SAXSdb — 4f44

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

Tumor necrosis factor receptor superfamily member 16

Rattus norvegicus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 334–418 Chain B； UniProt 334–418	Fragment：death domain	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

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 4F44	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 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 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
3BUK Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex Deposited 2008-01-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 29–189（161 aa） Fragment：ectodomain Chain D 29–189（161 aa） Fragment：ectodomain	Not recorded	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
3IJ2 Ligand-receptor structure Deposited 2009-08-03	Different construct Different oligomeric state 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 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

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–86； UniProt 334–418 Author chain B； PDBConstruct 2–86； UniProt 334–418

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	4f44
Deposition date deposition_date	2012-05-10
Structure title title	Neurotrophin p75NTR intracellular domain
Keywords keywords	death domain, signaling tranduction, 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	17.96 Å
Radius of gyration Rg (electron density) rg_electron	16.81 Å
Forward intensity I(0) i0	7098720.00
Molecular weight molecular_weight	18821.0 kDa
Excluded volume excluded_volume	23313 Å³
Envelope volume envelope_volume	27332 Å³
Hydration-shell volume shell_volume	14115 Å³
Envelope diameter envelope_diameter	55.6 Å
Shell Rg shell_rg	22.05 Å
Envelope Rg envelope_rg	16.93 Å
Shape Rg shape_rg	16.79 Å
Total Rg total_rg	17.77 Å
Total atoms total_atoms	1324
Residues n_residues	166
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	58.2 Å
Rg (real space) rg_real	17.92 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	7.0990e+06
I(0) uncertainty (real space) i0_real_error	8.0120e+04
Rg (reciprocal space) rg_reciprocal	17.93 Å
I(0) (reciprocal space) i0_reciprocal	7099000.0000
Solution quality estimate total_estimate	0.8066
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.285
Kurtosis Kurtosis kurtosis	-0.420
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1818000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor receptor superfamily member 16
Molecular weight formula_weight	10631.9 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	1377

MGNLYSSLPLTKREEVEKLLNGDTWRHLAGELGYQPEHIDSFTHEACPVRALLASWGAQDSATLDALLAALRRIQRADIVESLCSELEHHHHHH

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	brown rat,rat,rats
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	5-MERCAPTO-2-NITRO-BENZOIC ACID
Molecular weight formula_weight	199.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4f44a_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.2 — DEATH domain, DD

Domain ID domain_id	d4f44b_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.2 — DEATH domain, DD

CATH v4.4 (2 domains)

Domain ID domain_id	4f44A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	4f44B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

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8. Citations (1)

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Unit-cell length a length_a	53.372 Å
Unit-cell length b length_b	53.372 Å
Unit-cell length c length_c	73.486 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	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.560 Å
R factor r_factor	0.2302
R_work r_work	0.2279
R_free r_free	0.2800

fit	/app/data/saxs_computation/f4/4f44/4f44.fit
pddf	/app/data/pr_computation/f4/4f44/4f44.pr.out
profile	/app/data/saxs_computation/f4/4f44/4f44.dat

Neurotrophin p75NTR intracellular domain

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

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