[English] 日本語
Yorodumi
- PDB-1jy2: Crystal Structure of the Central Region of Bovine Fibrinogen (E5 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jy2
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 / extracellular matrix structural constituent / 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 ...blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / extracellular matrix structural constituent / 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 / innate immune response / signaling receptor binding / 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 / MOLECULAR REPLACEMENT / Resolution: 1.4 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
Revision 1.4Apr 3, 2024Group: 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
Remark 999SEQUENCE AN APPROPRIATE DATABASE MATCH WAS NOT AVAILABLE FOR FIBRINOGEN ALPHA CHAIN AT THE TIME OF PROCESSING.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-137 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.376, 66.222, 50.658
Angle α, β, γ (deg.)90.00, 106.55, 90.00
Int Tables number4
Space group name H-MP1211

-
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


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.5 %
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
Temperature: 4 ℃ / 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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 61149 / Num. obs: 61149 / % possible obs: 99.2 % / Redundancy: 5.8 % / Rsym value: 0.058
Reflection shellResolution: 1.4→1.45 Å / Rsym value: 0.339 / % possible all: 93.1
Reflection
*PLUS
Num. measured all: 359638 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Rmerge(I) obs: 0.334

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1.6 Angstrom resolution structure of bovine E5 in the orthorhombic space group

Resolution: 1.4→100 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2949 5 %RANDOM
Rwork0.216 ---
all-58431 --
obs-58431 94.9 %-
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.074 Å20 Å23.614 Å2
2---10.707 Å20 Å2
3---4.633 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 0 318 2514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.4-1.450.4112620.398X-RAY DIFFRACTION478978.2
2.09-2.390.4113000.398X-RAY DIFFRACTION614199.6
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.411 / Rfactor Rwork: 0.398

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more