3buk

Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex

Method: X-RAY DIFFRACTION D_max: 101.3 Å Quality: GOOD

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

Neurotrophin-3

Homo sapiens

UniProt P20783

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 139–257 Chain B； UniProt 139–257	Not recorded	Tumor necrosis factor receptor superfamily member 16 × 2 （P07174） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5；290 K；0.9M Lithium Sulfate, 0.05M Na Citrate, 0.7M Ammonium Sulfate, pH 5.0, EVAPORATION, temperature 290K	Resolution 2.60 Å R-free 0.288

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 3BUK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B8K Neurotrophin-3 from Human Deposited 1999-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 139–257（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；CRYSTALLIZATION CONDITIONS: 7% ISOPROPANOL 185 MM NACITRATE PH 5.6	Resolution 2.15 Å R-free 0.302
1BND STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER Deposited 1994-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 139–257（119 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1BND STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER Deposited 1994-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 139–257（119 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1NT3 HUMAN NEUROTROPHIN-3 Deposited 1999-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 139–257（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；200 MM AMMONIUM SULFATE, 32% PEG 400, 100 MM MES AT PH 5.6, pH 7.5	Resolution 2.40 Å R-free 0.263
9FIK Structure of the FAB fragment of the Antibody NTF30037 in complex with NTF3 Deposited 2024-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 139–257（119 aa）	Not recorded	GOL GLYCEROL × 5 PEG DI(HYDROXYETHYL)ETHER × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15 % w/v Polyethylene glycol 8,000, 0.2 M Sodium Acetate, 0.1 M MES pH 6.5	Resolution 1.86 Å R-free 0.186

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NT3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 139–257 Author chain B； PDBConstruct 1–119； UniProt 139–257

Tumor necrosis factor receptor superfamily member 16

Rattus norvegicus

UniProt P07174

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 29–189 Chain D； UniProt 29–189	Fragment：ectodomain	Neurotrophin-3 × 2 （P20783） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5；290 K；0.9M Lithium Sulfate, 0.05M Na Citrate, 0.7M Ammonium Sulfate, pH 5.0, EVAPORATION, temperature 290K	Resolution 2.60 Å R-free 0.288

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3BUK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NGR DEATH DOMAIN OF P75 LOW AFFINITY NEUROTROPHIN RECEPTOR, RESIDUES 334-418, NMR, 20 STRUCTURES Deposited 1997-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 334–418（85 aa） Fragment：DEATH DOMAIN, RESIDUES 281 - 425	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；301 K	Resolution not provided
1SG1 Crystal Structure of the Receptor-Ligand Complex between Nerve Growth Factor and the Common Neurotrophin Receptor p75 Deposited 2004-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 30–190（161 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；295 K；PEG 1000, isoproponal, sodium chloride, citrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.269
2MIC NMR structure of p75 transmembrane domain in DPC micelles Deposited 2013-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 245–284（40 aa） Fragment：UNP residues 245-284 Chain B 245–284（40 aa） Fragment：UNP residues 245-284	Mutation：C36S (chain A), C136S (chain B) Mutation：C36S (chain A), C136S (chain B)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；318 K；Pressure ambient NMR sample composition 1.9 mM [U-100% 13C; U-100% 15N] p75-TM-wt, 95 mM [U-98% 2H] DPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MJO NMR structure of p75 transmembrane domain C257A mutant in DPC micelles Deposited 2014-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 245–284（40 aa） Fragment：UNP residues 245-284 Chain B 245–284（40 aa） Fragment：UNP residues 245-284	Mutation：C14A, C36S chain A, C114A, C136S chain B Mutation：C14A, C36S chain A, C114A, C136S chain B	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；318 K；Pressure ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] p75-TM-C257A, 30 mM [U-98% 2H] DPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3IJ2 Ligand-receptor structure Deposited 2009-08-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 33–193（161 aa） Fragment：UNP RESIDUES 30-190 Chain Y 33–193（161 aa） Fragment：UNP RESIDUES 30-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.75 Å R-free 0.274
4F42 Neurotrophin p75NTR intracellular domain Deposited 2012-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 334–418（85 aa） Fragment：death domain, UNP RESIDUES 334-418	Not recorded	MNB 5-MERCAPTO-2-NITRO-BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Bis-Tris propane pH 7.0, 1.2M sodium citrate tribasic dehydrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.38 Å R-free 0.260
4F44 Neurotrophin p75NTR intracellular domain Deposited 2012-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 334–418（85 aa） Fragment：death domain Chain B 334–418（85 aa） Fragment：death domain	Not recorded	MNB 5-MERCAPTO-2-NITRO-BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Bis-Tris propane, 1.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.280

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNR16_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–161； UniProt 29–189 Author chain D； PDBConstruct 1–161； UniProt 29–189

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3buk
Deposition date deposition_date	2008-01-02
Structure title title	Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex
Keywords keywords	;Ligand-receptor complex, BETA-sheet, Neurotrophin-3, p75NTR, Cleavage on pair of basic residues, Glycoprotein, Growth factor, Secreted, Apoptosis, Developmental protein, Differentiation, Membrane, Neurogenesis, Transmembrane, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	30.16 Å
Radius of gyration Rg (electron density) rg_electron	29.58 Å
Forward intensity I(0) i0	70428000.00
Molecular weight molecular_weight	59276.0 kDa
Excluded volume excluded_volume	71286 Å³
Envelope volume envelope_volume	99126 Å³
Hydration-shell volume shell_volume	29657 Å³
Envelope diameter envelope_diameter	107.2 Å
Shell Rg shell_rg	34.56 Å
Envelope Rg envelope_rg	30.07 Å
Shape Rg shape_rg	29.53 Å
Total Rg total_rg	30.18 Å
Total atoms total_atoms	4108
Residues n_residues	540
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	101.3 Å
Rg (real space) rg_real	30.30 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	7.0430e+07
I(0) uncertainty (real space) i0_real_error	1.1540e+06
Rg (reciprocal space) rg_reciprocal	30.24 Å
I(0) (reciprocal space) i0_reciprocal	70420000.0000
Solution quality estimate total_estimate	0.8732
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.6 Å
Skewness Skewness skewness	0.449
Kurtosis Kurtosis kurtosis	-0.224
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5431000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.879

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Neurotrophin-3
Molecular weight formula_weight	13649.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4251

YAEHKSHRGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRKIGRT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 16
Molecular weight formula_weight	18059.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

KETCSTGLYTHSGECCKACNLGEGVAQPCGANQTVCEPCLDSVTFSDVVSATEPCKPCTECLGLQSMSAPCVEADDAVCRCAYGYYQDEETGHCEACSVCEVGSGLVFSCQDKQNTVCEECPEGTYSDEANHVDPCLPCTVCEDTERQLRECTPWADAECEHHHHHH

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	143

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3buka_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.3 — Neurotrophin

Domain ID domain_id	d3bukb_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.3 — Neurotrophin

Domain ID domain_id	d3bukc1
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d3bukc2
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d3bukc3
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d3bukc4
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d3bukd1
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d3bukd2
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d3bukd3
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d3bukd4
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

CATH v4.4 (6 domains)

Domain ID domain_id	3bukA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	3bukB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	3bukC01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3bukC02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3bukD01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3bukD02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	125.800 Å
Unit-cell length b length_b	125.800 Å
Unit-cell length c length_c	133.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2275
R_work r_work	0.2242
R_free r_free	0.2877

fit	/app/data/saxs_computation/bu/3buk/3buk.fit
pddf	/app/data/pr_computation/bu/3buk/3buk.pr.out
profile	/app/data/saxs_computation/bu/3buk/3buk.dat

Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex

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

Neurotrophin-3

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor receptor superfamily member 16

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)