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- PDB-3v4u: Structure of a monoclonal antibody complexed with its MHC-I antigen -

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Basic information

Entry
Database: PDB / ID: 3v4u
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: 1.64 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 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


Theoretical massNumber of molelcules
Total (without water)48,2473
Polymers48,2473
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-34 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.140, 40.643, 59.069
Angle α, β, γ (deg.)90.00, 103.07, 90.00
Int Tables number5
Space group name H-MC121

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
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 10, 2010
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→41.67 Å / Num. all: 56165 / Num. obs: 55324 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.1
Reflection shellResolution: 1.68→1.72 Å / % possible all: 88.4

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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: 1.64→41.67 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 2734 5.08 %
Rwork0.2128 --
obs0.2146 53846 95.72 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.34 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1695 Å2-0 Å23.7943 Å2
2--3.4375 Å20 Å2
3----4.6071 Å2
Refinement stepCycle: LAST / Resolution: 1.64→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 0 355 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143577
X-RAY DIFFRACTIONf_angle_d1.2084713
X-RAY DIFFRACTIONf_dihedral_angle_d13.781233
X-RAY DIFFRACTIONf_chiral_restr0.09536
X-RAY DIFFRACTIONf_plane_restr0.006600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.66670.39541070.3691991X-RAY DIFFRACTION75
1.6667-1.6970.42071470.35992356X-RAY DIFFRACTION88
1.697-1.72970.37641130.32232349X-RAY DIFFRACTION90
1.7297-1.7650.38541330.33832498X-RAY DIFFRACTION93
1.765-1.80340.32581350.32212421X-RAY DIFFRACTION93
1.8034-1.84530.31511160.31122531X-RAY DIFFRACTION94
1.8453-1.89150.36211440.29222508X-RAY DIFFRACTION95
1.8915-1.94260.28341430.28082548X-RAY DIFFRACTION96
1.9426-1.99980.29781420.24872560X-RAY DIFFRACTION97
1.9998-2.06430.32231200.26932619X-RAY DIFFRACTION98
2.0643-2.13810.26731220.25022671X-RAY DIFFRACTION98
2.1381-2.22370.30851410.24222606X-RAY DIFFRACTION99
2.2237-2.32490.28381480.23632631X-RAY DIFFRACTION99
2.3249-2.44740.26421600.24292623X-RAY DIFFRACTION99
2.4474-2.60080.31291560.2332622X-RAY DIFFRACTION99
2.6008-2.80150.26861550.21822660X-RAY DIFFRACTION99
2.8015-3.08340.23991330.22032690X-RAY DIFFRACTION100
3.0834-3.52930.24621470.20062683X-RAY DIFFRACTION100
3.5293-4.44580.21441350.16682733X-RAY DIFFRACTION100
4.4458-41.68750.16391370.16212812X-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)
10.2424-0.3451-0.1320.52690.10290.437-0.05380.0574-0.30870.01140.0854-0.0258-0.0976-0.1485-0.0360.27060.0576-0.04770.1813-0.12940.466711.2791-0.829818.1985
20.174-0.4823-0.16361.420.53630.21640.1133-0.0163-0.678-0.2351-0.13140.40920.0873-0.0687-0.03060.1676-0.0425-0.02080.18930.0920.489116.7118-8.42924.2622
31.0538-0.60260.51820.55720.24761.641-0.1066-0.4235-0.18460.03840.01320.0133-0.3703-0.35140.01560.24760.0290.05310.28080.05230.288918.1005-2.092728.8497
40.482-0.2911-0.12120.4404-0.10070.1093-0.08210.27240.21730.1009-0.1432-0.2976-0.23490.0687-0.0570.19990.01520.02010.19870.04040.267415.95052.65266.324
50.35680.0907-0.20250.32240.4260.79110.03510.41980.16880.0546-0.05630.08740.1016-0.1239-0.00430.2010.04950.02370.45370.08030.247611.45370.5155-6.0169
61.1548-0.08650.04830.6844-0.40890.41580.11380.3320.02610.1473-0.142-0.0112-0.15390.131-0.02020.21990.0546-0.01650.19350.0080.204741.5064-4.770318.5422
70.8449-0.13410.35850.3744-0.46820.23630.21380.5332-0.06030.1456-0.1069-0.07310.14250.26710.01950.13120.102-0.00810.307-0.05490.177332.4018-6.09568.32
80.07670.13630.05720.37570.3580.7126-0.04920.29450.074-0.06960.2659-0.2275-0.11360.86390.43770.2034-0.10190.03140.73730.1370.061524.41312.2279-12.7838
90.50570.23510.36540.33970.24020.53380.1056-0.1065-0.13710.06230.03220.0060.1848-0.0787-0.13720.44720.08490.06310.34960.14970.341629.3022-9.951734.9157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resseq 1:17)
2X-RAY DIFFRACTION2chain 'H' and (resseq 18:40)
3X-RAY DIFFRACTION3chain 'H' and (resseq 41:83)
4X-RAY DIFFRACTION4chain 'H' and (resseq 84:149)
5X-RAY DIFFRACTION5chain 'H' and (resseq 150:216)
6X-RAY DIFFRACTION6chain 'L' and (resseq 1:37)
7X-RAY DIFFRACTION7chain 'L' and (resseq 38:132)
8X-RAY DIFFRACTION8chain 'L' and (resseq 133:218)
9X-RAY DIFFRACTION9chain 'P'

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