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9vj0

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

Method: ELECTRON MICROSCOPY D_max: 206.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vj0
deposition_date	2025-06-19
last_revision	2025-10-01
title	Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ATP form)
keywords	ion pump, P-type ATPase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	58.17 Å
rg_electron	57.38 Å
i0	2746000000.00
molecular_weight	298530.0 kDa
excluded_volume	293070 Å³
envelope_volume	637430 Å³
shell_volume	95259 Å³
envelope_diameter	210.9 Å
shell_rg	56.23 Å
envelope_rg	56.87 Å
shape_rg	57.24 Å
total_rg	57.60 Å
total_atoms	22600
n_residues	2632
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	206.7 Å
rg_real	58.44 Å
rg_real_error	2.35 Å
i0_real	2.7460e+09
i0_real_error	5.9060e+07
rg_reciprocal	57.93 Å
i0_reciprocal	2744000000.0000
total_estimate	0.8510
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	68.9 Å
skewness	0.420
kurtosis	-0.358
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0001
highest_alpha	111200000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.717

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4. Crystallography & Experiment

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5. Entities & Polymer Info (13)

Entity 1 polymer

description	Na+,K+-ATPase beta subunit
formula_weight	35176.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,B
atom_count	22600

MARGKSKETDGGWKKFLWDSEKKEFLGRTGSSWFKIFLFYLIFYGCLAGIFIGTIQVLLLTLSDFEPKYQDRVAPPGLSHAPYAIKTEISFSISNPKSYESFVKSMHKLMDLYNESSQAGNSPFEDCSDTPADYIKRGDLDDSQGQKKACRFSRMWLKNCSGLDDTTYGYAEGKPCVVAKLNRIIGFYPKPLKNTTDLPEELQANYNQYVLPLRCAAKREEDREKIGSIEYFGLGGYAGFPLQYYPYYGKRLQKKYLQPLLAIQFTNLTQNMELRIECKVYGENIDYSEKDRFRGRFEVKIEVKS

Entity 2 polymer

description	Na, K-ATPase alpha subunit
formula_weight	113309.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,A

MGKGTASDKYEPAATSENATKSKKKGKKDKIDKKRDLDELKKEVSMDDHKLSLDELHNKYGTDLTRGLTNARAKEILARDGPNSLTPPPTTPEWIKFCRQLFGGFSILLWIGAILCFLAYGIQAATEDEPANDNLYLGVVLSTVVIVTGCFSYYQEAKSSRIMDSFKNMVPQQALVIRDGEKSTINAEFVVAGDLVEVKGGDRIPADLRIISAHGCKVDNSSLTGESEPQTRSPEFSSENPLETRNIAFFSTNCVEGTARGVVVYTGDRTVMGRIATLASGLEVGRTPIAIEIEHFIHIITGVAVFLGVSFFILSLILGYSWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGAAFDKTSATWSALSRIAALCNRAVFQAGQDNVPILKRSVAGDASESALLKCIELCCGSVQGMRDRNPKIVEIPFNSTNKYQLSIHENEKSSESRYLLVMKGAPERILDRCSTILLNGAEEPLKEDMKEAFQNAYLELGGLGERVLGFCHFALPEDKYNEGYPFDADEPNFPTTDLCFVGLMAMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETIEDIAARLNIPIGQVNPRDAKACVVHGSDLKDLSTEVLDDILHYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLVFIIGNVPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPMDLIGKRVRWDDRWISDVEDSFGQQWTYEQRKIVEFTCHTSFFISIVVVQWADLIICKTRRNSIFQQGMKNKILIFGLFEETALAAFLSYCPGTDVALRMYPLKPSWWFCAFPYSLIIFLYDEMRRFIIRRSPGGWVEQETYY

Entity 3 polymer

description	FXYD domain-containing ion transport regulator
formula_weight	10195.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,G

MLGAATGLMVLVAVTQGVWAMDPEGPDNDERFTYDYYRLRVVGLIVAAVLCVIGIIILLAGKCRCKFNQNKRTRSNSGTATAQHLLQPGEATEC

Entity 4 branched

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 ;
formula_weight	1057.0 kDa
src_method	man
entity_count	2

Entity 5 branched

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 ;
formula_weight	1114.0 kDa
src_method	man
entity_count	2

Entity 6 branched

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 ;
formula_weight	894.8 kDa
src_method	man
entity_count	2

Entity 7 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 8 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	10

Entity 9 non-polymer

description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	787.1 kDa
src_method	syn
entity_count	16

Entity 10 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 12 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	8

Entity 13 non-polymer

description	palytoxin
formula_weight	2680.1 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.70 Å
resolution_method	—
num_particles	31891

fit	/app/data/saxs_computation/vj/9vj0/9vj0.fit
pddf	/app/data/pr_computation/vj/9vj0/9vj0.pr.out
profile	/app/data/saxs_computation/vj/9vj0/9vj0.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (13)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 branched

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)