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- PDB-3mql: Crystal structure of the fibronectin 6FnI1-2FnII7FnI fragment -

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Basic information

Entry
Database: PDB / ID: 3mql
TitleCrystal structure of the fibronectin 6FnI1-2FnII7FnI fragment
ComponentsFibronectin 1
KeywordsCELL ADHESION / fibronectin / collagen / GBD / Fn2 / Fn1
Function / homology
Function and homology information


neutrophil degranulation / 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 ...neutrophil degranulation / 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 / poly(A) binding / cell-substrate junction assembly / U2-type catalytic step 2 spliceosome / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / cyclosporin A binding / 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 / basement membrane / endoplasmic reticulum-Golgi intermediate compartment / ECM proteoglycans / positive regulation of axon extension / Integrin cell surface interactions / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / collagen binding / Degradation of the extracellular matrix / catalytic step 2 spliceosome / Integrin signaling / substrate adhesion-dependent cell spreading / mRNA Splicing - Major Pathway / cell-matrix adhesion / extracellular matrix / regulation of ERK1 and ERK2 cascade / platelet alpha granule lumen / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / Signaling by ALK fusions and activated point mutants / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / response to wounding / mRNA splicing, via spliceosome / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / protein folding / Platelet degranulation / heparin binding / nervous system development / heart development / regulation of cell shape / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / angiogenesis / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / nuclear speck / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / mRNA binding / Neutrophil degranulation / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm
Similarity search - Function
Fibronectin, type II, collagen-binding / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Seminal Fluid Protein PDC-109 (Domain B) / Complement Module, domain 1 ...Fibronectin, type II, collagen-binding / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Seminal Fluid Protein PDC-109 (Domain B) / 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 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Kringle-like fold / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / RNA recognition motif / Fibronectin type-III domain profile. / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Fibronectin type III / Fibronectin type III superfamily / RNA-binding domain superfamily / Ribbon / Nucleotide-binding alpha-beta plait domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase E / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsErat, M.C. / Campbell, I.D. / Vakonakis, I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Implications for collagen binding from the crystallographic structure of fibronectin 6FnI1-2FnII7FnI
Authors: Erat, M.C. / Schwarz-Linek, U. / Pickford, A.R. / Farndale, R.W. / Campbell, I.D. / Vakonakis, I.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4505
Polymers24,8741
Non-polymers5764
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.947, 103.947, 102.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-530-

HOH

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Components

#1: Protein Fibronectin 1 / / Fibronectin 1 / isoform CRA_g


Mass: 24874.469 Da / Num. of mol.: 1 / Fragment: 6FnI1-2FnII7FnI, UNP residues 305-515 / Mutation: H307D
Source method: isolated from a genetically manipulated source
Details: gene integrated in the AOX1 locus / Source: (gene. exp.) Homo sapiens (human) / Description: genomic integration / Gene: FN1, hCG_1813428 / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: B7ZLF0, UniProt: P02751*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1:1 drops of of protein in 100 mM NaCl, 10mM HEPES pH 7.2 buffer at 17.5 mg/ml concentration, and a 0.2 M (NH4)H2PO4, 0.1 M Tris-Cl pH 8.5, 50% MPD buffer, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2010
RadiationMonochromator: Bartels monochromator with dual channel cut crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.004→51.974 Å / Num. obs: 5835 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.055 / Net I/σ(I): 27
Reflection shellResolution: 3→3.17 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.473 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XSCALEdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INDIVIDUAL DOMAINS FROM PDB ENTRIES 2CG7, 2RKY, 3EJH, 1EAK, 1H8P, 1L6J

2cg7

2rky

3ejh

1eak

1h8p

1l6j


Resolution: 3.004→51.973 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.4 / Phase error: 23.3 / Stereochemistry target values: ML
Details: 1. Used one TLS restraint for entire polypeptide chain; 2. SF file contains Friedel pairs.
RfactorNum. reflection% reflection
Rfree0.2305 528 4.97 %
Rwork0.2012 --
obs0.2026 5835 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.177 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 287.1 Å2 / Biso min: 35.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.583 Å20 Å2-0 Å2
2--4.583 Å2-0 Å2
3----9.166 Å2
Refinement stepCycle: LAST / Resolution: 3.004→51.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 38 2 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041715
X-RAY DIFFRACTIONf_angle_d0.7762314
X-RAY DIFFRACTIONf_dihedral_angle_d14.039590
X-RAY DIFFRACTIONf_chiral_restr0.054237
X-RAY DIFFRACTIONf_plane_restr0.002302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0041-3.30640.32581300.27962523X-RAY DIFFRACTION99
3.3064-3.78470.23181340.20032504X-RAY DIFFRACTION100
3.7847-4.76780.17341370.1662542X-RAY DIFFRACTION100
4.7678-51.98130.24751270.20282536X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.5081 Å / Origin y: -23.3915 Å / Origin z: 36.3732 Å
111213212223313233
T0.2979 Å20.0792 Å20.0836 Å2-0.2836 Å20.0861 Å2--0.2803 Å2
L1.203 °20.9195 °2-0.4607 °2-0.1318 °20.7422 °2--0.6996 °2
S0.0391 Å °-0.203 Å °0.1946 Å °0.0021 Å °0.0414 Å °0.1163 Å °-0.2242 Å °-0.1353 Å °-0.0444 Å °
Refinement TLS groupSelection details: chain A

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