[English] 日本語
Yorodumi
- PDB-4b60: Structure of rFnBPA(189-505) in complex with fibrinogen gamma cha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b60
TitleStructure of rFnBPA(189-505) in complex with fibrinogen gamma chain C- terminal peptide
Components
  • FIBRINOGEN GAMMA CHAIN
  • FIBRONECTIN-BINDING PROTEIN A
KeywordsCELL ADHESION / FNBPA / FIBRINOGEN / FIBRINOGEN BINDING
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 / 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 / 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
Fibronectin binding repeat / Fibronectin binding repeat / 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 ...Fibronectin binding repeat / Fibronectin binding repeat / 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. / YSIRK type signal peptide / Adhesion domain superfamily / 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 / Fibronectin-binding protein A
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsStemberk, V. / Moroz, O. / Atkin, K.E. / Turkenburg, J.P. / Potts, J.R.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Evidence for Steric Regulation of Fibrinogen Binding to Staphylococcus Aureus Fibronectin-Binding Protein a (Fnbpa).
Authors: Stemberk, V. / Jones, R.P. / Moroz, O. / Atkin, K.E. / Edwards, A.M. / Turkenburg, J.P. / Leech, A.P. / Massey, R.C. / Potts, J.R.
History
DepositionAug 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FIBRONECTIN-BINDING PROTEIN A
B: FIBRONECTIN-BINDING PROTEIN A
C: FIBRINOGEN GAMMA CHAIN
D: FIBRINOGEN GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9345
Polymers74,8944
Non-polymers401
Water7,314406
1
A: FIBRONECTIN-BINDING PROTEIN A
C: FIBRINOGEN GAMMA CHAIN


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers37,4472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-7.4 kcal/mol
Surface area14650 Å2
MethodPISA
2
B: FIBRONECTIN-BINDING PROTEIN A
D: FIBRINOGEN GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4873
Polymers37,4472
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.510, 59.050, 73.490
Angle α, β, γ (deg.)91.86, 98.05, 97.87
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein FIBRONECTIN-BINDING PROTEIN A / RFNBPA


Mass: 35755.328 Da / Num. of mol.: 2 / Fragment: N2N3, RESIDUES 189-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14738
#2: Protein/peptide FIBRINOGEN GAMMA CHAIN


Mass: 1691.780 Da / Num. of mol.: 2 / Fragment: C-TERMINUS, RESIDUES 421-433 / Source method: obtained synthetically
Details: REPRESENTS THE LAST 17 C-TERMINAL RESIDUES OF THE FIBRINOGEN GAMMA CHAIN, ISOFORM GAMMA-A
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02679
#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.: 406 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGPAM N-TERMINAL RESISDUES FROM VECTOR THE LAST 17 C-TERMINAL RESIDUES OF THE FIBRINOGEN GAMMA ...GPAM N-TERMINAL RESISDUES FROM VECTOR THE LAST 17 C-TERMINAL RESIDUES OF THE FIBRINOGEN GAMMA CHAIN, ISOFORM GAMMA-A

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.93 % / Description: NONE
Crystal growDetails: PEG 2K MME 25%, 0.2 M CA AC, ISOPROPANOL 10%

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91731
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91731 Å / Relative weight: 1
ReflectionResolution: 1.8→58.4 Å / Num. obs: 51268 / % possible obs: 93.6 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 67.4

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B5Z

4b5z


Resolution: 1.83→58.41 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.414 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 189-194, 479-489 AND 504-505 FROM CHAINS A AND B ARE ABSENT AND RESIDUES 1-3 FORM THE C CHAIN AND 1-5 FROM THE D CHAIN ARE ABSENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24593 2600 5.1 %RANDOM
Rwork0.19847 ---
obs0.20088 48668 93.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.04 Å2-0.03 Å2
2--0.08 Å2-0.09 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.83→58.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4791 0 1 406 5198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194871
X-RAY DIFFRACTIONr_bond_other_d0.0010.024518
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9316594
X-RAY DIFFRACTIONr_angle_other_deg0.777310363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43926.22246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87415817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9781512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021143
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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: 1.827→1.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 136 -
Rwork0.275 2629 -
obs--67.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36960.07760.1470.33580.41511.39710.0007-0.025-0.00410.0371-0.00530.00760.02270.00640.00460.0665-0.01110.00730.02670.05320.12830.917-2.134-6.2325
21.0041-0.4855-1.21470.46890.88123.35130.0188-0.0281-0.0612-0.03950.04850.04720.07970.1551-0.06730.0777-0.0123-0.0070.03690.04440.136210.027623.718-17.8594
36.48531.962111.14681.84954.696921.3794-0.10370.2550.1975-0.25620.05320.0021-0.49380.37570.05060.0718-0.02160.00130.04290.05340.1099-3.19571.3615-21.7883
46.1396-2.6554-12.30333.00786.65626.2738-0.3767-0.2437-0.38380.2435-0.11080.18050.77070.25860.48750.03870.00450.03690.0720.06470.16459.189526.37077.644
50.06780.06840.01910.22310.16390.32410.0055-0.0302-0.00820.0018-0.00340.01450.03260.0351-0.00220.0353-0.00340.0020.04620.05420.10427.516414.0635-6.3726
600000000000000-00.1128-0.0880.02920.11630.01250.036525.659316.6407-41.8716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A195 - 345
2X-RAY DIFFRACTION1A346 - 501
3X-RAY DIFFRACTION2B195 - 345
4X-RAY DIFFRACTION2B346 - 501
5X-RAY DIFFRACTION3C4 - 17
6X-RAY DIFFRACTION4D6 - 17
7X-RAY DIFFRACTION5A2001 - 2201
8X-RAY DIFFRACTION5B2001 - 2196
9X-RAY DIFFRACTION5C - B2001 - 2005
10X-RAY DIFFRACTION5D - B2001 - 2004
11X-RAY DIFFRACTION6B1502

+
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