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- PDB-8tq6: Crystal structure of Fab.B1.23.2 in complex with MHC-I (HLA-B*44:05) -

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Basic information

Entry
Database: PDB / ID: 8tq6
TitleCrystal structure of Fab.B1.23.2 in complex with MHC-I (HLA-B*44:05)
Components
  • Beta-2-microglobulin
  • Fab B1.23.2 Heavy Chain
  • Fab B1.23.2 Light Chain
  • HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)
  • MHC class II antigen peptide
KeywordsIMMUNE SYSTEM / histocompatibility complex class I / MHC-I / immune response / immune system Fab / antibody / anti-MHC antibody / cancer tumor
Function / homology
Function and homology information


antigen processing and presentation / antigen processing and presentation of peptide antigen via MHC class I / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation / antigen processing and presentation of peptide antigen via MHC class I / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / 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 / 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 / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / 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 II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
Beta-2-microglobulin / MHC class I antigen / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJiang, J. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of Fab.B1.23.2 in complex with MHC-I (HLA-B*44:05)
Authors: Jiang, J. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
History
DepositionAug 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)
D: Beta-2-microglobulin
E: MHC class II antigen peptide
F: Fab B1.23.2 Heavy Chain
G: Fab B1.23.2 Light Chain
H: Fab B1.23.2 Heavy Chain
L: Fab B1.23.2 Light Chain
P: MHC class II antigen peptide


Theoretical massNumber of molelcules
Total (without water)182,30210
Polymers182,30210
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)
B: Beta-2-microglobulin
H: Fab B1.23.2 Heavy Chain
L: Fab B1.23.2 Light Chain
P: MHC class II antigen peptide


Theoretical massNumber of molelcules
Total (without water)91,1515
Polymers91,1515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)
D: Beta-2-microglobulin
E: MHC class II antigen peptide

F: Fab B1.23.2 Heavy Chain
G: Fab B1.23.2 Light Chain


Theoretical massNumber of molelcules
Total (without water)91,1515
Polymers91,1515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_764-x+5/2,-y+1,z-1/21
Unit cell
Length a, b, c (Å)89.500, 92.840, 229.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 43 or resid 45...
d_2ens_1(chain "C" and (resid 1 through 43 or resid 45...
d_1ens_2(chain "B" and (resid 0 through 1 or (resid 2...
d_2ens_2(chain "D" and (resid 0 through 44 or resid 46...
d_1ens_3(chain "E" and (resid 1 through 4 or resid 6 through 9))
d_2ens_3(chain "P" and (resid 1 through 4 or resid 6...
d_1ens_4(chain "F" and (resid 2 through 62 or (resid 63...
d_2ens_4(chain "H" and (resid 2 through 12 or (resid 13...
d_1ens_5(chain "G" and (resid 2 through 14 or (resid 15...
d_2ens_5(chain "L" and ((resid 2 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYPROPROAA1 - 431 - 43
d_12ens_1LYSLYSLYSLYSAA4545
d_13ens_1PROPROGLYGLYAA47 - 10747 - 107
d_14ens_1LEULEULEULEUAA109 - 110109 - 110
d_15ens_1GLYGLYTRPTRPAA112 - 147112 - 147
d_16ens_1ALAALAPROPROAA149 - 185149 - 185
d_17ens_1THRTHRALAALAAA187 - 211187 - 211
d_18ens_1ILEILEGLNGLNAA213 - 218213 - 218
d_19ens_1ASPASPTHRTHRAA220 - 225220 - 225
d_110ens_1ASPASPHISHISAA227 - 263227 - 263
d_111ens_1GLYGLYLYSLYSAA265 - 268265 - 268
d_21ens_1GLYGLYPROPROCC1 - 431 - 43
d_22ens_1LYSLYSLYSLYSCC4545
d_23ens_1PROPROGLYGLYCC47 - 10747 - 107
d_24ens_1LEULEULEULEUCC109 - 110109 - 110
d_25ens_1GLYGLYTRPTRPCC112 - 147112 - 147
d_26ens_1ALAALAPROPROCC149 - 185149 - 185
d_27ens_1THRTHRALAALACC187 - 211187 - 211
d_28ens_1ILEILEGLNGLNCC213 - 218213 - 218
d_29ens_1ASPASPTHRTHRCC220 - 225220 - 225
d_210ens_1ASPASPHISHISCC227 - 263227 - 263
d_211ens_1GLYGLYLYSLYSCC265 - 268265 - 268
d_11ens_2METMETGLUGLUBB0 - 441 - 45
d_12ens_2ILEILEGLUGLUBB46 - 7447 - 75
d_13ens_2ASPASPMETMETBB76 - 9977 - 100
d_21ens_2METMETGLUGLUDD0 - 441 - 45
d_22ens_2ILEILEGLUGLUDD46 - 7447 - 75
d_23ens_2ASPASPMETMETDD76 - 9977 - 100
d_11ens_3GLUGLUGLYGLYEE1 - 41 - 4
d_12ens_3ALAALAPHEPHEEE6 - 96 - 9
d_21ens_3GLUGLUGLYGLYPJ1 - 41 - 4
d_22ens_3ALAALAPHEPHEPJ6 - 96 - 9
d_11ens_4VALVALASPASPFF2 - 1731 - 172
d_12ens_4TYRTYRALAALAFF175 - 213174 - 212
d_21ens_4VALVALASPASPHH2 - 1731 - 172
d_22ens_4TYRTYRALAALAHH175 - 213174 - 212
d_11ens_5THRTHRGLYGLYGG2 - 411 - 40
d_12ens_5SERSERASNASNGG43 - 5242 - 51
d_13ens_5LEULEUTYRTYRGG54 - 8053 - 79
d_14ens_5ASPASPGLUGLUGG82 - 9381 - 92
d_15ens_5TYRTYRSERSERGG95 - 12194 - 120
d_16ens_5GLNGLNGLUGLUGG123 - 186122 - 185
d_17ens_5HISHISCYSCYSGG188 - 193187 - 192
d_18ens_5ALAALAARGARGGG195 - 210194 - 209
d_21ens_5THRTHRGLYGLYLI2 - 411 - 40
d_22ens_5SERSERASNASNLI43 - 5242 - 51
d_23ens_5LEULEUTYRTYRLI54 - 8053 - 79
d_24ens_5ASPASPGLUGLULI82 - 9381 - 92
d_25ens_5TYRTYRSERSERLI95 - 12194 - 120
d_26ens_5GLNGLNGLUGLULI123 - 186122 - 185
d_27ens_5HISHISCYSCYSLI188 - 193187 - 192
d_28ens_5ALAALAARGARGLI195 - 210194 - 209

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(0.786625179881, -0.14837533579, -0.599337622802), (0.182953969899, 0.98311607443, -0.003260229473), (0.58970218863, -0.107086618806, 0.80048971561)88.017846056, -4.12709174463, -95.9369258268
2given(0.819067252701, -0.124726729258, -0.559975069589), (0.161495421399, 0.986736601183, 0.0164349856353), (0.55049801491, -0.103894768369, 0.828346432772)82.3232217055, -4.33191162752, -95.3850007836
3given(0.754195778041, 0.0730665628029, 0.652571839559), (-0.0988237348496, 0.995101029202, 0.00279483673354), (-0.649170700059, -0.0665974405076, 0.757721705577)-3.1287809561, 4.38355036024, 135.996649095
4given(-0.764531798929, -0.179992487681, 0.618945743022), (0.146146715676, -0.98361931988, -0.105518581571), (0.627799542787, 0.00978457653527, 0.77831355901)106.395097508, 77.4578953207, -98.9290730546
5given(-0.780180708521, -0.151979002677, 0.606811704564), (0.136383868802, -0.988028335087, -0.0721072076566), (0.610505939677, 0.0265026755441, 0.791568130869)108.037348583, 76.3934696632, -98.3436388926

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Components

#1: Protein HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05) / MHC-I HLA-B44*05 A-chain


Mass: 31802.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q860B7
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide MHC class II antigen peptide


Mass: 1090.165 Da / Num. of mol.: 2
Fragment: HLA-DPA1*02:01 derived peptide 77-85 (UNP residues 36-44)
Source method: isolated from a natural source / Source: (natural) synthetic construct (others) / References: UniProt: Q9TQB0
#4: Antibody Fab B1.23.2 Heavy Chain


Mass: 22719.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCDNA3.1 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
#5: Antibody Fab B1.23.2 Light Chain


Mass: 23660.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCDNA3.1 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 16% PEG3350, 0.04 M sodium citrate, 0.06 M Bis-Tris, pH 8.8

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→72.21 Å / Num. obs: 31179 / % possible obs: 95.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 45.1 Å2 / CC1/2: 0.938 / CC star: 0.984 / Rmerge(I) obs: 0.329 / Rpim(I) all: 0.171 / Net I/σ(I): 5.6
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3011 / CC1/2: 0.435 / CC star: 0.778 / Rpim(I) all: 0.694

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7TUE

7tue


Resolution: 3.2→72.21 Å / Cross valid method: FREE R-VALUE / σ(F): 2.68 / Phase error: 29.2907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.268 1612 5.2 %
Rwork0.24 29408 -
obs0.2527 31020 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.74 Å2
Refinement stepCycle: LAST / Resolution: 3.2→72.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12516 0 0 0 12516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003312834
X-RAY DIFFRACTIONf_angle_d0.719717479
X-RAY DIFFRACTIONf_chiral_restr0.04781901
X-RAY DIFFRACTIONf_plane_restr0.00652263
X-RAY DIFFRACTIONf_dihedral_angle_d17.4814575
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.17300110642
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.986556217031
ens_3d_2EEX-RAY DIFFRACTIONTorsion NCS0.532732084759
ens_4d_2FFX-RAY DIFFRACTIONTorsion NCS1.01417640653
ens_5d_2GGX-RAY DIFFRACTIONTorsion NCS0.989146904029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30.32061370.29662599X-RAY DIFFRACTION89.78
3.3-3.420.3261320.27732600X-RAY DIFFRACTION90.09
3.42-3.560.3331380.25882631X-RAY DIFFRACTION90.98
3.56-3.720.32251360.24842652X-RAY DIFFRACTION91.01
3.72-3.920.31471390.2472652X-RAY DIFFRACTION91.13
3.92-4.160.25081410.24262669X-RAY DIFFRACTION91.59
4.16-4.480.24421390.22622706X-RAY DIFFRACTION92.01
4.48-4.930.22011400.22152664X-RAY DIFFRACTION90.89
4.93-5.650.28921390.25742680X-RAY DIFFRACTION90.79
5.65-7.110.34161440.30342728X-RAY DIFFRACTION90.63
7.12-72.210.24441530.23392901X-RAY DIFFRACTION92.33

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