5zea

Crystal structure of the nucleotide-free mutant A3B3

Method: X-RAY DIFFRACTION

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

V-type sodium ATPase catalytic subunit A

Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase subunit B × 3 （Q08637） GLYCEROL × 12 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase subunit B × 3 （Q08637） GLYCEROL × 5 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPA_ENTHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–594； UniProt 1–587 Author chain B； PDBConstruct 8–594； UniProt 1–587 Author chain C； PDBConstruct 8–594； UniProt 1–587 Author chain G； PDBConstruct 8–594； UniProt 1–587 Author chain H； PDBConstruct 8–594； UniProt 1–587 Author chain I； PDBConstruct 8–594； UniProt 1–587

V-type sodium ATPase subunit B

Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)

UniProt Q08637

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase catalytic subunit A × 3 （Q08636） GLYCEROL × 12 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase catalytic subunit A × 3 （Q08636） GLYCEROL × 5 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPB_ENTHA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 8–462； UniProt 1–455 Author chain E； PDBConstruct 8–462； UniProt 1–455 Author chain F； PDBConstruct 8–462； UniProt 1–455 Author chain J； PDBConstruct 8–462； UniProt 1–455 Author chain K； PDBConstruct 8–462； UniProt 1–455 Author chain L； PDBConstruct 8–462； UniProt 1–455

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	5zea
Deposition date deposition_date	2018-02-27
Structure title title	Crystal structure of the nucleotide-free mutant A3B3
Keywords keywords	V-ATPase, rotary motor, 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.

5zea__assembly_2__model_1

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

Download this curve (.dat)

5zea__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5zea__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	45.68 Å
Rg (electron density)	44.82 Å
Total Rg	45.19 Å
Atom count	23898
Residues	3121
Excluded volume	424450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5zea__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5zea__assembly_2__model_1`	hexameric （6）	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	V-type sodium ATPase catalytic subunit A
Molecular weight formula_weight	65771.2 kDa
EC 编号 ec_number	3.6.3.15
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,G,H,I
Atom count atom_count	47987

GSSGSSGMQIGKIIKVSGPLVMAENMSEASIQDMCLVGDLGVIGEIIEMRQDVASIQVYEETSGIGPGEPVRSTGEALSVELGPGIISQMFDGIQRPLDTFMEVTQSNFLGRGVQLPALDHEKQWWFEATIEEGTEVSAGDIIGYVDETKIIQHKIMVPNGIKGTVQKIESGSFTIDDPICVIETEQGLKELTMMQKWPVRRGRPIKQKLNPDVPMITGQRVIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWSDVDLVVYVGCGERGNEMTDVVNEFPELIDPNTGESLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVAIMADSTSRWAEALREMSGRLEEMPGDEGYPAYLGSRLAEYYERSGRVIALGSDQREGSITAISAVSPSGGDISEPVTQNTLRVVKVFWGLDSSLAQKRHFPSINWIQSYSLYSTEVGRYMDQILQQDWSDMVTEGMRILQEEEQLNEIVRLVGIDSLSDNDRLTLEVAKSIREDYLQQNAFDDVDTFTSREKQFNMLKVILTFGKEARKALSLGAYFNEIMEGTVAVRERISRSKYIPEEELAKISSINEEIKETIQLIVSE

Source Source

Source organism organism	Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	V-type sodium ATPase subunit B
Molecular weight formula_weight	51455.6 kDa
Mutation mutation	L65Y
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,J,K,L

GSSGSSGMIKEYRTIKEVVGPLMAVEKVSGVKYEELIEVRMQNGEIRRGQVLEVQEDKAMVQIFEGTSGINYKNSSVRFLGHPLQLGVSEDMIGRVFDGLGRPKDNGPEILPEKYLDINGEVINPIARDYPDEFIQTGISAIDHLNTLVRGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMTDMTNYAEALREISAARREVPGRRGYPGYLYTNLATLFERAGRIRGLKGSVTQIPILTMPEDDKTHPIPDLTGYITEGQIILTRELYKSGIQPPIDVLPSLSRLKDKGTGAGKTREDHAATMNQLFAAYAQGKQAKELAVVLGESALSDIDKIYAKFAERFENEYVNQGFYTNRTITETLDLGWELLAMLPRTELKRIKDDLLDKYLP

Source Source

Source organism organism	Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258)
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	5zeaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5zeaA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	5zeaA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5zeaB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5zeaB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	5zeaB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5zeaC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5zeaC03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	5zeaC04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5zeaD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

Domain ID domain_id	5zeaE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

Domain ID domain_id	5zeaF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

Domain ID domain_id	5zeaG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5zeaG03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	5zeaG04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5zeaH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5zeaH03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	5zeaH04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5zeaI02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5zeaI03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	5zeaI04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	5zeaJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

Domain ID domain_id	5zeaK00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

Domain ID domain_id	5zeaL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

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Unit-cell length a length_a	180.840 Å
Unit-cell length b length_b	107.770 Å
Unit-cell length c length_c	193.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	3.384 Å
Low-resolution limit resolution_low	48.199 Å
R factor r_factor	0.2172
R_work r_work	0.2151
R_free r_free	0.2575

Crystal structure of the nucleotide-free mutant A3B3

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

V-type sodium ATPase catalytic subunit A

State in the Current Structure

Other States of the Same Protein in the Database

V-type sodium ATPase subunit B

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

5zea__assembly_2__model_1

5zea__assembly_2__model_1 | I(q)

5zea__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of the nucleotide-free mutant A3B3

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

V-type sodium ATPase catalytic subunit A

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 sodium ATPase subunit B

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

5zea__assembly_2__model_1

5zea__assembly_2__model_1 | I(q)

5zea__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)