[English] 日本語
Yorodumi
- PDB-3kex: Crystal structure of the catalytically inactive kinase domain of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kex
TitleCrystal structure of the catalytically inactive kinase domain of the human epidermal growth factor receptor 3 (HER3)
ComponentsReceptor tyrosine-protein kinase erbB-3
KeywordsTRANSFERASE / kinase domain / inactive kinase / HER3 / ErbB3 / ATP-binding / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Tyrosine-protein kinase
Function / homology
Function and homology information


neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / ErbB-3 class receptor binding / negative regulation of cell adhesion / negative regulation of motor neuron apoptotic process / motor neuron apoptotic process / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / Signaling by ERBB4 / growth factor binding / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / lateral plasma membrane / Schwann cell development / negative regulation of signal transduction / extrinsic apoptotic signaling pathway in absence of ligand / Signaling by ERBB2 / myelination / Downregulation of ERBB2:ERBB3 signaling / SHC1 events in ERBB2 signaling / neurogenesis / basal plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signaling by ERBB2 TMD/JMD mutants / wound healing / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / heart development / regulation of cell population proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / apical plasma membrane / protein heterodimerization activity / phosphorylation / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
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 ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Receptor tyrosine-protein kinase erbB-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.797 Å
AuthorsJura, N. / Shan, Y. / Cao, X. / Shaw, D.E. / Kuriyan, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3.
Authors: Jura, N. / Shan, Y. / Cao, X. / Shaw, D.E. / Kuriyan, J.
History
DepositionOct 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-3
B: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9596
Polymers72,8982
Non-polymers1,0614
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-38 kcal/mol
Surface area26900 Å2
MethodPISA
2
A: Receptor tyrosine-protein kinase erbB-3
hetero molecules

B: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9596
Polymers72,8982
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area3110 Å2
ΔGint-28 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.164, 47.637, 81.281
Angle α, β, γ (deg.)90.000, 108.040, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 677:846 or resseq 851:955 )A677 - 846
121chain A and (resseq 677:846 or resseq 851:955 )A851 - 955
211chain B and (resseq 677:844 or resseq 852:955 )B677 - 844
221chain B and (resseq 677:844 or resseq 852:955 )B852 - 955

-
Components

#1: Protein Receptor tyrosine-protein kinase erbB-3 / c-erbB3 / Tyrosine kinase-type cell surface receptor HER3


Mass: 36449.207 Da / Num. of mol.: 2 / Fragment: UNP residues 698-1019
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, ErbB3/HER3, HER3 / Plasmid: pFASTBacHTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P21860, receptor protein-tyrosine kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5mM AMP-PNP, 2mM MgCl2, 1mM DTT, 1mM TCEP, 0.1M Tris pH8.5, 0.2M lithium sulfate, 25% w/v PEG 3350 supplemented with 0.2% w/v 1,2- Diaminocyclohexane sulfate, 0.2% w/v Diloxanite Furoate, 0. ...Details: 5mM AMP-PNP, 2mM MgCl2, 1mM DTT, 1mM TCEP, 0.1M Tris pH8.5, 0.2M lithium sulfate, 25% w/v PEG 3350 supplemented with 0.2% w/v 1,2- Diaminocyclohexane sulfate, 0.2% w/v Diloxanite Furoate, 0.2% w/v Fumaric Acid, 0.2% w/v Spermine, 0.2% w/v Sulfaguanidine, 0.02M Hepes sodium pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2009 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KOHZU Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 17822 / Num. obs: 17502 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 62.94 Å2 / Rmerge(I) obs: 0.101 / Χ2: 1 / Net I/σ(I): 6.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1618 / Χ2: 0.725 / % possible all: 93

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.3 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å46.46 Å
Translation2.8 Å46.46 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inactive EGFR kinase domain

Resolution: 2.797→46.463 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 1.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 894 5.12 %
Rwork0.241 --
obs0.243 17472 98.2 %
all-17792 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.617 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 158.72 Å2 / Biso mean: 71.101 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--27.573 Å20 Å20.72 Å2
2--16.173 Å2-0 Å2
3---11.4 Å2
Refinement stepCycle: LAST / Resolution: 2.797→46.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 64 30 4627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044691
X-RAY DIFFRACTIONf_angle_d0.8336377
X-RAY DIFFRACTIONf_chiral_restr0.05702
X-RAY DIFFRACTIONf_plane_restr0.003800
X-RAY DIFFRACTIONf_dihedral_angle_d17.9241767
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2123X-RAY DIFFRACTIONPOSITIONAL0.016
12B2123X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.797-2.9730.3721430.332562270548
2.973-3.2020.3771470.3082741288851
3.202-3.5240.3031450.262781292652
3.524-4.0340.2781470.2232807295452
4.034-5.0810.2611540.2032804295852
5.081-46.470.2441580.2332883304153

+
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