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- PDB-1bbr: THE STRUCTURE OF RESIDUES 7-16 OF THE A ALPHA CHAIN OF HUMAN FIBR... -

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Entry
Database: PDB / ID: 1bbr
TitleTHE STRUCTURE OF RESIDUES 7-16 OF THE A ALPHA CHAIN OF HUMAN FIBRINOGEN BOUND TO BOVINE THROMBIN AT 2.3 ANGSTROMS RESOLUTION
Components
  • (EPSILON-THROMBIN) x 4
  • FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR
KeywordsSERINE PROTEASE
Function / homology
Function and homology information


induction of bacterial agglutination / blood coagulation, common pathway / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / platelet alpha granule / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) ...induction of bacterial agglutination / blood coagulation, common pathway / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / platelet alpha granule / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / 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 / thrombin / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein polymerization / Integrin cell surface interactions / positive regulation of blood coagulation / 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 / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / acute-phase response / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet 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 / extracellular vesicle / Platelet degranulation / protein-macromolecule adaptor activity / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / structural molecule activity / cell surface / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion 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. / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Prothrombin / Fibrinogen alpha chain
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMartin, P. / Edwards, B.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: The structure of residues 7-16 of the A alpha-chain of human fibrinogen bound to bovine thrombin at 2.3-A resolution.
Authors: Martin, P.D. / Robertson, W. / Turk, D. / Huber, R. / Bode, W. / Edwards, B.F.
History
DepositionApr 27, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: EPSILON-THROMBIN
H: EPSILON-THROMBIN
E: EPSILON-THROMBIN
F: FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR
J: EPSILON-THROMBIN
K: EPSILON-THROMBIN
G: FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR
M: EPSILON-THROMBIN
N: EPSILON-THROMBIN
I: FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)109,68210
Polymers109,68210
Non-polymers00
Water12,719706
1
L: EPSILON-THROMBIN
H: EPSILON-THROMBIN
E: EPSILON-THROMBIN
F: FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)36,5734
Polymers36,5734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-54 kcal/mol
Surface area13340 Å2
MethodPISA
2
J: EPSILON-THROMBIN
K: EPSILON-THROMBIN
G: FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)36,5553
Polymers36,5553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-18 kcal/mol
Surface area13330 Å2
MethodPISA
3
M: EPSILON-THROMBIN
N: EPSILON-THROMBIN
I: FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)36,5553
Polymers36,5553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-16 kcal/mol
Surface area13740 Å2
MethodPISA
4
M: EPSILON-THROMBIN
N: EPSILON-THROMBIN
I: FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR

J: EPSILON-THROMBIN
K: EPSILON-THROMBIN
G: FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)73,1106
Polymers73,1106
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area9390 Å2
ΔGint-40 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.020, 89.410, 99.300
Angle α, β, γ (deg.)90.00, 106.64, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO H 37 / 2: CIS PROLINE - PRO K 37 / 3: CIS PROLINE - PRO N 37

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Components

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Protein/peptide , 2 types, 6 molecules LJMFGI

#1: Protein/peptide EPSILON-THROMBIN


Mass: 5735.240 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#4: Protein/peptide FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR


Mass: 1047.144 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02671

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Protein , 3 types, 4 molecules HEKN

#2: Protein EPSILON-THROMBIN


Mass: 17525.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#3: Protein EPSILON-THROMBIN


Mass: 12265.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#5: Protein EPSILON-THROMBIN


Mass: 29772.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00735, thrombin

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Non-polymers , 1 types, 706 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 40 % / Common name: ammonium sulfate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 9999 Å / Num. obs: 47459 / % possible obs: 78.9 % / Num. measured all: 176974 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 39 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→7 Å / Rfactor obs: 0.167 / σ(I): 1
Details: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA ...Details: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA THROMBIN. FIBRINOPEPTIDE I HAS AN OCCUPANCY THAT MAKES THE AVERAGE B OF ARG-318 ROUGHLY EQUAL TO THAT IN FIBRINOPEPTIDES II AND III. THE DEPOSITORS DO NOT SEE ANY DENSITY AT ALL FOR THROMBIN RESIDUES 1U - 1I, AND POOR DENSITY FOR THE N AND C TERMINI OF THE LIGHT CHAINS, THE C TERMINUS OF THE HEAVY CHAINS, AND THE FIVE RESIDUES BORDERING 149B IN MOLECULES II AND III. EPSILON THROMBIN IN COMPLEX I HAS BEEN ASSIGNED CHAIN INDICATORS *L*, *H*, AND *E*. THE FIBRINOPEPTIDE IN COMPLEX I HAS BEEN ASSIGNED CHAIN INDICATOR *F*. ALPHA THROMBIN IN COMPLEX II HAS BEEN ASSIGNED CHAIN INDICATORS *J* AND *K*. THE FIBRINOPEPTIDE IN COMPLEX II HAS BEEN ASSIGNED CHAIN INDICATOR *G*. ALPHA THROMBIN IN COMPLEX III HAS BEEN ASSIGNED CHAIN INDICATORS *M* AND *N*. THE FIBRINOPEPTIDE IN COMPLEX III HAS BEEN ASSIGNED CHAIN INDICATOR *I*.
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7378 0 0 706 8084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d3.3
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection obs: 47459
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.3
X-RAY DIFFRACTIONp_planar_d0.037
X-RAY DIFFRACTIONp_chiral_restr0.141

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