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- PDB-7t0l: HLA-B*27:05 in complex with the pan-HLA-Ia monoclonal antibody W6/32 -

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Basic information

Entry
Database: PDB / ID: 7t0l
TitleHLA-B*27:05 in complex with the pan-HLA-Ia monoclonal antibody W6/32
Components
  • Beta-2-microglobulin
  • IgG2a heavy chain
  • Light chain kappa
  • MHC class I antigen
  • PHE-ARG-TYR-ASN-GLY-LEU-ILE-HIS-ARG peptide
KeywordsIMMUNE SYSTEM / HLA / antibody
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / 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 / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / 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 / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / 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, 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. ...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
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsVivian, J.P. / Rossjohn, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HLA-B*27:05 in complex with the pan-HLA-Ia monoclonal antibody W6/32
Authors: Vivian, J.P.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: PHE-ARG-TYR-ASN-GLY-LEU-ILE-HIS-ARG peptide
D: MHC class I antigen
E: Beta-2-microglobulin
F: PHE-ARG-TYR-ASN-GLY-LEU-ILE-HIS-ARG peptide
G: IgG2a heavy chain
H: IgG2a heavy chain
K: Light chain kappa
L: Light chain kappa


Theoretical massNumber of molelcules
Total (without water)182,93910
Polymers182,93910
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: PHE-ARG-TYR-ASN-GLY-LEU-ILE-HIS-ARG peptide
H: IgG2a heavy chain
L: Light chain kappa


Theoretical massNumber of molelcules
Total (without water)91,4705
Polymers91,4705
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: PHE-ARG-TYR-ASN-GLY-LEU-ILE-HIS-ARG peptide
G: IgG2a heavy chain
K: Light chain kappa


Theoretical massNumber of molelcules
Total (without water)91,4705
Polymers91,4705
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.785, 146.660, 177.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MHC class I antigen


Mass: 31911.109 Da / Num. of mol.: 2 / Mutation: C67S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A3F718
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide PHE-ARG-TYR-ASN-GLY-LEU-ILE-HIS-ARG peptide


Mass: 1178.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Antibody IgG2a heavy chain


Mass: 23245.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma
#5: Antibody Light chain kappa


Mass: 23386.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma

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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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 5000 MME, 0.1 M Bis-Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 37696 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 72.66 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.7
Reflection shellResolution: 3→3.2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.71 / Num. unique obs: 5427 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A83 and 2Q8A

2a83

2q8a


Resolution: 3→42.58 Å / Cor.coef. Fo:Fc: 0.9171 / Cor.coef. Fo:Fc free: 0.8852 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.427
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 1884 5 %RANDOM
Rwork0.1979 ---
obs0.2006 37652 99.96 %-
Displacement parametersBiso max: 209.64 Å2 / Biso mean: 92.94 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--2.2465 Å20 Å20 Å2
2--0.479 Å20 Å2
3---1.7676 Å2
Refine analyzeLuzzati coordinate error obs: 0.413 Å
Refinement stepCycle: final / Resolution: 3→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12866 0 0 0 12866
Num. residues----1623
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5977SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes319HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1945HARMONIC5
X-RAY DIFFRACTIONt_it13287HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1736SEMIHARMONIC5
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_contact14132SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13287HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg18127HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion3.41
LS refinement shellResolution: 3→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2817 147 5.1 %
Rwork0.2333 2735 -
all0.2359 2882 -
obs--100 %
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)
12.5487-0.3558-1.59360.44331.07983.1807-0.11-0.26050.2404-0.0288-0.0458-0.01640.07510.02240.1559-0.05450.29320.2934-0.13770.23550.3549-38.109412.7368-15.6039
24.4691-1.203-1.55074.8046-0.85762.8225-0.053-0.06530.65860.2611-0.0924-0.2705-0.67480.25240.1454-0.14020.25620.2175-0.30020.28710.6032-46.790929.4329-19.8783
31.5836-0.63170.65194.496-1.36052.6776-0.24140.071-0.7315-0.23660.03490.6289-0.01410.0030.2065-0.1960.3040.304-0.13690.0770.2656-13.9505-35.2803-29.98
45.0935-2.9741-1.89633.0473-1.09261.6929-0.10350.1699-0.1167-0.06840.04440.83690.3541-0.63420.0591-0.24160.27780.304-0.15080.22740.5866-30.5786-26.2456-26.2491
52.2139-0.0263-1.66013.5881-0.39013.0509-0.143-0.25-0.02690.46090.3326-0.2688-0.5310.5367-0.18970.13590.04960.05850.1153-0.0505-0.30193.0220.5314-32.6203
62.1640.75920.1342.5502-1.1264.33270.27980.12710.04-0.45030.0287-0.32520.5178-0.9886-0.3085-0.18960.01510.02390.15570.2601-0.09-73.3869-3.1684-12.0952
74.56133.1375-0.54116.40821.55330.8208-0.3278-0.85180.39560.85160.4662-0.0427-0.4770.5273-0.13840.49090.122-0.19090.0008-0.114-0.52249.89256.4051-16.7529
86.06114.39860.70415.08020.02931.52310.28860.20460.119-0.9476-0.03010.07580.5584-0.8159-0.2585-0.1171-0.0998-0.13280.29640.2135-0.2983-80.1109-10.9781-27.2616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 276
2X-RAY DIFFRACTION2{ B|* }B1 - 99
3X-RAY DIFFRACTION3{ D|* }D1 - 276
4X-RAY DIFFRACTION4{ E|* }E1 - 99
5X-RAY DIFFRACTION5{ G|* }G1 - 218
6X-RAY DIFFRACTION6{ H|* }H1 - 215
7X-RAY DIFFRACTION7{ K|* }K2 - 212
8X-RAY DIFFRACTION8{ L|* }L2 - 212

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