2k4a

FGF-1-C2A binary complex structure: a key component in the fibroblast growthfactor non-classical pathway

Method: SOLUTION NMR Dmax: 65.3 Å Quality: GOOD

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

Synaptotagmin-1

Homo sapiens

UniProt P21579

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 141–268 Fragment:C2 domain, UNP residues 141-268 Heparin-binding growth factor 1 × 1 (P05230) SOLUTION NMR NMR measurement conditions:pH 6;298 K;Ionic strength (raw mmCIF value) 50mM (NH4)2SO4;Pressure ambient NMR sample composition:1.2mM FGF-1-C2A; 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.

21 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYT1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–128; UniProt 141–268

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 B; UniProt 23–155 Fragment:UNP residues 23-155 Synaptotagmin-1 × 1 (P21579) SOLUTION NMR NMR measurement conditions:pH 6;298 K;Ionic strength (raw mmCIF value) 50mM (NH4)2SO4;Pressure ambient NMR sample composition:1.2mM FGF-1-C2A; 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.

96 other PDB entries and 217 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGF1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–133; UniProt 23–155

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 2k4a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2k4a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2k4a
Deposition date deposition_date2008-06-02
Structure title titleFGF-1-C2A binary complex structure: a key component in the fibroblast growthfactor non-classical pathway
Keywords keywords;beta barrel, FGF1-C2A binary complex, Calcium, Cell junction, Cytoplasmic vesicle, Glycoprotein, Lipoprotein, Membrane, Metal-binding, Palmitate, Phosphoprotein, Synapse, Transmembrane, Acetylation, Angiogenesis, Developmental protein, Differentiation, Growth factor, Heparin-binding, Mitogen, Polymorphism, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier19.76
Radius of gyration Rg (electron density) rg_electron19.64
Forward intensity I(0) i04697260000.00
Molecular weight molecular_weight597180.0 kDa
Excluded volume excluded_volume751630 ų
Envelope volume envelope_volume54116 ų
Hydration-shell volume shell_volume21932 ų
Envelope diameter envelope_diameter72.5
Shell Rg shell_rg27.10
Envelope Rg envelope_rg20.85
Shape Rg shape_rg19.65
Total Rg total_rg19.67
Total atoms total_atoms84020
Residues n_residues5220
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 dmax65.3
Rg (real space) rg_real19.71
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real4.6970e+09
I(0) uncertainty (real space) i0_real_error5.9110e+07
Rg (reciprocal space) rg_reciprocal19.72
I(0) (reciprocal space) i0_reciprocal4697000000.0000
Solution quality estimate total_estimate0.8922
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.1
Skewness Skewness skewness0.237
Kurtosis Kurtosis kurtosis-0.498
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1502000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2k4aa_
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.2 — Synaptotagmin-like (S variant)
Domain ID domain_idd2k4ab_
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)

CATH v4.4 (2 domains)

Domain ID domain_id2k4aA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
Domain ID domain_id2k4aB00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50

8. Citations (1)

9. Files and Curves (10)