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- PDB-2rl0: Crystal structure of the fourth and fifth fibronectin F1 modules ... -

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Basic information

Entry
Database: PDB / ID: 2rl0
TitleCrystal structure of the fourth and fifth fibronectin F1 modules in complex with a fragment of staphylococcus aureus fnbpa-5
Components
  • Fibronectin-binding protein
  • Fibronectin
KeywordsCELL ADHESION / FIBRONECTIN / 4F15F1 / 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 / 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 / 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 / Non-integrin membrane-ECM interactions / fibronectin binding / Signaling by ALK fusions and activated point mutants / basement membrane / ECM proteoglycans / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of axon extension / Integrin cell surface interactions / Nuclear events stimulated by ALK signaling in cancer / collagen binding / extracellular matrix / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / platelet alpha granule lumen / integrin-mediated signaling pathway / Post-translational protein phosphorylation / acute-phase response / Cell surface interactions at the vascular wall / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / 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) / 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 / 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 / collagen-containing extracellular matrix / angiogenesis / blood microparticle / Interleukin-4 and Interleukin-13 signaling / protease binding / 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, 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 / YSIRK type signal peptide / Adhesion domain superfamily / 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)
synthetic construct (others)
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 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_entity_src_syn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibronectin
G: Fibronectin-binding protein
B: Fibronectin
C: Fibronectin-binding protein
D: Fibronectin
E: Fibronectin-binding protein
F: Fibronectin
H: Fibronectin-binding protein
I: Fibronectin
J: Fibronectin-binding protein
K: Fibronectin
L: Fibronectin-binding protein


Theoretical massNumber of molelcules
Total (without water)72,90812
Polymers72,90812
Non-polymers00
Water8,323462
1
A: Fibronectin
G: Fibronectin-binding protein


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-5.8 kcal/mol
Surface area6230 Å2
MethodPISA
2
B: Fibronectin
C: Fibronectin-binding protein


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-5.1 kcal/mol
Surface area6440 Å2
MethodPISA
3
D: Fibronectin
E: Fibronectin-binding protein


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-8.3 kcal/mol
Surface area6290 Å2
MethodPISA
4
F: Fibronectin
H: Fibronectin-binding protein


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-5.6 kcal/mol
Surface area6430 Å2
MethodPISA
5
I: Fibronectin
J: Fibronectin-binding protein


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-4.3 kcal/mol
Surface area5410 Å2
MethodPISA
6
K: Fibronectin
L: Fibronectin-binding protein


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-5.5 kcal/mol
Surface area6380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.580, 85.580, 230.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-254-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12A
22B
13I
23A
33B
43D
14B
24D
15D
25K

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEU6DE218 - 22466 - 72
21LYSLYSLEULEU6AA218 - 22466 - 72
12LYSLYSLEULEU6AA218 - 22466 - 72
22LYSLYSLEULEU6BC218 - 22466 - 72
13LEULEUGLYGLY6II185 - 19033 - 38
23LEULEUGLYGLY6AA185 - 19033 - 38
33LEULEUGLYGLY6BC185 - 19033 - 38
43LEULEUGLYGLY6DE185 - 19033 - 38
14LYSLYSLEULEU6BC218 - 22466 - 72
24LYSLYSLEULEU6DE218 - 22466 - 72
15GLNGLNTRPTRP4DE175 - 17723 - 25
25GLNGLNTRPTRP4KK175 - 17723 - 25

NCS ensembles :
IDDetails
1D A
2A B
3I A B D
4B D
5D K

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Components

#1: Protein
Fibronectin / / Human fibronectin module pair 4F1-5F1


Mass: 10137.293 Da / Num. of mol.: 6 / Fragment: UNP residues 184-272
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
Fibronectin-binding protein / Staphylococcus aureus fibronectin binding protein / FNBP


Mass: 2014.082 Da / Num. of mol.: 6 / Fragment: UNP residues 638-655 / Source method: obtained synthetically / Details: Peptide synthesis / Source: (synth.) synthetic construct (others) / References: UniProt: P14738
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2M NACL, 0.1M BIS TRIS, 14% PEG3350, pH6.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2006 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→28.161 Å / Num. all: 58479 / Num. obs: 58383 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.7 / Redundancy: 7.3 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.8 / Num. measured all: 42415 / Num. unique all: 8238 / Rsym value: 0.3 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Previous low resolution structure

Resolution: 2→28.16 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.348 / SU ML: 0.123 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.176 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2954 5.1 %RANDOM
Rwork0.218 ---
all0.221 58383 --
obs0.221 55429 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.859 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2--1.78 Å20 Å2
3----3.57 Å2
Refinement stepCycle: LAST / Resolution: 2→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 0 462 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214978
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9146717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96924.313262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43615853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8531544
X-RAY DIFFRACTIONr_chiral_restr0.0050.02696
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023810
X-RAY DIFFRACTIONr_nbd_refined0.2760.2305
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4010.29
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.29
X-RAY DIFFRACTIONr_mcbond_it1.0481.53029
X-RAY DIFFRACTIONr_mcangle_it1.84724847
X-RAY DIFFRACTIONr_scbond_it2.67931949
X-RAY DIFFRACTIONr_scangle_it4.3814.51869
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A56LOOSE POSITIONAL0.455
12B56LOOSE POSITIONAL0.455
11A56LOOSE THERMAL18.2910
12B56LOOSE THERMAL18.2910
21C56LOOSE POSITIONAL0.125
22D56LOOSE POSITIONAL0.125
21C56LOOSE THERMAL1.0810
22D56LOOSE THERMAL1.0810
31E35LOOSE POSITIONAL0.395
32F35LOOSE POSITIONAL0.240.14
33G35LOOSE POSITIONAL0.230
34H35LOOSE POSITIONAL0.220
31E35LOOSE THERMAL8.2710
32F35LOOSE THERMAL9.060.29
33G35LOOSE THERMAL5.730.01
34H35LOOSE THERMAL6.370
41I56LOOSE POSITIONAL0.455
42J56LOOSE POSITIONAL0.455
41I56LOOSE THERMAL18.0210
42J56LOOSE THERMAL18.0210
51K27MEDIUM POSITIONAL0.440.5
52L27MEDIUM POSITIONAL0.440.5
51K27MEDIUM THERMAL0.632
52L27MEDIUM THERMAL0.632
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 213 -
Rwork0.256 3945 -
all-4158 -
obs-4158 97.08 %

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