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- PDB-6ddm: Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody -

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Basic information

Entry
Database: PDB / ID: 6ddm
TitleCrystal Structure Analysis of the Epitope of an Anti-MICA Antibody
Components
  • Anti-MICA Fab fragment heavy chain clone 1D5
  • Anti-MICA Fab fragment light chain clone 1D5
  • MHC class I polypeptide-related sequence A
KeywordsIMMUNE SYSTEM / Fab fragment-antigen complex / immunoglobulin domain
Function / homology
Function and homology information


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 / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / immune response / external side of plasma membrane / signaling receptor binding / extracellular space / metal ion binding
Similarity search - Function
Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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
MHC class I chain-related protein A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMatsumoto, M.L.
CitationJournal: MAbs / Year: 2019
Title: High-resolution glycosylation site-engineering method identifies MICA epitope critical for shedding inhibition activity of anti-MICA antibodies.
Authors: Lombana, T.N. / Matsumoto, M.L. / Berkley, A.M. / Toy, E. / Cook, R. / Gan, Y. / Du, C. / Schnier, P. / Sandoval, W. / Ye, Z. / Schartner, J.M. / Kim, J. / Spiess, C.
History
DepositionMay 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.page_first / _citation.page_last
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-MICA Fab fragment light chain clone 1D5
C: MHC class I polypeptide-related sequence A
B: Anti-MICA Fab fragment heavy chain clone 1D5


Theoretical massNumber of molelcules
Total (without water)57,2403
Polymers57,2403
Non-polymers00
Water11,133618
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.690, 50.177, 88.633
Angle α, β, γ (deg.)90.000, 90.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Anti-MICA Fab fragment light chain clone 1D5


Mass: 23219.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimeric Fab fragment consisting of murine variable domains with human constant domains
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4
#2: Protein MHC class I polypeptide-related sequence A / MHC class I polypeptide-related sequence A / isoform CRA_c / MICA / Stress inducible class I ...MHC class I polypeptide-related sequence A / isoform CRA_c / MICA / Stress inducible class I homolog / cDNA FLJ60820 / highly similar to Homo sapiens MHC class I polypeptide-related sequence A (MICA) / mRNA


Mass: 10578.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: alpha 3 domain of the MICA*008 allele co-expressed with Streptomyces plicatu EndoH in the presence of kifunensine
Source: (gene. exp.) Homo sapiens (human) / Gene: MICA, hCG_2001511 / Plasmid: pAcgp67 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96QC4
#3: Antibody Anti-MICA Fab fragment heavy chain clone 1D5


Mass: 23441.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: himeric Fab fragment consisting of murine variable domains with human constant domains
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBR322 / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.28 Å3/Da / Density % sol: 46.17 % / Mosaicity: 0.498 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate, pH 4.6, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→35 Å / Num. obs: 126363 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.037 / Rrim(I) all: 0.07 / Χ2: 0.997 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.322.90.5661000.7930.380.680.41596.4
1.32-1.353.20.53662370.8360.3530.6450.41999.6
1.35-1.373.30.47563220.8620.3070.5670.428100
1.37-1.43.40.4263030.8870.2690.5010.448100
1.4-1.433.40.3863510.9020.2430.4520.474100
1.43-1.463.40.31962500.9120.2040.380.491100
1.46-1.53.40.27163120.9430.1720.3220.5499.9
1.5-1.543.50.21963140.960.1390.260.574100
1.54-1.593.50.1962980.9670.120.2260.639100
1.59-1.643.50.16463320.9750.1030.1940.70699.9
1.64-1.73.50.1463030.9790.0880.1660.773100
1.7-1.763.60.11863410.9840.0740.1390.87899.9
1.76-1.843.60.09863470.9880.0610.1160.97999.9
1.84-1.943.60.07963150.9910.0490.0941.069100
1.94-2.063.70.07163310.9910.0440.0831.26299.9
2.06-2.223.70.06963480.9910.0420.0811.62799.9
2.22-2.453.80.06163760.9930.0370.0721.685100
2.45-2.83.80.05363920.9940.0320.0621.793100
2.8-3.533.70.04763860.9950.0280.0552.06599.8
3.53-353.60.04264050.9950.0260.051.9397.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3D, 4M1G, 1HYR, 1NZ8

1f3d

4m1g

1hyr

1nz8


Resolution: 1.3→35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.755 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.054
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 6152 4.9 %RANDOM
Rwork0.1884 ---
obs0.1892 120157 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.47 Å2 / Biso mean: 20.983 Å2 / Biso min: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.79 Å2
2---1.75 Å2-0 Å2
3---1.72 Å2
Refinement stepCycle: final / Resolution: 1.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 0 625 4505
Biso mean---32.51 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194331
X-RAY DIFFRACTIONr_bond_other_d0.0020.023840
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9445977
X-RAY DIFFRACTIONr_angle_other_deg0.8633.0028929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96524.371151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36615651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9581511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215113
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02966
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 385 -
Rwork0.288 8651 -
all-9036 -
obs--96.81 %
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)
10.46240.38020.34570.53120.30510.42950.0383-0.02580.0219-0.0461-0.03610.04110.0558-0.0747-0.00220.0388-0.0041-0.01080.05560.0160.012774.8516-2.063319.2172
22.9721.1927-1.05051.305-0.45531.18770.0202-0.1718-0.10060.02830.0125-0.0063-0.02770.1019-0.03270.0350.0176-0.00090.07640.01240.0119114.29718.055636.3747
30.67210.36380.32460.54710.31320.4550.02120.0947-0.0189-0.08540.0218-0.095-0.01240.0205-0.04310.03120.01060.02250.03510.02230.038391.8976-9.134817.1848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 214
2X-RAY DIFFRACTION2C204 - 297
3X-RAY DIFFRACTION3B2 - 216

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