[English] 日本語
Yorodumi
- PDB-3vrr: Crystal structure of the tyrosine kinase binding domain of Cbl-c ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vrr
TitleCrystal structure of the tyrosine kinase binding domain of Cbl-c (PL mutant) in complex with phospho-EGFR peptide
Components
  • Epidermal growth factor receptor
  • Signal transduction protein CBL-C
KeywordsPROTEIN BINDING/TRANSFERASE / PTB domain / TKB (tyrosine kinase binding) domain / four-helix bundle (4H) / calcium-binding EF hand / divergent SH2 domain / Regulator of EGFR mediated signal transduction / Ubiquitously expressed / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


response to glial cell derived neurotrophic factor / negative regulation of epidermal growth factor-activated receptor activity / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle ...response to glial cell derived neurotrophic factor / negative regulation of epidermal growth factor-activated receptor activity / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / epidermal growth factor receptor binding / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to cadmium ion / positive regulation of DNA repair / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / phosphotyrosine residue binding / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / cellular response to dexamethasone stimulus / ossification / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / neuron projection morphogenesis / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / lung development / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / negative regulation of protein catabolic process
Similarity search - Function
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 / 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 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Zinc finger, C3HC4 type (RING finger) / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / SH2 domain / SHC Adaptor Protein / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Growth factor receptor cysteine-rich domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Tyrosine-protein kinase, catalytic domain / Tyrosine 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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
Epidermal growth factor receptor / E3 ubiquitin-protein ligase CBL-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsTakeshita, K. / Tezuka, T. / Isozaki, Y. / Yamashita, E. / Suzuki, M. / Yamanashi, Y. / Yamamoto, T. / Nakagawa, A.
CitationJournal: J.Biochem. / Year: 2012
Title: Structural flexibility regulates phosphopeptide-binding activity of the tyrosine kinase binding domain of Cbl-c.
Authors: Takeshita, K. / Tezuka, T. / Isozaki, Y. / Yamashita, E. / Suzuki, M. / Kim, M. / Yamanashi, Y. / Yamamoto, T. / Nakagawa, A.
History
DepositionApr 13, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal transduction protein CBL-C
C: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3733
Polymers38,3332
Non-polymers401
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-22 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.240, 108.683, 54.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Signal transduction protein CBL-C / RING finger protein 57 / SH3-binding protein CBL-3 / SH3-binding protein CBL-C


Mass: 36707.113 Da / Num. of mol.: 1 / Fragment: tyrosine kinase binding domain / Mutation: P265L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLC / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q9ULV8
#2: Protein/peptide Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 1625.564 Da / Num. of mol.: 1 / Fragment: phospho-EGFR peptide, UNP residues 1062-1074 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human)
References: UniProt: P00533, receptor protein-tyrosine kinase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.81 Å3/Da / Density % sol: 31.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG3350, 0.1M sodium fluoride, 0.6M NDSB-201, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 19, 2008
Diffraction measurementDetails: 1.00 degrees, 1.0 sec, detector distance 350.00 mm
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionAv R equivalents: 0.066 / Number: 96327
ReflectionResolution: 2→50 Å / Num. all: 96327 / Num. obs: 96327 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 26.064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2-2.0350.4244.4559440.424100
2.03-2.0750.3765.149280.37699.9
2.07-2.1150.3415.8329530.341100
2.11-2.1550.2926.7549370.292100
2.15-2.25.10.2597.599480.259100
2.2-2.255.10.2268.2479420.22699.9
2.25-2.3150.21310.399460.21399.5
2.31-2.375.10.17910.6839440.17999.9
2.37-2.445.10.14213.0779360.142100
2.44-2.525.10.12414.2549500.124100
2.52-2.615.10.10716.3789520.107100
2.61-2.715.10.09717.2489510.097100
2.71-2.845.10.08320.0339570.083100
2.84-2.995.10.06823.7259640.068100
2.99-3.175.10.05629.2549450.056100
3.17-3.425.10.04435.0969740.04499.9
3.42-3.7650.03840.5549670.038100
3.76-4.3150.0347.2739710.03100
4.31-5.434.90.02750.2269940.027100
5.43-504.60.02950.49410450.02999.7
Cell measurementReflection used: 96327

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.13 Å35.48 Å
Translation2.13 Å35.48 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.71 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.826 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 982 5.1 %RANDOM
Rwork0.1865 ---
obs0.189 19105 99.54 %-
all-1325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.51 Å2 / Biso mean: 25.6566 Å2 / Biso min: 4.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 1 115 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222439
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9713308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57122.072111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33215397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8091525
X-RAY DIFFRACTIONr_chiral_restr0.1140.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211874
X-RAY DIFFRACTIONr_mcbond_it1.1171.51499
X-RAY DIFFRACTIONr_mcangle_it1.95822401
X-RAY DIFFRACTIONr_scbond_it2.9563940
X-RAY DIFFRACTIONr_scangle_it4.6484.5907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.999-2.050.264690.20212561387132595.53
2.05-2.1060.257790.19112731357135299.632
2.106-2.1670.236630.17112321300129599.615
2.167-2.2330.215600.17112271289128799.845
2.233-2.3060.252710.18611791253125099.761
2.306-2.3860.2580.17711561222121499.345
2.386-2.4760.212620.16310991162116199.914
2.476-2.5760.194720.16410541127112699.911
2.576-2.690.25460.183102010661066100
2.69-2.820.255470.1949971045104499.904
2.82-2.9710.225460.191937983983100
2.971-3.1490.234450.184898943943100
3.149-3.3640.233530.183829882882100
3.364-3.630.246350.18980784384299.881
3.63-3.970.251360.185729765765100
3.97-4.4290.269420.182649691691100
4.429-5.0950.2350.188594629629100
5.095-6.1950.273310.217507538538100
6.195-8.5770.186180.226412430430100
8.577-29.7060.226140.191268282282100

+
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://pdbjlvh1.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