[English] 日本語
Yorodumi
- PDB-7qvk: NM-02 in complex with HER2-ECD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qvk
TitleNM-02 in complex with HER2-ECD
Components
  • NM-02
  • Receptor tyrosine-protein kinase erbB-2
KeywordsONCOPROTEIN / receptor tyrosine protein kinase
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 / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse ...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 / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neuromuscular junction development / positive regulation of Rho protein signal transduction / ERBB2 Activates PTK6 Signaling / 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 / enzyme-linked receptor protein signaling pathway / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / myelination / Downregulation of ERBB2:ERBB3 signaling / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / neurogenesis / basal plasma membrane / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of translation / positive regulation of epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / neuromuscular junction / Signaling by ERBB2 ECD mutants / neuron differentiation / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / early endosome / cell surface receptor signaling pathway / receptor complex / endosome membrane / intracellular signal transduction / apical plasma membrane / positive regulation of protein phosphorylation / protein heterodimerization activity / protein phosphorylation / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane
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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCowan, R. / Hall, G. / Carr, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Plos One / Year: 2023
Title: Co-crystallisation and humanisation of an anti-HER2 single-domain antibody as a theranostic tool.
Authors: Sawmynaden, K. / Wong, N. / Davies, S. / Cowan, R. / Brown, R. / Tang, D. / Henry, M. / Tickle, D. / Matthews, D. / Carr, M. / Bakrania, P. / Hoi Ting, H. / Hall, G.
History
DepositionJan 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Derived calculations / Category: citation / citation_author / pdbx_struct_assembly
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_assembly.details
Revision 1.2Feb 7, 2024Group: 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
AAA: Receptor tyrosine-protein kinase erbB-2
BBB: NM-02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7654
Polymers83,9572
Non-polymers8082
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint1 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.767, 105.767, 185.882
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 69622.977 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): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Antibody NM-02


Mass: 14334.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.578768 Å3/Da / Density % sol: 65.65199 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 13% PEG6000 (w/v), 0.1 M MES pH 6.5, 7% 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96872 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96872 Å / Relative weight: 1
ReflectionResolution: 3.1→65.324 Å / Num. obs: 22490 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 101.26 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.1
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 19.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4001 / CC1/2: 0.34 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MY6

5my6


Resolution: 3.1→65.324 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.777 / Cross valid method: FREE R-VALUE / ESU R: 1.38 / ESU R Free: 0.497
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3299 1186 5.284 %Random selection
Rwork0.2751 21261 --
all0.278 ---
obs0.2747 22447 99.858 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 105.683 Å2
Baniso -1Baniso -2Baniso -3
1--3.441 Å2-1.721 Å20 Å2
2---3.441 Å2-0 Å2
3---11.163 Å2
Refinement stepCycle: LAST / Resolution: 3.1→65.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 0 53 0 4836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134963
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174457
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6586767
X-RAY DIFFRACTIONr_angle_other_deg2.5861.58610284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73522.627255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89115764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7871530
X-RAY DIFFRACTIONr_chiral_restr0.050.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025706
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021139
X-RAY DIFFRACTIONr_nbd_refined0.2230.21145
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2510.24754
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22367
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0820.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1070.29
X-RAY DIFFRACTIONr_nbd_other0.1920.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5860.21
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1420.21
X-RAY DIFFRACTIONr_mcbond_it5.05211.3372504
X-RAY DIFFRACTIONr_mcbond_other5.05311.3352503
X-RAY DIFFRACTIONr_mcangle_it8.35816.9833123
X-RAY DIFFRACTIONr_mcangle_other8.35716.9853124
X-RAY DIFFRACTIONr_scbond_it4.34511.632459
X-RAY DIFFRACTIONr_scbond_other4.34511.632459
X-RAY DIFFRACTIONr_scangle_it7.34617.3553644
X-RAY DIFFRACTIONr_scangle_other7.34517.3563645
X-RAY DIFFRACTIONr_lrange_it11.966134.5545371
X-RAY DIFFRACTIONr_lrange_other11.966134.5725372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.399570.4471538X-RAY DIFFRACTION99.563
3.18-3.2670.456950.4171511X-RAY DIFFRACTION99.9378
3.267-3.3620.418800.3941447X-RAY DIFFRACTION100
3.362-3.4660.361030.3651423X-RAY DIFFRACTION100
3.466-3.5790.415750.3561380X-RAY DIFFRACTION100
3.579-3.7050.366530.3021362X-RAY DIFFRACTION100
3.705-3.8450.281860.2731287X-RAY DIFFRACTION100
3.845-4.0010.279700.2581248X-RAY DIFFRACTION100
4.001-4.1790.283780.2531195X-RAY DIFFRACTION99.9215
4.179-4.3830.25570.2231156X-RAY DIFFRACTION100
4.383-4.620.275690.2021099X-RAY DIFFRACTION100
4.62-4.90.203570.1961026X-RAY DIFFRACTION100
4.9-5.2380.307570.2181003X-RAY DIFFRACTION99.9057
5.238-5.6580.274400.226916X-RAY DIFFRACTION100
5.658-6.1970.338420.234863X-RAY DIFFRACTION100
6.197-6.9280.277460.234774X-RAY DIFFRACTION100
6.928-7.9970.389510.243680X-RAY DIFFRACTION100
7.997-9.790.281320.251593X-RAY DIFFRACTION100
9.79-13.8260.373200.258481X-RAY DIFFRACTION100
13.826-65.3240.534180.458279X-RAY DIFFRACTION97.3771

+
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