSTLRIVGAFWRLDASLAFRRHFPAINWNGSYSLFTSALDPWYRENVAEDYPELRDAISELLQREAGLQEIVQLVGPDALQDAERLVIEVGRIIREDFLQQNAYHEVDAYCSMKKAYGIMKMILAFYKEAEAAIKRGVSIDEILQLPVLERIGRARYVSEEEFPAYFEEAMKEIQGAFKALA

Entity 2 Entity 2 polymer

Description description	V-type ATP synthase beta chain
Molecular weight formula_weight	53219.5 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,L,M,N

MDLLKKEYTGITYISGPLLFVENAKDLAYGAIVDIKDGTGRVRGGQVIEVSEEYAVIQVFEETTGLDLATTSVSLVEDVARLGVSKEMLGRRFNGIGKPIDGLPPITPEKRLPITGLPLNPVARRKPEQFIQTGISTIDVMNTLVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMTNYCEALREIGAAREEIPGRRGYPGYMYTDLATIYERAGVVEGKKGSVTQIPILSMPDDDRTHPIPDLTGYITEGQIQLSRELHRKGIYPPIDPLPSLSRLMNNGVGKGKTREDHKQVSDQLYSAYANGVDIRKLVAIIGEDALTENDRRYLQFADAFERFFINQGQQNRSIEESLQIAWALLSMLPQGELKRISKDHIGKYYGQKLEEIWGAPQALD

Entity 3 Entity 3 polymer

Description description	V-type ATP synthase subunit D
Molecular weight formula_weight	24715.6 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,O

MSQVSPTRMNLLQRRGQLRLAQKGVDLLKKKRDALVAEFFGLVREAMEARKALDQAAKEAYAALLLAQAFDGPEVVAGAALGVPPLEGVEAEVENVWGSKVPRLKATFPDGALLSPVGTPAYTLEASRAFRRYAEALIRVANTETRLKKIGEEIKKTTRRVNALEQVVIPGIRAQIRFIQQVLEQREREDTFRLKRIKGKIEAREAEEEGGRPNPQVEIGAGL

Entity 4 Entity 4 polymer

Description description	V-type ATP synthase subunit F
Molecular weight formula_weight	11294.9 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,P

MAVIADPETAQGFRLAGLEGYGASSAEEAQSLLETLVERGGYALVAVDEALLPDPERAVERLMRGRDLPVLLPIAGLKEAFQGHDVEGYMRELVRKTIGFDIKL

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

▼

6. Fold Classification (SCOP + CATH) 46 domains

SCOP 2.08 (46 domains)

Domain ID domain_id	d3a5ca1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5ca2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5ca3
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family family	b.84.5.1 — V1 ATP synthase A subunit, bulge domain-like

Domain ID domain_id	d3a5ca4
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cb1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5cb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5cb3
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family family	b.84.5.1 — V1 ATP synthase A subunit, bulge domain-like

Domain ID domain_id	d3a5cb4
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cc1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5cc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5cc3
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family family	b.84.5.1 — V1 ATP synthase A subunit, bulge domain-like

Domain ID domain_id	d3a5cc4
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cd1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5cd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5cd3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5ce1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5ce2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5ce3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cf1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5cf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5cf3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cg_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.20 — V-type ATPase central rotor subunit D
Family Family family	h.4.20.1 — V1 ATP synthase D subunit

Domain ID domain_id	d3a5ch_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.149 — AtpF-like
Superfamily Superfamily superfamily	c.149.1 — AtpF-like
Family Family family	c.149.1.1 — AtpF-like

Domain ID domain_id	d3a5ci1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5ci2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5ci3
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family family	b.84.5.1 — V1 ATP synthase A subunit, bulge domain-like

Domain ID domain_id	d3a5ci4
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cj1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5cj2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5cj3
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family family	b.84.5.1 — V1 ATP synthase A subunit, bulge domain-like

Domain ID domain_id	d3a5cj4
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5ck1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5ck2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5ck3
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family family	b.84.5.1 — V1 ATP synthase A subunit, bulge domain-like

Domain ID domain_id	d3a5ck4
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cl1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5cl2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5cl3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cm1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5cm2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5cm3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5cn1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase

Domain ID domain_id	d3a5cn2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d3a5cn3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

Domain ID domain_id	d3a5co_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.20 — V-type ATPase central rotor subunit D
Family Family family	h.4.20.1 — V1 ATP synthase D subunit

Domain ID domain_id	d3a5cp_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.149 — AtpF-like
Superfamily Superfamily superfamily	c.149.1 — AtpF-like
Family Family family	c.149.1.1 — AtpF-like

▶

Unit-cell length a length_a	381.578 Å
Unit-cell length b length_b	381.578 Å
Unit-cell length c length_c	147.672 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	4.510 Å
Low-resolution limit resolution_low	29.920 Å
R factor r_factor	—
R_work r_work	0.4290
R_free r_free	0.4370

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase

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

V-type ATP synthase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

V-type ATP synthase beta chain

State in the Current Structure

Other States of the Same Protein in the Database

V-type ATP synthase subunit D

State in the Current Structure

Other States of the Same Protein in the Database

V-type ATP synthase subunit F

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

3a5c__assembly_2__model_1

3a5c__assembly_2__model_1 | I(q)

3a5c__assembly_2__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 (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 non-polymer

6. Fold Classification (SCOP + CATH) 46 domains

SCOP 2.08 (46 domains)

7. Citations (1)

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase

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

V-type ATP synthase alpha chain

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 beta chain

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 D

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 F

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

3a5c__assembly_2__model_1

3a5c__assembly_2__model_1 | I(q)

3a5c__assembly_2__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 (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 non-polymer

6. Fold Classification (SCOP + CATH) 46 domains

SCOP 2.08 (46 domains)

7. Citations (1)