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- PDB-8ds5: X-ray structure of the MK5890 Fab - CD27 antibody-antigen complex -

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Basic information

Entry
Database: PDB / ID: 8ds5
TitleX-ray structure of the MK5890 Fab - CD27 antibody-antigen complex
Components
  • CD27 antigen
  • MK-5890 Fab heavy chain
  • MK-5890 Fab light chain
KeywordsIMMUNE SYSTEM / Complex
Function / homology
Function and homology information


TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / positive regulation of T cell differentiation / positive regulation of B cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / immunoglobulin mediated immune response / extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity ...TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / positive regulation of T cell differentiation / positive regulation of B cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / immunoglobulin mediated immune response / extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity / response to ethanol / cell surface receptor signaling pathway / external side of plasma membrane / negative regulation of apoptotic process / extracellular region / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 7 / Tumour necrosis factor receptor 7, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.926 Å
AuthorsFischmann, T.O.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J Immunother Cancer / Year: 2022
Title: Preclinical characterization and clinical translation of pharmacodynamic markers for MK-5890: a human CD27 activating antibody for cancer immunotherapy.
Authors: Guelen, L. / Fischmann, T.O. / Wong, J. / Mauze, S. / Guadagnoli, M. / Babala, N. / Wagenaars, J. / Juan, V. / Rosen, D. / Prosise, W. / Habraken, M. / Lodewijks, I. / Gu, D. / Stammen- ...Authors: Guelen, L. / Fischmann, T.O. / Wong, J. / Mauze, S. / Guadagnoli, M. / Babala, N. / Wagenaars, J. / Juan, V. / Rosen, D. / Prosise, W. / Habraken, M. / Lodewijks, I. / Gu, D. / Stammen-Vogelzangs, J. / Yu, Y. / Baker, J. / Lutje Hulsik, D. / Driessen-Engels, L. / Malashock, D. / Kreijtz, J. / Bertens, A. / de Vries, E. / Bovens, A. / Bramer, A. / Zhang, Y. / Wnek, R. / Troth, S. / Chartash, E. / Dobrenkov, K. / Sadekova, S. / van Elsas, A. / Cheung, J.K. / Fayadat-Dilman, L. / Borst, J. / Beebe, A.M. / Van Eenennaam, H.
History
DepositionJul 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD27 antigen
B: MK-5890 Fab light chain
C: MK-5890 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,90610
Polymers65,8173
Non-polymers1,0897
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.246, 126.105, 131.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-10100-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CD27 antigen / CD27L receptor / T-cell activation antigen CD27 / T14 / Tumor necrosis factor receptor superfamily member 7


Mass: 18459.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD27, TNFRSF7 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Expi293 / References: UniProt: P26842

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Antibody , 2 types, 2 molecules BC

#2: Antibody MK-5890 Fab light chain


Mass: 23426.932 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) / Strain (production host): Expi293
#3: Antibody MK-5890 Fab heavy chain


Mass: 23929.734 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) / Strain (production host): Expi293

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Non-polymers , 3 types, 282 molecules

#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.6 Å3/Da / Density % sol: 65.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris Cl pH 8.5, 40% v/v PEG400, 8.0mM CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.926→52.4 Å / Num. obs: 45883 / % possible obs: 91.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.927-2.10560.9521369322950.7180.4081.0381.662.6
6.218-52.46.10.0391393722930.9980.0170.04339.899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTER2.11.7 (23-SEP-2019)refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XTJ

2xtj


Resolution: 1.926→22 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 2190 4.78 %RANDOM
Rwork0.2093 ---
obs0.2101 45831 63.8 %-
Displacement parametersBiso max: 123.99 Å2 / Biso mean: 59.95 Å2 / Biso min: 24.74 Å2
Baniso -1Baniso -2Baniso -3
1-6.0659 Å20 Å20 Å2
2---3.3694 Å20 Å2
3----2.6966 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 1.926→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 309 0 4289
Biso mean--51.45 --
Num. residues----520
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1678SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1266HARMONIC5
X-RAY DIFFRACTIONt_it4127HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion539SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4691SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7969HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg14319HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion16.05
LS refinement shellResolution: 1.93→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2759 42 4.58 %
Rwork0.2257 875 -
all0.228 917 -
obs--9.69 %
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)
15.6075-1.78970.44475.2766-0.47922.27880.1166-0.0958-0.20190.0475-0.0721-0.05350.0292-0.0982-0.0444-0.0593-0.01450.0309-0.2580.0191-0.171-6.4342-54.516532.877
20.2902-0.4140.00833.8549-0.73961.04550.0146-0.2340.06060.3143-0.1482-0.7978-0.31140.38370.1336-0.1296-0.0817-0.0859-0.11370.0335-0.0656-17.1825-2.284819.1054
31.0999-1.04130.34754.5334-1.03241.8077-0.0154-0.1378-0.15680.05320.06180.1307-0.11920.0213-0.0464-0.0724-0.0143-0.0112-0.10610.0122-0.2054-32.6154-11.389115.6993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A26 - 9922
2X-RAY DIFFRACTION2{ B|* }B1 - 9911
3X-RAY DIFFRACTION3{ C|* }C1 - 9902

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