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- PDB-4f7p: Crystal Structure of HLA-A*2402 Complexed with a Newly Identified... -

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Basic information

Entry
Database: PDB / ID: 4f7p
TitleCrystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009H1N1 PB1 (496-505)
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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / MHC class II protein complex / 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 / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / RNA-directed RNA polymerase / viral RNA genome replication / focal adhesion / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / Neutrophil degranulation / endoplasmic reticulum membrane
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: 1.9 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 1.3Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)44,8473
Polymers44,8473
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-18 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.122, 64.787, 50.229
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121

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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.: 1 / 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.: 1 / 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: 1284.441 Da / Num. of mol.: 1 / Fragment: unp residues 496-505 / Source method: obtained synthetically
Details: in vitro synthesized peptide from polymerase basic protein 1
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.: 330 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
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 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: 1.9→50 Å / Num. obs: 40018 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 24.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.38 / Rsym value: 0.512 / % possible all: 95.8

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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: 1.9→19.69 Å / SU ML: 0.24 / σ(F): 0.1 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1923 5.01 %
Rwork0.185 --
obs0.186 38401 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.96 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5479 Å20 Å2-0.7257 Å2
2--6.8745 Å20 Å2
3----1.3266 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3122 0 0 330 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053224
X-RAY DIFFRACTIONf_angle_d0.9144366
X-RAY DIFFRACTIONf_dihedral_angle_d18.1711169
X-RAY DIFFRACTIONf_chiral_restr0.068440
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.903-1.95050.27941090.23592217X-RAY DIFFRACTION80
1.9505-2.00320.2821140.21572387X-RAY DIFFRACTION86
2.0032-2.06210.24141300.19632454X-RAY DIFFRACTION89
2.0621-2.12860.2331400.19252476X-RAY DIFFRACTION90
2.1286-2.20460.24061390.18852564X-RAY DIFFRACTION93
2.2046-2.29270.22631420.18142629X-RAY DIFFRACTION94
2.2927-2.39690.23591090.19122631X-RAY DIFFRACTION94
2.3969-2.5230.22261420.18662644X-RAY DIFFRACTION96
2.523-2.68070.22721300.1972655X-RAY DIFFRACTION97
2.6807-2.88710.23291400.19052720X-RAY DIFFRACTION97
2.8871-3.17660.20521520.18512727X-RAY DIFFRACTION99
3.1766-3.63370.2241690.16912752X-RAY DIFFRACTION99
3.6337-4.56870.15611620.15312794X-RAY DIFFRACTION100
4.5687-19.69450.20631450.1782828X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.2985 Å / Origin y: -26.8695 Å / Origin z: -14.022 Å
111213212223313233
T0.159 Å2-0.004 Å20.0015 Å2-0.1611 Å20.0116 Å2--0.1583 Å2
L0.4374 °2-0.0995 °20.071 °2-0.5028 °20.2715 °2--0.5734 °2
S0.0045 Å °-0.0919 Å °-0.0559 Å °-0.0713 Å °-0.0414 Å °0.0762 Å °-0.0137 Å °-0.0645 Å °0 Å °
Refinement TLS groupSelection details: all

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