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9w63

Cryo-EM structure of C20:5-CoA bound state human ABCD3 in inward-facing conformation

Method: ELECTRON MICROSCOPY D_max: 127.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w63
deposition_date	2025-08-03
title	Cryo-EM structure of C20:5-CoA bound state human ABCD3 in inward-facing conformation
keywords	ABC transporter, 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	36.14 Å
rg_electron	36.32 Å
i0	66457700.00
molecular_weight	69134.0 kDa
excluded_volume	88582 Å³
envelope_volume	129070 Å³
shell_volume	32054 Å³
envelope_diameter	129.5 Å
shell_rg	39.13 Å
envelope_rg	35.36 Å
shape_rg	36.34 Å
total_rg	36.50 Å
total_atoms	4868
n_residues	573
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	127.0 Å
rg_real	36.44 Å
rg_real_error	1.48 Å
i0_real	6.6460e+07
i0_real_error	1.1250e+06
rg_reciprocal	36.26 Å
i0_reciprocal	66450000.0000
total_estimate	0.8522
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	37.5 Å
skewness	0.472
kurtosis	-0.412
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	4166000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.729; Smooth: 0.930

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Isoform 1 of ATP-binding cassette sub-family D member 3,Green fluorescent protein
formula_weight	104527.6 kDa
ec_number	3.1.2.-,7.6.2.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4868

MAAFSKYLTARNSSLAGAAFLLLCLLHKRRRALGLHGKKSGKPPLQNNEKEGKKERAVVDKVFFSRLIQILKIMVPRTFCKETGYLVLIAVMLVSRTYCDVWMIQNGTLIESGIIGRSRKDFKRYLLNFIAAMPLISLVNNFLKYGLNELKLCFRVRLTKYLYEEYLQAFTYYKMGNLDNRIANPDQLLTQDVEKFCNSVVDLYSNLSKPFLDIVLYIFKLTSAIGAQGPASMMAYLVVSGLFLTRLRRPIGKMTITEQKYEGEYRYVNSRLITNSEEIAFYNGNKREKQTVHSVFRKLVEHLHNFILFRFSMGFIDSIIAKYLATVVGYLVVSRPFLDLSHPRHLKSTHSELLEDYYQSGRMLLRMSQALGRIVLAGREMTRLAGFTARITELMQVLKDLNHGKYERTMVSQQEKGIEGVQVIPLIPGAGEIIIADNIIKFDHVPLATPNGDVLIRDLNFEVRSGANVLICGPNGCGKSSLFRVLGELWPLFGGRLTKPERGKLFYVPQRPYMTLGTLRDQVIYPDGREDQKRKGISDLVLKEYLDNVQLGHILEREGGWDSVQDWMDVLSGGEKQRMAMARLFYHKPQFAILDECTSAVSVDVEGYIYSHCRKVGITLFTVSHRKSLWKHHEYYLHMDGRGNYEFKQITEDTVEFGSLEVLFQGPAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	;S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate ;
formula_weight	1054.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	5

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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	—

resolution	3.29 Å
resolution_method	—
num_particles	119378

fit	/app/data/saxs_computation/w6/9w63/9w63.fit
pddf	/app/data/pr_computation/w6/9w63/9w63.pr.out
profile	/app/data/saxs_computation/w6/9w63/9w63.dat