[English] 日本語
Yorodumi
- PDB-2vr3: Structural and Biochemical Characterization of Fibrinogen binding... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vr3
TitleStructural and Biochemical Characterization of Fibrinogen binding to ClfA from Staphylocccus aureus
Components
  • CLUMPING FACTOR A
  • FIBRINOGEN GAMMA-CHAIN
KeywordsCELL ADHESION / PLATELET AGGREGATION / PEPTIDOGLYCAN-ANCHOR / STAPHYLOCOCCUS AUREUS / FIBRINOGEN GAMMA-CHAIN / SECRETED / CELL WALL / VIRULENCE / CLUMPING FACTOR
Function / homology
Function and homology information


aggregation of unicellular organisms / fibrinogen complex / platelet alpha granule / Regulation of TLR by endogenous ligand / fibrinogen binding / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent ...aggregation of unicellular organisms / fibrinogen complex / platelet alpha granule / Regulation of TLR by endogenous ligand / fibrinogen binding / 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 / fibronectin binding / protein secretion / positive regulation of exocytosis / 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 / cell adhesion / 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-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family ...: / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / 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. / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibrinogen gamma chain / Clumping factor A
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGanesh, V.K. / Rivera, J.J. / Smeds, E. / Bowden, M.G. / Wann, E.R. / Gurusidappa, S. / Fitzgerald, J.R. / Hook, M.
CitationJournal: Plos Pathog. / Year: 2008
Title: A Structural Model of the Staphylococcus Aureus Clfa-Fibrinogen Interaction Opens New Avenues for the Design of Anti-Staphylococcal Therapeutics.
Authors: Ganesh, V.K. / Rivera, J.J. / Smeds, E. / Ko, Y.P. / Bowden, M.G. / Wann, E.R. / Gurusiddappa, S. / Fitzgerald, J.R. / Hook, M.
History
DepositionMar 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CLUMPING FACTOR A
B: CLUMPING FACTOR A
C: FIBRINOGEN GAMMA-CHAIN
D: FIBRINOGEN GAMMA-CHAIN


Theoretical massNumber of molelcules
Total (without water)74,1564
Polymers74,1564
Non-polymers00
Water9,494527
1
A: CLUMPING FACTOR A
C: FIBRINOGEN GAMMA-CHAIN


Theoretical massNumber of molelcules
Total (without water)37,0782
Polymers37,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-7 kcal/mol
Surface area14350 Å2
MethodPISA
2
B: CLUMPING FACTOR A
D: FIBRINOGEN GAMMA-CHAIN


Theoretical massNumber of molelcules
Total (without water)37,0782
Polymers37,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6.5 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.427, 61.836, 81.777
Angle α, β, γ (deg.)85.44, 81.84, 82.45
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein CLUMPING FACTOR A / FIBRINOGEN-BINDING PROTEIN A / FIBRINOGEN RECEPTOR A


Mass: 35801.477 Da / Num. of mol.: 2 / Fragment: N2N3, RESIDUES 229-545 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED DISULFIDE BOND BETWEEN 327 AND 541 / Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2G015
#2: Protein/peptide FIBRINOGEN GAMMA-CHAIN


Mass: 1276.424 Da / Num. of mol.: 2
Fragment: C-TERMINAL GAMMA-CHAIN PEPTIDE ANALOG, RESIDUES 425-437
Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02679
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 327 TO CYS ENGINEERED RESIDUE IN CHAIN A, LYS 541 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, ASP 327 TO CYS ENGINEERED RESIDUE IN CHAIN A, LYS 541 TO CYS ENGINEERED RESIDUE IN CHAIN B, ASP 327 TO CYS ENGINEERED RESIDUE IN CHAIN B, LYS 541 TO CYS ENGINEERED RESIDUE IN CHAIN C, ASP 436 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASP 436 TO ALA
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6 / Details: 16-20% PEG 8000, 100MM SUCCINIC ACID PH 6.0

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→15 Å / Num. obs: 49456 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 2.7 / % possible all: 88.7

-
Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N67

1n67


Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 3.108 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27931 941 2 %RANDOM
Rwork0.21116 ---
obs0.21264 45132 93.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.927 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.63 Å2-0.27 Å2
2--0.82 Å2-0.3 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 0 527 5226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224787
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9486558
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3675634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.09426.421190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07315673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.466155
X-RAY DIFFRACTIONr_chiral_restr0.1160.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.32251
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.53303
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.30.5719
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 67
Rwork0.218 3145

+
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