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- PDB-3vfv: crystal structure of HLA B*3508 LPEP-P9Ala, peptide mutant P9-ala -

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Basic information

Entry
Database: PDB / ID: 3vfv
Titlecrystal structure of HLA B*3508 LPEP-P9Ala, peptide mutant P9-ala
Components
  • Beta-2-microglobulin
  • LPEP peptide from EBV, P9A, LPEPLPQGALTAY
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA B*3508 / Epstein Barr virus / TCR / T cell / antigen-presenting molecule
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / antigen processing and presentation of peptide antigen via MHC class I / 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 ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / antigen processing and presentation of peptide antigen via MHC class I / 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 / : / : / secretory granule membrane / 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 / 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 / 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 / defense response / 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 receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / protein-folding chaperone binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 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-B*3507 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsLiu, Y.C. / Rossjohn, J. / Gras, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Energetic Basis Underpinning T-cell Receptor Recognition of a Super-bulged Peptide Bound to a Major Histocompatibility Complex Class I Molecule.
Authors: Liu, Y.C. / Chen, Z. / Burrows, S.R. / Purcell, A.W. / McCluskey, J. / Rossjohn, J. / Gras, S.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Sep 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 1.4Oct 16, 2024Group: Structure summary / Category: 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: MHC class I antigen
B: Beta-2-microglobulin
C: LPEP peptide from EBV, P9A, LPEPLPQGALTAY


Theoretical massNumber of molelcules
Total (without water)45,2333
Polymers45,2333
Non-polymers00
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-26 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.800, 81.500, 110.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen


Mass: 31984.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5MK56, UniProt: P01889*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 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide LPEP peptide from EBV, P9A, LPEPLPQGALTAY


Mass: 1369.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GL biochem
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 16% PEG 4K, 0.1M sodium citrate pH5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionNumber: 485952 / Rmerge(I) obs: 0.049 / D res high: 1.55 Å / Num. obs: 66782 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
610100299.810.033
5689099.910.031
35745499.910.034
2.53683599.810.044
2.22.5747399.610.051
2.052.2549899.610.059
1.952.05466499.210.067
1.851.95568898.910.087
1.751.85706599.110.12
1.651.75879398.510.162
1.551.651117098.210.234
ReflectionResolution: 1.55→65.611 Å / Num. obs: 66782 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.176 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 24.04
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 8.01 / Num. measured obs: 82794 / Num. unique obs: 11170 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZHK

1zhk


Resolution: 1.55→19.681 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8819 / SU ML: 0.38 / σ(F): 1.36 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 3379 5.06 %
Rwork0.1701 --
obs0.1717 66779 99.12 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.509 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 66.48 Å2 / Biso mean: 18.4699 Å2 / Biso min: 2.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.8973 Å20 Å20 Å2
2---2.9789 Å20 Å2
3---3.8762 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 0 569 3760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063439
X-RAY DIFFRACTIONf_angle_d1.0734698
X-RAY DIFFRACTIONf_chiral_restr0.077480
X-RAY DIFFRACTIONf_plane_restr0.005631
X-RAY DIFFRACTIONf_dihedral_angle_d12.5491301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57210.21951390.20842562270198
1.5721-1.59560.20181240.18112610273498
1.5956-1.62050.22221260.18142583270999
1.6205-1.64710.21471440.1762576272098
1.6471-1.67550.21891450.18032615276099
1.6755-1.70590.2111370.17252578271598
1.7059-1.73870.20181350.1732632276799
1.7387-1.77420.21831250.17112586271198
1.7742-1.81270.21941480.17312625277398
1.8127-1.85490.19181510.1725992750100
1.8549-1.90120.19541350.16812625276099
1.9012-1.95260.21881220.17532629275199
1.9526-2.010.20651600.184626172777100
2.01-2.07480.21821490.17432595274499
2.0748-2.14880.19691340.17952652278699
2.1488-2.23480.21071650.17942617278299
2.2348-2.33630.21511440.169126772821100
2.3363-2.45930.21691300.177926682798100
2.4593-2.6130.19381530.172926382791100
2.613-2.81430.22771420.18327022844100
2.8143-3.09650.20191390.180926812820100
3.0965-3.54230.20661350.164127282863100
3.5423-4.45440.16741380.139127552893100
4.4544-19.68210.2021590.16428503009100

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