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- PDB-2rkz: Crystal structure of the second and third fibronectin f1 modules ... -

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Basic information

Entry
Database: PDB / ID: 2rkz
TitleCrystal structure of the second and third fibronectin f1 modules in complex with a fragment of staphylococcus aureus fnbpa-1
Components
  • Fibronectin
  • peptide from Fibronectin-binding protein A
KeywordsCELL ADHESION / fibrronectin / 2F13F1 / beta zipper / staphylococcus aureus / Acute phase / Alternative splicing / Extracellular matrix / Glycoprotein / Heparin-binding / Phosphorylation / 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 / 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 ...aggregation of unicellular organisms / 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 / fibrinogen binding / ALK mutants bind TKIs / cell-substrate junction assembly / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / Molecules associated with elastic fibres / peptidase activator activity / Syndecan interactions / biological process involved in interaction with symbiont / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / regulation of protein phosphorylation / 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 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / acute-phase response / Cell surface interactions at the vascular wall / integrin-mediated signaling pathway / Post-translational protein phosphorylation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / integrin binding / 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 / Signaling by ALK fusions and activated point mutants / Platelet degranulation / nervous system development / GPER1 signaling / regulation of cell shape / heparin binding / : / heart development / protease binding / angiogenesis / Interleukin-4 and Interleukin-13 signaling / blood microparticle / 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 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 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 / 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 / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
SUCCINIC ACID / Fibronectin / Fibronectin-binding protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionOct 18, 2007Deposition 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_distant_solvent_atoms / 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_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
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_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_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct.pdbx_descriptor / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_asym_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 / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Apr 3, 2024Group: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibronectin
B: Fibronectin
C: Fibronectin
D: Fibronectin
E: Fibronectin
F: Fibronectin
M: peptide from Fibronectin-binding protein A
N: peptide from Fibronectin-binding protein A
O: peptide from Fibronectin-binding protein A
P: peptide from Fibronectin-binding protein A
Q: peptide from Fibronectin-binding protein A
R: peptide from Fibronectin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,83415
Polymers75,48012
Non-polymers3543
Water14,808822
1
A: Fibronectin
M: peptide from Fibronectin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6983
Polymers12,5802
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-3.2 kcal/mol
Surface area6500 Å2
MethodPISA
2
B: Fibronectin
N: peptide from Fibronectin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6983
Polymers12,5802
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-4.1 kcal/mol
Surface area6470 Å2
MethodPISA
3
C: Fibronectin
O: peptide from Fibronectin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6983
Polymers12,5802
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-3.5 kcal/mol
Surface area6730 Å2
MethodPISA
4
D: Fibronectin
P: peptide from Fibronectin-binding protein A


Theoretical massNumber of molelcules
Total (without water)12,5802
Polymers12,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-4.8 kcal/mol
Surface area6790 Å2
MethodPISA
5
E: Fibronectin
Q: peptide from Fibronectin-binding protein A


Theoretical massNumber of molelcules
Total (without water)12,5802
Polymers12,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6.6 kcal/mol
Surface area6320 Å2
MethodPISA
6
F: Fibronectin
R: peptide from Fibronectin-binding protein A


Theoretical massNumber of molelcules
Total (without water)12,5802
Polymers12,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-6.3 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.590, 109.720, 71.470
Angle α, β, γ (deg.)90.000, 96.940, 90.000
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.: 6 / Fragment: UNP residues 93-182
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: 2459.572 Da / Num. of mol.: 6 / Fragment: UNP residues 529-549 / Source method: obtained synthetically / Details: Peptide synthesis
Source: (synth.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: P14738
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8M 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: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2006
Details: Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→26.038 Å / Num. all: 61539 / Num. obs: 58424 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.7 / Redundancy: 3.6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4.2 / Num. measured all: 33090 / Num. unique all: 8970 / Rsym value: 0.272 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.4.0013refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A previous lower resolution structure

Resolution: 2→25.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 4.723 / SU ML: 0.132 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3086 5 %RANDOM
Rwork0.197 ---
all0.2 61510 --
obs0.2 58424 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.358 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å20 Å2-0.13 Å2
2---2.17 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2→25.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 28 822 5928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215230
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9467079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg23.1225639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41823.74254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56615878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7651542
X-RAY DIFFRACTIONr_chiral_restr0.0280.02731
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024018
X-RAY DIFFRACTIONr_nbd_refined0.310.2338
X-RAY DIFFRACTIONr_nbtor_refined0.3380.2730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2162
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.29
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.29
X-RAY DIFFRACTIONr_mcbond_it3.1061.53156
X-RAY DIFFRACTIONr_mcangle_it4.34925075
X-RAY DIFFRACTIONr_scbond_it6.61932074
X-RAY DIFFRACTIONr_scangle_it9.2924.51998
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 218 -
Rwork0.235 4326 -
all-4544 -
obs-4544 100 %

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