[English] 日本語
Yorodumi
- PDB-6o03: Monobody (MC17) bound to tyrosine kinase binding domain of E3 ubi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o03
TitleMonobody (MC17) bound to tyrosine kinase binding domain of E3 ubiquitin ligase CBL
Components
  • E3 ubiquitin-protein ligase CBL
  • Monobody (MC17)
Keywordstransferase/protein binding / inhibitor / Monobody / SH2 domain / E3 ligase / Synthetic binder / PROTEIN BINDING / transferase-protein binding / inhibitor complex
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / cellular response to platelet-derived growth factor stimulus / negative regulation of epidermal growth factor receptor signaling pathway / response to starvation / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / protein autoubiquitination / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / phosphotyrosine residue binding / ephrin receptor binding / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / response to activity / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / response to gamma radiation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / SH3 domain binding / positive regulation of receptor-mediated endocytosis / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / male gonad development / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / membrane raft / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / plasma membrane / cytosol
Similarity search - Function
Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily ...Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily / UBA/TS-N domain / Ubiquitin associated domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKukenshoner, T. / Pojer, F. / Hantschel, O.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2016-CoG 682311-ONCOINTRABODYEuropean Union
CitationJournal: To Be Published
Title: Monobody (MC17) bound to tyrosine kinase binding domain of E3 ligase CBL
Authors: Kukenshoner, T. / Pojer, F. / Hantschel, O.
History
DepositionFeb 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: E3 ubiquitin-protein ligase CBL
C: Monobody (MC17)
A: E3 ubiquitin-protein ligase CBL
D: Monobody (MC17)


Theoretical massNumber of molelcules
Total (without water)91,4554
Polymers91,4554
Non-polymers00
Water0
1
B: E3 ubiquitin-protein ligase CBL
C: Monobody (MC17)


Theoretical massNumber of molelcules
Total (without water)45,7282
Polymers45,7282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-13 kcal/mol
Surface area18460 Å2
MethodPISA
2
A: E3 ubiquitin-protein ligase CBL
D: Monobody (MC17)


Theoretical massNumber of molelcules
Total (without water)45,7282
Polymers45,7282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-11 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.104, 67.156, 167.882
Angle α, β, γ (deg.)90.00, 96.22, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein E3 ubiquitin-protein ligase CBL / Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / RING- ...Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / RING-type E3 ubiquitin transferase CBL / Signal transduction protein CBL


Mass: 35862.453 Da / Num. of mol.: 2 / Mutation: G306E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P22681, RING-type E3 ubiquitin transferase
#2: Antibody Monobody (MC17)


Mass: 9865.075 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3000, 100mM tris base/hydrochloric acid pH 7, 200mM calcium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→43.49 Å / Num. obs: 14407 / % possible obs: 98 % / Redundancy: 3 % / Net I/σ(I): 8.66
Reflection shellResolution: 3.3→3.418 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→46.19 Å / SU ML: 0.75 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3297 2620 10.04 %
Rwork0.2846 --
obs0.2891 26106 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6279 0 0 0 6279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056450
X-RAY DIFFRACTIONf_angle_d0.8028744
X-RAY DIFFRACTIONf_dihedral_angle_d15.063843
X-RAY DIFFRACTIONf_chiral_restr0.043953
X-RAY DIFFRACTIONf_plane_restr0.0051100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2999-3.35990.4731320.40041219X-RAY DIFFRACTION87
3.3599-3.42450.40251410.36581257X-RAY DIFFRACTION93
3.4245-3.49430.42611340.35471217X-RAY DIFFRACTION93
3.4943-3.57030.33761430.34111251X-RAY DIFFRACTION94
3.5703-3.65330.4421470.34621222X-RAY DIFFRACTION88
3.6533-3.74460.37931190.32551121X-RAY DIFFRACTION86
3.7446-3.84580.37461450.33931268X-RAY DIFFRACTION95
3.8458-3.95890.35761460.33671292X-RAY DIFFRACTION93
3.9589-4.08670.38261330.3271233X-RAY DIFFRACTION94
4.0867-4.23260.35281450.31611276X-RAY DIFFRACTION91
4.2326-4.4020.34671200.29651118X-RAY DIFFRACTION86
4.402-4.60210.33811490.28241305X-RAY DIFFRACTION95
4.6021-4.84450.32561430.26281270X-RAY DIFFRACTION96
4.8445-5.14770.30861380.25441281X-RAY DIFFRACTION96
5.1477-5.54450.29281490.25111295X-RAY DIFFRACTION94
5.5445-6.10140.31531350.26931276X-RAY DIFFRACTION93
6.1014-6.98160.34841280.29011134X-RAY DIFFRACTION86
6.9816-8.78620.31481360.26191214X-RAY DIFFRACTION91
8.7862-46.19470.23621370.21671237X-RAY DIFFRACTION91

+
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