[English] 日本語
Yorodumi
- PDB-1bbr: THE STRUCTURE OF RESIDUES 7-16 OF THE A ALPHA CHAIN OF HUMAN FIBR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / blood coagulation, fibrin clot formation / platelet alpha granule / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / blood coagulation, fibrin clot formation / platelet alpha granule / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / 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 exocytosis / positive regulation of peptide hormone secretion / 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 / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 aggregation / platelet activation / response to calcium ion / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / 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 / external side of plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / innate immune response / 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 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 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. / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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, 1992-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Non-polymers , 1 types, 706 molecules

#6: Water ChemComp-HOH / water / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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 %

-
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

+
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://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