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

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Basic information

Entry
Database: PDB / ID: 6ddr
TitleCrystal Structure Analysis of the Epitope of an Anti-MICA Antibody
Components
  • (Anti-MICA Fab fragment ...) x 2
  • MHC class I polypeptide-related sequence A
KeywordsIMMUNE SYSTEM / Fab fragment-antigen complex / immunoglobulin domain
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-MICA Fab fragment light chain clone 13A9
B: Anti-MICA Fab fragment heavy chain clone 13A9
C: MHC class I polypeptide-related sequence A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,47613
Polymers57,5783
Non-polymers89810
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-76 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.549, 61.833, 172.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules C

#3: 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

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Antibody , 2 types, 2 molecules AB

#1: Antibody Anti-MICA Fab fragment light chain clone 13A9


Mass: 23529.072 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
#2: Antibody Anti-MICA Fab fragment heavy chain clone 13A9


Mass: 23470.141 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

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Non-polymers , 4 types, 270 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.44 % / Mosaicity: 0.367 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.01 M ZnSO4, 0.1 M MES, pH 6.5, 16% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 42120 / % possible obs: 95 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.038 / Rrim(I) all: 0.093 / Χ2: 1.062 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9340.48616350.7240.2540.5510.86274.6
1.93-1.973.80.46417300.7410.2540.5320.85280.1
1.97-2.014.40.40218050.8340.1980.450.9182.8
2.01-2.054.60.38618990.8420.1860.430.90187.5
2.05-2.094.70.35419760.8750.1690.3940.93991
2.09-2.144.70.3320900.8870.1590.3680.93394.2
2.14-2.194.90.30620890.910.1460.340.92997.2
2.19-2.2550.28321500.9310.1350.3150.9997.8
2.25-2.324.90.25821740.9440.1240.2870.9698.6
2.32-2.394.70.23321730.9550.1160.2610.95499.1
2.39-2.485.10.20721920.9620.0980.230.99199.1
2.48-2.585.10.17421960.9740.0830.1931.0199
2.58-2.75.80.14721900.9850.0640.1611.04399.4
2.7-2.845.80.12421920.990.0540.1361.09299.6
2.84-3.025.90.122080.9930.0430.1091.07199.5
3.02-3.255.80.07722320.9950.0340.0841.10199.9
3.25-3.575.70.06322140.9960.0280.0691.14199.6
3.57-4.096.10.05522610.9970.0240.061.23699.7
4.09-5.156.40.05123040.9980.0210.0561.33799.7
5.15-355.80.0524100.9970.0220.0551.36999.5

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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: 1A2Y, 4J8R, 1NZ8, 6DDM

1a2y

4j8r

1nz8

6ddm


Resolution: 1.9→35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.984 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.16
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 2050 4.9 %RANDOM
Rwork0.2084 ---
obs0.2103 40023 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.61 Å2 / Biso mean: 33.709 Å2 / Biso min: 21.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2--4.52 Å2-0 Å2
3----2.41 Å2
Refinement stepCycle: final / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 54 260 4259
Biso mean--53.58 38.02 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194163
X-RAY DIFFRACTIONr_bond_other_d0.0010.023691
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.945684
X-RAY DIFFRACTIONr_angle_other_deg0.82638523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50124.756164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4615596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9051512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02952
LS refinement shellResolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 124 -
Rwork0.314 2295 -
all-2419 -
obs--75.76 %
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)
11.02160.2206-0.80560.2384-0.23971.3019-0.0429-0.10530.0189-0.0065-0.0158-0.0440.05060.07360.05870.15130.0219-0.0330.01480.00620.15776.3635-10.844-23.6198
20.6670.058-1.02890.2721-0.1542.43790.06470.13530.15810.03870.0438-0.0346-0.1744-0.2434-0.10850.13080.026-0.03750.03480.03760.213-1.53372.7669-30.545
32.0313-0.04461.03611.6191-0.65794.10130.1210.1943-0.1036-0.2979-0.064-0.13880.35750.262-0.05690.12490.03440.03970.03390.01260.075319.5164-3.3481-66.2825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 214
2X-RAY DIFFRACTION2B1 - 217
3X-RAY DIFFRACTION3C204 - 297

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