5knc

Crystal structure of the 3 ADP-bound V1 complex

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 ATCC 9790

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 sodium ATPase subunit B × 3 （Q08637） V-type sodium ATPase subunit D × 1 （P43435） V-type sodium ATPase subunit NtpG (F) × 1 （P43455） MAGNESIUM ION × 3 SULFATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 3 GLYCEROL × 14 water × 8	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 8–600； UniProt 1–593 Author chain B； PDBConstruct 8–600； UniProt 1–593 Author chain C； PDBConstruct 8–600； UniProt 1–593

V-type sodium ATPase subunit B

Enterococcus hirae ATCC 9790

UniProt Q08637

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 sodium ATPase catalytic subunit A × 3 （Q08636） V-type sodium ATPase subunit D × 1 （P43435） V-type sodium ATPase subunit NtpG (F) × 1 （P43455） MAGNESIUM ION × 3 SULFATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 3 GLYCEROL × 14 water × 8	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 8–465； UniProt 1–458 Author chain E； PDBConstruct 8–465； UniProt 1–458 Author chain F； PDBConstruct 8–465； UniProt 1–458

V-type sodium ATPase subunit D

Enterococcus hirae ATCC 9790

UniProt P43435

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 sodium ATPase catalytic subunit A × 3 （Q08636） V-type sodium ATPase subunit B × 3 （Q08637） V-type sodium ATPase subunit NtpG (F) × 1 （P43455） MAGNESIUM ION × 3 SULFATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 3 GLYCEROL × 14 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPD_ENTHA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 8–217； UniProt 1–210

V-type sodium ATPase subunit NtpG (F)

Enterococcus hirae ATCC 9790

UniProt P43455

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 sodium ATPase catalytic subunit A × 3 （Q08636） V-type sodium ATPase subunit B × 3 （Q08637） V-type sodium ATPase subunit D × 1 （P43435） MAGNESIUM ION × 3 SULFATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 3 GLYCEROL × 14 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPG_ENTHA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–103； UniProt 1–103

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	5knc
Deposition date deposition_date	2016-06-28
Structure title title	Crystal structure of the 3 ADP-bound V1 complex
Keywords keywords	P-loop, Hydrolase, Na(+)-ATPase, ATP Binding; 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.

5knc__assembly_1__model_1

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

Download this curve (.dat)

5knc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5knc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.90 Å
Rg (electron density)	44.19 Å
Total Rg	44.51 Å
Atom count	26705
Residues	3421
Excluded volume	475740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5knc__assembly_1__model_1`	octameric （8）	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 (9)

Entity 1 Entity 1 polymer

Description description	V-type sodium ATPase catalytic subunit A
Molecular weight formula_weight	66347.8 kDa
EC 编号 ec_number	3.6.3.15
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	26799

GSSGSSGMQIGKIIKVSGPLVMAENMSEASIQDMCLVGDLGVIGEIIEMRQDVASIQVYEETSGIGPGEPVRSTGEALSVELGPGIISQMFDGIQRPLDTFMEVTQSNFLGRGVQLPALDHEKQWWFEATIEEGTEVSAGDIIGYVDETKIIQHKIMVPNGIKGTVQKIESGSFTIDDPICVIETEQGLKELTMMQKWPVRRGRPIKQKLNPDVPMITGQRVIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWSDVDLVVYVGCGERGNEMTDVVNEFPELIDPNTGESLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVAIMADSTSRWAEALREMSGRLEEMPGDEGYPAYLGSRLAEYYERSGRVIALGSDQREGSITAISAVSPSGGDISEPVTQNTLRVVKVFWGLDSSLAQKRHFPSINWIQSYSLYSTEVGRYMDQILQQDWSDMVTEGMRILQEEEQLNEIVRLVGIDSLSDNDRLTLEVAKSIREDYLQQNAFDDVDTFTSREKQFNMLKVILTFGKEARKALSLGAYFNEIMEGTVAVRERISRSKYIPEEELAKISSINEEIKETIQLIVSEGGMTDD

Source Source

Source organism organism	Enterococcus hirae ATCC 9790
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	51720.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

GSSGSSGMIKEYRTIKEVVGPLMAVEKVSGVKYEELIEVRMQNGEIRRGQVLEVQEDKAMVQIFEGTSGINLKNSSVRFLGHPLQLGVSEDMIGRVFDGLGRPKDNGPEILPEKYLDINGEVINPIARDYPDEFIQTGISAIDHLNTLVRGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMTDMTNYAEALREISAARREVPGRRGYPGYLYTNLATLFERAGRIRGLKGSVTQIPILTMPEDDKTHPIPDLTGYITEGQIILTRELYKSGIQPPIDVLPSLSRLKDKGTGAGKTREDHAATMNQLFAAYAQGKQAKELAVVLGESALSDIDKIYAKFAERFENEYVNQGFYTNRTITETLDLGWELLAMLPRTELKRIKDDLLDKYLPEGK

Source Source

Source organism organism	Enterococcus hirae ATCC 9790
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	V-type sodium ATPase subunit D
Molecular weight formula_weight	25119.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GSSGSSGMRLNVNPTRMELTRLKKQLTTATRGHKLLKDKQDELMRQFILLIRKNNELRQAIEKETQTAMKDFVLAKSTVEEAFIDELLALPAENVSISVVEKNIMSVKVPLMNFQYDETLNETPLEYGYLHSNAELDRSIDGFTQLLPKLLKLAEVEKTCQLMAEEIEKTRRRVNALEYMTIPQLEETIYYIKMKLEENERAEVTRLIKVKNMGTEE

Source Source

Source organism organism	Enterococcus hirae ATCC 9790
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	V-type sodium ATPase subunit NtpG (F)
Molecular weight formula_weight	12689.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MTYKIGVVGDKDSVSPFRLFGFDVQHGTTKTEIRKTIDEMAKNEYGVIYITEQCANLVPETIERYKGQLTPAIILIPSHQGTLGIGLEEIQNSVEKAVGQNILSGPSSGENLYFQ

Source Source

Source organism organism	Enterococcus hirae ATCC 9790
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d5kncd1
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.49.1.0 — automated matches

Domain ID domain_id	d5kncd2
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.37.1.0 — automated matches

Domain ID domain_id	d5kncd3
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.69.1.0 — automated matches

Domain ID domain_id	d5knce1
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.49.1.0 — automated matches

Domain ID domain_id	d5knce2
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.37.1.0 — automated matches

Domain ID domain_id	d5knce3
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.69.1.0 — automated matches

Domain ID domain_id	d5kncf1
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.49.1.0 — automated matches

Domain ID domain_id	d5kncf2
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.37.1.0 — automated matches

Domain ID domain_id	d5kncf3
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.69.1.0 — automated matches

Domain ID domain_id	d5kncg_
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.4.20.0 — automated matches

CATH v4.4 (13 domains)

Domain ID domain_id	5kncA02
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	5kncA03
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	5kncA04
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	5kncB02
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	5kncB03
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	5kncB04
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	5kncC02
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	5kncC03
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	5kncC04
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	5kncD00
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	5kncE00
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	5kncF00
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	5kncH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10580 — ATPase, V1 complex, subunit F

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Unit-cell length a length_a	121.680 Å
Unit-cell length b length_b	126.490 Å
Unit-cell length c length_c	225.260 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.015 Å
Low-resolution limit resolution_low	48.372 Å
R factor r_factor	0.2160
R_work r_work	0.2140
R_free r_free	0.2532

Crystal structure of the 3 ADP-bound V1 complex

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

V-type sodium ATPase 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 sodium ATPase subunit NtpG (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

5knc__assembly_1__model_1

5knc__assembly_1__model_1 | I(q)

5knc__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 (9)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (10 domains)

CATH v4.4 (13 domains)

7. Citations (1)