[English] 日本語
Yorodumi
- PDB-2rfe: Crystal structure of the complex between the EGFR kinase domain a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rfe
TitleCrystal structure of the complex between the EGFR kinase domain and a Mig6 peptide
Components
  • ERBB receptor feedback inhibitor 1
  • Epidermal growth factor receptor
KeywordsTRANSFERASE / kinase domain / inhibition / dimer / Alternative splicing / Anti-oncogene / ATP-binding / Cell cycle / Disease mutation / Glycoprotein / Membrane / Nucleotide-binding / Phosphorylation / Polymorphism / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase / Ubl conjugation / Cytoplasm
Function / homology
Function and homology information


regulation of type B pancreatic cell proliferation / negative regulation of epidermal growth factor-activated receptor activity / lung epithelium development / lung vasculature development / negative regulation of protein autophosphorylation / regulation of keratinocyte differentiation / skin morphogenesis / negative regulation of collagen biosynthetic process / lung alveolus development / cellular hyperosmotic response ...regulation of type B pancreatic cell proliferation / negative regulation of epidermal growth factor-activated receptor activity / lung epithelium development / lung vasculature development / negative regulation of protein autophosphorylation / regulation of keratinocyte differentiation / skin morphogenesis / negative regulation of collagen biosynthetic process / lung alveolus development / cellular hyperosmotic response / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / cellular response to dexamethasone stimulus / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor activity / epidermal growth factor binding / response to UV-A / regulation of peptidyl-tyrosine phosphorylation / negative regulation of interleukin-1 beta production / negative regulation of cardiac muscle hypertrophy in response to stress / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / PTK6 promotes HIF1A stabilization / Signaling by EGFR / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / ERBB2 Regulates Cell Motility / Developmental Lineage of Mammary Gland Myoepithelial Cells / protein insertion into membrane / Signaling by ERBB4 / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / negative regulation of tumor necrosis factor production / cellular response to platelet-derived growth factor stimulus / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / GAB1 signalosome / protein tyrosine kinase activator activity / ossification / positive regulation of G1/S transition of mitotic cell cycle / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / positive regulation of epithelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / positive regulation of fibroblast proliferation / SHC1 events in ERBB2 signaling / cellular response to amino acid stimulus / cellular response to epidermal growth factor stimulus / basal plasma membrane / positive regulation of DNA replication / positive regulation of DNA repair / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signal transduction by L1 / GTPase activator activity / cellular response to estradiol stimulus / positive regulation of protein localization to plasma membrane / negative regulation of protein catabolic process / clathrin-coated endocytic vesicle membrane / NOTCH3 Activation and Transmission of Signal to the Nucleus / cell-cell adhesion / Signaling by ERBB2 TMD/JMD mutants / negative regulation of ERK1 and ERK2 cascade / EGFR downregulation / Constitutive Signaling by EGFRvIII / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / SH3 domain binding / positive regulation of miRNA transcription / positive regulation of protein phosphorylation / cell junction / epidermal growth factor receptor signaling pathway / kinase binding / ruffle membrane / small GTPase binding / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / HCMV Early Events / positive regulation of canonical Wnt signaling pathway / actin filament binding / cellular response to insulin stimulus / PIP3 activates AKT signaling / neuron differentiation / transmembrane signaling receptor activity / positive regulation of cell growth / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / nuclear membrane / ATPase binding
Similarity search - Function
Cdc42 binding domain-like / : / GTPase binding / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain ...Cdc42 binding domain-like / : / GTPase binding / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / 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 / Growth factor receptor cysteine-rich domain superfamily / : / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor / ERBB receptor feedback inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsZhang, X. / Pickin, K.A. / Bose, R. / Jura, N. / Cole, P.A. / Kuriyan, J.
CitationJournal: Nature / Year: 2007
Title: Inhibition of the EGF receptor by binding of MIG6 to an activating kinase domain interface.
Authors: Zhang, X. / Pickin, K.A. / Bose, R. / Jura, N. / Cole, P.A. / Kuriyan, J.
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epidermal growth factor receptor
B: Epidermal growth factor receptor
C: Epidermal growth factor receptor
D: Epidermal growth factor receptor
E: ERBB receptor feedback inhibitor 1
F: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)156,3716
Polymers156,3716
Non-polymers00
Water64936
1
A: Epidermal growth factor receptor
E: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)41,2192
Polymers41,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
MethodPISA
2
B: Epidermal growth factor receptor
F: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)41,2192
Polymers41,2192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
MethodPISA
3
C: Epidermal growth factor receptor


Theoretical massNumber of molelcules
Total (without water)36,9671
Polymers36,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Epidermal growth factor receptor


Theoretical massNumber of molelcules
Total (without water)36,9671
Polymers36,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.508, 98.425, 101.496
Angle α, β, γ (deg.)90.000, 112.590, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Epidermal growth factor receptor / Receptor tyrosine-protein kinase ErbB-1


Mass: 36966.801 Da / Num. of mol.: 4 / Fragment: Protein kinase domain / Mutation: K799E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Plasmid: pFASTBAC-HT / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Protein/peptide ERBB receptor feedback inhibitor 1 / Mitogen-inducible gene 6 protein / Mig-6


Mass: 4251.812 Da / Num. of mol.: 2 / Fragment: sequence database residues, 325-364 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UJM3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% PEG3350, 100 mM NaNO3, 100 mM Bis-Tris propane, pH 7.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 32555 / % possible obs: 90.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.082 / Χ2: 1.047 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-31.80.32421030.99458.4
3-3.121.90.32425391.02870.9
3.12-3.271.90.25429701.07182.7
3.27-3.4420.19133481.08793.2
3.44-3.652.10.15635191.05898.3
3.65-3.942.10.10636331.06399.9
3.94-4.332.10.07935871.07599.8
4.33-4.962.10.06336151.0299.5
4.96-6.242.10.06435961.04199.2
6.24-502.10.03136451.01598.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GS7

2gs7


Resolution: 2.9→49.85 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1514 4.1 %random
Rwork0.229 ---
obs-30226 82.6 %-
Solvent computationBsol: 32.294 Å2
Displacement parametersBiso mean: 61.158 Å2
Baniso -1Baniso -2Baniso -3
1-27.155 Å20 Å2-13.079 Å2
2--9.424 Å20 Å2
3----36.578 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8853 0 0 36 8889
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3371.5
X-RAY DIFFRACTIONc_scbond_it1.7152
X-RAY DIFFRACTIONc_mcangle_it2.3922
X-RAY DIFFRACTIONc_scangle_it2.8072.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.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