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- PDB-5sxp: STRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX -

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Basic information

Entry
Database: PDB / ID: 5sxp
TitleSTRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX
Components
  • E3 ubiquitin-protein ligase Itchy homolog
  • Rho guanine nucleotide exchange factor 7
KeywordsSIGNALING PROTEIN/LIGASE / SH3 DOMAIN PEPTIDE LIGAND COMPLEX / LIGASE / SIGNALING PROTEIN-LIGASE complex
Function / homology
Function and homology information


negative regulation of microtubule nucleation / regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein K29-linked ubiquitination / T cell anergy / positive regulation of T cell anergy / regulation of necroptotic process ...negative regulation of microtubule nucleation / regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein K29-linked ubiquitination / T cell anergy / positive regulation of T cell anergy / regulation of necroptotic process / protein branched polyubiquitination / CXCR chemokine receptor binding / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / HECT-type E3 ubiquitin transferase / negative regulation of JNK cascade / focal adhesion assembly / arrestin family protein binding / gamma-tubulin binding / positive regulation of fibroblast migration / positive regulation of lamellipodium morphogenesis / Ephrin signaling / regulation of hematopoietic stem cell differentiation / lamellipodium assembly / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / Activation of RAC1 downstream of NMDARs / positive regulation of receptor catabolic process / RHOV GTPase cycle / NRAGE signals death through JNK / ligase activity / mitotic spindle pole / Golgi organization / RHOJ GTPase cycle / negative regulation of NF-kappaB transcription factor activity / RHOQ GTPase cycle / ubiquitin-like protein ligase binding / RHOU GTPase cycle / CDC42 GTPase cycle / ephrin receptor signaling pathway / protein K63-linked ubiquitination / RHOA GTPase cycle / protein monoubiquitination / Rho protein signal transduction / protein K48-linked ubiquitination / ribonucleoprotein complex binding / protein autoubiquitination / ruffle / positive regulation of substrate adhesion-dependent cell spreading / RAC1 GTPase cycle / Downregulation of ERBB4 signaling / positive regulation of GTPase activity / Activated NOTCH1 Transmits Signal to the Nucleus / guanyl-nucleotide exchange factor activity / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / EGFR downregulation / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / receptor internalization / Regulation of necroptotic cell death / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / G alpha (12/13) signalling events / lamellipodium / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / early endosome membrane / cell cortex / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynapse / protein ubiquitination / neuron projection / positive regulation of apoptotic process / inflammatory response / symbiont entry into host cell / intracellular membrane-bounded organelle / innate immune response / focal adhesion / neuronal cell body / centrosome / apoptotic process / negative regulation of apoptotic process / protein kinase binding / signal transduction / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / E3 ubiquitin-protein ligase, SMURF1 type / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / : / HECT domain / HECT, E3 ligase catalytic domain ...Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / E3 ubiquitin-protein ligase, SMURF1 type / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Variant SH3 domain / Calponin homology domain / Calponin homology (CH) domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / SH3 Domains / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 7 / E3 ubiquitin-protein ligase Itchy homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCappadocia, L. / Desrochers, G. / Lussier-Price, M. / Angers, A. / Omichinski, J.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)312158 Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Molecular basis of interactions between SH3 domain-containing proteins and the proline-rich region of the ubiquitin ligase Itch.
Authors: Desrochers, G. / Cappadocia, L. / Lussier-Price, M. / Ton, A.T. / Ayoubi, R. / Serohijos, A. / Omichinski, J.G. / Angers, A.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Data collection / Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
C: Rho guanine nucleotide exchange factor 7
D: Rho guanine nucleotide exchange factor 7
F: E3 ubiquitin-protein ligase Itchy homolog
G: E3 ubiquitin-protein ligase Itchy homolog


Theoretical massNumber of molelcules
Total (without water)34,0116
Polymers34,0116
Non-polymers00
Water6,900383
1
A: Rho guanine nucleotide exchange factor 7
C: Rho guanine nucleotide exchange factor 7
G: E3 ubiquitin-protein ligase Itchy homolog


Theoretical massNumber of molelcules
Total (without water)17,0063
Polymers17,0063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rho guanine nucleotide exchange factor 7
D: Rho guanine nucleotide exchange factor 7
F: E3 ubiquitin-protein ligase Itchy homolog


Theoretical massNumber of molelcules
Total (without water)17,0063
Polymers17,0063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.845, 43.451, 61.482
Angle α, β, γ (deg.)90.37, 101.01, 105.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Rho guanine nucleotide exchange factor 7 / Beta-Pix / COOL-1 / PAK-interacting exchange factor beta / p85


Mass: 7094.742 Da / Num. of mol.: 4 / Fragment: UNP residues 183-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ARHGEF7, COOL1, KIAA0142, P85SPR, PAK3BP, PIXB, Nbla10314
Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14155
#2: Protein/peptide E3 ubiquitin-protein ligase Itchy homolog / Itch / Atrophin-1-interacting protein 4 / AIP4 / NFE2-associated polypeptide 1 / NAPP1


Mass: 2816.185 Da / Num. of mol.: 2 / Fragment: UNP residues 249-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MIB buffer pH 5.0 and 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 32525 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 18.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 6.9 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P4R

2p4r


Resolution: 1.65→41.847 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 16.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1613 1390 4.27 %
Rwork0.1389 --
obs0.1398 32519 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→41.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 0 383 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042390
X-RAY DIFFRACTIONf_angle_d0.7143251
X-RAY DIFFRACTIONf_dihedral_angle_d17.6451421
X-RAY DIFFRACTIONf_chiral_restr0.049323
X-RAY DIFFRACTIONf_plane_restr0.005441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.7090.18161240.14153041X-RAY DIFFRACTION93
1.709-1.77740.17471390.13753035X-RAY DIFFRACTION94
1.7774-1.85830.17611430.13293073X-RAY DIFFRACTION94
1.8583-1.95630.15211370.13033097X-RAY DIFFRACTION95
1.9563-2.07880.16331440.13543110X-RAY DIFFRACTION95
2.0788-2.23930.19471400.1323125X-RAY DIFFRACTION96
2.2393-2.46470.1651370.14383126X-RAY DIFFRACTION97
2.4647-2.82120.17211410.15113142X-RAY DIFFRACTION97
2.8212-3.55420.14821400.14073184X-RAY DIFFRACTION98
3.5542-41.86010.14631450.13643196X-RAY DIFFRACTION98

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