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- PDB-3uyr: Structure of a monoclonal antibody complexed with its MHC-I antigen -

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Basic information

Entry
Database: PDB / ID: 3uyr
TitleStructure of a monoclonal antibody complexed with its MHC-I antigen
Components
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • antibody Fab heavy chain
  • antibody Fab light chain
KeywordsIMMUNE SYSTEM / Ig-fold 3 / 10 helix
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / T cell receptor binding / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / antibacterial humoral response / protein-folding chaperone binding / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / metal ion binding / plasma membrane
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 / Immunoglobulin V-Type / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain ...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 / Immunoglobulin V-Type / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Mainly Beta
Similarity search - Domain/homology
If kappa light chain / H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMargulies, D.H. / Mage, M.G. / Wang, R. / Natarajan, K.
CitationJournal: J.Immunol. / Year: 2012
Title: The Peptide-receptive transition state of MHC class I molecules: insight from structure and molecular dynamics.
Authors: Mage, M.G. / Dolan, M.A. / Wang, R. / Boyd, L.F. / Revilleza, M.J. / Robinson, H. / Natarajan, K. / Myers, N.B. / Hansen, T.H. / Margulies, D.H.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: antibody Fab heavy chain
L: antibody Fab light chain
P: H-2 class I histocompatibility antigen, L-D alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1814
Polymers48,1193
Non-polymers621
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-24 kcal/mol
Surface area20240 Å2
Unit cell
Length a, b, c (Å)193.524, 40.423, 59.265
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-281-

HOH

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Components

#1: Antibody antibody Fab heavy chain


Mass: 23163.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody Fab light chain


Mass: 23967.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3*PLUS
#3: Protein/peptide H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 987.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P01897
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M LiSO4, 0.1M Tris pH 8.5, 30% (w/v) PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→45.07 Å / Num. all: 49985 / Num. obs: 49813 / % possible obs: 99.57 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.067 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 2523 5.07 %Random
Rwork0.1924 ---
all0.1941 49809 --
obs0.1941 49809 99.57 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.458 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4735 Å2-0 Å22.8875 Å2
2---0.8414 Å20 Å2
3----1.6321 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 4 328 3681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063438
X-RAY DIFFRACTIONf_angle_d1.1684678
X-RAY DIFFRACTIONf_dihedral_angle_d12.5161215
X-RAY DIFFRACTIONf_chiral_restr0.07534
X-RAY DIFFRACTIONf_plane_restr0.005593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.75710.35222220.29624637X-RAY DIFFRACTION97
1.7571-1.82750.32642600.25634657X-RAY DIFFRACTION100
1.8275-1.91070.272440.22554713X-RAY DIFFRACTION100
1.9107-2.01140.24582370.21754712X-RAY DIFFRACTION100
2.0114-2.13740.27112270.21564764X-RAY DIFFRACTION100
2.1374-2.30250.2412830.20644674X-RAY DIFFRACTION100
2.3025-2.53410.23722810.20074742X-RAY DIFFRACTION100
2.5341-2.90080.2342630.19794748X-RAY DIFFRACTION100
2.9008-3.65440.22222590.19394744X-RAY DIFFRACTION99
3.6544-45.08330.18862470.16434895X-RAY DIFFRACTION99
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)
12.4354-0.97750.49540.78130.20180.99060.10780.1002-0.3965-0.115-0.29710.1504-0.1225-0.15580.05860.24570.01230.01730.2159-0.03020.316.6961-9.576521.9977
23.0456-0.46730.80560.7155-0.05391.7369-0.0215-0.0687-0.23390.0553-0.11470.1078-0.2208-0.22460.06070.24640.01280.04770.2325-0.01590.233517.6698-8.078325.9935
30.6925-0.6334-0.60890.74690.96061.57010.07790.17460.0764-0.0303-0.0549-0.03720.0027-0.0993-0.01830.23770.04780.03870.28770.04870.226211.3633-3.4727-6.9798
42.0114-0.19910.02142.3052-0.81850.59390.08010.28980.0610.3029-0.1113-0.0148-0.2490.2061-0.00850.11060.0242-0.0280.14490.00630.156641.1176-10.56318.6678
51.1619-0.2023-0.57170.4579-0.11830.64110.08770.3004-0.25890.022-0.125-0.06140.21160.0296-0.05690.25260.0316-0.02840.1719-0.06530.258135.9038-18.097215.7519
61.0208-0.21690.86610.4792-0.44940.96770.17360.4152-0.01090.0133-0.0935-0.01740.04570.47590.13410.16640.090.01030.2655-0.00440.164728.8866-6.62661.9602
70.72030.39640.11250.9534-0.30171.680.0990.12080.1501-0.0267-0.0178-0.035-0.12850.69290.08320.1964-0.02360.02420.34810.04140.153924.33766.0313-12.8802
81.36051.30320.6311.48121.08551.61590.37640.0815-0.29020.06290.3072-0.48170.1351-0.177-0.38180.8132-0.07790.07780.51620.09260.616529.4924-15.617934.8121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resseq 2:51)
2X-RAY DIFFRACTION2chain 'H' and (resseq 52:115)
3X-RAY DIFFRACTION3chain 'H' and (resseq 116:216)
4X-RAY DIFFRACTION4chain 'L' and (resseq 1:37)
5X-RAY DIFFRACTION5chain 'L' and (resseq 38:80)
6X-RAY DIFFRACTION6chain 'L' and (resseq 81:132)
7X-RAY DIFFRACTION7chain 'L' and (resseq 133:218)
8X-RAY DIFFRACTION8chain 'P'

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