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- PDB-2fib: RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RE... -

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Basic information

Entry
Database: PDB / ID: 2fib
TitleRECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) COMPLEXED TO THE PEPTIDE GLY-PRO-ARG-PRO AT PH 6.0
Components
  • FIBRINOGEN
  • GLY-PRO-ARG-PRO
KeywordsCOMPLEX (BLOOD COAGULATION/PEPTIDE) / FIBRINOGEN / BLOOD COAGULATION / FIBRIN POLYMERIZATION / COMPLEX (BLOOD COAGULATION-PEPTIDE) / COMPLEX (BLOOD COAGULATION-PEPTIDE) complex
Function / homology
Function and homology information


fibrinogen complex / platelet alpha granule / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation ...fibrinogen complex / platelet alpha granule / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / 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 vasoconstriction / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of exocytosis / protein secretion / 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 / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / 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 / response to calcium ion / platelet aggregation / 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 / : / ER-Phagosome pathway / protein-containing complex assembly / blood microparticle / positive regulation of ERK1 and ERK2 cascade / endoplasmic reticulum lumen / signaling receptor binding / external side of plasma membrane / structural molecule activity / cell surface / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. ...Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Fibrinogen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH PDB ENTRY 1FIB / Resolution: 2.01 Å
AuthorsPratt, K.P. / Cote, H.C.F. / Chung, D.W. / Stenkamp, R.E. / Davie, E.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro.
Authors: Pratt, K.P. / Cote, H.C. / Chung, D.W. / Stenkamp, R.E. / Davie, E.W.
History
DepositionJun 3, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBRINOGEN
B: GLY-PRO-ARG-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7103
Polymers30,6702
Non-polymers401
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-13 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.330, 68.200, 47.600
Angle α, β, γ (deg.)90.00, 105.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FIBRINOGEN


Mass: 30243.422 Da / Num. of mol.: 1
Fragment: GAMMA CHAIN, CARBOXYL TERMINAL FRAGMENT RESIDUES 143 - 411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD PLASMA
Gene: HUMAN FIBRINOGEN GAMMA CHAIN CDNA ENCODING VAL 143 - VAL 411
Organ: BLOOD / Plasmid: PPIC9K / Production host: Pichia pastoris (fungus) / References: UniProt: P02679
#2: Protein/peptide GLY-PRO-ARG-PRO


Mass: 426.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNO DENSITY FOR RESIDUES BEYOND LEU 392 WAS OBSERVED. MASS SPECTROMETRY SHOWED HETEROGENEITY AT THE C-TERMINUS.

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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: 1.91 Å3/Da / Density % sol: 35.52 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG8000, 70MM CACL2, 0.1 M MES, PH 6.0, 0.02%NAN3, ROOM TEMPERATURE, SITTING DROPS. THE CRYSTAL WAS SOAKED OVERNIGHT IN THE ORIGINAL SOLUTION PLUS 0.01M GLY- ...Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG8000, 70MM CACL2, 0.1 M MES, PH 6.0, 0.02%NAN3, ROOM TEMPERATURE, SITTING DROPS. THE CRYSTAL WAS SOAKED OVERNIGHT IN THE ORIGINAL SOLUTION PLUS 0.01M GLY-PRO-ARG-PRO (SIGMA), THEN BACK-SOAKED FOR 10 MINUTES., vapor diffusion - sitting drop
Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG80001reservoir
270 mM1reservoirCaCl2
30.1 MMES1reservoir
40.02 %1reservoirNaN3
515 mg/mlprotain1drop
66 %PEG80001drop
735 mM1dropCaCl2
80.05 MMES1drop
90.01 %1dropNaN3

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→68.2 Å / Num. obs: 12275 / % possible obs: 76.9 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.054 / Rsym value: 0.052 / Net I/σ(I): 11
Reflection shellResolution: 2.01→2.25 Å / Mean I/σ(I) obs: 3.17 / % possible all: 61.3

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Processing

Software
NameVersionClassification
RIGAKUSOFTWAREdata collection
RIGAKUSOFTWAREdata reduction
X-PLOR3.1model building
XTALVIEWrefinement
X-PLOR3.1refinement
RIGAKUdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1FIB
Starting model: PDB ENTRY 1FIB

1fib


Resolution: 2.01→10 Å / σ(F): 3
Details: MODIFIED TOPOLOGY AND PARAMETER FILES WERE CREATED SO THAT X-PLOR WOULD ACCEPT A CIS PEPTIDE BOND THAT DID NOT PRECEDE A PROLINE RESIDUE. THE PDB INPUT FILE FOR X-PLOR SHOULD SPECIFY CYS 339 ...Details: MODIFIED TOPOLOGY AND PARAMETER FILES WERE CREATED SO THAT X-PLOR WOULD ACCEPT A CIS PEPTIDE BOND THAT DID NOT PRECEDE A PROLINE RESIDUE. THE PDB INPUT FILE FOR X-PLOR SHOULD SPECIFY CYS 339 AS CCY 339. THE BACKBONE ANGLES PHI AND PSI OF ASN 337 ARE STRAINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1205 10 %RANDOM
Rwork0.186 ---
obs0.186 12275 --
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 2.01→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 1 117 2152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.903
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.43
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→10 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3957 39
Rwork0.2542 380
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM.CALCIUMTOPCISPEP.PRO
X-RAY DIFFRACTION2PARAM.TIPS3PTOPOLOGY.CALCIUM
X-RAY DIFFRACTION3PARAMCISPEP.PROTOPOLOGY.TIPS3P
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.43
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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