[English] 日本語
Yorodumi- PDB-1fzd: STRUCTURE OF RECOMBINANT ALPHAEC DOMAIN FROM HUMAN FIBRINOGEN-420 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fzd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF RECOMBINANT ALPHAEC DOMAIN FROM HUMAN FIBRINOGEN-420 | |||||||||
Components | FIBRINOGEN-420 | |||||||||
Keywords | BLOOD COAGULATION / FIBRINOGEN-420 / ALPHAEC DOMAIN / FIBRINOGEN RELATED DOMAIN / GLYCOSYLATED PROTEIN | |||||||||
Function / homology | Function and homology information blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein polymerization / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Spraggon, G. / Applegate, D. / Everse, S.J. / Zhang, J.-Z. / Veerapandian, L. / Redman, C. / Doolittle, R.F. / Grieninger, G. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Crystal structure of a recombinant alphaEC domain from human fibrinogen-420. Authors: Spraggon, G. / Applegate, D. / Everse, S.J. / Zhang, J.Z. / Veerapandian, L. / Redman, C. / Doolittle, R.F. / Grieninger, G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fzd.cif.gz | 337.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fzd.ent.gz | 279.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fzd_validation.pdf.gz | 912.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fzd_full_validation.pdf.gz | 1009.4 KB | Display | |
Data in XML | 1fzd_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 1fzd_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fzd ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fzd | HTTPS FTP |
-Related structure data
Related structure data | 1fczS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 22840.660 Da / Num. of mol.: 8 / Fragment: ALPHA-EC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD / Production host: Pichia pastoris (fungus) / References: UniProt: P02671 |
---|
-Sugars , 4 types, 10 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 2 types, 504 molecules
#5: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 Details: PROTEIN WAS CRYSTALLIZED BY SITTING DROP VAPOUR DIFFUSION FROM 20% PEG 3350, 0.15 M CACL2, 0.1M IMIDAZOLE- ACETATE PH 5.5 0.002 M SODIUM AZIDE, vapor diffusion - sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.08 |
Detector | Detector: CCD / Date: Feb 20, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 110459 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.098 |
Reflection | *PLUS Num. measured all: 1169328 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FCZ (GAMMA DOMAIN) Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: CARBOHYDRATE RESIDUES 12 - 15 FOR CHAINS A, B, C, AND D WERE MODELLED INTO WEAK ELECTRON DENSITY. THERE WAS NO ELECTRON DENSITY OBSERVED FOR THESE RESIDUES IN CHAINS E, F, G, AND H.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|