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9w65

Cryo-EM structure of ATP bound state human ABCD3 in inward-facing conformation

Method: ELECTRON MICROSCOPY D_max: 128.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w65
deposition_date	2025-08-03
title	Cryo-EM structure of ATP 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	37.42 Å
rg_electron	37.40 Å
i0	68635600.00
molecular_weight	68215.0 kDa
excluded_volume	86412 Å³
envelope_volume	126550 Å³
shell_volume	30768 Å³
envelope_diameter	128.6 Å
shell_rg	39.84 Å
envelope_rg	36.25 Å
shape_rg	37.43 Å
total_rg	37.47 Å
total_atoms	4794
n_residues	575
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	128.3 Å
rg_real	37.66 Å
rg_real_error	1.53 Å
i0_real	6.8640e+07
i0_real_error	1.3260e+06
rg_reciprocal	37.52 Å
i0_reciprocal	68630000.0000
total_estimate	0.8675
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.6 Å
skewness	0.324
kurtosis	-0.669
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	3693000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.785; Smooth: 0.927

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	ATP-binding cassette sub-family D member 3,Green fluorescent protein
formula_weight	104526.6 kDa
ec_number	3.1.2.-,7.6.2.-
mutation	E596Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4794

MAAFSKYLTARNSSLAGAAFLLLCLLHKRRRALGLHGKKSGKPPLQNNEKEGKKERAVVDKVFFSRLIQILKIMVPRTFCKETGYLVLIAVMLVSRTYCDVWMIQNGTLIESGIIGRSRKDFKRYLLNFIAAMPLISLVNNFLKYGLNELKLCFRVRLTKYLYEEYLQAFTYYKMGNLDNRIANPDQLLTQDVEKFCNSVVDLYSNLSKPFLDIVLYIFKLTSAIGAQGPASMMAYLVVSGLFLTRLRRPIGKMTITEQKYEGEYRYVNSRLITNSEEIAFYNGNKREKQTVHSVFRKLVEHLHNFILFRFSMGFIDSIIAKYLATVVGYLVVSRPFLDLSHPRHLKSTHSELLEDYYQSGRMLLRMSQALGRIVLAGREMTRLAGFTARITELMQVLKDLNHGKYERTMVSQQEKGIEGVQVIPLIPGAGEIIIADNIIKFDHVPLATPNGDVLIRDLNFEVRSGANVLICGPNGCGKSSLFRVLGELWPLFGGRLTKPERGKLFYVPQRPYMTLGTLRDQVIYPDGREDQKRKGISDLVLKEYLDNVQLGHILEREGGWDSVQDWMDVLSGGEKQRMAMARLFYHKPQFAILDQCTSAVSVDVEGYIYSHCRKVGITLFTVSHRKSLWKHHEYYLHMDGRGNYEFKQITEDTVEFGSLEVLFQGPAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

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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	2.94 Å
resolution_method	—
num_particles	65336

fit	/app/data/saxs_computation/w6/9w65/9w65.fit
pddf	/app/data/pr_computation/w6/9w65/9w65.pr.out
profile	/app/data/saxs_computation/w6/9w65/9w65.dat