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- PDB-1qr1: POOR BINDING OF A HER-2/NEU EPITOPE (GP2) TO HLA-A2.1 IS DUE TO A... -

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Basic information

Entry
Database: PDB / ID: 1qr1
TitlePOOR BINDING OF A HER-2/NEU EPITOPE (GP2) TO HLA-A2.1 IS DUE TO A LACK OF INTERACTIONS IN THE CENTER OF THE PEPTIDE
Components
  • BETA-2 MICROGLOBULIN
  • GP2 PEPTIDE
  • HLA-A2.1 HEAVY CHAIN
KeywordsIMMUNE SYSTEM / PEPTIDE-BINDING SUPERDOMAIN
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 / regulation of microtubule-based process / ErbB-3 class receptor binding / 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 / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / positive regulation of Rho protein signal transduction / ERBB2-EGFR signaling pathway / neuromuscular junction development / 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 / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of cell adhesion / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / regulation of angiogenesis / endoplasmic reticulum exit site / coreceptor activity / beta-2-microglobulin binding / Schwann cell development / TAP binding / protection from natural killer cell mediated cytotoxicity / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / myelination / Downregulation of ERBB2:ERBB3 signaling / detection of bacterium / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / T cell receptor binding / neurogenesis / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / basal plasma membrane / regulation of ERK1 and ERK2 cascade / positive regulation of translation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / positive regulation of epithelial cell proliferation / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Signaling by ERBB2 TMD/JMD mutants / neuromuscular junction / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / positive regulation of MAP kinase activity / wound healing / negative regulation of forebrain neuron differentiation / Signaling by ERBB2 ECD mutants / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / Signaling by ERBB2 KD Mutants / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / receptor tyrosine kinase binding
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 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Growth factor receptor cysteine-rich domain superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Tyrosine-protein kinase, active site / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Receptor tyrosine-protein kinase erbB-2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsKuhns, J.J. / Batalia, M.A. / Yan, S. / Collins, E.J.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Poor binding of a HER-2/neu epitope (GP2) to HLA-A2.1 is due to a lack of interactions with the center of the peptide.
Authors: Kuhns, J.J. / Batalia, M.A. / Yan, S. / Collins, E.J.
History
DepositionJun 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.name / _software.version
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Nov 3, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-A2.1 HEAVY CHAIN
B: BETA-2 MICROGLOBULIN
C: GP2 PEPTIDE
D: HLA-A2.1 HEAVY CHAIN
E: BETA-2 MICROGLOBULIN
F: GP2 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)89,2356
Polymers89,2356
Non-polymers00
Water1,856103
1
A: HLA-A2.1 HEAVY CHAIN
B: BETA-2 MICROGLOBULIN
C: GP2 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,6183
Polymers44,6183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-23 kcal/mol
Surface area19010 Å2
MethodPISA
2
D: HLA-A2.1 HEAVY CHAIN
E: BETA-2 MICROGLOBULIN
F: GP2 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,6183
Polymers44,6183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-23 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.337, 63.609, 75.135
Angle α, β, γ (deg.)81.88, 76.25, 77.83
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein HLA-A2.1 HEAVY CHAIN


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-275 OF EXTRACELLULAR PORTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid details: T7 promoter system / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2 MICROGLOBULIN /


Mass: 11879.356 Da / Num. of mol.: 2
Mutation: B2M HAS AN ADDED METHIONINE FOR BACTERIAL EXPRESSION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid details: T7 promoter system / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): pHN1 / References: UniProt: P61769
#3: Protein/peptide GP2 PEPTIDE


Mass: 884.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide by FMOC chemistry / References: UniProt: P04626
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Details: Zhao, R., (1999) J.Exp.Med., 189, 359.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-16 %PEG60001reservoir
26 %dioxane1reservoir
325 mMMES1reservoir
410 mg/mlprotein1drop
525 mMMES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.91
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 34412 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.233 / Num. unique all: 1900 / % possible all: 97.6
Reflection
*PLUS
Num. obs: 34962 / Num. measured all: 66839
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 97.6 % / Mean I/σ(I) obs: 3.46

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Processing

Software
NameVersionClassification
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
Adxvdata processing
RefinementResolution: 2.4→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 997316.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1701 5.1 %RANDOM
Rwork0.242 ---
obs0.284 33261 98.2 %-
all-34962 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.99 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å20.08 Å20.25 Å2
2---1.05 Å20.06 Å2
3----3.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6292 0 0 103 6395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 273 5 %
Rwork0.362 5189 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / % reflection Rfree: 5 % / Rfactor Rwork: 0.362

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