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2jp2

Solution structure and resonance assignment of the N-terminal EVH1 domain from the human Spred2 protein (Sprouty-related protein with EVH1 domain isoform 2)

Method: SOLUTION NMR Dmax: 51.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sprouty-related, EVH1 domain-containing protein 2

Homo sapiens

UniProt Q7Z698

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 1–124 Fragment：EVH1/WH1 domain, sequence database residues 1-124 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition：1 mM [U-100% 15N] Spred2 EVH1, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-100% 13C; U-100% 15N] Spred2 EVH1, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-100% 13C; U-100% 15N] Spred2 EVH1, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 100% D2O | 100% D2O NMR sample composition：1 mM [U-100% 15N] Spred2 EVH1, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 100% D2O | 100% 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 2JP2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8EQ5 Crystal structure of the N-terminal kinase domain of RSK2 in complex with SPRED2 (131-160) Deposited 2022-10-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 131–160（30 aa） Fragment：Residues 131-160
Not recorded QCT 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；30% w/v PEG 2K MME, 0.1 M Tris, pH 8.0
Resolution 1.80 Å R-free 0.225

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

View Construct and Data Evidence
UniProt name SPRE2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–126； UniProt 1–124

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 2jp2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2jp2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2jp2
Deposition date deposition_date2007-04-18
Structure title titleSolution structure and resonance assignment of the N-terminal EVH1 domain from the human Spred2 protein (Sprouty-related protein with EVH1 domain isoform 2)
Keywords keywordsEVH1 domain, solution structure, Structural Genomics, Structural Genomics Consortium, SGC, 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_guinier15.22 Å
Radius of gyration Rg (electron density) rg_electron14.60 Å
Forward intensity I(0) i01205040000.00
Molecular weight molecular_weight283860.0 kDa
Excluded volume excluded_volume351030 ų
Envelope volume envelope_volume40796 ų
Hydration-shell volume shell_volume18790 ų
Envelope diameter envelope_diameter57.2 Å
Shell Rg shell_rg24.80 Å
Envelope Rg envelope_rg18.59 Å
Shape Rg shape_rg14.55 Å
Total Rg total_rg14.95 Å
Total atoms total_atoms39480
Residues n_residues2520
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 dmax51.7 Å
Rg (real space) rg_real15.14 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real1.2050e+09
I(0) uncertainty (real space) i0_real_error1.4650e+07
Rg (reciprocal space) rg_reciprocal15.15 Å
I(0) (reciprocal space) i0_reciprocal1205000000.0000
Solution quality estimate total_estimate0.8760
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.6 Å
Skewness Skewness skewness0.161
Kurtosis Kurtosis kurtosis-0.341
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha430000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.996
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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2jp2a1
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd2jp2a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2jp2A00
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)