[English] 日本語
Yorodumi
- PDB-5kwg: Crystal structure of extracellular domain of HER2 in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kwg
TitleCrystal structure of extracellular domain of HER2 in complex with Fcab H10-03-6
Components
  • Ig gamma-1 chain C region
  • Receptor tyrosine-protein kinase erbB-2
KeywordsIMMUNE SYSTEM / antibody engineering / immunoglobulin G1 / Fc fragment / glycosylations / CH3 domain / Fcab / human epidermal growth factor receptor 2 / HER2/neu / erbB-2 / cell surface receptor
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / Fc-gamma receptor I complex binding / ErbB-3 class receptor binding / regulation of microtubule-based process ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / Fc-gamma receptor I complex binding / ErbB-3 class receptor binding / regulation of microtubule-based process / complement-dependent cytotoxicity / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / Classical antibody-mediated complement activation / positive regulation of Rho protein signal transduction / ERBB2 Activates PTK6 Signaling / neuromuscular junction development / positive regulation of transcription by RNA polymerase I / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / Initial triggering of complement / immunoglobulin complex, circulating / enzyme-linked receptor protein signaling pathway / immunoglobulin receptor binding / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / FCGR activation / positive regulation of protein targeting to membrane / Role of phospholipids in phagocytosis / regulation of angiogenesis / coreceptor activity / complement activation, classical pathway / Schwann cell development / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / antigen binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of ERK1 and ERK2 cascade / SHC1 events in ERBB2 signaling / positive regulation of cell adhesion / Downregulation of ERBB2:ERBB3 signaling / Constitutive Signaling by Overexpressed ERBB2 / FCGR3A-mediated IL10 synthesis / neurogenesis / positive regulation of epithelial cell proliferation / basal plasma membrane / positive regulation of translation / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / neuromuscular junction / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / neuron differentiation / cellular response to growth factor stimulus / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / ruffle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / antibacterial humoral response / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of cell growth / Interleukin-4 and Interleukin-13 signaling / basolateral plasma membrane / blood microparticle / adaptive immune response
Similarity search - Function
: / 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 ...: / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsHumm, A. / Lobner, E. / Goritzer, K. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
Funding support Austria, 2items
OrganizationGrant numberCountry
Christian Doppler Research AssociationChristian Doppler Laboratory for Antibody Engineering Austria
Austrian Science FundFWF W1224 (Doctoral Program on Biomolecular Technology of Proteins , BioToP) Austria
CitationJournal: Structure / Year: 2017
Title: Fcab-HER2 Interaction: a Menage a Trois. Lessons from X-Ray and Solution Studies.
Authors: Lobner, E. / Humm, A.S. / Goritzer, K. / Mlynek, G. / Puchinger, M.G. / Hasenhindl, C. / Ruker, F. / Traxlmayr, M.W. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionJul 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4Jan 10, 2024Group: 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Receptor tyrosine-protein kinase erbB-2
A: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)95,2782
Polymers95,2782
Non-polymers00
Water00
1
C: Receptor tyrosine-protein kinase erbB-2
A: Ig gamma-1 chain C region

C: Receptor tyrosine-protein kinase erbB-2
A: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)190,5564
Polymers190,5564
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
MethodPISA
Unit cell
Length a, b, c (Å)109.770, 109.770, 176.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Receptor tyrosine-protein kinase erbB-2 / Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / ...Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / Tyrosine kinase-type cell surface receptor HER2 / p185erbB2


Mass: 69507.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, MLN19, NEU, NGL / Cell line (production host): CHO Lec1 / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Protein Ig gamma-1 chain C region


Mass: 25770.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Plasmid: Plasmid / Cell line (production host): HEK 293-6E / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P01857
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 50 mM Citric acid, 18% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 5, 2015 / Details: CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 4.3→47.532 Å / Num. all: 55512 / Num. obs: 8755 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 174.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1898 / Net I/σ(I): 6.48
Reflection shellResolution: 4.3→4.454 Å / Redundancy: 6 % / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 0.99 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2247: ???)refinement
EDNAdata collection
XDSv.Oct-2015data reduction
XDSv.Oct-2015data scaling
PHENIX1.10-2247phasing
XDSv.Oct-2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K33

5k33


Resolution: 4.3→47.532 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 41.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3686 1606 9.97 %
Rwork0.3237 --
obs0.3283 8754 99.86 %
all-16114 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.3→47.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6025 0 0 0 6025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026191
X-RAY DIFFRACTIONf_angle_d0.5958437
X-RAY DIFFRACTIONf_dihedral_angle_d8.4583755
X-RAY DIFFRACTIONf_chiral_restr0.043928
X-RAY DIFFRACTIONf_plane_restr0.0041105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3004-4.43910.36581520.39981300X-RAY DIFFRACTION100
4.4391-4.59760.38011470.38381344X-RAY DIFFRACTION100
4.5976-4.78160.39811420.38851353X-RAY DIFFRACTION100
4.7816-4.9990.37011500.37321289X-RAY DIFFRACTION100
4.999-5.26220.40321530.38831291X-RAY DIFFRACTION100
5.2622-5.59140.40061440.3711321X-RAY DIFFRACTION100
5.5914-6.02230.38231380.37981332X-RAY DIFFRACTION100
6.0223-6.6270.43871370.35591321X-RAY DIFFRACTION100
6.627-7.58250.35761480.31171323X-RAY DIFFRACTION100
7.5825-9.54050.36331430.32371315X-RAY DIFFRACTION100
9.5405-47.53470.33741520.24791319X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.1196-3.6312-0.39736.04773.0571.9273-0.5614-0.3228-0.03510.75890.3911-1.04120.7263-0.06250.00012.02990.00120.11382.1659-0.14531.893955.59812.872-4.5736
21.6341-1.44720.70835.1544-2.52111.1892-0.41220.4997-1.3225-0.66860.1748-0.36580.6561-0.522501.80870.0383-0.03271.9913-0.14992.417949.1028.113-34.0927
30.80081.38051.81974.92052.23434.7181-0.94270.08130.1631.6293-0.3841.31510.19490.4945-0.91070.99570.4459-0.02492.8202-0.47071.918226.324521.8094-45.9081
41.8583-0.8748-2.24940.6570.95332.7242-1.4850.089-0.14551.07481.74310.4087-1.66410.9454-0.00112.8479-0.13060.11274.0218-0.60183.0939-31.27718.0373-42.8983
52.2005-4.88320.39292.0011-0.26325.1080.3010.1919-0.6339-2.5214-2.1043-1.4654-1.1603-0.0601-0.83511.9031-0.2515-0.63333.0847-0.25972.89423.77686.1212-61.562
65.37330.69274.38210.1060.52673.56780.4543-0.3188-0.54590.5668-1.82370.1535-0.60350.0382-0.00062.16980.333-0.11252.9564-0.56422.2004-3.45936.2524-50.1383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 224 )
2X-RAY DIFFRACTION2chain 'C' and (resid 225 through 429 )
3X-RAY DIFFRACTION3chain 'C' and (resid 430 through 575 )
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 346 )
5X-RAY DIFFRACTION5chain 'A' and (resid 347 through 364 )
6X-RAY DIFFRACTION6chain 'A' and (resid 365 through 443 )

+
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