+Open data
-Basic information
Entry | Database: PDB / ID: 1n8e | ||||||
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Title | Fragment Double-D from Human Fibrin | ||||||
Components |
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Keywords | BLOOD CLOTTING / Cross-linked fibrin / D:D interfaces / crystal packing | ||||||
Function / homology | Function and homology information platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / 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 secretion / protein polymerization / cellular response to interleukin-1 / 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 / cell adhesion molecule binding / 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 / cell cortex / ER-Phagosome pathway / protein-folding chaperone binding / 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 / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | ||||||
Authors | Yang, Z. / Pandi, L. / Doolittle, R.F. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: The Crystal Structure of Fragment Double-D from Cross-Linked Lamprey Fibrin Reveals Isopeptide Linkages across an Unexpected D-D Interface Authors: Yang, Z. / Pandi, L. / Doolittle, R.F. #1: Journal: Biochemistry / Year: 1998 Title: Crystal Structure of Fragment Double-D from Human Fibrin with Two Different Bound Ligands Authors: Everse, S.J. / Spraggon, G. / Veerapandian, L. / Riley, M. / Doolittle, R.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n8e.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n8e.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 1n8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n8e_validation.pdf.gz | 339.7 KB | Display | wwPDB validaton report |
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Full document | 1n8e_full_validation.pdf.gz | 339.6 KB | Display | |
Data in XML | 1n8e_validation.xml.gz | 978 B | Display | |
Data in CIF | 1n8e_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/1n8e ftp://data.pdbj.org/pub/pdb/validation_reports/n8/1n8e | HTTPS FTP |
-Related structure data
Related structure data | 1n73C 1n86C 1fzcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10517.244 Da / Num. of mol.: 2 / Fragment: double-D alpha chain / Source method: isolated from a natural source / Details: Fibrinogen prepared from blood bank plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P02671 #2: Protein | Mass: 37691.992 Da / Num. of mol.: 2 / Fragment: double-D beta chain / Source method: isolated from a natural source / Details: Fibrinogen prepared from blood bank plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P02675 #3: Protein | Mass: 36693.754 Da / Num. of mol.: 2 / Fragment: double-D gamma chain / Source method: isolated from a natural source / Details: Fibrinogen prepared from blood bank plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P02679 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.27 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG-3350, 50 mM Tris, 7.5 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 2, 1999 |
Radiation | Monochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→30 Å / Num. all: 12247 / Num. obs: 10214 / % possible obs: 83.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.138 |
Reflection shell | Resolution: 4.5→4.6 Å / % possible all: 53.3 |
Reflection | *PLUS Num. measured all: 71273 |
Reflection shell | *PLUS % possible obs: 53.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: fragment D of 1FZC Resolution: 4.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The coordinates contain C-Alphas only.
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Refinement step | Cycle: LAST / Resolution: 4.5→30 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |