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- PDB-3kww: Crystal structure of the 'restriction triad' mutant of HLA B*3508... -

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Basic information

Entry
Database: PDB / ID: 3kww
TitleCrystal structure of the 'restriction triad' mutant of HLA B*3508, beta-2-microglobulin and EBV peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • peptide from Trans-activator protein BZLF1
KeywordsIMMUNE SYSTEM / MHC-peptide / HLA / Disulfide bond / Immune response / Membrane / MHC I / Polymorphism / Immunoglobulin domain
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / sequence-specific DNA binding / adaptive immune response / learning or memory / protein dimerization activity / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / host cell nucleus / chromatin / Neutrophil degranulation / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / endoplasmic reticulum
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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 ...Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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
ACETIC ACID / DI(HYDROXYETHYL)ETHER / HLA class I histocompatibility antigen, B alpha chain / Lytic switch protein BZLF1 / 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: 2.18 Å
AuthorsArchbold, J.K. / Tynan, F.E. / Gras, S. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Hard wiring of T cell receptor specificity for the major histocompatibility complex is underpinned by TCR adaptability
Authors: Burrows, S.R. / Chen, Z. / Archbold, J.K. / Tynan, F.E. / Beddoe, T. / Kjer-Nielsen, L. / Miles, J.J. / Khanna, R. / Moss, D.J. / Liu, Y.C. / Gras, S. / Kostenko, L. / Brennan, R.M. / ...Authors: Burrows, S.R. / Chen, Z. / Archbold, J.K. / Tynan, F.E. / Beddoe, T. / Kjer-Nielsen, L. / Miles, J.J. / Khanna, R. / Moss, D.J. / Liu, Y.C. / Gras, S. / Kostenko, L. / Brennan, R.M. / Clements, C.S. / Brooks, A.G. / Purcell, A.W. / McCluskey, J. / Rossjohn, J.
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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, B-35 alpha chain
B: Beta-2-microglobulin
C: peptide from Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,37619
Polymers45,0153
Non-polymers1,36116
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-22 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.972, 81.454, 110.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / MHC class I antigen B*35


Mass: 31840.152 Da / Num. of mol.: 1 / Fragment: residues in UNP 25-300 / Mutation: Q65A, T69A, Q155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide peptide from Trans-activator protein BZLF1 / / EB1 / Protein zebra


Mass: 1426.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P03206

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Non-polymers , 4 types, 364 molecules

#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS SEQUENCE IS VARIANT, B*3508.

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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: 2.55 Å3/Da / Density % sol: 51.67 % / Mosaicity: 0.362 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.6
Details: 0.1M cacodlyate, 0.2M ammonium acetate, 18% PEG3350, pH 7.6, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1
DetectorDate: May 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 3.2 % / Number: 79157 / Rmerge(I) obs: 0.079 / Χ2: 1.34 / D res high: 2.18 Å / D res low: 50 Å / Num. obs: 24588 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.7509610.0341.2493.2
3.734.798.810.041.4433.2
3.263.7399.610.0561.5443.3
2.963.2699.910.0831.4613.2
2.752.9610010.1171.3713.2
2.582.7510010.1631.3553.2
2.462.5810010.21.2983.2
2.352.4610010.2521.2223.2
2.262.3510010.2791.2183.2
2.182.2699.910.3411.2443.2
ReflectionResolution: 2.18→50 Å / Num. all: 24588 / Num. obs: 24588 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.7
Reflection shellResolution: 2.18→2.26 Å / Mean I/σ(I) obs: 3.8 / Num. unique all: 2428 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zhl

1zhl


Resolution: 2.18→33.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.755 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 989 4 %RANDOM
Rwork0.186 ---
obs0.188 23559 99.46 %-
all-24588 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.54 Å2 / Biso mean: 17.066 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.18→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 90 348 3615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213456
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9534683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12222.819188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3915557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8751538
X-RAY DIFFRACTIONr_chiral_restr0.0720.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022742
X-RAY DIFFRACTIONr_nbd_refined0.1780.21573
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2337
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.220
X-RAY DIFFRACTIONr_mcbond_it0.95432087
X-RAY DIFFRACTIONr_mcangle_it1.53253238
X-RAY DIFFRACTIONr_scbond_it2.54871604
X-RAY DIFFRACTIONr_scangle_it3.443101430
LS refinement shellResolution: 2.18→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 58 -
Rwork0.201 1724 -
all-1782 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5792-0.61440.2241.528-0.10020.49490.07190.11530.0101-0.2126-0.0689-0.15030.0297-0.0128-0.003-0.02360.00170.0202-0.0337-0.0029-0.047720.59178.874825.2516
21.0197-0.4277-0.00251.4609-0.2130.53540.02440.13250.2404-0.2676-0.049-0.2959-0.0396-0.03530.0246-0.00780.01760.046-0.04680.0150.015319.367220.809423.7566
30.8868-0.2236-1.14320.82660.4484.39670.0023-0.2179-0.03080.28430.08890.0886-0.2149-0.0256-0.09120.03930.03630.04790.06420.0115-0.0293-0.267114.957454.1381
46.58940.6941-1.47172.867-0.41722.6863-0.5329-0.5143-0.44170.3430.260.47750.1492-0.11840.27290.02090.07640.1541-0.05980.09760.04825.1245-0.019544.9654
55.04010.8167-1.31893.2743-0.76281.9895-0.332-0.4738-0.73560.34210.14050.16650.22940.10270.19150.00870.08330.1197-0.05050.10340.050811.3862-3.626143.5956
65.5108-1.1821.35931.15290.72881.49290.23690.38360.4473-0.1919-0.2605-0.24470.0491-0.02150.02360.03830.02880.0801-0.0210.08190.070525.933613.742716.1698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2A125 - 185
3X-RAY DIFFRACTION3A186 - 276
4X-RAY DIFFRACTION4B1 - 22
5X-RAY DIFFRACTION5B23 - 99
6X-RAY DIFFRACTION6C1 - 13

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