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- PDB-4qrp: Crystal Structure of HLA B*0801 in complex with HSKKKCDEL and DD31 TCR -

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Basic information

Entry
Database: PDB / ID: 4qrp
TitleCrystal Structure of HLA B*0801 in complex with HSKKKCDEL and DD31 TCR
Components
  • Beta-2-microglobulin
  • DD31 TCR alpha chain
  • DD31 TCR beta chain
  • HLA class I histocompatibility antigen, B-8 alpha chain
  • NS3-4A protein
KeywordsIMMUNE SYSTEM / HLA B*0801 / human hepatitis C virus / TCR / T cell
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 / symbiont-mediated transformation of host cell / 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 / symbiont-mediated transformation of host cell / 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 / serine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / 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 / viral capsid / 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 / RNA helicase activity / immune response / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / Neutrophil degranulation / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / proteolysis / extracellular space / extracellular exosome
Similarity search - Function
: / NS3 RNA helicase, C-terminal helical domain / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...: / NS3 RNA helicase, C-terminal helical domain / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease 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 / DEAD box, Flavivirus / Flavivirus DEAD domain / 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. / helicase superfamily c-terminal domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsGras, S. / Berry, R. / Lucet, I.S. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2014
Title: An Extensive Antigenic Footprint Underpins Immunodominant TCR Adaptability against a Hypervariable Viral Determinant.
Authors: Nivarthi, U.K. / Gras, S. / Kjer-Nielsen, L. / Berry, R. / Lucet, I.S. / Miles, J.J. / Tracy, S.L. / Purcell, A.W. / Bowden, D.S. / Hellard, M. / Rossjohn, J. / McCluskey, J. / Bharadwaj, M.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Sep 16, 2020Group: Database references / Derived calculations / Structure summary
Category: struct_keywords / struct_ref_seq_dif / struct_site
Item: _struct_keywords.text / _struct_ref_seq_dif.details ..._struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.6Nov 6, 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, B-8 alpha chain
B: Beta-2-microglobulin
C: NS3-4A protein
D: DD31 TCR alpha chain
E: DD31 TCR beta chain
F: HLA class I histocompatibility antigen, B-8 alpha chain
G: Beta-2-microglobulin
H: NS3-4A protein
I: DD31 TCR beta chain
J: DD31 TCR alpha chain
K: DD31 TCR alpha chain
L: DD31 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,51727
Polymers240,92512
Non-polymers1,59215
Water1,00956
1
A: HLA class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: NS3-4A protein
D: DD31 TCR alpha chain
E: DD31 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6789
Polymers95,2755
Non-polymers4044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, B-8 alpha chain
G: Beta-2-microglobulin
H: NS3-4A protein
I: DD31 TCR beta chain
J: DD31 TCR alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,80510
Polymers95,2755
Non-polymers5315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: DD31 TCR alpha chain
L: DD31 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0348
Polymers50,3762
Non-polymers6586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: HLA class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: NS3-4A protein
I: DD31 TCR beta chain
J: DD31 TCR alpha chain
hetero molecules

D: DD31 TCR alpha chain
E: DD31 TCR beta chain
F: HLA class I histocompatibility antigen, B-8 alpha chain
G: Beta-2-microglobulin
H: NS3-4A protein
K: DD31 TCR alpha chain
L: DD31 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,51727
Polymers240,92512
Non-polymers1,59215
Water1629
TypeNameSymmetry operationNumber
crystal symmetry operation1_454x-1,y,z-11
identity operation1_555x,y,z1
Buried area29680 Å2
ΔGint-160 kcal/mol
Surface area97240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.160, 252.190, 79.450
Angle α, β, γ (deg.)90.00, 101.97, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

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Protein , 4 types, 10 molecules AFBGDJKEIL

#1: Protein HLA class I histocompatibility antigen, B-8 alpha chain / MHC class I antigen B*8


Mass: 31927.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30460, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein DD31 TCR alpha chain


Mass: 22741.139 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein DD31 TCR beta chain


Mass: 27634.908 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide NS3-4A protein


Mass: 1091.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: X2G898

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Non-polymers , 3 types, 71 molecules

#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 16% PEG 4K, 0.1 tri-Na citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 62727 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 9.62
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.9-30.5742.82199.9
3-3.10.4383.68199.8
3.1-3.20.3584.391100
3.2-3.30.2815.45199.9
3.3-3.40.2376.23199.8
3.4-3.50.2067.121100
3.5-40.1439.54199.9
4-50.08814.11199.8
5-60.08114.87199.8
6-100.06416.85199.8
100.04821.25187

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M05, PDB ENTRY 1KGC

1m05

1kgc


Resolution: 2.9→19.85 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.8428 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 3181 5.07 %RANDOM
Rwork0.2065 ---
obs0.2086 62723 99.93 %-
Displacement parametersBiso mean: 61.24 Å2
Baniso -1Baniso -2Baniso -3
1-3.5789 Å20 Å214.6239 Å2
2---10.4416 Å20 Å2
3---6.8627 Å2
Refine analyzeLuzzati coordinate error obs: 0.439 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16833 0 15 56 16904
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00717250HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9923437HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5888SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes493HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2489HARMONIC5
X-RAY DIFFRACTIONt_it17250HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.01
X-RAY DIFFRACTIONt_other_torsion19.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2190SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18156SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3152 236 5.07 %
Rwork0.2559 4416 -
all0.2588 4652 -
obs--99.93 %

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