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- PDB-8g2m: The tumor activated anti-CTLA-4 monoclonal antibody XTX101 demons... -

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Basic information

Entry
Database: PDB / ID: 8g2m
TitleThe tumor activated anti-CTLA-4 monoclonal antibody XTX101 demonstrates tumor-growth inhibition and tumor-selective pharmacodynamics in mouse models of cancer
Components
  • Heavy chain of humanized IgG
  • Light chain of humanized IgG
  • masking peptide
KeywordsIMMUNE SYSTEM / Engineered antibody
Function / homologyCITRIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
Peptide display vector fth1 (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWilliams, J.C. / Williams, J.C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J Immunother Cancer / Year: 2023
Title: XTX101, a tumor-activated, Fc-enhanced anti-CTLA-4 monoclonal antibody, demonstrates tumor-growth inhibition and tumor-selective pharmacodynamics in mouse models of cancer.
Authors: Jenkins, K.A. / Park, M. / Pederzoli-Ribeil, M. / Eskiocak, U. / Johnson, P. / Guzman, W. / McLaughlin, M. / Moore-Lai, D. / O'Toole, C. / Liu, Z. / Nicholson, B. / Flesch, V. / Qiu, H. / ...Authors: Jenkins, K.A. / Park, M. / Pederzoli-Ribeil, M. / Eskiocak, U. / Johnson, P. / Guzman, W. / McLaughlin, M. / Moore-Lai, D. / O'Toole, C. / Liu, Z. / Nicholson, B. / Flesch, V. / Qiu, H. / Clackson, T. / O'Hagan, R.C. / Rodeck, U. / Karow, M. / O'Neil, J. / Williams, J.C.
History
DepositionFeb 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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

Downloads & links

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Assembly

Deposited unit
F: masking peptide
H: Heavy chain of humanized IgG
L: Light chain of humanized IgG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1034
Polymers46,9113
Non-polymers1921
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-23 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.180, 55.230, 73.860
Angle α, β, γ (deg.)90.00, 118.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-591-

HOH

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Components

#1: Protein/peptide masking peptide


Mass: 992.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Peptide display vector fth1 (others)
#2: Antibody Heavy chain of humanized IgG


Mass: 23624.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Light chain of humanized IgG


Mass: 22294.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium Citrate Dibasic pH 5.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28.98 Å / Num. obs: 42381 / % possible obs: 96.99 % / Redundancy: 8.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0645 / Rpim(I) all: 0.0228 / Rrim(I) all: 0.06861 / Net I/σ(I): 21.67
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.5691 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 3390 / CC1/2: 0.848 / Rpim(I) all: 0.3137

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Processing

Software
NameVersionClassification
PHENIXv1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.741 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21395 2120 5.1 %RANDOM
Rwork0.1798 ---
obs0.18155 39463 97.02 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.199 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.3 Å2
2---0.18 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 13 541 3852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0163456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163027
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.814718
X-RAY DIFFRACTIONr_angle_other_deg0.4441.5637114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1195.12458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50310550
X-RAY DIFFRACTIONr_chiral_restr0.0670.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02678
X-RAY DIFFRACTIONr_mcbond_it1.8320.9261756
X-RAY DIFFRACTIONr_mcbond_other1.8270.9261756
X-RAY DIFFRACTIONr_mcangle_it2.4711.3712197
X-RAY DIFFRACTIONr_mcangle_other2.4711.3722198
X-RAY DIFFRACTIONr_scbond_it3.5591.1751700
X-RAY DIFFRACTIONr_scbond_other3.4091.1651697
X-RAY DIFFRACTIONr_scangle_other4.8051.6432516
X-RAY DIFFRACTIONr_long_range_B_refined7.28717.533805
X-RAY DIFFRACTIONr_long_range_B_other7.16214.1023625
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 108 -
Rwork0.259 2320 -
obs--76.79 %
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)
16.193-1.3462-7.70280.7849-0.235817.0596-0.0178-0.07470.6350.32470.2745-0.2453-1.1507-0.8038-0.25670.28770.1177-0.01830.21190.00790.2423-34.59232.9018.323
25.0702-0.51442.62554.087-0.52232.84040.00311.0271-0.24040.2681-0.0492-0.7928-0.14850.79130.04610.0399-0.0187-0.09750.2561-0.04110.2911-8.48227.17810.776
34.3389-0.41523.8831.56240.47483.95570.06990.21980.0938-0.1459-0.0471-0.2483-0.04150.2103-0.02270.0733-0.0394-0.02170.12850.0680.0806-17.64131.7242.571
43.26740.3020.35823.82170.61234.05960.0079-0.14580.19380.35310.0007-0.0649-0.3457-0.0875-0.00860.11050.0108-0.04440.0196-0.00870.0547-20.95731.47314.256
53.1925-2.21482.36892.9049-0.68825.8877-0.1847-0.34220.29160.43270.3072-0.1292-0.2588-0.5614-0.12260.22330.0252-0.07620.09160.05280.1856-11.72431.26817.79
63.419-1.74520.72742.2918-1.26060.8621-0.13860.33170.47390.1268-0.123-0.4057-0.13170.12060.26150.0529-0.0415-0.05310.07720.0670.1038-10.9219.91613.412
74.1904-2.34312.065913.13530.55883.5094-0.02460.1547-0.36160.45780.0438-0.32320.44490.1343-0.01920.08640.02320.02630.18440.02880.11317.163-4.0324.196
82.4419-1.01680.76516.82190.94721.4153-0.10220.35830.2333-0.292-0.0447-0.5333-0.00810.34860.14690.0998-0.01070.00610.25090.06320.10297.0913.20717.868
96.3373-4.505-2.08619.52292.04462.47530.0907-0.30750.04870.2705-0.0328-0.46630.1528-0.0516-0.0580.1205-0.0139-0.02730.07060.03260.044-28.1950.82117.496
102.79540.51432.72775.87480.15324.5185-0.04990.1501-0.03560.126-0.01660.1182-0.1562-0.14090.06650.01710.0076-0.0110.0567-0.01510.0193-26.33713.89610.534
112.0796-1.6484-0.14596.13412.84825.55410.03680.137-0.1133-0.0469-0.19120.1433-0.1128-0.28470.15440.01610.006-0.01160.077-0.01330.0134-34.3868.7879.35
122.1441-1.88370.169210.6739-0.66291.5064-0.04240.0099-0.10230.6165-0.00810.1047-0.0536-0.1210.05050.0477-0.0174-0.0060.09780.00610.015-26.35310.64415.148
135.79861.8823.13232.44281.2462.1910.00450.11360.0845-0.0491-0.0539-0.0533-0.0620.08570.04940.05270.0163-0.03150.0560.00640.0328-0.928-3.47429.757
142.69270.94710.29390.41910.94688.40480.08520.0054-0.18390.0467-0.0269-0.06630.2753-0.5325-0.05840.17350.007-0.05360.1204-0.01520.0893-2.7591.31938.061
155.78781.06244.0822.19750.97364.51770.01590.15030.08170.075-0.0737-0.06520.00180.25150.05790.02070.0178-0.00070.0569-0.00050.03290.219-1.59931.779
1617.49372.64636.51283.16080.63993.80610.55870.0011-0.82070.1283-0.1442-0.19210.42190.1129-0.41440.14360.0116-0.010.0721-0.01510.1044-0.968-10.80534.699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN F AND RESID 1:9 )F1 - 9
2X-RAY DIFFRACTION2( CHAIN H AND RESID 1:17 )H1 - 17
3X-RAY DIFFRACTION3( CHAIN H AND RESID 18:32 )H18 - 32
4X-RAY DIFFRACTION4( CHAIN H AND RESID 33:76 )H33 - 76
5X-RAY DIFFRACTION5( CHAIN H AND RESID 77:91 )H77 - 91
6X-RAY DIFFRACTION6( CHAIN H AND RESID 92:130 )H92 - 130
7X-RAY DIFFRACTION7( CHAIN H AND RESID 131:151 )H131 - 151
8X-RAY DIFFRACTION8( CHAIN H AND RESID 152:221 )H152 - 221
9X-RAY DIFFRACTION9( CHAIN L AND RESID 9:25 )L9 - 25
10X-RAY DIFFRACTION10( CHAIN L AND RESID 26:48 )L26 - 48
11X-RAY DIFFRACTION11( CHAIN L AND RESID 49:75 )L49 - 75
12X-RAY DIFFRACTION12( CHAIN L AND RESID 76:107 )L76 - 107
13X-RAY DIFFRACTION13( CHAIN L AND RESID 108:150 )L108 - 150
14X-RAY DIFFRACTION14( CHAIN L AND RESID 151:163 )L151 - 163
15X-RAY DIFFRACTION15( CHAIN L AND RESID 164:197 )L164 - 197
16X-RAY DIFFRACTION16( CHAIN L AND RESID 198:213 )L198 - 213

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