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- PDB-4b60: Structure of rFnBPA(189-505) in complex with fibrinogen gamma cha... -

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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 / platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion ...aggregation of unicellular organisms / platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to interleukin-6 / 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 / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / fibronectin binding / protein secretion / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / 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 / cell adhesion molecule binding / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / 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) / Signaling by BRAF and RAF1 fusions / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / blood microparticle / cell adhesion / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / structural molecule activity / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / 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 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. / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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

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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

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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

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