[English] 日本語
Yorodumi
- PDB-3bux: Crystal structure of c-Cbl-TKB domain complexed with its binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bux
TitleCrystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met
Components
  • 13-meric peptide from Hepatocyte growth factor receptor
  • E3 ubiquitin-protein ligase CBL
KeywordsLIGASE/SIGNALING PROTEIN / Cbl / TKB / ligase / signal transduction / proto-oncogene / complex / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / Calcium / Cytoplasm / Metal-binding / SH2 domain / Ubl conjugation pathway / Zinc / Zinc-finger / LIGASE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / cellular response to oxygen-glucose deprivation / regulation of Rap protein signal transduction / hepatocyte growth factor receptor activity / negative regulation of epidermal growth factor-activated receptor activity / entry of bacterium into host cell / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / cellular response to oxygen-glucose deprivation / regulation of Rap protein signal transduction / hepatocyte growth factor receptor activity / negative regulation of epidermal growth factor-activated receptor activity / entry of bacterium into host cell / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / flotillin complex / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / phosphatidylinositol 3-kinase regulatory subunit binding / semaphorin receptor activity / Sema4D mediated inhibition of cell attachment and migration / MET receptor recycling / positive regulation of epidermal growth factor receptor signaling pathway / MET activates PTPN11 / pancreas development / negative regulation of Rho protein signal transduction / MET activates RAP1 and RAC1 / MET activates PI3K/AKT signaling / protein monoubiquitination / neuron death / negative regulation of stress fiber assembly / response to testosterone / negative regulation of thrombin-activated receptor signaling pathway / response to starvation / mast cell degranulation / semaphorin-plexin signaling pathway / Interleukin-6 signaling / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / Regulation of KIT signaling / positive chemotaxis / negative regulation of epidermal growth factor receptor signaling pathway / TGF-beta receptor signaling activates SMADs / cellular response to platelet-derived growth factor stimulus / establishment of skin barrier / MECP2 regulates neuronal receptors and channels / protein autoubiquitination / positive regulation of microtubule polymerization / MET activates RAS signaling / phagocytosis / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / negative regulation of autophagy / cellular response to nerve growth factor stimulus / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / phosphotyrosine residue binding / liver development / response to activity / ephrin receptor binding / cilium / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / EGFR downregulation / Negative regulation of FGFR2 signaling / RING-type E3 ubiquitin transferase / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / response to gamma radiation / negative regulation of neuron death / Negative regulation of MET activity / receptor tyrosine kinase binding / Constitutive Signaling by EGFRvIII / neuron differentiation / cytokine-mediated signaling pathway / receptor protein-tyrosine kinase / transmembrane receptor protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / SH3 domain binding / ubiquitin protein ligase activity / protein polyubiquitination / ubiquitin-protein transferase activity / male gonad development / positive regulation of receptor-mediated endocytosis / positive regulation of kinase activity / Constitutive Signaling by Aberrant PI3K in Cancer / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / growth cone / PIP3 activates AKT signaling / nervous system development / ubiquitin-dependent protein catabolic process / positive regulation of phosphatidylinositol 3-kinase signaling / transmembrane receptor protein tyrosine kinase signaling pathway / cell migration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / response to ethanol / protein tyrosine kinase activity / positive regulation of protein kinase B signaling
Similarity search - Function
Adaptor protein Cbl, N-terminal domain / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / CBL proto-oncogene N-terminus, EF hand-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / CBL proto-oncogene N-terminus, SH2-like domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / CBL proto-oncogene N-terminal domain 1 / Adaptor protein Cbl, PTB domain ...Adaptor protein Cbl, N-terminal domain / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / CBL proto-oncogene N-terminus, EF hand-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / CBL proto-oncogene N-terminus, SH2-like domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / CBL proto-oncogene N-terminal domain 1 / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / Adaptor protein Cbl, N-terminal domain superfamily / Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Transcription Elongation Factor S-II; Chain A / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain superfamily / Sema domain profile. / Sema domain / UBA/TS-N domain / IPT/TIG domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / ig-like, plexins, transcription factors / domain found in Plexins, Semaphorins and Integrins / PSI domain / IPT domain / UBA-like superfamily / SH2 domain / SHC Adaptor Protein / Zinc finger RING-type signature. / Zinc finger, RING-type, conserved site / EF-hand / Ring finger / Recoverin; domain 1 / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Immunoglobulin E-set / Tyrosine kinase, catalytic domain / Tyrosine-protein kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Zinc finger, RING/FYVE/PHD-type / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor / E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsNg, C. / Jackson, R.A. / Buschdorf, J.P. / Sun, Q. / Guy, G.R. / Sivaraman, J.
CitationJournal: Embo J. / Year: 2008
Title: Structural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates
Authors: Ng, C. / Jackson, R.A. / Buschdorf, J.P. / Sun, Q. / Guy, G.R. / Sivaraman, J.
History
DepositionJan 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 13-meric peptide from Hepatocyte growth factor receptor
B: E3 ubiquitin-protein ligase CBL
C: 13-meric peptide from Hepatocyte growth factor receptor
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)79,5754
Polymers79,5754
Non-polymers00
Water12,358686
1
A: 13-meric peptide from Hepatocyte growth factor receptor


Theoretical massNumber of molelcules
Total (without water)1,5961
Polymers1,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)38,1921
Polymers38,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 13-meric peptide from Hepatocyte growth factor receptor


Theoretical massNumber of molelcules
Total (without water)1,5961
Polymers1,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)38,1921
Polymers38,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: 13-meric peptide from Hepatocyte growth factor receptor
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7882
Polymers39,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5.4 kcal/mol
Surface area14820 Å2
MethodPISA
6
C: 13-meric peptide from Hepatocyte growth factor receptor
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7882
Polymers39,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5.5 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.175, 104.800, 52.598
Angle α, β, γ (deg.)90.000, 90.410, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide 13-meric peptide from Hepatocyte growth factor receptor / HGF receptor / Scatter factor receptor / SF receptor / HGF/SF receptor / Met proto-oncogene ...HGF receptor / Scatter factor receptor / SF receptor / HGF/SF receptor / Met proto-oncogene tyrosine kinase / c-Met


Mass: 1595.537 Da / Num. of mol.: 2 / Fragment: UNP residues 997-1009, pTyr-1003 phosphopeptide / Source method: obtained synthetically / Details: synthetic construct / References: UniProt: P08581
#2: Protein E3 ubiquitin-protein ligase CBL / Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto-oncogene ...Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto-oncogene / RING finger protein 55


Mass: 38192.090 Da / Num. of mol.: 2
Fragment: c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55
Plasmid details: Cas-Br-M (murine) ecotropic retroviral transforming sequence
Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15M malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 142289 / % possible obs: 95 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Χ2: 0.608 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.35-1.44.90.236130010.35587.2
1.4-1.455.50.203137140.36391.8
1.45-1.5260.156140430.39893.9
1.52-1.66.30.119141380.43994.5
1.6-1.76.60.087142860.44795.4
1.7-1.836.80.067144040.48796.3
1.83-2.0270.053144780.61296.7
2.02-2.317.20.044146030.82297.6
2.31-2.917.20.034147910.7998.3
2.91-507.60.03148311.03697.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.6 Å29.1 Å
Translation1.6 Å29.1 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBL
Resolution: 1.35→20 Å / Cross valid method: THROUGHOUT / σ(F): 11808
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2208 1.5 %RANDOM
Rwork0.225 ---
obs-130160 87 %-
Solvent computationBsol: 52.376 Å2
Displacement parametersBiso mean: 18.448 Å2
Baniso -1Baniso -2Baniso -3
1--3.011 Å20 Å20.733 Å2
2--1.438 Å20 Å2
3---1.573 Å2
Refinement stepCycle: LAST / Resolution: 1.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 0 686 5820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.112
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ptr.param

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more