SAXSdb — 9r10

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1. Structure Basics

entry_id	9r10
deposition_date	2025-04-24
last_revision	2025-11-05
title	Cryo-EM structure of human MATE1 in complex with cimetidine
keywords	SLC47A1, inhibitor, Fab, multidrug 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	39.26 Å
rg_electron	39.36 Å
i0	137467000.00
molecular_weight	103950.0 kDa
excluded_volume	134060 Å³
envelope_volume	174490 Å³
shell_volume	40241 Å³
envelope_diameter	139.0 Å
shell_rg	40.44 Å
envelope_rg	39.69 Å
shape_rg	39.31 Å
total_rg	39.62 Å
total_atoms	7334
n_residues	921
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	129.1 Å
rg_real	39.98 Å
rg_real_error	1.38 Å
i0_real	1.3750e+08
i0_real_error	2.4320e+06
rg_reciprocal	39.54 Å
i0_reciprocal	137400000.0000
total_estimate	0.7579
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	32.3 Å
skewness	0.615
kurtosis	-0.383
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	12590000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.715; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.646; Smooth: 0.058

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Multidrug and toxin extrusion protein 1
formula_weight	61967.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7335

MEAPEEPAPVRGGPEATLEVRGSRCLRLSAFREELRALLVLAGPAFLVQLMVFLISFISSVFCGHLGKLELDAVTLAIAVINVTGVSVGFGLSSACDTLISQTYGSQNLKHVGVILQRSALVLLLCCFPCWALFLNTQHILLLFRQDPDVSRLTQTYVTIFIPALPATFLYMLQVKYLLNQGIVLPQIVTGVAANLVNALANYLFLHQLHLGVIGSALANLISQYTLALLLFLYILGKKLHQATWGGWSLECLQDWASFLRLAIPSMLMLCMEWWAYEVGSFLSGILGMVELGAQSIVYELAIIVYMVPAGFSVAASVRVGNALGAGDMEQARKSSTVSLLITVLFAVAFSVLLLSCKDHVGYIFTTDRDIINLVAQVVPIYAVSHLFEALACTSGGVLRGSGNQKVGAIVNTIGYYVVGLPIGIALMFATTLGVMGLWSGIIICTVFQAVCFLGFIIQLNWKKACQQAQVHANLKVNNVPRSGNSALPQDPLHPGCPENLEGILTNDVGKTGEPQSDQQMRQEEPLPEHPQDGAKLSRKQLVLRRGLLLLGVFLILLVGILVRFYVRIQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Heavy chain of Fab
formula_weight	24250.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

VQLVESGGGLVQPGGSLRLSCAASGFNFSYSYIHWVRQAPGKGLEWVASISSYYGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWANTSSYGWRFWSNGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 polymer

description	Light chain of Fab
formula_weight	23140.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYWWPLTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 4 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	9

Entity 5 non-polymer

description	Cimetidine
formula_weight	252.3 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
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	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	588461

fit	/app/data/saxs_computation/r1/9r10/9r10.fit
pddf	/app/data/pr_computation/r1/9r10/9r10.pr.out
profile	/app/data/saxs_computation/r1/9r10/9r10.dat

Cryo-EM structure of human MATE1 in complex with cimetidine

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)