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- PDB-1n8e: Fragment Double-D from Human Fibrin -

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Basic information

Entry
Database: PDB / ID: 1n8e
TitleFragment Double-D from Human Fibrin
Components
  • Fibrin alpha/alpha-E chain
  • Fibrin beta chain
  • Fibrin gamma chain
KeywordsBLOOD 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 / positive regulation of heterotypic cell-cell adhesion ...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 / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / 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 / cellular response to interleukin-1 / protein polymerization / Integrin cell surface interactions / Common Pathway of Fibrin Clot Formation / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / cell adhesion molecule binding / positive regulation of vasoconstriction / positive regulation of substrate adhesion-dependent cell spreading / Integrin signaling / platelet alpha granule lumen / cell-matrix adhesion / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / 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 / Signaling by BRAF and RAF1 fusions / Platelet degranulation / extracellular vesicle / protein-folding chaperone binding / ER-Phagosome pathway / cell cortex / protein-containing complex assembly / protein-macromolecule adaptor activity / : / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / innate immune response / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain ...Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Fibrinogen alpha chain / Fibrinogen beta chain / Fibrinogen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsYang, 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
DepositionNov 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibrin alpha/alpha-E chain
B: Fibrin beta chain
C: Fibrin gamma chain
D: Fibrin alpha/alpha-E chain
E: Fibrin beta chain
F: Fibrin gamma chain


Theoretical massNumber of molelcules
Total (without water)169,8066
Polymers169,8066
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.000, 125.350, 312.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fibrin alpha/alpha-E chain / Coordinate model: Cα atoms only


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 Fibrin beta chain / Coordinate model: Cα atoms only


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 Fibrin gamma chain / PRO2061 / Coordinate model: Cα atoms only


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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris1droppH7.0
35 mM1dropCaCl2
413.25 %PEG33501drop
510 mM1reservoirCaCl2
650 mMTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 2, 1999
RadiationMonochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 4.5→4.6 Å / % possible all: 53.3
Reflection
*PLUS
Num. measured all: 71273
Reflection shell
*PLUS
% possible obs: 53.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fragment D of 1FZC

1fzc


Resolution: 4.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The coordinates contain C-Alphas only.
RfactorNum. reflectionSelection details
Rfree0.416 511 random
Rwork0.415 --
all0.415 10214 -
obs0.415 9703 -
Refinement stepCycle: LAST / Resolution: 4.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 0 1352
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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