3oj2

Crystal structure of FGF1 complexed with the ectodomain of FGFR2b harboring the A172F Pfeiffer syndrome mutation

Method: X-RAY DIFFRACTION Dmax: 104.1 Å Quality: GOOD

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

Heparin-binding growth factor 1

Homo sapiens

UniProt P05230

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 1–155 Not recorded Fibroblast growth factor receptor 2 × 1 (P21802) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M Hepes, 20% PEG4000, 0.2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.294
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–155 Not recorded Fibroblast growth factor receptor 2 × 1 (P21802) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M Hepes, 20% PEG4000, 0.2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.294

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.

96 other PDB entries and 216 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGF1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–155; UniProt 1–155 Author chain B; PDBConstruct 1–155; UniProt 1–155

Fibroblast growth factor receptor 2

Homo sapiens

UniProt P21802

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 C; UniProt 140–313 Mutation:A172F Heparin-binding growth factor 1 × 1 (P05230) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M Hepes, 20% PEG4000, 0.2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.294
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 140–313 Mutation:A172F Heparin-binding growth factor 1 × 1 (P05230) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1M Hepes, 20% PEG4000, 0.2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.294

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.

60 other PDB entries and 122 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGFR2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 2–175; UniProt 140–313 Author chain D; PDBConstruct 2–175; UniProt 140–313

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 3oj2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3oj2
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3oj2
Deposition date deposition_date2010-08-20
Structure title titleCrystal structure of FGF1 complexed with the ectodomain of FGFR2b harboring the A172F Pfeiffer syndrome mutation
Keywords keywords;beta trefoil motif, Immunoglobulin-like domain, growth factor, growth factor receptor, extracellular, Cytokine-Signaling Protein complex ;; Cytokine/Signaling Protein
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.63
Radius of gyration Rg (electron density) rg_electron29.66
Forward intensity I(0) i098173600.00
Molecular weight molecular_weight76634.0 kDa
Excluded volume excluded_volume95269 ų
Envelope volume envelope_volume121670 ų
Hydration-shell volume shell_volume34345 ų
Envelope diameter envelope_diameter110.8
Shell Rg shell_rg36.60
Envelope Rg envelope_rg29.40
Shape Rg shape_rg29.65
Total Rg total_rg30.32
Total atoms total_atoms5397
Residues n_residues688
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 dmax104.1
Rg (real space) rg_real30.56
Rg uncertainty (real space) rg_real_error0.95
I(0) (real space) i0_real9.8170e+07
I(0) uncertainty (real space) i0_real_error1.7870e+06
Rg (reciprocal space) rg_reciprocal30.59
I(0) (reciprocal space) i0_reciprocal98180000.0000
Solution quality estimate total_estimate0.8894
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.0
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.389
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11190000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3oj2a_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3oj2b_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3oj2c1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd3oj2c2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3oj2d1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd3oj2d2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id3oj2A00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3oj2B00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3oj2C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3oj2C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3oj2D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3oj2D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)