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- PDB-3uo1: Structure of a monoclonal antibody complexed with its MHC-I antigen -

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Basic information

Entry
Database: PDB / ID: 3uo1
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-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: 1.641 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
DepositionNov 16, 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)48,3434
Polymers48,2473
Non-polymers961
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-43 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.583, 40.291, 59.353
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-338-

HOH

21H-439-

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: 1115.213 Da / Num. of mol.: 1 / Fragment: H-2L(d) PEPTIDE SEGMENT 46-54 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P01897
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: antibody at 6.8 mg/ml mixed with equimolar peptide and then 1:1 with 0.1 M LiSO4, 0.1 M TRIS, 30% w/v PEG 3000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→46.93 Å / Num. obs: 54890

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 1.641 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 2776 5.08 %RANDOM
Rwork0.185 ---
obs0.1861 54694 99.77 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.766 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8747 Å2-0 Å23.8943 Å2
2---3.0039 Å20 Å2
3----0.8708 Å2
Refinement stepCycle: LAST / Highest resolution: 1.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 5 478 3869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063476
X-RAY DIFFRACTIONf_angle_d1.0464731
X-RAY DIFFRACTIONf_dihedral_angle_d11.971237
X-RAY DIFFRACTIONf_chiral_restr0.072537
X-RAY DIFFRACTIONf_plane_restr0.005602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.641-1.66920.35781150.29992500X-RAY DIFFRACTION96
1.6692-1.69950.31111240.27132585X-RAY DIFFRACTION100
1.6995-1.73220.27531390.26012542X-RAY DIFFRACTION100
1.7322-1.76760.27491250.24622605X-RAY DIFFRACTION100
1.7676-1.8060.28951350.22732573X-RAY DIFFRACTION100
1.806-1.8480.23281460.22162607X-RAY DIFFRACTION100
1.848-1.89420.24861340.20382579X-RAY DIFFRACTION100
1.8942-1.94540.23561540.19192549X-RAY DIFFRACTION100
1.9454-2.00270.20091370.18162599X-RAY DIFFRACTION100
2.0027-2.06730.21751470.18032571X-RAY DIFFRACTION100
2.0673-2.14120.21881350.18052609X-RAY DIFFRACTION100
2.1412-2.22690.17371440.18132585X-RAY DIFFRACTION100
2.2269-2.32830.20351490.17242567X-RAY DIFFRACTION100
2.3283-2.4510.20031220.18642632X-RAY DIFFRACTION100
2.451-2.60460.20231490.1822585X-RAY DIFFRACTION100
2.6046-2.80570.22321500.19142607X-RAY DIFFRACTION100
2.8057-3.0880.22271500.18972616X-RAY DIFFRACTION100
3.088-3.53470.19841380.1752622X-RAY DIFFRACTION100
3.5347-4.45280.17041330.16072667X-RAY DIFFRACTION100
4.4528-46.95170.18381500.17932718X-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)
13.9844-1.9630.69892.63370.31852.18470.19540.4392-0.40850.0786-0.46880.2598-0.1331-0.2433-0.03170.06880.0540.05390.2079-0.0960.137616.8694-2.075324.1798
22.2808-1.2138-1.54151.20512.11315.04970.03810.0762-0.0196-0.0696-0.0113-0.0618-0.1056-0.0934-0.01070.16920.00860.02030.13750.01920.163711.3463.3839-7.0282
31.0827-0.6886-0.31513.88574.31826.72590.19340.36320.177-0.1351-0.0082-0.2671-0.22190.1915-0.08740.16270.0185-0.00730.24510.02850.198841.5554-2.279112.0391
42.2046-0.24820.46192.0265-0.34483.9530.08050.1113-0.19730.01910.05850.08490.0225-0.1786-0.17140.08610.0195-0.0070.080.00090.137333.9159-7.600121.2672
53.00270.29360.75383.0620.21224.04710.0570.3569-0.2904-0.1086-0.13860.06430.39060.09840.08790.16570.0383-0.00270.147-0.05640.19639.3966-13.404717.0552
60.6045-0.1610.57660.715-0.74522.21150.0850.2716-0.0612-0.0532-0.1033-0.03520.20940.176-0.00180.12340.0556-0.02480.2403-0.02710.163935.3063-4.74548.4598
71.3293-0.91440.18942.1294-0.76192.48820.07780.06630.44730.0319-0.0075-0.0674-0.19090.1952-0.04370.1474-0.01650.03160.10620.00870.188921.458612.5449-12.7415
82.2014-1.56490.64573.6036-1.19472.31870.11520.02970.3264-0.0496-0.0266-0.0468-0.14340.3007-0.13940.1308-0.02990.0320.1356-0.00120.180723.315512.7418-13.1904
96.51833.461.25976.09223.30763.25120.0704-1.0415-1.16281.85320.3667-0.81630.90620.55280.16520.47310.05510.0640.35260.15030.340229.0155-8.280736.1044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resseq 1:115)
2X-RAY DIFFRACTION2chain 'H' and (resseq 116:216)
3X-RAY DIFFRACTION3chain 'L' and (resseq 1:25)
4X-RAY DIFFRACTION4chain 'L' and (resseq 26:53)
5X-RAY DIFFRACTION5chain 'L' and (resseq 54:80)
6X-RAY DIFFRACTION6chain 'L' and (resseq 81:117)
7X-RAY DIFFRACTION7chain 'L' and (resseq 118:159)
8X-RAY DIFFRACTION8chain 'L' and (resseq 160:218)
9X-RAY DIFFRACTION9chain 'P'

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