2dyf

Solution structure of the first WW domain of FBP11 / HYPA (FBP11 WW1) complexed with a PL (PPLP) motif peptide ligand

Method: SOLUTION NMR Dmax: 36.2 Å Quality: GOOD

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

Huntingtin-interacting protein HYPA/FBP11

Homo sapiens

UniProt O75400

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 146–173 Fragment:THE FIRST WW DOMAIN PL (PPLP) motif peptide from Myosin tail region-interacting protein MTI1 × 1 (P47068) SOLUTION NMR NMR measurement conditions:pH 5;283 K;Ionic strength (raw mmCIF value) 0.3;Pressure 1 NMR sample composition:1.5MM FBP11 WW1 U-15N, 13C 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.5MM FBP11 WW1 U- 15N, 13C; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.5MM FBP11 WW1 U-15N; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRP40_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–30; UniProt 146–173

PL (PPLP) motif peptide from Myosin tail region-interacting protein MTI1

Saccharomyces cerevisiae

UniProt P47068

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 796–802 Not recorded Huntingtin-interacting protein HYPA/FBP11 × 1 (O75400) SOLUTION NMR NMR measurement conditions:pH 5;283 K;Ionic strength (raw mmCIF value) 0.3;Pressure 1 NMR sample composition:1.5MM FBP11 WW1 U-15N, 13C 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.5MM FBP11 WW1 U- 15N, 13C; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.5MM FBP11 WW1 U-15N; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 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.

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BBC1_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 3–9; UniProt 796–802

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 2dyf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2dyf
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2dyf
Deposition date deposition_date2006-09-11
Structure title titleSolution structure of the first WW domain of FBP11 / HYPA (FBP11 WW1) complexed with a PL (PPLP) motif peptide ligand
Keywords keywords;WW DOMAIN, COMPLEX, FBP11, HYPA, PL MOTIF, PPLP MOTIF, SOLUTION STRUCTURE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, PROTEIN BINDING ;; PROTEIN BINDING
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier10.23
Radius of gyration Rg (electron density) rg_electron9.79
Forward intensity I(0) i0128471000.00
Molecular weight molecular_weight89355.0 kDa
Excluded volume excluded_volume109080 ų
Envelope volume envelope_volume12110 ų
Hydration-shell volume shell_volume8968 ų
Envelope diameter envelope_diameter39.1
Shell Rg shell_rg17.24
Envelope Rg envelope_rg12.15
Shape Rg shape_rg9.72
Total Rg total_rg10.27
Total atoms total_atoms12040
Residues n_residues780
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 dmax36.2
Rg (real space) rg_real10.22
Rg uncertainty (real space) rg_real_error0.31
I(0) (real space) i0_real1.2850e+08
I(0) uncertainty (real space) i0_real_error1.5060e+06
Rg (reciprocal space) rg_reciprocal10.22
I(0) (reciprocal space) i0_reciprocal128500000.0000
Solution quality estimate total_estimate0.8613
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary12.4
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.199
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37090.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.952

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2dyfa2
Class classb — All beta proteins
Fold Fold foldb.72 — WW domain-like
Superfamily Superfamily superfamilyb.72.1 — WW domain
Family Family familyb.72.1.1 — WW domain
Domain ID domain_idd2dyfa3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

8. Citations (1)

9. Files and Curves (10)