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9qzq

CryoEM structure of nanodisc-reconstituted human NTCP in complex with grafted NTCP_Nb1 and NabFab

Method: ELECTRON MICROSCOPY D_max: 140.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qzq
deposition_date	2025-04-23
title	CryoEM structure of nanodisc-reconstituted human NTCP in complex with grafted NTCP_Nb1 and NabFab
keywords	Solute Carrier Protein, Bile salt transporter, HBV/ HDV receptor, Sodium-coupled transport, 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	39.74 Å
rg_electron	40.77 Å
i0	121183000.00
molecular_weight	92140.0 kDa
excluded_volume	116620 Å³
envelope_volume	160760 Å³
shell_volume	36166 Å³
envelope_diameter	149.0 Å
shell_rg	41.18 Å
envelope_rg	40.61 Å
shape_rg	40.68 Å
total_rg	41.12 Å
total_atoms	6479
n_residues	831
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	140.0 Å
rg_real	40.42 Å
rg_real_error	1.53 Å
i0_real	1.2120e+08
i0_real_error	2.1890e+06
rg_reciprocal	40.00 Å
i0_reciprocal	121100000.0000
total_estimate	0.5636
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	31.5 Å
skewness	0.542
kurtosis	-0.462
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	9814000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.642; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.437; Smooth: 0.772

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Sodium/bile acid cotransporter
formula_weight	38149.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6479

MEAHNASAPFNFTLPPNFGKRPTDLALSVILVFMLFFIMLSLGCTMEFSKIKAHLWKPKGLAIALVAQYGIMPLTAFVLGKVFRLKNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSIVMTTCSTFCALGMMPLLLYIYSRGIYDGDLKDKVPYKGIVISLVLVLIPCTIGIVLKSKRPQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVLSALFCLNGRCRRTVSMETGCQNVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLLIAIFWCYEKFKTPKDKTKMIYTAATTEETIPGALGNGTYKGEDCSPCTA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	NabFab - Heavy Chain
formula_weight	25684.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSYYSIHWVRQAPGKGLEWVAYISSSSSYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGYQYWQYHASWYWNGGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	NabFab - Light Chain
formula_weight	23258.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Grafted Nanobody NTCP_Nb1
formula_weight	15233.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

QRQLVESGGGLVQPGGSLRLSCAASRFTFDDYTIGWFRQAPGKEREGVSYMSSRDGSTYYADSVKGRFIISRDNVKNTVYLQMNSLEPEDTAVYYCAAAYRPWGLIGGNFDFSGAYWGKGTPVTVSSHHHHHHEPEA

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 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	3.11 Å
resolution_method	—
num_particles	133506

fit	/app/data/saxs_computation/qz/9qzq/9qzq.fit
pddf	/app/data/pr_computation/qz/9qzq/9qzq.pr.out
profile	/app/data/saxs_computation/qz/9qzq/9qzq.dat

CryoEM structure of nanodisc-reconstituted human NTCP in complex with grafted NTCP_Nb1 and NabFab

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)