SAXSdb — 9r1f

▼

1. Structure Basics

entry_id	9r1f
deposition_date	2025-04-26
last_revision	2025-11-05
title	Cryo-EM structure of human MATE1 in complex with metformin
keywords	SLC47A1, ligand, Fab, multidrug transporter, TRANSPORT PROTEIN; TRANSPORT PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	39.15 Å
rg_electron	39.39 Å
i0	135784000.00
molecular_weight	101570.0 kDa
excluded_volume	130260 Å³
envelope_volume	170130 Å³
shell_volume	39130 Å³
envelope_diameter	135.4 Å
shell_rg	40.61 Å
envelope_rg	39.82 Å
shape_rg	39.35 Å
total_rg	39.66 Å
total_atoms	7165
n_residues	916
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

▼

3. P(r) Analysis (GNOM)

dmax	127.4 Å
rg_real	39.86 Å
rg_real_error	1.50 Å
i0_real	1.3580e+08
i0_real_error	2.4800e+06
rg_reciprocal	39.43 Å
i0_reciprocal	135700000.0000
total_estimate	0.7578
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.0 Å
skewness	0.613
kurtosis	-0.390
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	12060000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.664; Smooth: 0.047

▶

4. Crystallography & Experiment

▶

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	7204

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	nat
entity_count	5

Entity 5 non-polymer

description	Metformin
formula_weight	129.2 kDa
src_method	nat
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	39

▶

6. Citations (1)

▶

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	2.31 Å
resolution_method	—
num_particles	431222

fit	/app/data/saxs_computation/r1/9r1f/9r1f.fit
pddf	/app/data/pr_computation/r1/9r1f/9r1f.pr.out
profile	/app/data/saxs_computation/r1/9r1f/9r1f.dat

Cryo-EM structure of human MATE1 in complex with metformin

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

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)