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- PDB-8t7r: Crystal structure of human leukocyte antigen A*0101 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8t7r
TitleCrystal structure of human leukocyte antigen A*0101 in complex with the Fab of alloreactive antibody E07
Components
  • Beta-2-microglobulin
  • Fab heavy chain from antibody JTK191b E07
  • Light chain from antibody JTK191b E07
  • MHC class I antigen (Fragment)
  • peptide
KeywordsIMMUNE SYSTEM / human leukocyte antigen / HLA / HLA class I / antibodies / autoimmunity / Fab / alloreactive
Function / homology
Function and homology information


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 / cellular response to iron(III) ion ...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 / 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 / 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 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)
Cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å
AuthorsGreen, T.J. / Killian Jr, J.T. / Qiu, S. / Macon, K.J. / Yang, G. / King, R.G. / Lund, F.E.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007051 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI142737 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)T32DK007545 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA013148 United States
National Institutes of Health/Office of the DirectorS10OD027000 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR025528 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR028976 United States
CitationJournal: To Be Published
Title: B cell and antibody targeting of transplant alloantigen epitopes is supported by both self and allo-recognition
Authors: Killian Jr, J.T. / King, R.G. / Kizziah, J.L. / Fucile, C.F. / Diaz-Avalos, R. / Qiu, S. / Silva-Sanchez, A. / Mousseau, B.J. / Macon, K.J. / Callahan, A.R. / Yang, G. / Hossain, E.M. / ...Authors: Killian Jr, J.T. / King, R.G. / Kizziah, J.L. / Fucile, C.F. / Diaz-Avalos, R. / Qiu, S. / Silva-Sanchez, A. / Mousseau, B.J. / Macon, K.J. / Callahan, A.R. / Yang, G. / Hossain, E.M. / Akther, J. / Good, D.B. / Kelso, S. / Houp, J.A. / Rosenblum, F. / Porrett, P.M. / Ong, S.C. / Kumar, V. / Ollmann Saphire, E. / Kearney, J.F. / Randall, T.D. / Rosenberg, A.F. / Green, T.J. / Lund, F.E.
History
DepositionJun 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain from antibody JTK191b E07
B: Fab heavy chain from antibody JTK191b E07
C: MHC class I antigen (Fragment)
0: peptide
D: Beta-2-microglobulin
E: Light chain from antibody JTK191b E07
F: Fab heavy chain from antibody JTK191b E07
G: MHC class I antigen (Fragment)
1: peptide
H: Beta-2-microglobulin
I: Light chain from antibody JTK191b E07
J: Fab heavy chain from antibody JTK191b E07
K: MHC class I antigen (Fragment)
2: peptide
L: Beta-2-microglobulin
M: Light chain from antibody JTK191b E07
N: Fab heavy chain from antibody JTK191b E07
O: MHC class I antigen (Fragment)
3: peptide
P: Beta-2-microglobulin
Q: Light chain from antibody JTK191b E07
R: Fab heavy chain from antibody JTK191b E07
S: MHC class I antigen (Fragment)
4: peptide
T: Beta-2-microglobulin
U: Light chain from antibody JTK191b E07
V: Fab heavy chain from antibody JTK191b E07
W: MHC class I antigen (Fragment)
5: peptide
X: Beta-2-microglobulin
Y: Light chain from antibody JTK191b E07
Z: Fab heavy chain from antibody JTK191b E07
a: MHC class I antigen (Fragment)
6: peptide
b: Beta-2-microglobulin
c: Light chain from antibody JTK191b E07
d: Fab heavy chain from antibody JTK191b E07
e: MHC class I antigen (Fragment)
7: peptide
f: Beta-2-microglobulin
g: Light chain from antibody JTK191b E07
h: Fab heavy chain from antibody JTK191b E07
i: MHC class I antigen (Fragment)
8: peptide
k: Light chain from antibody JTK191b E07
l: Fab heavy chain from antibody JTK191b E07
o: Light chain from antibody JTK191b E07
p: Fab heavy chain from antibody JTK191b E07
s: Light chain from antibody JTK191b E07
t: Fab heavy chain from antibody JTK191b E07


Theoretical massNumber of molelcules
Total (without water)972,57850
Polymers972,57850
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)357.076, 259.582, 255.361
Angle α, β, γ (deg.)90.00, 133.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
Light chain from antibody JTK191b E07


Mass: 22731.115 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Fab heavy chain from antibody JTK191b E07


Mass: 25938.840 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein
MHC class I antigen (Fragment)


Mass: 31636.955 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: F6IQR9
#4: Protein/peptide
peptide


Mass: 1091.191 Da / Num. of mol.: 9 / Source method: obtained synthetically / Source: (synth.) Cytomegalovirus
#5: Protein
Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
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: 4.44 Å3/Da / Density % sol: 72.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium citrate tribasic dihydrate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.84→30.13 Å / Num. obs: 154424 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.1 / Rrim(I) all: 0.199 / Net I/σ(I): 8.05
Reflection shellResolution: 3.89→3.977 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 7737 / CC1/2: 0.71 / CC star: 0.911 / Rpim(I) all: 0.36 / Rrim(I) all: 0.699 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIXv1.20.1_4487refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.84→30.13 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 2017 1.31 %
Rwork0.2165 --
obs0.2171 154388 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.84→30.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63621 0 0 0 63621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00465320
X-RAY DIFFRACTIONf_angle_d0.77688925
X-RAY DIFFRACTIONf_dihedral_angle_d14.29623527
X-RAY DIFFRACTIONf_chiral_restr0.0489543
X-RAY DIFFRACTIONf_plane_restr0.00611575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.84-3.930.3557840.27366499X-RAY DIFFRACTION57
3.93-4.040.30571490.253311207X-RAY DIFFRACTION99
4.04-4.160.27911530.247111199X-RAY DIFFRACTION99
4.16-4.290.27281500.230211217X-RAY DIFFRACTION99
4.29-4.450.24791520.216511229X-RAY DIFFRACTION99
4.45-4.620.23371450.201511232X-RAY DIFFRACTION99
4.62-4.830.21931550.192311196X-RAY DIFFRACTION99
4.83-5.090.2491510.196711148X-RAY DIFFRACTION98
5.09-5.40.21621520.194511206X-RAY DIFFRACTION98
5.4-5.820.2351380.208211069X-RAY DIFFRACTION97
5.82-6.40.27291530.223811266X-RAY DIFFRACTION99
6.4-7.310.3081410.226511369X-RAY DIFFRACTION99
7.31-9.170.2351570.208211307X-RAY DIFFRACTION99
9.17-30.130.30721370.219711227X-RAY DIFFRACTION97

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