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- PDB-4f7t: Crystal Structure of HLA-A*2402 Complexed with a Newly Identified... -

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Basic information

Entry
Database: PDB / ID: 4f7t
TitleCrystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009 H1N1 PB1 (498-505)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • RNA-directed RNA polymerase catalytic subunit
KeywordsIMMUNE SYSTEM / HLA-A*2402 / 2009H1N1 / HLA-A3 supertype / cross-allele recognition
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 / Golgi medial cisterna / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / viral transcription / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / immune response / symbiont-mediated suppression of host gene expression / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / RNA-directed RNA polymerase / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / 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 ...Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / 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 / RNA-directed RNA polymerase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus H3N2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, J. / Zhang, S. / Tan, S. / Yi, Y. / Wu, B. / Zhu, F. / Wang, H. / Qi, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2012
Title: Cross-Allele Cytotoxic T Lymphocyte Responses against 2009 Pandemic H1N1 Influenza A Virus among HLA-A24 and HLA-A3 Supertype-Positive Individuals.
Authors: Liu, J. / Zhang, S. / Tan, S. / Yi, Y. / Wu, B. / Cao, B. / Zhu, F. / Wang, C. / Wang, H. / Qi, J. / Gao, G.F.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: RNA-directed RNA polymerase catalytic subunit
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: RNA-directed RNA polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)89,0736
Polymers89,0736
Non-polymers00
Water15,871881
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: RNA-directed RNA polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)44,5373
Polymers44,5373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-17 kcal/mol
Surface area18770 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: RNA-directed RNA polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)44,5373
Polymers44,5373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-18 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.838, 66.583, 70.362
Angle α, β, γ (deg.)97.70, 101.03, 111.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HLA class I histocompatibility antigen, A-24 alpha chain / Aw-24 / HLA class I histocompatibility antigen / A-9 alpha chain / MHC class I antigen A*24


Mass: 31683.086 Da / Num. of mol.: 2 / Fragment: unp residues 25-298
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: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: unp residues 21-119
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 RNA-directed RNA polymerase catalytic subunit


Mass: 974.094 Da / Num. of mol.: 2 / Fragment: unp residues 498-505 / Source method: obtained synthetically
Details: in vitro synthesized peptide from 2009H1N1 PB1(498-505)
Source: (synth.) Influenza A virus H3N2 / References: UniProt: Q9YXL6, RNA-directed RNA polymerase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 0.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 13, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 90267 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 25.58
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 4.264 / Rsym value: 0.289 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I6L

3i6l


Resolution: 1.7→24.42 Å / SU ML: 0.23 / σ(F): 0.09 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 4329 5.01 %
Rwork0.196 --
obs0.197 86431 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.93 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7703 Å27.8818 Å2-0.2931 Å2
2---2.7935 Å2-2.0969 Å2
3----4.9768 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6242 0 0 881 7123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056432
X-RAY DIFFRACTIONf_angle_d0.9128710
X-RAY DIFFRACTIONf_dihedral_angle_d17.6982334
X-RAY DIFFRACTIONf_chiral_restr0.079880
X-RAY DIFFRACTIONf_plane_restr0.0031152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6973-1.71660.27821130.24642275X-RAY DIFFRACTION77
1.7166-1.73680.31521150.2352392X-RAY DIFFRACTION80
1.7368-1.7580.25441270.22882535X-RAY DIFFRACTION83
1.758-1.78020.26051220.22382493X-RAY DIFFRACTION84
1.7802-1.80360.27311560.21732572X-RAY DIFFRACTION85
1.8036-1.82830.28941480.22732522X-RAY DIFFRACTION87
1.8283-1.85440.24451160.21732643X-RAY DIFFRACTION88
1.8544-1.88210.28061490.22622671X-RAY DIFFRACTION89
1.8821-1.91150.23411490.21332622X-RAY DIFFRACTION90
1.9115-1.94280.25341540.21052718X-RAY DIFFRACTION91
1.9428-1.97630.24341480.20982711X-RAY DIFFRACTION92
1.9763-2.01220.26731560.20112743X-RAY DIFFRACTION92
2.0122-2.05090.2421530.22780X-RAY DIFFRACTION93
2.0509-2.09280.22261620.19612802X-RAY DIFFRACTION94
2.0928-2.13820.23431420.19992829X-RAY DIFFRACTION95
2.1382-2.18790.23831420.19332852X-RAY DIFFRACTION95
2.1879-2.24260.21321520.19832816X-RAY DIFFRACTION95
2.2426-2.30320.23821790.19092883X-RAY DIFFRACTION96
2.3032-2.37090.21921450.19872836X-RAY DIFFRACTION96
2.3709-2.44740.21791290.19372892X-RAY DIFFRACTION97
2.4474-2.53480.21211530.19952885X-RAY DIFFRACTION97
2.5348-2.63620.22491540.1972906X-RAY DIFFRACTION97
2.6362-2.7560.21691560.19872885X-RAY DIFFRACTION97
2.756-2.90110.24141600.18852887X-RAY DIFFRACTION97
2.9011-3.08250.19891440.1932945X-RAY DIFFRACTION98
3.0825-3.320.23031400.18152932X-RAY DIFFRACTION98
3.32-3.65310.18611420.1732893X-RAY DIFFRACTION97
3.6531-4.17940.20361640.1592836X-RAY DIFFRACTION95
4.1794-5.25690.17731380.16062730X-RAY DIFFRACTION91
5.2569-24.42060.21521210.19662616X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -16.6265 Å / Origin y: -14.8161 Å / Origin z: -24.1268 Å
111213212223313233
T0.1122 Å20.0105 Å2-0.0213 Å2-0.1354 Å20.001 Å2--0.1266 Å2
L0.0089 °2-0.0463 °2-0.1672 °2-0.2684 °20.2655 °2--0.2555 °2
S0.0068 Å °0.0131 Å °0.0066 Å °0.0089 Å °0.0168 Å °-0.0276 Å °0.0317 Å °0.0261 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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