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9vdl

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

Method: ELECTRON MICROSCOPY D_max: 123.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdl
deposition_date	2025-06-09
title	Cryo-EM structure of human ATP9A in BeF-bound E2P state closed form
keywords	P-type ATPase, flippase, human, TRANSPORT PROTEIN; TRANSPORT 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	35.87 Å
rg_electron	36.51 Å
i0	184471000.00
molecular_weight	113350.0 kDa
excluded_volume	143480 Å³
envelope_volume	180890 Å³
shell_volume	43275 Å³
envelope_diameter	130.2 Å
shell_rg	40.42 Å
envelope_rg	36.62 Å
shape_rg	36.57 Å
total_rg	36.58 Å
total_atoms	7971
n_residues	999
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	123.6 Å
rg_real	36.14 Å
rg_real_error	1.07 Å
i0_real	1.8450e+08
i0_real_error	3.2770e+06
rg_reciprocal	35.98 Å
i0_reciprocal	184400000.0000
total_estimate	0.8402
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.5 Å
skewness	0.559
kurtosis	-0.157
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0002
highest_alpha	38100000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.723

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	8241

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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	270

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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	2.31 Å
resolution_method	—
num_particles	84464

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