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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bum
TitleCrystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty2
Components
  • E3 ubiquitin-protein ligase CBL
  • Protein sprouty homolog 2
KeywordsLIGASE / signal transduction / proto-oncogene / complex / Cytoplasm / Developmental protein / Membrane / Microtubule / Polymorphism / Calcium / Metal-binding / Phosphoprotein / SH2 domain / Ubl conjugation pathway / Zinc / Zinc-finger
Function / homology
Function and homology information


microtubule end / negative regulation of lens fiber cell differentiation / negative regulation of cell projection organization / lung growth / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of fibroblast growth factor receptor signaling pathway / ubiquitin-dependent endocytosis / animal organ development ...microtubule end / negative regulation of lens fiber cell differentiation / negative regulation of cell projection organization / lung growth / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of fibroblast growth factor receptor signaling pathway / ubiquitin-dependent endocytosis / animal organ development / regulation of Rap protein signal transduction / ubiquitin-protein transferase inhibitor activity / bud elongation involved in lung branching / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / negative regulation of epithelial to mesenchymal transition / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / inner ear morphogenesis / Interleukin-6 signaling / mast cell degranulation / response to starvation / response to testosterone / negative regulation of epidermal growth factor receptor signaling pathway / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / protein serine/threonine kinase inhibitor activity / cellular response to vascular endothelial growth factor stimulus / fibroblast growth factor receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / protein monoubiquitination / cell fate commitment / protein autoubiquitination / ephrin receptor binding / cellular response to platelet-derived growth factor stimulus / ERK1 and ERK2 cascade / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / negative regulation of protein ubiquitination / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / InlB-mediated entry of Listeria monocytogenes into host cell / protein serine/threonine kinase activator activity / response to activity / response to gamma radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / sensory perception of sound / Spry regulation of FGF signaling / negative regulation of transforming growth factor beta receptor signaling pathway / Negative regulation of MET activity / Constitutive Signaling by EGFRvIII / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / negative regulation of ERK1 and ERK2 cascade / positive regulation of receptor-mediated endocytosis / SH3 domain binding / ruffle membrane / male gonad development / protein polyubiquitination / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / actin cytoskeleton / Clathrin-mediated endocytosis / microtubule cytoskeleton / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol / cellular response to hypoxia / cytoskeleton / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cilium / positive regulation of cell migration / cadherin binding / membrane raft / negative regulation of cell population proliferation / focal adhesion / calcium ion binding / DNA damage response / positive regulation of gene expression / symbiont entry into host cell / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction
Similarity search - Function
: / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / Adaptor protein Cbl, N-terminal domain / 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 ...: / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / Adaptor protein Cbl, N-terminal domain / 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 / Transcription Elongation Factor S-II; Chain A / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein sprouty homolog 2 / E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNg, C. / Jackson, A.R. / Buschdorf, P.J. / Sun, Q. / Guy, R.G. / 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 16, 2020Group: Database references / Derived calculations / Structure summary
Category: entity / struct ...entity / struct / struct_conn / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct.pdbx_descriptor ..._entity.pdbx_description / _struct.pdbx_descriptor / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein sprouty homolog 2
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7672
Polymers39,7672
Non-polymers00
Water5,350297
1
A: Protein sprouty homolog 2


Theoretical massNumber of molelcules
Total (without water)1,5751
Polymers1,5751
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


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.256, 122.256, 54.707
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein/peptide Protein sprouty homolog 2 / Spry-2


Mass: 1574.562 Da / Num. of mol.: 1 / Fragment: UNP residues 49-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPRY2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O43597
#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.: 1 / Fragment: c-Cbl TKB domain, UNP residues 25-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / 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


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG3350, pH7.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Sep 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 32750 / % possible obs: 99.9 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.083 / Χ2: 1.162 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.98-2.058.20.34632350.54699.1
2.05-2.1312.10.32832450.615100
2.13-2.2313.60.27232490.704100
2.23-2.3514.50.2332550.764100
2.35-2.4915.70.1932800.8499.9
2.49-2.69170.14832320.92399.9
2.69-2.96180.11332801.038100
2.96-3.3919.80.07632841.253100
3.39-4.2621.20.06433061.95100
4.26-5021.10.05233841.854100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBL

2cbl


Resolution: 2→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.263 2221 7 %
Rwork0.224 --
obs-31690 99.9 %
Solvent computationBsol: 55.439 Å2
Displacement parametersBiso mean: 31.025 Å2
Baniso -1Baniso -2Baniso -3
1-1.778 Å2-0.579 Å20 Å2
2--1.778 Å20 Å2
3----3.556 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 0 297 2860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.236
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