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9vj2

Crystal structure of palytoxin-bound Na+,K+-ATPase in the E2P state

Method: X-RAY DIFFRACTION D_max: 168.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vj2
deposition_date	2025-06-19
last_revision	2025-10-01
title	Crystal structure of palytoxin-bound Na+,K+-ATPase in the E2P state
keywords	ion pump, P-type ATPase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	X-RAY DIFFRACTION

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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	46.47 Å
rg_electron	47.05 Å
i0	661520000.00
molecular_weight	142650.0 kDa
excluded_volume	138990 Å³
envelope_volume	270610 Å³
shell_volume	52244 Å³
envelope_diameter	170.8 Å
shell_rg	45.35 Å
envelope_rg	47.17 Å
shape_rg	47.02 Å
total_rg	47.03 Å
total_atoms	10793
n_residues	1318
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	168.9 Å
rg_real	47.21 Å
rg_real_error	2.53 Å
i0_real	6.6150e+08
i0_real_error	1.4560e+07
rg_reciprocal	46.48 Å
i0_reciprocal	660900000.0000
total_estimate	0.7597
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.8 Å
skewness	0.590
kurtosis	-0.405
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	42480000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.515; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.625; Smooth: 0.702

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Sodium/potassium-transporting ATPase subunit alpha
formula_weight	112937.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10796

MGKGVGRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGVSFDKTSATWLALSRIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTAFFVSIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Entity 2 polymer

description	Sodium/potassium-transporting ATPase subunit beta-1
formula_weight	35204.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLTISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDDMIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKLNRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPLQYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIEVKS

Entity 3 polymer

description	FXYD domain-containing ion transport regulator
formula_weight	7094.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPINEDEL

Entity 4 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	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	787.1 kDa
src_method	syn
entity_count	6

Entity 8 non-polymer

description	palytoxin
formula_weight	2680.1 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3

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6. Citations (1)

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length_a	85.022 Å
length_b	85.022 Å
length_c	646.129 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	3.790 Å
resolution_low	10.000 Å
r_factor	0.2293
r_work	0.2267
r_free	0.2757

fit	/app/data/saxs_computation/vj/9vj2/9vj2.fit
pddf	/app/data/pr_computation/vj/9vj2/9vj2.pr.out
profile	/app/data/saxs_computation/vj/9vj2/9vj2.dat

Crystal structure of palytoxin-bound Na+,K+-ATPase in the E2P state

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

Refinement

Diffraction

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)