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- PDB-4pz5: Crystal structure of the second and third fibronectin F1 modules ... -

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Basic information

Entry
Database: PDB / ID: 4pz5
TitleCrystal structure of the second and third fibronectin F1 modules in complex with a fragment of BBK32 from Borrelia burgdorferi
Components
  • Fibronectin
  • Fibronectin-binding protein BBK32
KeywordsCELL ADHESION / Fibronectin type one / Bacterial adhesion / Fibronectin binding / Extracellular matrix / Plasma
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / peptide cross-linking / integrin activation ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / regulation of protein phosphorylation / proteoglycan binding / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / peptidase activator activity / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / endodermal cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / fibronectin binding / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / endothelial cell migration / regulation of ERK1 and ERK2 cascade / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / integrin-mediated signaling pathway / acute-phase response / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / integrin binding / Signaling by ALK fusions and activated point mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of fibroblast proliferation / 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 / GPER1 signaling / Platelet degranulation / nervous system development / regulation of cell shape / heparin binding / : / heart development / protease binding / blood microparticle / angiogenesis / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Fibronectin-binding protein BBK32 / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
Borrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsHarris, G. / Potts, J.R.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Borrelia burgdorferi Protein BBK32 Binds to Soluble Fibronectin via the N-terminal 70-kDa Region, Causing Fibronectin to Undergo Conformational Extension.
Authors: Harris, G. / Ma, W. / Maurer, L.M. / Potts, J.R. / Mosher, D.F.
History
DepositionMar 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 29, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 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
A: Fibronectin
B: Fibronectin-binding protein BBK32


Theoretical massNumber of molelcules
Total (without water)11,9822
Polymers11,9822
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-3 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.580, 86.580, 63.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-282-

HOH

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Components

#1: Protein Fibronectin / FN / Cold-insoluble globulin / CIG / Anastellin / Ugl-Y1 / Ugl-Y2 / Ugl-Y3


Mass: 10120.389 Da / Num. of mol.: 1 / Fragment: 2FN1-3FN1, UNP RESIDUES 93-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Pichia pastoris (fungus) / References: UniProt: P02751
#2: Protein/peptide Fibronectin-binding protein BBK32


Mass: 1861.823 Da / Num. of mol.: 1 / Fragment: BBK32TwL, UNP RESIDUES 175-189 / Source method: obtained synthetically
Source: (synth.) Borrelia burgdorferi (Lyme disease spirochete)
References: UniProt: O50835
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.4 M Na/K phosphate, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0039 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2007
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0039 Å / Relative weight: 1
ReflectionResolution: 1.96→48.49 Å / Num. all: 10551 / Num. obs: 10524 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.9
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1033 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
REFMACrefinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CG7

2cg7


Resolution: 1.96→48.49 Å / SU ML: 0.11 / Isotropic thermal model: Isotropic / σ(F): 1.34 / σ(I): 2 / Phase error: 18.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.199 512 4.87 %Random
Rwork0.1612 ---
obs0.163 10524 99.8 %-
all-10551 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9 Å2
Refinement stepCycle: LAST / Resolution: 1.96→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms820 0 0 129 949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007852
X-RAY DIFFRACTIONf_angle_d0.9691147
X-RAY DIFFRACTIONf_dihedral_angle_d11.621317
X-RAY DIFFRACTIONf_chiral_restr0.041116
X-RAY DIFFRACTIONf_plane_restr0.003150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9613-2.15860.20211040.18822454X-RAY DIFFRACTION100
2.1586-2.4710.19911450.17712440X-RAY DIFFRACTION100
2.471-3.11310.24951260.17552489X-RAY DIFFRACTION100
3.1131-48.50340.17441370.14192610X-RAY DIFFRACTION99
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)
18.2479-2.893-2.40574.31664.0213.82480.17530.48950.1223-0.16430.0334-0.6028-0.21210.2957-0.2160.3-0.01610.04890.16640.02610.1989-28.695210.634648.4557
25.88752.64330.84065.6321.53222.00330.00220.01-0.2705-0.10630.2169-1.63170.00450.7476-0.18660.20020.00750.02820.2567-0.01070.3385-24.90515.598950.6579
33.2171-3.4317-3.36955.47564.24444.64970.1677-0.03540.2887-0.059-0.001-0.3316-0.06210.0319-0.18810.1818-0.0410.00290.12470.01470.1709-33.243410.250258.2352
41.9346-1.2253-1.75161.3958-0.4595.8751-0.04120.07210.01470.1083-0.13760.0799-0.05590.00570.12540.1491-0.0448-0.00430.10350.01560.1326-36.61298.446260.2537
52.6851-0.110.00485.77494.07533.12470.0736-0.07520.1569-0.05960.0067-0.3405-0.42210.1823-0.06940.1669-0.01610.04750.12650.03470.1822-33.447310.76677.3595
64.6809-0.5778-4.53331.43051.44694.9772-0.1451-0.27991.4569-0.4784-0.17690.2348-1.0413-0.77380.26970.3660.0652-0.01460.2012-0.09710.4022-42.496719.241488.604
70.1759-0.5872-0.63466.57085.48654.6858-0.0148-0.0125-0.03980.31480.0497-0.10230.50980.0952-0.03590.1279-0.00850.02790.08440.01160.1276-39.46277.500779.5083
82.28431.4989-2.64121.0337-1.82523.1939-0.1388-0.07280.0128-0.1603-0.0404-0.11220.33960.33560.16740.22130.01940.00030.2837-0.00380.177-42.17659.990950.9239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 132 )
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 151 )
8X-RAY DIFFRACTION8chain 'B' and (resid 175 through 188 )

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