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- PDB-4mj6: Crystal Structure of HLA-A*1101 in complex with H7-22, an influen... -

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Basic information

Entry
Database: PDB / ID: 4mj6
TitleCrystal Structure of HLA-A*1101 in complex with H7-22, an influenza A(H7N9) virus epitope
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-11 alpha chain
  • Nucleoprotein
KeywordsIMMUNE SYSTEM/PEPTIDE / MHC / T cell responses / IMMUNE SYSTEM-PEPTIDE complex
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / helical viral capsid / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / helical viral capsid / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / detection of bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / viral penetration into host nucleus / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / host cell / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / immune response / defense response to Gram-positive bacterium / endoplasmic reticulum lumen / Amyloid fiber formation / ribonucleoprotein complex / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / symbiont entry into host cell / endoplasmic reticulum membrane / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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 / Beta-2-microglobulin / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsLiu, J. / Tan, S. / Zhao, M. / Qi, J. / Gao, G.F.
CitationJournal: J.Infect.Dis. / Year: 2016
Title: Cross-immunity Against Avian Influenza A(H7N9) Virus in the Healthy Population Is Affected by Antigenicity-Dependent Substitutions.
Authors: Liu, W.J. / Tan, S. / Zhao, M. / Quan, C. / Bi, Y. / Wu, Y. / Zhang, S. / Zhang, H. / Xiao, H. / Qi, J. / Yan, J. / Liu, W. / Yu, H. / Shu, Y. / Wu, G. / Gao, G.F.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references / Structure summary
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,9723
Polymers44,9723
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-20 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.993, 65.052, 109.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, A-11 alpha chain / MHC class I antigen A*11


Mass: 31725.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P13746, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Nucleoprotein


Mass: 1366.798 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 188-198 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Influenza A virus / References: UniProt: R4X2K3, UniProt: Q9Q0U8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Ammonium acetate, 0.1M BIS0TRIS PH5.5, 17% w/v Polyethylene glycol 10K, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 12933 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→38.842 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 630 4.89 %RANDOM
Rwork0.1865 ---
obs0.1893 12877 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→38.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 0 98 3262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053250
X-RAY DIFFRACTIONf_angle_d0.8884400
X-RAY DIFFRACTIONf_dihedral_angle_d16.2531212
X-RAY DIFFRACTIONf_chiral_restr0.066448
X-RAY DIFFRACTIONf_plane_restr0.003580
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.57-2.82850.3271470.2692288094
2.8285-3.23760.3011710.24453052100
3.2376-4.07840.25281570.18533091100
4.0784-38.84660.20521550.1523322499
Refinement TLS params.Method: refined / Origin x: -15.1253 Å / Origin y: 4.2237 Å / Origin z: -13.6801 Å
111213212223313233
T0.0933 Å2-0.0083 Å2-0.0038 Å2-0.0921 Å20.0096 Å2--0.0682 Å2
L0.7898 °2-0.0722 °2-0.1193 °2-0.7782 °20.3056 °2--0.4953 °2
S0.0049 Å °-0.002 Å °-0.0474 Å °-0.018 Å °-0.0332 Å °0.1136 Å °-0.0078 Å °-0.0066 Å °-0.0005 Å °
Refinement TLS groupSelection details: ALL

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