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- PDB-3zrz: Crystal structure of the second and third fibronectin F1 modules ... -

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Basic information

Entry
Database: PDB / ID: 3zrz
TitleCrystal structure of the second and third fibronectin F1 modules in complex with a fragment of Streptococcus pyogenes SfbI-5
Components
  • FIBRONECTIN-BINDING PROTEIN
  • FIBRONECTIN
KeywordsCELL ADHESION / PRTF / BETA ZIPPER
Function / homology
Function and homology information


negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / Signaling by ALK fusions and activated point mutants / Non-integrin membrane-ECM interactions / basement membrane / : / endoplasmic reticulum-Golgi intermediate compartment / ECM proteoglycans / positive regulation of axon extension / Integrin cell surface interactions / Nuclear events stimulated by ALK signaling in cancer / collagen binding / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / extracellular matrix / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / platelet alpha granule lumen / integrin-mediated signaling pathway / acute-phase response / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / wound healing / response to wounding / GPER1 signaling / 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) / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / heparin binding / nervous system development / heart development / regulation of cell shape / angiogenesis / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / blood microparticle / protease binding / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / 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 binding repeat / Fibronectin binding repeat / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain ...Fibronectin binding repeat / Fibronectin binding repeat / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / 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 / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Fibronectin / Fibronectin-binding protein / Fibronectin-binding protein I
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
STREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNorris, N.C. / Bingham, R.J. / Potts, J.R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Analysis of the Tandem Beta-Zipper Interaction of a Streptococcal Protein with Human Fibronectin.
Authors: Norris, N.C. / Bingham, R.J. / Harris, G. / Speakman, A. / Jones, R.P.O. / Leech, A. / Turkenburg, J.P. / Potts, J.R.
History
DepositionJun 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Nov 9, 2011Group: Database references / Non-polymer description
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: FIBRONECTIN
C: FIBRONECTIN-BINDING PROTEIN
D: FIBRONECTIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4257
Polymers24,1454
Non-polymers2803
Water4,252236
1
A: FIBRONECTIN
C: FIBRONECTIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2614
Polymers12,0732
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-14.1 kcal/mol
Surface area6230 Å2
MethodPISA
2
B: FIBRONECTIN
D: FIBRONECTIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1653
Polymers12,0732
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-9.3 kcal/mol
Surface area6150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.055, 50.055, 93.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein FIBRONECTIN / / FN / COLD-INSOLUBLE GLOBULIN / CIG


Mass: 10120.389 Da / Num. of mol.: 2 / Fragment: SECOND AND THIRD F1 MODULES, RESIDUES 93-182
Source method: isolated from a genetically manipulated source
Details: IN BOTH A AND B THERE ARE DISULFIDE BONDS BETWEEN RESIDUES C 97 AND C 125, C 123 AND C 135, C 141 AND C 169, C 167 AND C 179
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPIC9K / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P02751
#2: Protein/peptide FIBRONECTIN-BINDING PROTEIN / STREPTOCOCCUS FIBRONECTIN-BINDING PROTEIN I


Mass: 1952.148 Da / Num. of mol.: 2 / Fragment: RESIDUES 560-577 / Source method: obtained synthetically
Details: ACETYLATED ON THE N-TERMINUS AND AMIDATED ON THE C-TERMINUS
Source: (synth.) STREPTOCOCCUS PYOGENES (bacteria) / References: UniProt: Q01924, UniProt: Q711B0*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.7 %
Description: 2F1 AND 3F1 FROM 2RKZ WERE SEARCHED SEPARATELY IN PHASER. THE PEPTIDE FROM THIS STRUCTURE WAS NOT USED.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: CRYSTALS OF THE PROTEIN/PEPTIDE COMPLEX (0.3 MM/3.5 MM, PH 7.7) WERE GROWN USING SITTING DROP VAPOUR DIFFUSION FROM A 1:1 DILUTION WITH WELL SOLUTION (0.1 M TRIS PH 7.0, 1.5 M (NH4)2SO4 AT 18 DEGREES CENTIGRADE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9804
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 8, 2008 / Details: BENT CYLINDRICAL MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 1.7→28.22 Å / Num. obs: 25333 / % possible obs: 100 % / Observed criterion σ(I): 1.9 / Redundancy: 6.1 % / Biso Wilson estimate: 22.64 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RKZ

2rkz


Resolution: 1.7→26.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.041 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22157 1289 5.1 %RANDOM
Rwork0.17389 ---
obs0.17621 24001 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 17 236 1881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211698
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9492302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.2623.42573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65615265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9661512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211296
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.2697
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21131
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8711.51060
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53521697
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3343638
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.74.5603
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 92 -
Rwork0.272 1744 -
obs--100 %

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