9vj1

Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ADP form)

Method: ELECTRON MICROSCOPY

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

Na+,K+-ATPase beta subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 其他Polymer 8	Na, K-ATPase alpha subunit × 2 （Q4H132） FXYD domain-containing ion transport regulator × 2 （Q70Q12） ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CHOLESTEROL × 10 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 18 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 2 SODIUM ION × 8 palytoxin × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C4IX13_SQUAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–305； UniProt 1–305 Author chain D； PDBConstruct 1–305； UniProt 1–305

Na, K-ATPase alpha subunit

OrganismNot specified

UniProt Q4H132

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 其他Polymer 8	Na+,K+-ATPase beta subunit × 2 （C4IX13） FXYD domain-containing ion transport regulator × 2 （Q70Q12） ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CHOLESTEROL × 10 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 18 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 2 SODIUM ION × 8 palytoxin × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4H132_SQUAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–1028； UniProt 1–1028 Author chain C； PDBConstruct 1–1028； UniProt 1–1028

FXYD domain-containing ion transport regulator

OrganismNot specified

UniProt Q70Q12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 其他Polymer 8	Na+,K+-ATPase beta subunit × 2 （C4IX13） Na, K-ATPase alpha subunit × 2 （Q4H132） ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CHOLESTEROL × 10 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 18 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 2 SODIUM ION × 8 palytoxin × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q70Q12_SQUAC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–94； UniProt 1–94 Author chain G； PDBConstruct 1–94； UniProt 1–94

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	9vj1
Deposition date deposition_date	2025-06-19
Last revision last_revision	2025-10-01
Structure title title	Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ADP form)
Keywords keywords	ion pump, P-type ATPase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

9vj1__assembly_1__model_1

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

Download this curve (.dat)

9vj1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vj1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	58.82 Å
Rg (electron density)	57.01 Å
Total Rg	56.94 Å
Atom count	22636
Residues	2632
Excluded volume	410040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vj1__assembly_1__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 (13)

Entity 1 Entity 1 polymer

Description description	Na+,K+-ATPase beta subunit
Molecular weight formula_weight	35176.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,B
Atom count atom_count	22636

MARGKSKETDGGWKKFLWDSEKKEFLGRTGSSWFKIFLFYLIFYGCLAGIFIGTIQVLLLTLSDFEPKYQDRVAPPGLSHAPYAIKTEISFSISNPKSYESFVKSMHKLMDLYNESSQAGNSPFEDCSDTPADYIKRGDLDDSQGQKKACRFSRMWLKNCSGLDDTTYGYAEGKPCVVAKLNRIIGFYPKPLKNTTDLPEELQANYNQYVLPLRCAAKREEDREKIGSIEYFGLGGYAGFPLQYYPYYGKRLQKKYLQPLLAIQFTNLTQNMELRIECKVYGENIDYSEKDRFRGRFEVKIEVKS

Entity 2 Entity 2 polymer

Description description	Na, K-ATPase alpha subunit
Molecular weight formula_weight	113309.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A

MGKGTASDKYEPAATSENATKSKKKGKKDKIDKKRDLDELKKEVSMDDHKLSLDELHNKYGTDLTRGLTNARAKEILARDGPNSLTPPPTTPEWIKFCRQLFGGFSILLWIGAILCFLAYGIQAATEDEPANDNLYLGVVLSTVVIVTGCFSYYQEAKSSRIMDSFKNMVPQQALVIRDGEKSTINAEFVVAGDLVEVKGGDRIPADLRIISAHGCKVDNSSLTGESEPQTRSPEFSSENPLETRNIAFFSTNCVEGTARGVVVYTGDRTVMGRIATLASGLEVGRTPIAIEIEHFIHIITGVAVFLGVSFFILSLILGYSWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGAAFDKTSATWSALSRIAALCNRAVFQAGQDNVPILKRSVAGDASESALLKCIELCCGSVQGMRDRNPKIVEIPFNSTNKYQLSIHENEKSSESRYLLVMKGAPERILDRCSTILLNGAEEPLKEDMKEAFQNAYLELGGLGERVLGFCHFALPEDKYNEGYPFDADEPNFPTTDLCFVGLMAMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETIEDIAARLNIPIGQVNPRDAKACVVHGSDLKDLSTEVLDDILHYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLVFIIGNVPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPMDLIGKRVRWDDRWISDVEDSFGQQWTYEQRKIVEFTCHTSFFISIVVVQWADLIICKTRRNSIFQQGMKNKILIFGLFEETALAAFLSYCPGTDVALRMYPLKPSWWFCAFPYSLIIFLYDEMRRFIIRRSPGGWVEQETYY

Entity 3 Entity 3 polymer

Description description	FXYD domain-containing ion transport regulator
Molecular weight formula_weight	10195.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MLGAATGLMVLVAVTQGVWAMDPEGPDNDERFTYDYYRLRVVGLIVAAVLCVIGIIILLAGKCRCKFNQNKRTRSNSGTATAQHLLQPGEATEC

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1057.0 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1114.0 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 branched

Description description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	894.8 kDa
Source method src_method	man
Copy count entity_count	2

Entity 7 Entity 7 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

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	10

Entity 9 Entity 9 non-polymer

Description description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	787.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 10 Entity 10 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 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 12 Entity 12 non-polymer

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

Entity 13 Entity 13 non-polymer

Description description	palytoxin
Molecular weight formula_weight	2680.1 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	28472

Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ADP form)

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

Na+,K+-ATPase beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Na, K-ATPase alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

FXYD domain-containing ion transport regulator

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

9vj1__assembly_1__model_1

9vj1__assembly_1__model_1 | I(q)

9vj1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

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 non-polymer

Entity 13 Entity 13 non-polymer

7. Citations (1)

Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ADP form)

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

Na+,K+-ATPase beta subunit

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 alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

FXYD domain-containing ion transport regulator

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

9vj1__assembly_1__model_1

9vj1__assembly_1__model_1 | I(q)

9vj1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

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 non-polymer

Entity 13 Entity 13 non-polymer

7. Citations (1)