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- PDB-3v52: Structure of a monoclonal antibody complexed with its MHC-I antigen -

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Basic information

Entry
Database: PDB / ID: 3v52
TitleStructure of a monoclonal antibody complexed with its MHC-I antigen
Components
  • ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 H CHAIN
  • ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 L CHAIN
  • H-2 class I histocompatibility antigen, L-D alpha chain
KeywordsIMMUNE SYSTEM / Ig domain / 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: 1.697 Å
AuthorsMage, 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.
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 15, 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: ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 H CHAIN
L: ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 L 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
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-36 kcal/mol
Surface area19240 Å2
MethodPISA
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-395-

HOH

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Components

#1: Protein ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 H CHAIN


Mass: 23163.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Protein ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 L 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 / Fragment: H-2Ld peptide p46-53 / 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.: 345 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M LiSO4, 0.1M Tris, 30% (w/v/) PEG 3000, pH 8.5, 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: Nov 9, 2010
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator; vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.697→50 Å / Num. obs: 49812 / % possible obs: 99.78 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.3
Reflection shellHighest resolution: 1.697 Å

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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: 1.697→45.067 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 2523 5.07 %
Rwork0.1968 --
obs0.1983 49809 99.57 %
all-31132 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.859 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5237 Å2-0 Å22.7754 Å2
2---0.8374 Å20 Å2
3----1.6864 Å2
Refinement stepCycle: LAST / Resolution: 1.697→45.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 4 345 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073438
X-RAY DIFFRACTIONf_angle_d1.2014678
X-RAY DIFFRACTIONf_dihedral_angle_d12.541215
X-RAY DIFFRACTIONf_chiral_restr0.086534
X-RAY DIFFRACTIONf_plane_restr0.006593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.697-1.72910.35471270.29832492X-RAY DIFFRACTION95
1.7291-1.76440.36631220.27192622X-RAY DIFFRACTION100
1.7644-1.80280.28541480.2552598X-RAY DIFFRACTION100
1.8028-1.84470.26331440.22782652X-RAY DIFFRACTION100
1.8447-1.89090.26021310.23012583X-RAY DIFFRACTION100
1.8909-1.9420.23711360.21742645X-RAY DIFFRACTION100
1.942-1.99910.24331360.21842628X-RAY DIFFRACTION100
1.9991-2.06370.2929990.2232644X-RAY DIFFRACTION100
2.0637-2.13740.24741470.22142619X-RAY DIFFRACTION100
2.1374-2.2230.25511590.21112604X-RAY DIFFRACTION100
2.223-2.32420.23821490.22332630X-RAY DIFFRACTION100
2.3242-2.44670.26141570.21162595X-RAY DIFFRACTION100
2.4467-2.60.23781530.21812641X-RAY DIFFRACTION100
2.6-2.80070.22821460.21482636X-RAY DIFFRACTION100
2.8007-3.08250.25381410.20782653X-RAY DIFFRACTION100
3.0825-3.52840.21151480.1952623X-RAY DIFFRACTION99
3.5284-4.44480.20111520.16452642X-RAY DIFFRACTION99
4.4448-45.08330.18461280.1672779X-RAY DIFFRACTION100
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)
15.1762-1.69331.17173.1013-0.03353.36870.00470.0003-0.39410.0229-0.14640.2549-0.1706-0.29930.12520.16360.00390.05490.165-0.02070.197317.2406-8.750524.2947
21.6147-0.926-0.96371.80872.15534.0460.08720.25490.087-0.0618-0.0491-0.0771-0.0578-0.1156-0.02910.24040.03850.04470.26860.05940.234411.3587-3.5201-6.977
32.6425-0.60690.2732.63211.87895.77840.23070.86280.2387-0.1421-0.2032-0.1826-0.31720.258-0.04810.2150.033-0.01240.34030.03750.220141.8069-9.048112.0601
43.1677-0.8987-0.02621.8146-0.59762.40.14440.361-0.4334-0.0281-0.10640.09580.2948-0.0032-0.01110.22660.0245-0.02540.1245-0.04710.241436.7481-17.163119.1648
51.0118-0.22821.45660.6671-0.93992.48280.15760.4698-0.0235-0.038-0.09620.00370.09180.5695-0.10740.1940.08080.01510.3194-0.01490.196128.8664-6.68081.9565
62.2064-1.06320.61362.7703-1.12582.59980.08930.19720.3296-0.0755-0.0485-0.1575-0.17240.7404-0.04580.217-0.04770.02850.38240.02540.192924.35675.9549-12.8731
75.67025.7510.91238.07932.94014.00630.4566-0.2802-1.3291.17720.4175-0.60230.8185-0.4253-0.70720.8164-0.0981-0.01230.67290.2270.690529.3811-15.583734.8345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resseq 2:115)
2X-RAY DIFFRACTION2chain 'H' and (resseq 116:216)
3X-RAY DIFFRACTION3chain 'L' and (resseq 1:25)
4X-RAY DIFFRACTION4chain 'L' and (resseq 26:80)
5X-RAY DIFFRACTION5chain 'L' and (resseq 81:132)
6X-RAY DIFFRACTION6chain 'L' and (resseq 133:218)
7X-RAY DIFFRACTION7chain 'P' and (resseq 46:53)

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