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9w62

Cryo-EM structure of human ABCD3 in inward-facing conformation in the presence of phytanoyl-CoA

Method: ELECTRON MICROSCOPY D_max: 122.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w62
deposition_date	2025-08-03
title	Cryo-EM structure of human ABCD3 in inward-facing conformation in the presence of phytanoyl-CoA
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	37.57 Å
rg_electron	37.36 Å
i0	64267900.00
molecular_weight	67781.0 kDa
excluded_volume	86604 Å³
envelope_volume	129720 Å³
shell_volume	31297 Å³
envelope_diameter	130.0 Å
shell_rg	40.47 Å
envelope_rg	36.27 Å
shape_rg	37.38 Å
total_rg	37.54 Å
total_atoms	4774
n_residues	574
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	122.0 Å
rg_real	37.80 Å
rg_real_error	1.15 Å
i0_real	6.4270e+07
i0_real_error	1.1190e+06
rg_reciprocal	37.66 Å
i0_reciprocal	64260000.0000
total_estimate	0.8524
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.7 Å
skewness	0.324
kurtosis	-0.639
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	3352000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.864; Smooth: 0.385

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	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	B
atom_count	4774

MAAFSKYLTARNSSLAGAAFLLLCLLHKRRRALGLHGKKSGKPPLQNNEKEGKKERAVVDKVFFSRLIQILKIMVPRTFCKETGYLVLIAVMLVSRTYCDVWMIQNGTLIESGIIGRSRKDFKRYLLNFIAAMPLISLVNNFLKYGLNELKLCFRVRLTKYLYEEYLQAFTYYKMGNLDNRIANPDQLLTQDVEKFCNSVVDLYSNLSKPFLDIVLYIFKLTSAIGAQGPASMMAYLVVSGLFLTRLRRPIGKMTITEQKYEGEYRYVNSRLITNSEEIAFYNGNKREKQTVHSVFRKLVEHLHNFILFRFSMGFIDSIIAKYLATVVGYLVVSRPFLDLSHPRHLKSTHSELLEDYYQSGRMLLRMSQALGRIVLAGREMTRLAGFTARITELMQVLKDLNHGKYERTMVSQQEKGIEGVQVIPLIPGAGEIIIADNIIKFDHVPLATPNGDVLIRDLNFEVRSGANVLICGPNGCGKSSLFRVLGELWPLFGGRLTKPERGKLFYVPQRPYMTLGTLRDQVIYPDGREDQKRKGISDLVLKEYLDNVQLGHILEREGGWDSVQDWMDVLSGGEKQRMAMARLFYHKPQFAILDECTSAVSVDVEGYIYSHCRKVGITLFTVSHRKSLWKHHEYYLHMDGRGNYEFKQITEDTVEFGSLEVLFQGPAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
formula_weight	760.1 kDa
src_method	syn
entity_count	1

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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	3.28 Å
resolution_method	—
num_particles	73450

fit	/app/data/saxs_computation/w6/9w62/9w62.fit
pddf	/app/data/pr_computation/w6/9w62/9w62.pr.out
profile	/app/data/saxs_computation/w6/9w62/9w62.dat