7wyz

Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP with ouabain

Method: ELECTRON MICROSCOPY

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

Sodium/potassium-transporting ATPase subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 4	Na+,K+-ATPase beta subunit × 1 （C4IX13） FXYD domain-containing ion transport regulator × 1 （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 ; × 1 ;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 ; × 1 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 1 SODIUM ION × 2 OUABAIN × 1 CHOLESTEROL × 4 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 water × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 4	Na+,K+-ATPase beta subunit × 1 （C4IX13） FXYD domain-containing ion transport regulator × 1 （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 ; × 1 ;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 ; × 1 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 1 SODIUM ION × 2 OUABAIN × 1 CHOLESTEROL × 4 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 water × 1	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1028； UniProt 1–1028 Author chain C； PDBConstruct 1–1028； UniProt 1–1028

Na+,K+-ATPase beta subunit

OrganismNot specified

UniProt C4IX13

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 4	Sodium/potassium-transporting ATPase subunit alpha × 1 （Q4H132） FXYD domain-containing ion transport regulator × 1 （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 ; × 1 ;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 ; × 1 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 1 SODIUM ION × 2 OUABAIN × 1 CHOLESTEROL × 4 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 water × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 4	Sodium/potassium-transporting ATPase subunit alpha × 1 （Q4H132） FXYD domain-containing ion transport regulator × 1 （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 ; × 1 ;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 ; × 1 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 1 SODIUM ION × 2 OUABAIN × 1 CHOLESTEROL × 4 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 water × 1	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–305； UniProt 1–305 Author chain D； PDBConstruct 1–305； UniProt 1–305

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 3 其他Polymer 4	Sodium/potassium-transporting ATPase subunit alpha × 1 （Q4H132） Na+,K+-ATPase beta subunit × 1 （C4IX13） ;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 ; × 1 ;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 ; × 1 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 1 SODIUM ION × 2 OUABAIN × 1 CHOLESTEROL × 4 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 water × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 4	Sodium/potassium-transporting ATPase subunit alpha × 1 （Q4H132） Na+,K+-ATPase beta subunit × 1 （C4IX13） ;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 ; × 1 ;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 ; × 1 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAGNESIUM ION × 1 SODIUM ION × 2 OUABAIN × 1 CHOLESTEROL × 4 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 water × 1	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	7wyz
Deposition date deposition_date	2022-02-16
Structure title title	Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP with ouabain
Keywords keywords	Na+, K+-ATPase, membrane protein, ion transport, TRANSPORT 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.

7wyz__assembly_1__model_1

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

Download this curve (.dat)

7wyz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7wyz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.54 Å
Rg (electron density)	48.14 Å
Total Rg	47.86 Å
Atom count	11339
Residues	1326
Excluded volume	206580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7wyz__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7wyz__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 (13)

Entity 1 Entity 1 polymer

Description description	Sodium/potassium-transporting ATPase subunit alpha
Molecular weight formula_weight	113389.9 kDa
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	22682

MGKGTASDKYEPAATSENATKSKKKGKKDKIDKKRDLDELKKEVSMDDHKLSLDELHNKYGTDLTRGLTNARAKEILARDGPNSLTPPPTTPEWIKFCRQLFGGFSILLWIGAILCFLAYGIQAATEDEPANDNLYLGVVLSTVVIVTGCFSYYQEAKSSRIMDSFKNMVPQQALVIRDGEKSTINAEFVVAGDLVEVKGGDRIPADLRIISAHGCKVDNSSLTGESEPQTRSPEFSSENPLETRNIAFFSTNCVEGTARGVVVYTGDRTVMGRIATLASGLEVGRTPIAIEIEHFIHIITGVAVFLGVSFFILSLILGYSWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGAAFDKTSATWSALSRIAALCNRAVFQAGQDNVPILKRSVAGDASESALLKCIELCCGSVQGMRDRNPKIVEIPFNSTNKYQLSIHENEKSSESRYLLVMKGAPERILDRCSTILLNGAEEPLKEDMKEAFQNAYLELGGLGERVLGFCHFALPEDKYNEGYPFDADEPNFPTTDLCFVGLMAMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETIEDIAARLNIPIGQVNPRDAKACVVHGSDLKDLSTEVLDDILHYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLVFIIGNVPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPMDLIGKRVRWDDRWISDVEDSFGQQWTYEQRKIVEFTCHTSFFISIVVVQWADLIICKTRRNSIFQQGMKNKILIFGLFEETALAAFLSYCPGTDVALRMYPLKPSWWFCAFPYSLIIFLYDEMRRFIIRRSPGGWVEQETYY

Entity 2 Entity 2 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	B,D

MARGKSKETDGGWKKFLWDSEKKEFLGRTGSSWFKIFLFYLIFYGCLAGIFIGTIQVLLLTLSDFEPKYQDRVAPPGLSHAPYAIKTEISFSISNPKSYESFVKSMHKLMDLYNESSQAGNSPFEDCSDTPADYIKRGDLDDSQGQKKACRFSRMWLKNCSGLDDTTYGYAEGKPCVVAKLNRIIGFYPKPLKNTTDLPEELQANYNQYVLPLRCAAKREEDREKIGSIEYFGLGGYAGFPLQYYPYYGKRLQKKYLQPLLAIQFTNLTQNMELRIECKVYGENIDYSEKDRFRGRFEVKIEVKS

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	G,E

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

Entity 9 Entity 9 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 non-polymer

Description description	OUABAIN
Molecular weight formula_weight	584.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 12 Entity 12 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	24

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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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	97465

Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP with ouabain

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

Sodium/potassium-transporting ATPase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Na+,K+-ATPase beta 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

7wyz__assembly_1__model_1

7wyz__assembly_1__model_1 | I(q)

7wyz__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 water

7. Citations (1)

Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP with ouabain

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

Sodium/potassium-transporting ATPase subunit alpha

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 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

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

7wyz__assembly_1__model_1

7wyz__assembly_1__model_1 | I(q)

7wyz__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 water

7. Citations (1)