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1n3h

Coupling of Folding and Binding in the PTB Domain of the Signaling Protein Shc

Method: SOLUTION NMR Dmax: 91.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SHC Transforming protein

Homo sapiens

UniProt P29353

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 111–317 Fragment：PTB domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；308 K；Ionic strength (raw mmCIF value) 200mM；Pressure 1 NMR sample composition：0.5mM Shc PTB Domain, 50mM Sodium phosphate, 20mM DTT-d10, pH 6.5 | 90% H2O/10% D2O Resolution not provided

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 1N3H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1MIL TRANSFORMING PROTEIN Deposited 1995-09-20 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 482–583（102 aa） Fragment：PHOSPHOTYROSINE RECOGNITION DOMAIN SH2
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1OY2 Coupling of Folding and Binding in the PTB Domain of the Signaling Protein Shc Deposited 2003-04-03 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–317（207 aa） Fragment：PTB Domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 200mM；Pressure 1
NMR sample composition 0.5mM Shc PTB Domain, 50mM Sodium phosphate, 20mM DTT-d10 | 90% D2O, 10% D2O
Resolution not provided
1QG1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN COMPLEXED WITH AN SHC-DERIVED PEPTIDE Deposited 1999-04-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 423–435（13 aa） Fragment：423-435
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；301 K
Resolution not provided
1SHC SHC PTB DOMAIN COMPLEXED WITH A TRKA RECEPTOR PHOSPHOPEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-03-27 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–317（192 aa） Fragment：PTB DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TCE SOLUTION NMR STRUCTURE OF THE SHC SH2 DOMAIN COMPLEXED WITH A TYROSINE-PHOSPHORYLATED PEPTIDE FROM THE T-CELL RECEPTOR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-03-27 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 480–583（104 aa） Fragment：SH2 DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
4JMH Crystal structure of synthetic protein in complex with double pY peptide Deposited 2013-03-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 344–356（13 aa） Fragment：unp residues 344-356
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.66% ammonium sulfate, 2.32% PEG400, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.41 Å R-free 0.276
4XWX Crystal structure of the PTB domain of SHC Deposited 2015-01-29 Different construct 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 37–201（165 aa） Fragment：residues 37-201
Not recorded EDO 1,2-ETHANEDIOL × 6 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.8 M sodium/potassium tartrate, 0.1 M Hepes pH 7.5
Resolution 1.87 Å R-free 0.191

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

View Construct and Data Evidence
UniProt name SHC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–207； UniProt 111–317

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

SAXS profile for 1n3h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1n3h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1n3h
Deposition date deposition_date2002-10-28
Structure title titleCoupling of Folding and Binding in the PTB Domain of the Signaling Protein Shc
Keywords keywordsFree Protein, Beta Sandwich, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.47 Å
Radius of gyration Rg (electron density) rg_electron20.79 Å
Forward intensity I(0) i010362300.00
Molecular weight molecular_weight22635.0 kDa
Excluded volume excluded_volume28023 ų
Envelope volume envelope_volume41623 ų
Hydration-shell volume shell_volume17995 ų
Envelope diameter envelope_diameter92.5 Å
Shell Rg shell_rg25.56 Å
Envelope Rg envelope_rg22.21 Å
Shape Rg shape_rg20.71 Å
Total Rg total_rg21.80 Å
Total atoms total_atoms3181
Residues n_residues207
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax91.4 Å
Rg (real space) rg_real21.74 Å
Rg uncertainty (real space) rg_real_error1.22 Å
I(0) (real space) i0_real1.0360e+07
I(0) uncertainty (real space) i0_real_error1.6010e+05
Rg (reciprocal space) rg_reciprocal21.68 Å
I(0) (reciprocal space) i0_reciprocal10360000.0000
Solution quality estimate total_estimate0.6978
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2 Å
Skewness Skewness skewness0.788
Kurtosis Kurtosis kurtosis0.777
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2102000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.248; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.337; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1n3ha_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.2 — Phosphotyrosine-binding domain (PTB)

CATH v4.4 (1 domains)

Domain ID domain_id1n3hA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)