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- PDB-8tq4: Crystal structure of Fab M142 in complex with MHC-I (H2-Dd) -

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Basic information

Entry
Database: PDB / ID: 8tq4
TitleCrystal structure of Fab M142 in complex with MHC-I (H2-Dd)
Components
  • Beta-2-microglobulin
  • Fab M142 Heavy Chain
  • Fab M142 Light Chain
  • H2 class I histocompatibility antigen D-d alpha chain (H2-Dd)
  • HV1: HIV-1 P18-I10
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


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / H-2 class I histocompatibility antigen, D-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 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 M142 in complex with MHC-I (H2-Dd)
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: H2 class I histocompatibility antigen D-d alpha chain (H2-Dd)
B: Beta-2-microglobulin
C: Fab M142 Heavy Chain
D: Fab M142 Light Chain
E: H2 class I histocompatibility antigen D-d alpha chain (H2-Dd)
F: Beta-2-microglobulin
G: HV1: HIV-1 P18-I10
H: Fab M142 Heavy Chain
L: Fab M142 Light Chain
P: HV1: HIV-1 P18-I10


Theoretical massNumber of molelcules
Total (without water)183,46910
Polymers183,46910
Non-polymers00
Water00
1
A: H2 class I histocompatibility antigen D-d alpha chain (H2-Dd)
B: Beta-2-microglobulin
H: Fab M142 Heavy Chain
L: Fab M142 Light Chain
P: HV1: HIV-1 P18-I10


Theoretical massNumber of molelcules
Total (without water)91,7355
Polymers91,7355
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fab M142 Heavy Chain
D: Fab M142 Light Chain
E: H2 class I histocompatibility antigen D-d alpha chain (H2-Dd)
F: Beta-2-microglobulin
G: HV1: HIV-1 P18-I10


Theoretical massNumber of molelcules
Total (without water)91,7355
Polymers91,7355
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.552, 121.552, 327.199
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: Protein H2 class I histocompatibility antigen D-d alpha chain (H2-Dd) / MHC-I (H2-Dd)


Mass: 31819.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin


Mass: 11529.153 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887
#3: Antibody Fab M142 Heavy Chain


Mass: 23754.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pCDNA3.1 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
#4: Antibody Fab M142 Light Chain


Mass: 23555.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pCDNA3.1 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
#5: Protein/peptide HV1: HIV-1 P18-I10


Mass: 1075.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG4000, 0.2 M sodium acetate, 0.1 M sodium citrate, pH 5.5

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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: Feb 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.59→97.57 Å / Num. obs: 28062 / % possible obs: 95 % / Redundancy: 9.2 % / Biso Wilson estimate: 91.75 Å2 / CC1/2: 0.995 / CC star: 0.995 / Rmerge(I) obs: 0.424 / Rpim(I) all: 0.139 / Net I/σ(I): 6.2
Reflection shellResolution: 3.59→3.72 Å / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2728 / CC1/2: 0.803 / CC star: 0.803 / Rpim(I) all: 0.613

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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 5WEU

5weu


Resolution: 3.59→97.57 Å / SU ML: 0.4882 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2696 1402 5 %
Rwork0.221 26653 -
obs0.2234 28055 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.54 Å2
Refinement stepCycle: LAST / Resolution: 3.59→97.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12671 0 0 0 12671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003813006
X-RAY DIFFRACTIONf_angle_d0.81617725
X-RAY DIFFRACTIONf_chiral_restr0.05771932
X-RAY DIFFRACTIONf_plane_restr0.00552286
X-RAY DIFFRACTIONf_dihedral_angle_d14.38354643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.720.31811360.27812592X-RAY DIFFRACTION95.45
3.72-3.870.33091390.26892643X-RAY DIFFRACTION96.36
3.87-4.050.31591390.25622649X-RAY DIFFRACTION95.77
4.05-4.260.31931380.24192610X-RAY DIFFRACTION95.45
4.26-4.530.25611400.20882670X-RAY DIFFRACTION95.48
4.53-4.880.24921390.18922643X-RAY DIFFRACTION95.67
4.88-5.370.25911410.2022675X-RAY DIFFRACTION95.55
5.37-6.140.29041420.22062687X-RAY DIFFRACTION95.25
6.14-7.740.28771410.23762684X-RAY DIFFRACTION93.92
7.75-97.570.20091470.19412800X-RAY DIFFRACTION91.75

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