3ojv

Crystal Structure of FGF1 complexed with the ectodomain of FGFR1c exhibiting an ordered ligand specificity-determining betaC'-betaE loop

Method: X-RAY DIFFRACTION Dmax: 133.4 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 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 21–155 Not recorded Basic fibroblast growth factor receptor 1 × 1 (P11362) ;4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;0.1M Tris, 15% PEG4000, 0.1M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.60 Å R-free 0.309
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 21–155 Not recorded Basic fibroblast growth factor receptor 1 × 1 (P11362) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;0.1M Tris, 15% PEG4000, 0.1M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.60 Å R-free 0.309

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 2–136; UniProt 21–155 Author chain B; PDBConstruct 2–136; UniProt 21–155

Basic fibroblast growth factor receptor 1

Homo sapiens

UniProt P11362

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 142–365 Fragment:FGFR1c Mutation:N185Q Heparin-binding growth factor 1 × 1 (P05230) ;4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;0.1M Tris, 15% PEG4000, 0.1M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.60 Å R-free 0.309
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 142–365 Fragment:FGFR1c Mutation:N185Q Heparin-binding growth factor 1 × 1 (P05230) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;0.1M Tris, 15% PEG4000, 0.1M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.60 Å R-free 0.309

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.

77 other PDB entries and 149 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGFR1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 3–226; UniProt 142–365 Author chain D; PDBConstruct 3–226; UniProt 142–365

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 3ojv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ojv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ojv
Deposition date deposition_date2010-08-23
Structure title titleCrystal Structure of FGF1 complexed with the ectodomain of FGFR1c exhibiting an ordered ligand specificity-determining betaC'-betaE loop
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_guinier34.92
Radius of gyration Rg (electron density) rg_electron35.83
Forward intensity I(0) i098425700.00
Molecular weight molecular_weight77290.0 kDa
Excluded volume excluded_volume95937 ų
Envelope volume envelope_volume129080 ų
Hydration-shell volume shell_volume33071 ų
Envelope diameter envelope_diameter145.3
Shell Rg shell_rg37.10
Envelope Rg envelope_rg36.85
Shape Rg shape_rg35.87
Total Rg total_rg35.80
Total atoms total_atoms5433
Residues n_residues692
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 dmax133.4
Rg (real space) rg_real35.42
Rg uncertainty (real space) rg_real_error2.21
I(0) (real space) i0_real9.8430e+07
I(0) uncertainty (real space) i0_real_error1.8240e+06
Rg (reciprocal space) rg_reciprocal35.11
I(0) (reciprocal space) i0_reciprocal98400000.0000
Solution quality estimate total_estimate0.7722
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.6
Skewness Skewness skewness0.759
Kurtosis Kurtosis kurtosis0.408
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10470000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.530; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.577; Smooth: 0.872

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_idd3ojva_
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_idd3ojvb_
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_idd3ojvc1
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_idd3ojvc2
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_idd3ojvd1
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_idd3ojvd2
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_id3ojvA00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3ojvB00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3ojvC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ojvC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ojvD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ojvD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)