SAXSdb — 9rsj

▼

1. Structure Basics

entry_id	9rsj
deposition_date	2025-07-01
title	Cryo-EM structure of MATE transporter NorM-VC in complex with doxorubicin
keywords	NabFab, substrate, 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	46.34 Å
rg_electron	47.38 Å
i0	209649000.00
molecular_weight	122800.0 kDa
excluded_volume	155340 Å³
envelope_volume	219810 Å³
shell_volume	42588 Å³
envelope_diameter	161.0 Å
shell_rg	44.88 Å
envelope_rg	47.06 Å
shape_rg	47.35 Å
total_rg	47.40 Å
total_atoms	8656
n_residues	1102
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	149.3 Å
rg_real	47.11 Å
rg_real_error	1.93 Å
i0_real	2.0960e+08
i0_real_error	4.4640e+06
rg_reciprocal	46.34 Å
i0_reciprocal	209400000.0000
total_estimate	0.7496
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	35.1 Å
skewness	0.552
kurtosis	-0.568
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	12120000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.692; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.664; Smooth: 0.003

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Multidrug resistance protein NorM
formula_weight	49892.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8664

MENSVHRYKKEASNLIKLATPVLIASVAQTGMGFVDTIMAGGVSAIDMAAVSIAASIWLPSILFGVGLLMALVPVVAQLNGAGRQHKIPFEVHQGLILALLVSVPIIAVLFQTQFIIRFMDVEEAMATKTVGYMHAVIFAVPAYLLFQALRSFTDGMSLTKPAMVIGFIGLLLNIPLNWIFVYGKFGAPELGGVGCGVATAIVYWIMLLLLLFYIVTSKRLAHVKVFETFHKPQPKELIRLFRLGFPVAAALFFEVTLFAVVALLVAPLGSTVVAAHQVALNFSSLVFMFPMSIGAAVSIRVGHKLGEQDTKGAAIAANVGLMTGLATACITALLTVLFREQIALLYTENQVVVALAMQLLLFAAIYQCMDAVQVVAAGSLRGYKDMTAIFHRTFISYWVLGLPTGYILGMTNWLTEQPLGAKGFWLGFIIGLSAAALMLGQRLYWLQKQSDDVQLHLAAK

Source

organism	Vibrio cholerae
ncbi_taxonomy_id	666
host_organism	Escherichia coli

Entity 2 polymer

description	NabFab HC
formula_weight	25684.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSYYSIHWVRQAPGKGLEWVAYISSSSSYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGYQYWQYHASWYWNGGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 polymer

description	NabFab LC
formula_weight	23258.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 4 polymer

description	NorM-Nb17_4
formula_weight	14357.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

QRQLVESGGGLVQPGGSLRLSCAASGIIFKINDMGWFRQAPGKEREGVAGITSGGRTNYADSVKGRFIISRDNVKNTVYLQMNSLEPEDTAVYYCKSDGLISYAASQLSTYWGKGTPVTVSSHHHHHHEPEA

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 5 polymer

description	Anti-Fab nanobody
formula_weight	13390.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 6 non-polymer

description	DOXORUBICIN
formula_weight	543.5 kDa
src_method	nat
entity_count	1

▶

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	triclinic

resolution	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	327809

fit	/app/data/saxs_computation/rs/9rsj/9rsj.fit
pddf	/app/data/pr_computation/rs/9rsj/9rsj.pr.out
profile	/app/data/saxs_computation/rs/9rsj/9rsj.dat

Cryo-EM structure of MATE transporter NorM-VC in complex with doxorubicin

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 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)