3b8e

Crystal structure of the sodium-potassium pump

Method: X-RAY DIFFRACTION

▼

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 × 1 RUBIDIUM ION × 3 TETRAFLUOROMAGNESATE(2-) × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	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 × 1 RUBIDIUM ION × 3 TETRAFLUOROMAGNESATE(2-) × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AT1A1_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–998； UniProt 19–1016 Author chain C； PDBConstruct 1–998； UniProt 19–1016

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 （P05024） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） MAGNESIUM ION × 1 RUBIDIUM ION × 3 TETRAFLUOROMAGNESATE(2-) × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （P05024） Na+/K+ ATPase gamma subunit transcript variant a × 1 （Q58K79） MAGNESIUM ION × 1 RUBIDIUM ION × 3 TETRAFLUOROMAGNESATE(2-) × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	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 1–46； UniProt 28–73 Author chain D； PDBConstruct 1–46； UniProt 28–73

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 （P05024） Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） MAGNESIUM ION × 1 RUBIDIUM ION × 3 TETRAFLUOROMAGNESATE(2-) × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sodium/potassium-transporting ATPase subunit alpha-1 × 1 （P05024） Sodium/potassium-transporting ATPase subunit beta-1 × 1 （P05027） MAGNESIUM ION × 1 RUBIDIUM ION × 3 TETRAFLUOROMAGNESATE(2-) × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	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 G； PDBConstruct 1–29； UniProt 23–51 Author chain H； PDBConstruct 1–29； UniProt 23–51

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	3b8e
Deposition date deposition_date	2007-11-01
Structure title title	Crystal structure of the sodium-potassium pump
Keywords keywords	;Na+, K+-ATPASE, P-TYPE ATPASE, CATION PUMP, MEMBRANE PROTEIN, HYDROLASE, ATP-BINDING, CALCIUM TRANSPORT, ION TRANSPORT, MEMBRANE POTENTIAL, PHOSPHORYLATION, Magnesium, Metal-binding, Nucleotide-binding, Potassium, Potassium transport, Sodium, Sodium transport, Sodium/potassium transport, Transmembrane, Glycoprotein, Signal-anchor, HYDROLASE-TRANSPORT PROTEIN COMPLEX ;; HYDROLASE/TRANSPORT PROTEIN
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.

3b8e__assembly_2__model_1

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

Download this curve (.dat)

3b8e__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b8e__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	39.14 Å
Rg (electron density)	39.66 Å
Total Rg	39.44 Å
Atom count	8359
Residues	1073
Excluded volume	150620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b8e__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3b8e__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Sodium/potassium-transporting ATPase subunit alpha-1
Molecular weight formula_weight	110320.7 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	16718

AKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALSRIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPASKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNEQLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTPFFVTIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Entity 2 Entity 2 polymer

Description description	Sodium/potassium-transporting ATPase subunit beta-1
Molecular weight formula_weight	5225.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

TGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLTISEFKPTYQDRVA

Entity 3 Entity 3 polymer

Description description	Na+/K+ ATPase gamma subunit transcript variant a
Molecular weight formula_weight	3221.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

YETVRNGGLIFAALAFIVGLIIILSKRLR

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	2

Entity 5 Entity 5 non-polymer

Description description	RUBIDIUM ION
Molecular weight formula_weight	85.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	TETRAFLUOROMAGNESATE(2-)
Molecular weight formula_weight	100.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 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	2

▼

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3b8ea1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.220 — Metal cation-transporting ATPase, ATP-binding domain N
Superfamily Superfamily superfamily	d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N
Family Family family	d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N

Domain ID domain_id	d3b8ea2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.7 — Meta-cation ATPase, catalytic domain P

Domain ID domain_id	d3b8ea3
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.7 — Metal cation-transporting ATPase, actuator domain A
Family Family family	b.82.7.1 — Metal cation-transporting ATPase, actuator domain A

Domain ID domain_id	d3b8ea4
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.33 — Metal cation-transporting ATPase, transmembrane domain
Superfamily Superfamily superfamily	f.33.1 — Metal cation-transporting ATPase, transmembrane domain
Family Family family	f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain

Domain ID domain_id	d3b8eb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.42 — Sodium/potassium-transporting ATPase, beta subunit transmembrane helix
Family Family family	f.23.42.1 — Sodium/potassium-transporting ATPase, beta subunit transmembrane helix

Domain ID domain_id	d3b8ec1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.220 — Metal cation-transporting ATPase, ATP-binding domain N
Superfamily Superfamily superfamily	d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N
Family Family family	d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N

Domain ID domain_id	d3b8ec2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.7 — Meta-cation ATPase, catalytic domain P

Domain ID domain_id	d3b8ec3
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.7 — Metal cation-transporting ATPase, actuator domain A
Family Family family	b.82.7.1 — Metal cation-transporting ATPase, actuator domain A

Domain ID domain_id	d3b8ec4
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.33 — Metal cation-transporting ATPase, transmembrane domain
Superfamily Superfamily superfamily	f.33.1 — Metal cation-transporting ATPase, transmembrane domain
Family Family family	f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain

Domain ID domain_id	d3b8ed_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.42 — Sodium/potassium-transporting ATPase, beta subunit transmembrane helix
Family Family family	f.23.42.1 — Sodium/potassium-transporting ATPase, beta subunit transmembrane helix

Domain ID domain_id	d3b8eg_
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	d3b8eh_
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	3b8eA01
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	3b8eA02
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	3b8eA03
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	3b8eA04
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	3b8eB00
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	170 —

Domain ID domain_id	3b8eC01
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	3b8eC02
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	3b8eC03
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	3b8eC04
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	3b8eD00
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	170 —

▶

Unit-cell length a length_a	68.930 Å
Unit-cell length b length_b	261.500 Å
Unit-cell length c length_c	334.780 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	3.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2774
R_free r_free	0.3129

Crystal structure of the sodium-potassium pump

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

Sodium/potassium-transporting ATPase subunit beta-1

State in the Current Structure

Other States of the Same Protein in the Database

Na+/K+ ATPase gamma subunit transcript variant a

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

3b8e__assembly_2__model_1

3b8e__assembly_2__model_1 | I(q)

3b8e__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 (7)

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

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of the sodium-potassium pump

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

3b8e__assembly_2__model_1

3b8e__assembly_2__model_1 | I(q)

3b8e__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 (7)

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

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

CATH v4.4 (10 domains)

7. Citations (1)