SAXSdb — 9vdk

▼

1. Structure Basics

entry_id	9vdk
deposition_date	2025-06-09
title	Cryo-EM structure of human ATP9A in BeF-bound E2P state open form
keywords	P-type ATPase, flippase, human, TRANSPORT PROTEIN; TRANSPORT PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.12 Å
rg_electron	36.86 Å
i0	187050000.00
molecular_weight	115680.0 kDa
excluded_volume	147000 Å³
envelope_volume	186810 Å³
shell_volume	44062 Å³
envelope_diameter	132.5 Å
shell_rg	40.87 Å
envelope_rg	37.23 Å
shape_rg	36.92 Å
total_rg	36.91 Å
total_atoms	8130
n_residues	996
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	123.8 Å
rg_real	36.41 Å
rg_real_error	1.18 Å
i0_real	1.8700e+08
i0_real_error	3.2190e+06
rg_reciprocal	36.23 Å
i0_reciprocal	187000000.0000
total_estimate	0.8370
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.6 Å
skewness	0.578
kurtosis	-0.128
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	37440000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.866; Smooth: 0.685

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Probable phospholipid-transporting ATPase IIA
formula_weight	115036.8 kDa
ec_number	7.6.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8428

GGEARPRTVWLGHPEKRDQRYPRNVINNQKYNFFTFLPGVLFNQFKYFFNLYFLLLACSQFVPEMRLGALYTYWVPLGFVLAVTVIREAVEEIRCYVRDKEVNSQVYSRLTARGTVKVKSSNIQVGDLIIVEKNQRVPADMIFLRTSEKNGSCFLRTDQLDGETDWKLRLPVACTQRLPTAADLLQIRSYVYAEEPNIDIHNFVGTFTREDSDPPISESLSIENTLWAGTVVASGTVVGVVLYTGRELRSVMNTSNPRSKIGLFDLEVNCLTKILFGALVVVSLVMVALQHFAGRWYLQIIRFLLLFSNIIPISLRVNLDMGKIVYSWVIRRDSKIPGTVVRSSTIPEQLGRISYLLTDKTGTLTQNEMIFKRLHLGTVAYGLDSMDEVQSHIFSIYTQQSQDPPAQKGPTLTTKVRRTMSSRVHEAVKAIALCHNVTPVYESNGVTDQAEAEKQYEDSCRVYQASSPDEVALVQWTESVGLTLVGRDQSSMQLRTPGDQILNFTILQIFPFTYESKRMGIIVRDESTGEITFYMKGADVVMAGIVQYNDWLEEECGNMAREGLRVLVVAKKSLAEEQYQDFEARYVQAKLSVHDRSLKVATVIESLEMEMELLCLTGVEDQLQADVRPTLETLRNAGIKVWMLTGDKLETATCTAKNAHLVTRNQDIHVFRLVTNRGEAHLELNAFRRKHDCALVISGDSLEVCLKYYEYEFMELACQCPAVVCCRCAPTQKAQIVRLLQERTGKLTCAVGDGGNDVSMIQESDCGVGVEGKEGKQASLAADFSITQFKHLGRLLMVHGRNSYKRSAALSQFVIHRSLCISTMQAVFSSVFYFASVPLYQGFLIIGYSTIYTMFPVFSLVLDKDVKSEVAMLYPELYKDLLKGRPLSYKTFLIWVLISIYQGSTIMYGALLLFESEFVHIVAISFTSLILTELLMVALTIQTWHWLMTVAELLSLACYIASLVFLHEFIDVYFIATLSFLWKVSVITLVSCLPLYVLKYLRRRFSPPSYSKLTS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
formula_weight	792.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

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

Entity 5 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	298

▶

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	2.18 Å
resolution_method	—
num_particles	126825

fit	/app/data/saxs_computation/vd/9vdk/9vdk.fit
pddf	/app/data/pr_computation/vd/9vdk/9vdk.pr.out
profile	/app/data/saxs_computation/vd/9vdk/9vdk.dat

Cryo-EM structure of human ATP9A in BeF-bound E2P state open form

SAXS Profile

P(r) Distribution