← Back to search

9viz

Cryo-EM structure of palytoxin-bound Na+,K+-ATPase in the transient state of dephosphorylation (E2~P)

Method: ELECTRON MICROSCOPY D_max: 195.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9viz
deposition_date	2025-06-19
last_revision	2025-10-01
title	Cryo-EM structure of palytoxin-bound Na+,K+-ATPase in the transient state of dephosphorylation (E2~P)
keywords	ion pump, P-type ATPase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	60.18 Å
rg_electron	59.51 Å
i0	2808420000.00
molecular_weight	302050.0 kDa
excluded_volume	296520 Å³
envelope_volume	631170 Å³
shell_volume	93209 Å³
envelope_diameter	209.4 Å
shell_rg	55.61 Å
envelope_rg	59.06 Å
shape_rg	59.38 Å
total_rg	59.67 Å
total_atoms	22862
n_residues	2654
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

▼

3. P(r) Analysis (GNOM)

dmax	195.6 Å
rg_real	60.54 Å
rg_real_error	1.86 Å
i0_real	2.8080e+09
i0_real_error	6.2160e+07
rg_reciprocal	59.85 Å
i0_reciprocal	2805000000.0000
total_estimate	0.8392
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	75.2 Å
skewness	0.445
kurtosis	-0.277
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	70840000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.116

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (13)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	22862

MGKGTASDKYEPAATSENATKSKKKGKKDKIDKKRDLDELKKEVSMDDHKLSLDELHNKYGTDLTRGLTNARAKEILARDGPNSLTPPPTTPEWIKFCRQLFGGFSILLWIGAILCFLAYGIQAATEDEPANDNLYLGVVLSTVVIVTGCFSYYQEAKSSRIMDSFKNMVPQQALVIRDGEKSTINAEFVVAGDLVEVKGGDRIPADLRIISAHGCKVDNSSLTGESEPQTRSPEFSSENPLETRNIAFFSTNCVEGTARGVVVYTGDRTVMGRIATLASGLEVGRTPIAIEIEHFIHIITGVAVFLGVSFFILSLILGYSWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGAAFDKTSATWSALSRIAALCNRAVFQAGQDNVPILKRSVAGDASESALLKCIELCCGSVQGMRDRNPKIVEIPFNSTNKYQLSIHENEKSSESRYLLVMKGAPERILDRCSTILLNGAEEPLKEDMKEAFQNAYLELGGLGERVLGFCHFALPEDKYNEGYPFDADEPNFPTTDLCFVGLMAMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETIEDIAARLNIPIGQVNPRDAKACVVHGSDLKDLSTEVLDDILHYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLVFIIGNVPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPMDLIGKRVRWDDRWISDVEDSFGQQWTYEQRKIVEFTCHTSFFISIVVVQWADLIICKTRRNSIFQQGMKNKILIFGLFEETALAAFLSYCPGTDVALRMYPLKPSWWFCAFPYSLIIFLYDEMRRFIIRRSPGGWVEQETYY

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	B,D

MARGKSKETDGGWKKFLWDSEKKEFLGRTGSSWFKIFLFYLIFYGCLAGIFIGTIQVLLLTLSDFEPKYQDRVAPPGLSHAPYAIKTEISFSISNPKSYESFVKSMHKLMDLYNESSQAGNSPFEDCSDTPADYIKRGDLDDSQGQKKACRFSRMWLKNCSGLDDTTYGYAEGKPCVVAKLNRIIGFYPKPLKNTTDLPEELQANYNQYVLPLRCAAKREEDREKIGSIEYFGLGGYAGFPLQYYPYYGKRLQKKYLQPLLAIQFTNLTQNMELRIECKVYGENIDYSEKDRFRGRFEVKIEVKS

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	G,E

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	8

Entity 9 non-polymer

description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	787.1 kDa
src_method	syn
entity_count	22

Entity 10 non-polymer

description	TETRAFLUOROALUMINATE ION
formula_weight	103.0 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 12 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 13 non-polymer

description	palytoxin
formula_weight	2680.1 kDa
src_method	syn
entity_count	2

▶

6. Citations (1)

▶

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	3.40 Å
resolution_method	—
num_particles	62516

fit	/app/data/saxs_computation/vi/9viz/9viz.fit
pddf	/app/data/pr_computation/vi/9viz/9viz.pr.out
profile	/app/data/saxs_computation/vi/9viz/9viz.dat

Cryo-EM structure of palytoxin-bound Na+,K+-ATPase in the transient state of dephosphorylation (E2~P)

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)