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- PDB-1jy3: Crystal Structure of the Central Region of Bovine Fibrinogen (E5 ... -

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Basic information

Entry
Database: PDB / ID: 1jy3
TitleCrystal Structure of the Central Region of Bovine Fibrinogen (E5 Fragment) at 1.4 Angstroms Resolution
Components
  • FIBRINOGEN ALPHA CHAIN
  • FIBRINOGEN BETA CHAIN
  • FIBRINOGEN GAMMA-B CHAIN
KeywordsBLOOD CLOTTING / fibrinogen / fragment E / disulfide bonds / asymmetry / coiled-coil / beta-sheet
Function / homology
Function and homology information


blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / positive regulation of peptide hormone secretion / protein polymerization / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / cell-matrix adhesion ...blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / positive regulation of peptide hormone secretion / protein polymerization / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / cell-matrix adhesion / platelet aggregation / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / signaling receptor binding / innate immune response / extracellular space / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Fibrinogen alpha chain / Fibrinogen beta chain / Fibrinogen gamma-B chain
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsMadrazo, J. / Brown, J.H. / Litvinovich, S. / Dominguez, R. / Yakovlev, S. / Medved, L. / Cohen, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4-A resolution.
Authors: Madrazo, J. / Brown, J.H. / Litvinovich, S. / Dominguez, R. / Yakovlev, S. / Medved, L. / Cohen, C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Crystal Structure of Modified Bovine Fibrinogen
Authors: Brown, J.H. / Volkmann, N. / Jun, G. / Henschen-Edman, A.H. / Cohen, C.
History
DepositionSep 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Remark 999SEQUENCE AN APPROPRIATE DATABASE MATCH WAS NOT AVAILABLE FOR FIBRINOGEN ALPHA CHAIN AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: FIBRINOGEN ALPHA CHAIN
O: FIBRINOGEN BETA CHAIN
P: FIBRINOGEN GAMMA-B CHAIN
Q: FIBRINOGEN ALPHA CHAIN
R: FIBRINOGEN BETA CHAIN
S: FIBRINOGEN GAMMA-B CHAIN


Theoretical massNumber of molelcules
Total (without water)35,8046
Polymers35,8046
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-132 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.700, 59.100, 97.300
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 FIBRINOGEN ALPHA CHAIN /


Mass: 6172.894 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Proteolytic fragment / Source: (natural) Bos taurus (cattle) / References: UniProt: P02672*PLUS
#2: Protein FIBRINOGEN BETA CHAIN /


Mass: 6253.134 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Proteolytic fragment / Source: (natural) Bos taurus (cattle) / References: UniProt: P02676
#3: Protein/peptide FIBRINOGEN GAMMA-B CHAIN


Mass: 5476.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Proteolytic fragment / Source: (natural) Bos taurus (cattle) / References: UniProt: P12799
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8
Details: PEG 3350, Calcium chloride, Tris, Dioxane, Sodium azide, pH 8.0, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
215.0 %PEG33501reservoir
3150 mM1reservoirCaCl2
43.5 %dioxane1reservoir
53 mM1reservoirNaN3
620 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.087 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 41785 / Num. obs: 41785 / % possible obs: 99.4 % / Redundancy: 31.6 % / Rsym value: 0.059
Reflection shellResolution: 1.6→1.66 Å / Rsym value: 0.147
Reflection
*PLUS
Num. measured all: 1321351 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Rmerge(I) obs: 0.147

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
SOLVEphasing
MLPHAREphasing
CNSrefinement
ARPmodel building
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→100 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2028 5 %Random
Rwork0.194 ---
all-40453 --
obs-40453 99.4 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--8.634 Å20 Å20 Å2
2--10.123 Å20 Å2
3----1.489 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 0 312 2537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.408
X-RAY DIFFRACTIONc_dihedral_angle_d19.745
X-RAY DIFFRACTIONc_improper_angle_d1.039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.6-1.660.2761540.232X-RAY DIFFRACTION3642
2.17-2.390.2762300.232X-RAY DIFFRACTION4107
Software
*PLUS
Name: 'CNS, ARP' / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.194 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.745
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.039
LS refinement shell
*PLUS
Rfactor Rfree: 0.276 / Rfactor Rwork: 0.232

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