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

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Basic information

Entry
Database: PDB / ID: 6ddv
TitleCrystal Structure Analysis of the Epitope of an Anti-MICA Antibody
Components
  • Anti-MICA Fab fragment heavy chain clone 6E1
  • Anti-MICA Fab fragment light chain clone 6E1
  • MHC class I chain-related protein A
KeywordsIMMUNE SYSTEM / Fab fragment-antigen complex / immunoglobulin domain
Function / homology
Function and homology information


negative regulation of defense response / natural killer cell lectin-like receptor binding / gamma-delta T cell activation / regulation of immune response / response to heat / killing of cells of another organism / metal ion binding / plasma membrane
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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
MHC class I chain-related protein A / 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: 2.05 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Anti-MICA Fab fragment heavy chain clone 6E1
C: MHC class I chain-related protein A
A: Anti-MICA Fab fragment light chain clone 6E1


Theoretical massNumber of molelcules
Total (without water)58,9163
Polymers58,9163
Non-polymers00
Water1,09961
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)66.505, 89.776, 89.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Anti-MICA Fab fragment heavy chain clone 6E1


Mass: 24192.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimeric Fab fragment heavy chain consisting of murine variable domain with human constant domain
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 chain-related protein A


Mass: 10562.569 Da / Num. of mol.: 1 / Mutation: C273S
Source method: isolated from a genetically manipulated source
Details: alpha 3 domain of the MICA*008 allele with C273S mutation co-expressed with Streptomyces plicatu EndoH in the presence of kifunensine
Source: (gene. exp.) Homo sapiens (human) / Gene: MICA / Plasmid: pAcgp67 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H9CTV0, UniProt: Q96QC4*PLUS
#3: Antibody Anti-MICA Fab fragment light chain clone 6E1


Mass: 24159.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimeric Fab fragment light chain consisting of murine variable domain with human constant domain
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.38 % / Mosaicity: 1.477 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M tri-sodium citrate, 15% isopropanol, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→35 Å / Num. obs: 26155 / % possible obs: 76 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.044 / Rrim(I) all: 0.1 / Χ2: 1.032 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.091.20.3163120.6360.2730.4211.29718.2
2.09-2.121.20.2724210.6730.2490.370.59225.5
2.12-2.161.30.285120.8080.2420.3720.64230.1
2.16-2.211.40.2757150.770.230.360.55942.1
2.21-2.261.70.33110100.5910.270.4310.87259.4
2.26-2.311.90.32311620.7090.2430.4080.58968
2.31-2.372.20.31913340.7330.2330.3990.58478.7
2.37-2.432.50.32514210.7590.2210.3960.58183.1
2.43-2.52.70.32114470.7570.2090.3860.59285.8
2.5-2.5830.28615260.8820.1790.340.59389.4
2.58-2.673.20.24714220.9070.1460.2890.6382.7
2.67-2.783.70.2315560.930.1270.2640.64491
2.78-2.9140.20415650.9490.1080.2320.68592.4
2.91-3.064.30.1616120.9760.0820.1810.79193.9
3.06-3.254.50.12216460.9860.060.1370.88795.2
3.25-3.54.60.09915780.9910.0480.111.13890.6
3.5-3.865.40.08916810.9910.040.0981.32797
3.86-4.415.70.07417160.9940.0330.0811.50198.2
4.41-5.565.50.06317090.9950.0280.071.43995.1
5.56-355.70.05518100.9970.0240.061.2496.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J8R, 1F3D, 1NZ8, 6DDM

4j8r

1f3d

1nz8

6ddm


Resolution: 2.05→35 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 21.247 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.256
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 1353 5.2 %RANDOM
Rwork0.2234 ---
obs0.2259 24785 75.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.1 Å2 / Biso mean: 38.068 Å2 / Biso min: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2---0.02 Å20 Å2
3----2.03 Å2
Refinement stepCycle: final / Resolution: 2.05→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 0 61 4087
Biso mean---33.36 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194153
X-RAY DIFFRACTIONr_bond_other_d0.0020.023714
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9355667
X-RAY DIFFRACTIONr_angle_other_deg0.83638581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3625534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44324.233163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31415624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6081514
X-RAY DIFFRACTIONr_chiral_restr0.0670.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02950
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 24 -
Rwork0.422 476 -
all-500 -
obs--19.96 %
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)
11.4274-0.37791.24230.3893-0.27021.9069-0.0721-0.0530.0602-0.020.0007-0.0703-0.1685-0.00440.07150.1517-0.01380.01020.0875-0.00680.01532.30312.657347.8304
22.2884-0.61330.0620.98340.56052.6518-0.14550.04360.0852-0.05250.0448-0.0225-0.2191-0.0550.10070.22810.0155-0.02120.08850.00020.0081-8.853713.43357.4635
31.0601-0.01910.90860.5041-0.24781.78410.1169-0.0463-0.05170.0689-0.06320.02820.23370.0374-0.05370.13950.00980.01140.123-0.01080.0072-0.821-4.827650.2054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 214
2X-RAY DIFFRACTION2C204 - 297
3X-RAY DIFFRACTION3A1 - 212

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