3wgv

Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state with oligomycin

Method: X-RAY DIFFRACTION

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

Sodium/potassium-transporting ATPase subunit alpha-1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） MAGNESIUM ION × 2 TETRAFLUOROALUMINATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 SODIUM ION × 4 CHOLESTEROL × 3 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Oligomycin A × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） MAGNESIUM ION × 2 TETRAFLUOROALUMINATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 SODIUM ION × 4 CHOLESTEROL × 3 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Oligomycin A × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I7HD36_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1016； UniProt 5–1020 Author chain C； PDBConstruct 1–1016； UniProt 5–1020

Sodium/potassium-transporting ATPase subunit beta-1

OrganismNot specified

UniProt P05027

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （I7HD36） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） MAGNESIUM ION × 2 TETRAFLUOROALUMINATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 SODIUM ION × 4 CHOLESTEROL × 3 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Oligomycin A × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （I7HD36） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） MAGNESIUM ION × 2 TETRAFLUOROALUMINATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 SODIUM ION × 4 CHOLESTEROL × 3 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Oligomycin A × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AT1B1_PIG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–303； UniProt 1–303 Author chain D； PDBConstruct 1–303； UniProt 1–303

Na+/K+ ATPase gamma subunit transcript variant a

OrganismNot specified

UniProt Q58K79

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （I7HD36） Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） MAGNESIUM ION × 2 TETRAFLUOROALUMINATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 SODIUM ION × 4 CHOLESTEROL × 3 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Oligomycin A × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （I7HD36） Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） MAGNESIUM ION × 2 TETRAFLUOROALUMINATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 SODIUM ION × 4 CHOLESTEROL × 3 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Oligomycin A × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q58K79_PIG
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–65； UniProt 1–65 Author chain G； PDBConstruct 1–65； UniProt 1–65

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	3wgv
Deposition date deposition_date	2013-08-09
Structure title title	Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state with oligomycin
Keywords keywords	;membrane protein, ion pump, ATPase, Na+ binding, Haloacid dehydrogenease superfamily, phosphate analogue, ATP-binding, Hydrolase, Ion transport, Nucleotide-binding, Phosphoprotein, HYDROLASE-TRANSPORT PROTEIN-ANTIBIOTIC complex ;; HYDROLASE/TRANSPORT PROTEIN/ANTIBIOTIC
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.

3wgv__assembly_1__model_1

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

Download this curve (.dat)

3wgv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wgv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.30 Å
Rg (electron density)	46.12 Å
Total Rg	45.83 Å
Atom count	10925
Residues	1331
Excluded volume	198340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wgv__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wgv__assembly_2__model_1`	trimeric （3）	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 (12)

Entity 1 Entity 1 polymer

Description description	Sodium/potassium-transporting ATPase subunit alpha-1
Molecular weight formula_weight	112399.1 kDa
EC 编号 ec_number	3.6.3.9
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	21909

GRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGVSFDKTSATWLALSRIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTAFFVSIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Entity 2 Entity 2 polymer

Description description	Sodium/potassium-transporting ATPase subunit beta-1
Molecular weight formula_weight	35204.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLTISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDDMIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKLNRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPLQYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIEVKS

Entity 3 Entity 3 polymer

Description description	Na+/K+ ATPase gamma subunit transcript variant a
Molecular weight formula_weight	7094.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPINEDEL

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	TETRAFLUOROALUMINATE ION
Molecular weight formula_weight	103.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 non-polymer

Description description	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	790.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 10 Entity 10 non-polymer

Description description	Oligomycin A
Molecular weight formula_weight	791.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3wgve_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.43 — ATP1G1/PLM/MAT8-like (FXYD-like)
Family Family family	f.23.43.1 — ATP1G1/PLM/MAT8-like (FXYD-like)

Domain ID domain_id	d3wgvg_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.43 — ATP1G1/PLM/MAT8-like (FXYD-like)
Family Family family	f.23.43.1 — ATP1G1/PLM/MAT8-like (FXYD-like)

CATH v4.4 (10 domains)

Domain ID domain_id	3wgvA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	150 — Calcium-transporting ATPase, cytoplasmic transduction domain A
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic transduction domain A

Domain ID domain_id	3wgvA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1110 — Calcium-transporting ATPase, transmembrane domain
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, transmembrane domain

Domain ID domain_id	3wgvA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	3wgvA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

Domain ID domain_id	3wgvB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1660 — Na, k-atpase alpha subunit.

Domain ID domain_id	3wgvC01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	150 — Calcium-transporting ATPase, cytoplasmic transduction domain A
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic transduction domain A

Domain ID domain_id	3wgvC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1110 — Calcium-transporting ATPase, transmembrane domain
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, transmembrane domain

Domain ID domain_id	3wgvC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	3wgvC04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

Domain ID domain_id	3wgvD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1660 — Na, k-atpase alpha subunit.

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Unit-cell length a length_a	106.285 Å
Unit-cell length b length_b	210.183 Å
Unit-cell length c length_c	256.086 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	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.995 Å
R factor r_factor	0.2704
R_work r_work	0.2696
R_free r_free	0.2982

Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state with oligomycin

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

Sodium/potassium-transporting ATPase subunit alpha-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Sodium/potassium-transporting ATPase subunit beta-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Na+/K+ ATPase gamma subunit transcript variant 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3wgv__assembly_1__model_1

3wgv__assembly_1__model_1 | I(q)

3wgv__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 (12)

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 non-polymer

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 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (2 domains)

CATH v4.4 (10 domains)

7. Citations (1)