SAXSdb — 9vvo

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1. Structure Basics

entry_id	9vvo
deposition_date	2025-07-16
title	cryo-EM structure of gastric proton pump bound to YK01
keywords	P-type ATPase, transporters, gastric, P-CABs, proton pump, 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	46.51 Å
rg_electron	47.08 Å
i0	577023000.00
molecular_weight	133670.0 kDa
excluded_volume	130490 Å³
envelope_volume	246050 Å³
shell_volume	48324 Å³
envelope_diameter	169.4 Å
shell_rg	44.55 Å
envelope_rg	46.98 Å
shape_rg	47.05 Å
total_rg	47.04 Å
total_atoms	10118
n_residues	1250
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	156.6 Å
rg_real	47.27 Å
rg_real_error	2.00 Å
i0_real	5.7700e+08
i0_real_error	1.2350e+07
rg_reciprocal	46.51 Å
i0_reciprocal	576500000.0000
total_estimate	0.7509
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.8 Å
skewness	0.584
kurtosis	-0.436
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	26030000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.647; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.692; Smooth: 0.126

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Sodium/potassium-transporting ATPase subunit alpha
formula_weight	108832.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10491

NDHQLSVAELEQKYQTSATKGLSASLAAELLLRDGPNALRPPRGTPEYVKFARQLAGGLQCLMWVAAAICLIAFAIQASEGDLTTDDNLYLALALIAVVVVTGCFGYYQEFKSTNIIASFKNLVPQQATVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILQAQGCKVDNSSLTGESEPQTRSPECTHESPLETRNIAFFSTMCLEGTAQGLVVNTGDRTIIGRIASLASGVENEKTPIAIEIEHFVDIIAGLAILFGATFFIVAMCIGYTFLRAMVFFMAIVVAYVPEGLLATVTVCLSLTAKRLASKNCVVKNLEAVETLGSTSVICSDKTGTLTQNRMTVSHLWFDNHIHSADTTEDQSGQTFDQSSETWRALCRVLTLCNRAAFKSGQDAVPVPKRIVIGDASETALLKFSELTLGNAMGYRERFPKVCEIPFNSTNKFQLSIHTLEDPRDPRHVLVMKGAPERVLERCSSILIKGQELPLDEQWREAFQTAYLSLGGLGERVLGFCQLYLSEKDYPPGYAFDVEAMNFPTSGLCFAGLVSMIDPPRATVPDAVLKCRTAGIRVIMVTGDHPITAKAIAASVGIISEGSETVEDIAARLRVPVDQVNRKDARACVINGMQLKDMDPSELVEALRTHPEMVFARTSPQQKLVIVESCQRLGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDAAKNAADMILLDDNFASIVTGVEQGRLIFDNLKKSIAYTLTKNIPELTPYLIYITVSVPLPLGCITILFIELCTDIFPSVSLAYEKAESDIMHLRPRNPKRDRLVNEPLAAYSYFQIGAIQSFAGFTDYFTAMAQEGWFPLLCVGLRPQWENHHLQDLQDSYGQEWTFGQRLYQQYTCYTVFFISIEMCQIADVLIRKTRRLSAFQQGFFRNRILVIAIVFQVCIGCFLCYCPGMPNIFNFMPIRFQWWLVPMPFSLLIFVYDEIRKLGVRCCPGSWWDQELYY

Source

organism	Sus scrofa
common_name	pig
ncbi_taxonomy_id	9823
host_organism	Homo sapiens

Entity 2 polymer

description	Potassium-transporting ATPase subunit beta
formula_weight	30374.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

NPDTGQMLGRTLSRWVWISLYYVAFYVVMSGIFALCIYVLMRTIDPYTPDYQDQLKSPGVTLRPDVYGEKGLDISYNVSDSTTWAGLAHTLHRFLAGYSPAAQEGSINCTSEKYFFQESFLAPNHTKFSCKFTADMLQNCSGRPDPTFGFAEGKPCFIIKMNRIVKFLPGNSTAPRVDCAFLDQPRDGPPLQVEYFPANGTYSLHYFPYYGKKAQPHYSNPLVAAKLLNVPRNRDVVIVCKILAEHVSFDNPHDPYEGKVEFKLKIQK

Source

organism	Sus scrofa
common_name	pig
ncbi_taxonomy_id	9823
host_organism	Homo sapiens

Entity 3 non-polymer

description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	787.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	YK01-b
formula_weight	347.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	373

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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	2.66 Å
resolution_method	—
num_particles	177544

fit	/app/data/saxs_computation/vv/9vvo/9vvo.fit
pddf	/app/data/pr_computation/vv/9vvo/9vvo.pr.out
profile	/app/data/saxs_computation/vv/9vvo/9vvo.dat

cryo-EM structure of gastric proton pump bound to YK01

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)