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- PDB-3ch8: The crystal structure of PDZ-Fibronectin fusion protein -

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Basic information

Entry
Database: PDB / ID: 3ch8
TitleThe crystal structure of PDZ-Fibronectin fusion protein
Components
  • C-terminal octapeptide from protein ARVCF
  • fusion protein PDZ-Fibronectin,Fibronectin
KeywordsSTRUCTURAL PROTEIN / fibronectin / PDZ
Function / homology
Function and homology information


basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / postsynaptic specialization / negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization ...basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / postsynaptic specialization / 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 / intermediate filament cytoskeleton organization / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / negative regulation of monocyte chemotactic protein-1 production / ALK mutants bind TKIs / cell-substrate junction assembly / establishment or maintenance of epithelial cell apical/basal polarity / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / RHOB GTPase cycle / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / negative regulation of NF-kappaB transcription factor activity / p130Cas linkage to MAPK signaling for integrins / RHOC GTPase cycle / endodermal cell differentiation / regulation of postsynaptic membrane neurotransmitter receptor levels / GRB2:SOS provides linkage to MAPK signaling for Integrins / response to muramyl dipeptide / Signaling by ALK fusions and activated point mutants / RHOG GTPase cycle / Non-integrin membrane-ECM interactions / basement membrane / endoplasmic reticulum-Golgi intermediate compartment / ECM proteoglycans / RHOA GTPase cycle / protein targeting / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of axon extension / Integrin cell surface interactions / Nuclear events stimulated by ALK signaling in cancer / Signaling by ERBB2 / RAC1 GTPase cycle / collagen binding / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / Constitutive Signaling by Overexpressed ERBB2 / extracellular matrix / basal plasma membrane / 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 / Signaling by ERBB2 TMD/JMD mutants / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / neuromuscular junction / MAP2K and MAPK activation / wound healing / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / structural constituent of cytoskeleton / Downregulation of ERBB2 signaling / 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 / cell junction / heparin binding / nervous system development / cellular response to tumor necrosis factor
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / 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 I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / 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 / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Kringle-like fold / EGF-like domain signature 1. / Leucine-rich repeat / PDZ domain / Fibronectin type III domain / Fibronectin type 3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Fibronectin type-III domain profile. / Leucine-rich repeat domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Roll / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMakabe, K. / Huang, J. / Koide, A. / Koide, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution.
Authors: Huang, J. / Makabe, K. / Biancalana, M. / Koide, A. / Koide, S.
History
DepositionMar 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fusion protein PDZ-Fibronectin,Fibronectin
P: C-terminal octapeptide from protein ARVCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9483
Polymers21,9232
Non-polymers241
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-16 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.008, 69.008, 46.706
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein fusion protein PDZ-Fibronectin,Fibronectin / / FN / Cold-insoluble globulin / CIG


Mass: 20996.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: see REMARK 400,see REMARK 400 / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET system / Gene: FN1, FN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02751, UniProt: Q96RT1*PLUS
#2: Protein/peptide C-terminal octapeptide from protein ARVCF


Mass: 927.011 Da / Num. of mol.: 1 / Fragment: C-terminal residues / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN IS A VARIANT OF PREVIOUSLY DEPOSITED FUSION PROTEIN (PDBID: 2QBW). THE CIRCULAR ...THIS PROTEIN IS A VARIANT OF PREVIOUSLY DEPOSITED FUSION PROTEIN (PDBID: 2QBW). THE CIRCULAR PERMUTATED ERVIN PDZ DOMAIN (UNIPROTKB ENTRY: Q96RT1 RESIDUES 1318-1410) WAS FUSED AT THE N-TERMINUS OF THE 10TH FIBRONECTIN TYPE III DOMAIN OF HUMAN FIBRONECTIN (UNIPROTKB: P02751) VIA GLY-GLY-SER-GLY-GLY LINKER. THE PDZ DOMAIN WAS CIRCULAR PERMUTATED FOR A CERTAIN ORIENTATION.

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 31% isopropanol, 0.1M HEPES, 0.2M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 23031 / Num. obs: 23031 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.74
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.712 / Num. unique all: 2256 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.257 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25984 973 5.1 %RANDOM
Rwork0.20071 ---
obs0.20354 18126 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.924 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0.42 Å20 Å2
2---0.84 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 1 89 1625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221575
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9612149
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14223.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70915239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.696159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021221
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2654
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21063
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9931.51002
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48821605
X-RAY DIFFRACTIONr_scbond_it2.353647
X-RAY DIFFRACTIONr_scangle_it3.6394.5542
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.583 68 -
Rwork0.542 1183 -
obs--88.66 %

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