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- PDB-3vfu: crystal structure of HLA B*3508 LPEP-P7Ala, peptide mutant P7-ala -

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Basic information

Entry
Database: PDB / ID: 3vfu
Titlecrystal structure of HLA B*3508 LPEP-P7Ala, peptide mutant P7-ala
Components
  • Beta-2-microglobulin
  • LPEP peptide from EBV, P7A, LPEPLPAGQLTAY
  • 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 / 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 / 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 / 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 / defense response / 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 / 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 / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / protein-folding chaperone binding / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / 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: 1.65 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 1.4Nov 6, 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, P7A, LPEPLPAGQLTAY


Theoretical massNumber of molelcules
Total (without water)45,2333
Polymers45,2333
Non-polymers00
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-24 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.316, 80.580, 109.545
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 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, P7A, LPEPLPAGQLTAY


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.: 542 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
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 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 9.1 / Number: 387310 / Rsym value: 0.078 / D res high: 1.65 Å / D res low: 64.91 Å / Num. obs: 54048 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.2219.8898.110.0290.0296.6
3.695.2299.910.0290.0297
3.013.6999.910.0380.0387.1
2.613.0199.910.0560.0567.2
2.332.6199.810.0810.0817.3
2.132.3399.710.1210.1217.2
1.972.1399.510.1440.1447.2
1.841.9799.210.2350.2357.2
1.741.8499.510.3540.3547.4
1.651.7498.610.4780.4787
ReflectionResolution: 1.65→64.91 Å / Num. all: 54048 / Num. obs: 54048 / % possible obs: 99.4 % / Redundancy: 7.2 % / Rsym value: 0.078 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.65-1.7470.4781.60.478198.6
1.74-1.847.40.3542.20.354199.5
1.84-1.977.20.2353.30.235199.2
1.97-2.137.20.1445.40.144199.5
2.13-2.337.20.1216.30.121199.7
2.33-2.617.30.0819.60.081199.8
2.61-3.017.20.05613.50.056199.9
3.01-3.697.10.03818.40.038199.9
3.69-5.2270.02922.70.029199.9
5.22-19.8846.60.02920.20.029198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZHK

1zhk


Resolution: 1.65→19.884 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.41 / σ(F): 1.33 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 2729 5.09 %
Rwork0.1897 --
obs0.1915 53656 98.74 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.145 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8387 Å2-0 Å20 Å2
2---3.1649 Å2-0 Å2
3---5.0035 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 0 542 3733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073426
X-RAY DIFFRACTIONf_angle_d1.1334673
X-RAY DIFFRACTIONf_dihedral_angle_d12.9961290
X-RAY DIFFRACTIONf_chiral_restr0.069477
X-RAY DIFFRACTIONf_plane_restr0.005626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.26391350.22782610X-RAY DIFFRACTION97
1.68-1.71230.24081440.21492645X-RAY DIFFRACTION100
1.7123-1.74720.23541520.20572650X-RAY DIFFRACTION98
1.7472-1.78520.26491450.20752649X-RAY DIFFRACTION100
1.7852-1.82670.23751410.19742656X-RAY DIFFRACTION99
1.8267-1.87240.26341390.23532631X-RAY DIFFRACTION98
1.8724-1.92290.35141480.31222607X-RAY DIFFRACTION97
1.9229-1.97950.21711410.18692633X-RAY DIFFRACTION99
1.9795-2.04330.18931510.16372680X-RAY DIFFRACTION99
2.0433-2.11630.20061490.17232686X-RAY DIFFRACTION99
2.1163-2.20090.23071330.20172600X-RAY DIFFRACTION97
2.2009-2.30090.32641250.26212587X-RAY DIFFRACTION95
2.3009-2.4220.24241230.19022721X-RAY DIFFRACTION100
2.422-2.57350.22611510.18542701X-RAY DIFFRACTION100
2.5735-2.77170.26641680.18922710X-RAY DIFFRACTION100
2.7717-3.04970.22591280.18712746X-RAY DIFFRACTION100
3.0497-3.4890.2211480.17092748X-RAY DIFFRACTION100
3.489-4.38790.1631490.15042754X-RAY DIFFRACTION99
4.3879-19.88510.17281590.16462913X-RAY DIFFRACTION100

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