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- PDB-4f7m: Crystal Structure of HLA-A*2402 Complexed with a Newly Identified... -

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Basic information

Entry
Database: PDB / ID: 4f7m
TitleCrystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009 H1N1 PA (649-658)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • PA polymerase subunit
KeywordsIMMUNE SYSTEM / HLA-A*2402 / Influenza A virus / 2009 H1N1 / HLA-A3 supertype
Function / homology
Function and homology information


T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 / cap snatching / antigen processing and presentation of exogenous peptide antigen via MHC class I ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 / cap snatching / antigen processing and presentation of exogenous peptide antigen via MHC class I / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / detection of bacterium / T cell receptor binding / 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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of type II interferon production / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / endonuclease activity / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / Hydrolases; Acting on ester bonds / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / viral RNA genome replication / signaling receptor binding / focal adhesion / innate immune response / DNA-templated transcription
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 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 ...Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Polymerase acidic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus H3N2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, J. / Zhang, S. / Tan, S. / Yi, Y. / Wu, B. / Zhu, F. / Wang, H. / Qi, J. / George, F.G.
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

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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-24 alpha chain
B: Beta-2-microglobulin
C: PA polymerase subunit
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: PA polymerase subunit


Theoretical massNumber of molelcules
Total (without water)89,3736
Polymers89,3736
Non-polymers00
Water7,242402
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: PA polymerase subunit


Theoretical massNumber of molelcules
Total (without water)44,6873
Polymers44,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-20 kcal/mol
Surface area19060 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: PA polymerase subunit


Theoretical massNumber of molelcules
Total (without water)44,6873
Polymers44,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-20 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.272, 67.092, 87.668
Angle α, β, γ (deg.)90.00, 101.30, 90.00
Int Tables number4
Space group name H-MP1211

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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 / 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 PA polymerase subunit


Mass: 1124.243 Da / Num. of mol.: 2 / Fragment: unp residues 649-658 / Source method: obtained synthetically
Details: in vitro synthesized peptide from influenza A virus polymerase
Source: (synth.) Influenza A virus H3N2 / References: UniProt: Q9YXL3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium nitrate and 20% (w/v) polyethylene glycol 3,350, 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 Å
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: 2.4→50 Å / Num. all: 33037 / Num. obs: 33004 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.18 / Rsym value: 0.18 / Net I/σ(I): 9.06
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.38 / Num. unique all: 3267 / Rsym value: 0.483 / % possible all: 99.8

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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: 2.4→40.671 Å / SU ML: 0.33 / σ(F): 0.15 / Phase error: 29.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1581 5.08 %random
Rwork0.2392 ---
obs0.2417 31150 93.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.263 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.5793 Å2-0 Å23.6486 Å2
2---1.8467 Å20 Å2
3----3.7326 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 0 402 6664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046448
X-RAY DIFFRACTIONf_angle_d0.7088732
X-RAY DIFFRACTIONf_dihedral_angle_d18.3662346
X-RAY DIFFRACTIONf_chiral_restr0.05885
X-RAY DIFFRACTIONf_plane_restr0.0031154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4035-2.4810.33061460.2742304X-RAY DIFFRACTION83
2.481-2.56970.3681400.27282544X-RAY DIFFRACTION89
2.5697-2.67260.33851220.272578X-RAY DIFFRACTION90
2.6726-2.79420.34691370.26672624X-RAY DIFFRACTION92
2.7942-2.94150.31581320.26022653X-RAY DIFFRACTION93
2.9415-3.12570.29531450.2592720X-RAY DIFFRACTION95
3.1257-3.36690.2981450.23842770X-RAY DIFFRACTION97
3.3669-3.70550.27691430.21962832X-RAY DIFFRACTION98
3.7055-4.24130.2481490.20262807X-RAY DIFFRACTION98
4.2413-5.34160.23271420.18682852X-RAY DIFFRACTION99
5.3416-40.67640.25421800.24112885X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.3064 Å / Origin y: -6.7243 Å / Origin z: -21.5987 Å
111213212223313233
T0.0505 Å20.0024 Å20.0058 Å2-0.0383 Å20.005 Å2--0.0428 Å2
L0.0754 °20.0343 °2-0.0149 °2-0.0724 °20.0084 °2--0.0329 °2
S-0.0042 Å °0.0244 Å °0.0293 Å °-0.008 Å °0.0052 Å °0.0133 Å °-0.0027 Å °0.0009 Å °0 Å °
Refinement TLS groupSelection details: all

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