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- PDB-7kgu: Structure of 2Q1-Fab, an antibody selective for IDH2R140Q-HLA-B*07:02 -

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Basic information

Entry
Database: PDB / ID: 7kgu
TitleStructure of 2Q1-Fab, an antibody selective for IDH2R140Q-HLA-B*07:02
Components
  • Heavy Chain, Fab, IGG, Fab
  • Light Chain, Fab fragment, IGG
KeywordsIMMUNE SYSTEM / antibody / Fab / 2Q1 / IGG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / GLYCINE / : / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMiller, M.S. / Aytenfisu, T.Y. / Wright, K.M. / Gabelli, S.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Other private
CitationJournal: Nat Commun / Year: 2021
Title: Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens.
Authors: Hwang, M.S. / Miller, M.S. / Thirawatananond, P. / Douglass, J. / Wright, K.M. / Hsiue, E.H. / Mog, B.J. / Aytenfisu, T.Y. / Murphy, M.B. / Aitana Azurmendi, P. / Skora, A.D. / Pearlman, A.H. ...Authors: Hwang, M.S. / Miller, M.S. / Thirawatananond, P. / Douglass, J. / Wright, K.M. / Hsiue, E.H. / Mog, B.J. / Aytenfisu, T.Y. / Murphy, M.B. / Aitana Azurmendi, P. / Skora, A.D. / Pearlman, A.H. / Paul, S. / DiNapoli, S.R. / Konig, M.F. / Bettegowda, C. / Pardoll, D.M. / Papadopoulos, N. / Kinzler, K.W. / Vogelstein, B. / Zhou, S. / Gabelli, S.B.
History
DepositionOct 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light Chain, Fab fragment, IGG
B: Heavy Chain, Fab, IGG, Fab
C: Light Chain, Fab fragment, IGG
D: Heavy Chain, Fab, IGG, Fab
E: Light Chain, Fab fragment, IGG
F: Heavy Chain, Fab, IGG, Fab
H: Heavy Chain, Fab, IGG, Fab
L: Light Chain, Fab fragment, IGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,72455
Polymers187,0298
Non-polymers4,69647
Water10,719595
1
A: Light Chain, Fab fragment, IGG
B: Heavy Chain, Fab, IGG, Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,42216
Polymers46,7572
Non-polymers1,66414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-23 kcal/mol
Surface area19240 Å2
MethodPISA
2
C: Light Chain, Fab fragment, IGG
D: Heavy Chain, Fab, IGG, Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,13216
Polymers46,7572
Non-polymers1,37514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area19440 Å2
MethodPISA
3
E: Light Chain, Fab fragment, IGG
F: Heavy Chain, Fab, IGG, Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,47510
Polymers46,7572
Non-polymers7188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area19450 Å2
MethodPISA
4
H: Heavy Chain, Fab, IGG, Fab
L: Light Chain, Fab fragment, IGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,69513
Polymers46,7572
Non-polymers93811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-24 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.462, 263.955, 91.237
Angle α, β, γ (deg.)90.000, 99.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 8 molecules ACELBDFH

#1: Antibody
Light Chain, Fab fragment, IGG


Mass: 23449.023 Da / Num. of mol.: 4 / Fragment: fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Strain (production host): HEK293
#2: Antibody
Heavy Chain, Fab, IGG, Fab


Mass: 23308.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Strain (production host): HEK293

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Non-polymers , 8 types, 642 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris pH 5.5, 25% (w/v) PEG 3350, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.4→45.53 Å / Num. obs: 68740 / % possible obs: 98.7 % / Redundancy: 2.866 % / Biso Wilson estimate: 38.118 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.118 / Χ2: 0.916 / Net I/σ(I): 8.82 / Num. measured all: 197009 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.462.6270.4682.0813096504749850.6760.59298.8
2.46-2.532.8830.422.514470502350190.7750.51699.9
2.53-2.62.9860.3852.814457489548410.8040.46998.9
2.6-2.682.9590.323.3813948473747140.8630.38999.5
2.68-2.772.9560.2594.0713546462145830.9050.31699.2
2.77-2.872.9760.2234.7512977439243610.9290.27299.3
2.87-2.982.9340.1755.8512588433842910.9550.21498.9
2.98-3.12.9390.1556.7911878407340410.9640.18899.2
3.1-3.242.880.1228.4111426400239670.9750.14899.1
3.24-3.392.910.09710.3410772375237020.9850.11898.7
3.39-3.582.8270.07812.4110100362235730.990.09698.6
3.58-3.792.770.07213.129359341333790.9910.08899
3.79-4.062.6240.06314.038103318030880.9920.07997.1
4.06-4.382.5250.05116.17430300829430.9930.06597.8
4.38-4.82.7020.04817.867360277827240.9950.0698.1
4.8-5.372.8260.04818.096756244923910.9950.05997.6
5.37-6.23.0790.05417.246622219521510.9940.06598
6.2-7.593.0790.05217.685668186518410.9950.06398.7
7.59-10.733.0610.03722.794209141413750.9970.04597.2
10.73-45.532.9110.03523.2622448087710.9970.04395.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.559
Highest resolutionLowest resolution
Rotation45.52 Å3.5 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UJ9

6uj9


Resolution: 2.4→45.53 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.2493 / WRfactor Rwork: 0.1945 / FOM work R set: 0.7753 / SU B: 21.498 / SU ML: 0.25 / SU R Cruickshank DPI: 0.5904 / SU Rfree: 0.3022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.59 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 3437 5 %RANDOM
Rwork0.2081 ---
obs0.2111 65303 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.27 Å2 / Biso mean: 39.047 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20.01 Å2
2--0.5 Å20 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 2.4→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12900 0 261 595 13756
Biso mean--67.79 35.54 -
Num. residues----1690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01313442
X-RAY DIFFRACTIONr_bond_other_d0.0030.01711909
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.64218297
X-RAY DIFFRACTIONr_angle_other_deg1.351.56927772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.24851679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55422.772570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.935152065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2051552
X-RAY DIFFRACTIONr_chiral_restr0.0780.21743
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214793
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022739
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 248 -
Rwork0.318 4720 -
all-4968 -
obs--98.83 %
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)
11.0852-0.40140.19792.10650.33671.6541-0.00220.1563-0.1157-0.01210.1285-0.07390.2787-0.0857-0.12630.1571-0.0453-0.03360.0611-0.01870.02846.829-5.676-5.44
20.8412-0.26220.36662.24550.94461.3879-0.02580.05420.0110.04110.2358-0.13420.18240.1009-0.210.07780.0111-0.01430.1003-0.02910.09258.2984.02810.353
30.55330.4643-0.11472.6423-1.15012.5125-0.0193-0.0799-0.050.23510.0887-0.0172-0.1391-0.1488-0.06940.0890.042-0.0080.0570.01420.01211.7038.16353.136
40.60260.37210.16691.298-1.17542.1136-0.0059-0.02580.00730.03430.0862-0.07570.105-0.188-0.08030.08310.0002-0.0160.12190.0160.096210.4919.93534.644
50.61480.3401-0.15673.31480.36541.50270.0286-0.18710.11930.12770.1872-0.2472-0.1981-0.0632-0.21580.08730.0230.04610.1034-0.05380.09046.93774.95936.69
60.60120.1362-0.39741.9280.78281.17840.0512-0.0840.048-0.10060.1613-0.2063-0.13750.0403-0.21250.0404-0.01540.03940.0803-0.04510.13578.54964.97921.1
70.87-0.6593-0.19132.089-1.69243.73990.17930.29020.158-0.45360.1234-0.0880.1626-0.4711-0.30260.16870.00560.06690.17770.06550.068411.92859.898-21.804
81.1856-0.3799-0.6330.9569-0.92832.33540.04080.17730.0866-0.10970.1358-0.0879-0.0022-0.4359-0.17660.06680.01550.03640.15330.03020.123310.76358.522-3.168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 211
2X-RAY DIFFRACTION1L301
3X-RAY DIFFRACTION2H2 - 218
4X-RAY DIFFRACTION3A1 - 212
5X-RAY DIFFRACTION4B1 - 218
6X-RAY DIFFRACTION5C1 - 212
7X-RAY DIFFRACTION6D2 - 218
8X-RAY DIFFRACTION7E1 - 211
9X-RAY DIFFRACTION8F1 - 218

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