2rmx

Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A

Method: SOLUTION NMR Dmax: 50.4 Å Quality: GOOD

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

Tyrosine-protein phosphatase non-receptor type 6

Homo sapiens

UniProt P29350

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 110–214 Fragment:SH2 domain NKG2-A/NKG2-B type II integral membrane protein × 1 (P26715) SOLUTION NMR NMR measurement conditions:pH 7.4;Ionic strength (raw mmCIF value) 120;Pressure ambient NMR sample composition:0.8mM [U-13C; U-15N] SHP-1 C-terminal SH2 domain; 0.8mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O | 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.

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTN6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 8–112; UniProt 110–214

NKG2-A/NKG2-B type II integral membrane protein

OrganismNot specified

UniProt P26715

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–15 Fragment:tyrosine phosphorylation site, UNP residues 1-15 Non-standard monomer:Yes (specific site not provided by mmCIF) Tyrosine-protein phosphatase non-receptor type 6 × 1 (P29350) SOLUTION NMR NMR measurement conditions:pH 7.4;Ionic strength (raw mmCIF value) 120;Pressure ambient NMR sample composition:0.8mM [U-13C; U-15N] SHP-1 C-terminal SH2 domain; 0.8mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O | 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.

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

View Construct and Data Evidence
UniProt name NKG2A_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–15; UniProt 1–15

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 2rmx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2rmx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2rmx
Deposition date deposition_date2007-11-30
Structure title titleSolution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A
Keywords keywords;SH2 domain, protein-peptide complex, phosphorylated peptide recognition, phosphotyrosine binding domain, signal transduction, Alternative splicing, Cytoplasm, Hydrolase, Nucleus, Phosphoprotein, Protein phosphatase, Glycoprotein, Lectin, Membrane, Receptor, Signal-anchor, Transmembrane, SIGNALING PROTEIN, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier15.05
Radius of gyration Rg (electron density) rg_electron14.44
Forward intensity I(0) i01196360000.00
Molecular weight molecular_weight286280.0 kDa
Excluded volume excluded_volume354630 ų
Envelope volume envelope_volume37637 ų
Hydration-shell volume shell_volume17685 ų
Envelope diameter envelope_diameter60.8
Shell Rg shell_rg24.01
Envelope Rg envelope_rg18.56
Shape Rg shape_rg14.41
Total Rg total_rg14.75
Total atoms total_atoms39400
Residues n_residues2640
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax50.4
Rg (real space) rg_real14.98
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real1.1960e+09
I(0) uncertainty (real space) i0_real_error1.3980e+07
Rg (reciprocal space) rg_reciprocal14.98
I(0) (reciprocal space) i0_reciprocal1196000000.0000
Solution quality estimate total_estimate0.7837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.4
Skewness Skewness skewness0.207
Kurtosis Kurtosis kurtosis-0.172
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha494500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.730; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2rmxA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain

8. Citations (1)

9. Files and Curves (10)