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

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Basic information

Entry
Database: PDB / ID: 3cal
TitleCrystal structure of the second and third fibronectin F1 modules in complex with a fragment of staphylococcus aureus fnbpa-5
Components
  • Fibronectin
  • peptide from Fibronectin-binding protein A
KeywordsCELL ADHESION / Fibronectin / 2F13F1 / Beta zipper / Staphylococcus Aureus / Acute phase / Alternative splicing / Extracellular matrix / Glycoprotein / Heparin-binding / Phosphoprotein / Polymorphism / Pyrrolidone carboxylic acid / Secreted / Sulfation / Cell wall / Peptidoglycan-anchor / Virulence
Function / homology
Function and homology information


aggregation of unicellular organisms / 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 ...aggregation of unicellular organisms / 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 / fibrinogen binding / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / proteoglycan binding / Molecules associated with elastic fibres / 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 / endoplasmic reticulum-Golgi intermediate compartment / fibronectin binding / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / substrate adhesion-dependent cell spreading / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Cell surface interactions at the vascular wall / wound healing / Signaling by high-kinase activity BRAF mutants / regulation of protein phosphorylation / MAP2K and MAPK activation / response to wounding / 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 / GPER1 signaling / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / heart development / heparin binding / nervous system development / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / protease binding / angiogenesis / collagen-containing extracellular matrix / blood microparticle / 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 / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Fibronectin type I domain / : ...: / Fibronectin binding repeat / Fibronectin binding repeat / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / 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 / 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 / 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 A
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBingham, R.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structures of fibronectin-binding sites from Staphylococcus aureus FnBPA in complex with fibronectin domains
Authors: Bingham, R.J. / Meenan, N.A. / Schwarz-Linek, U. / Turkenburg, J.P. / Garman, E.F. / Potts, J.R.
History
DepositionFeb 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 19, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct.pdbx_descriptor / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Nov 1, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.2Oct 30, 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: peptide from Fibronectin-binding protein A
C: Fibronectin
D: peptide from Fibronectin-binding protein A


Theoretical massNumber of molelcules
Total (without water)24,0114
Polymers24,0114
Non-polymers00
Water3,675204
1
A: Fibronectin
B: peptide from Fibronectin-binding protein A


Theoretical massNumber of molelcules
Total (without water)12,0052
Polymers12,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-5.2 kcal/mol
Surface area6160 Å2
MethodPISA
2
C: Fibronectin
D: peptide from Fibronectin-binding protein A


Theoretical massNumber of molelcules
Total (without water)12,0052
Polymers12,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-7.4 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.495, 73.438, 36.742
Angle α, β, γ (deg.)90.00, 95.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 10120.389 Da / Num. of mol.: 2 / Fragment: UNP residues 93-182, Second and third F1 modules
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P02751
#2: Protein/peptide peptide from Fibronectin-binding protein A / FnbpA


Mass: 1885.081 Da / Num. of mol.: 2 / Fragment: UNP residues 655-672 / Source method: obtained synthetically / Details: Peptide synthesis
Source: (synth.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: P14738
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.95M succinic acid, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→36.588 Å / Num. all: 21298 / Num. obs: 19459 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.7 / Redundancy: 3.8 % / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 20.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 2952 / Rsym value: 0.321 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0013refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RKZ

2rkz


Resolution: 1.7→36.588 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.332 / SU ML: 0.079 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.7 / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21665 1051 5.1 %RANDOM
Rwork0.17656 ---
all0.17865 21298 --
obs0.17865 19459 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0.51 Å2
2---0.75 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 7 204 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211684
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9372278
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10322.87773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07215281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8061514
X-RAY DIFFRACTIONr_chiral_restr0.0060.02238
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021272
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.2107
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.2236
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.22
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.390.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0341.51046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79221678
X-RAY DIFFRACTIONr_scbond_it2.5363638
X-RAY DIFFRACTIONr_scangle_it4.0364.5598
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
Rfree0.308 109 -
Rwork0.23 1421 -
obs-1530 95.62 %

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