SAXSdb — 9jf4

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neuromedin-B receptor,de novo design protein

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–237 Chain A； UniProt 256–340	Not recorded	A1D63 (2~{S})-3-(1~{H}-indol-3-yl)-2-methyl-2-[(4-nitrophenyl)carbamoylamino]-~{N}-[(1-pyridin-2-ylcyclohexyl)methyl]propanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9JF4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H0P Structure of the NMB30-NMBR and Gq complex Deposited 2022-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–390（390 aa）	Mutation：L134Q	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NMBR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–244； UniProt 1–237 Author chain A； PDBConstruct 430–514； UniProt 256–340

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9jf4
Deposition date deposition_date	2024-09-03
Structure title title	cryo-EM structure of Neuromedin B receptor in complex with PD168368
Keywords keywords	GPCR, inactive-state, de novo protein, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.52 Å
Radius of gyration Rg (electron density) rg_electron	28.63 Å
Forward intensity I(0) i0	45044900.00
Molecular weight molecular_weight	36492.0 kDa
Excluded volume excluded_volume	36104 Å³
Envelope volume envelope_volume	64748 Å³
Hydration-shell volume shell_volume	20948 Å³
Envelope diameter envelope_diameter	102.6 Å
Shell Rg shell_rg	32.46 Å
Envelope Rg envelope_rg	28.95 Å
Shape Rg shape_rg	28.62 Å
Total Rg total_rg	28.98 Å
Total atoms total_atoms	2782
Residues n_residues	392
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	98.1 Å
Rg (real space) rg_real	29.01 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	4.5040e+07
I(0) uncertainty (real space) i0_real_error	7.4760e+05
Rg (reciprocal space) rg_reciprocal	28.86 Å
I(0) (reciprocal space) i0_reciprocal	45040000.0000
Solution quality estimate total_estimate	0.7424
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.550
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11450000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.482; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.319; Smooth: 0.882

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Neuromedin-B receptor,de novo design protein
Molecular weight formula_weight	56911.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2782

DYKDDDAMPSKSLSNLSVTTGANESGSVPEGWERDFLPASDGTTTELVIRCVIPSLYLLIITVGLLGNIMLVKIFITNSAMRSVPNIFISNLAAGDLLLLLTCVPVDASRYFFDEWMFGKVGCKLIPVIQLTSVGVSVWTLTALSADRYRAIVNPMDMQTSGALLRTCVKAMGIWVVSVLLAVPEAVFSEVARISSLDNSSFTACIPYPQTDELHPKIHSVLIFLVYFLIPLAIISIYYYHIAKHLKEKAKAGAEIAAHPDAFLFLLFAAFGVVLTGDPEDRALWAELLALVERAAPGIARALAAAYRAAEEAYRAGGPVAGFRAGILGACAGVDAETRLPLTARIVDLLRTIRALRDDEAALRALVDALGAELRALLAPVAADAEELDALLARLADLALVALRELAKLSESEMDAFIADLTAAVEAMAKQMETRKRLAKIVLVFVGCFIFCWFPNHILYMYRSFNYNEIDPSLGHMIVTLVARVLSFGNSCVNPFALYLLSESFRRHFNSQLCHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	(2~{S})-3-(1~{H}-indol-3-yl)-2-methyl-2-[(4-nitrophenyl)carbamoylamino]-~{N}-[(1-pyridin-2-ylcyclohexyl)methyl]propanamide
Molecular weight formula_weight	554.6 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	149635

fit	/app/data/saxs_computation/jf/9jf4/9jf4.fit
pddf	/app/data/pr_computation/jf/9jf4/9jf4.pr.out
profile	/app/data/saxs_computation/jf/9jf4/9jf4.dat

cryo-EM structure of Neuromedin B receptor in complex with PD168368

1. Protein Identity and Related Structures Protein Identity & Related Structures

Neuromedin-B receptor,de novo design protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)