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- PDB-6y8k: Crystal structure of CD137 in complex with the cyclic peptide BCY10916 -

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Basic information

Entry
Database: PDB / ID: 6y8k
TitleCrystal structure of CD137 in complex with the cyclic peptide BCY10916
Components
  • BCY10916
  • Tumor necrosis factor receptor superfamily member 9
KeywordsSIGNALING PROTEIN / TNFRSF9 / CD137 / 4-1BB / bicyclic peptide / Bicycle / BCY10916
Function / homology
Function and homology information


TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, 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 / Growth factor receptor cysteine-rich domain superfamily
Similarity search - Domain/homology
Chem-29N / ACETATE ION / Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å
AuthorsUpadhyaya, P. / Kublin, J. / Dods, R. / Kristensson, J. / Lahdenranta, J. / Kleyman, M. / Repash, E. / Ma, J. / Mudd, G. / Van Rietschoten, K. ...Upadhyaya, P. / Kublin, J. / Dods, R. / Kristensson, J. / Lahdenranta, J. / Kleyman, M. / Repash, E. / Ma, J. / Mudd, G. / Van Rietschoten, K. / Haines, E. / Harrison, H. / Beswick, P. / Chen, L. / McDonnell, K. / Battula, S. / Hurov, K. / Keen, N.
CitationJournal: J Immunother Cancer / Year: 2021
Title: Anticancer immunity induced by a synthetic tumor-targeted CD137 agonist.
Authors: Upadhyaya, P. / Lahdenranta, J. / Hurov, K. / Battula, S. / Dods, R. / Haines, E. / Kleyman, M. / Kristensson, J. / Kublin, J. / Lani, R. / Ma, J. / Mudd, G. / Repash, E. / Van Rietschoten, ...Authors: Upadhyaya, P. / Lahdenranta, J. / Hurov, K. / Battula, S. / Dods, R. / Haines, E. / Kleyman, M. / Kristensson, J. / Kublin, J. / Lani, R. / Ma, J. / Mudd, G. / Repash, E. / Van Rietschoten, K. / Stephen, T. / You, F. / Harrison, H. / Chen, L. / McDonnell, K. / Brandish, P. / Keen, N.
History
DepositionMar 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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
AAA: Tumor necrosis factor receptor superfamily member 9
PPP: BCY10916
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2079
Polymers19,5192
Non-polymers6887
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-42 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.470, 122.470, 122.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232
Components on special symmetry positions
IDModelComponents
11AAA-206-

NA

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AAAPPP

#1: Protein Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / CDw137 / T-cell antigen 4-1BB homolog / T-cell antigen ILA


Mass: 17765.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q07011
#2: Protein/peptide BCY10916


Mass: 1753.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BCY10916 / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 37 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-29N / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)triprop-2-en-1-one, bound form


Mass: 255.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.6
Details: 1.5 M lithium sulfate monohydrate, 0.1M sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.01→40.857 Å / Num. obs: 21496 / % possible obs: 100 % / Redundancy: 39.1 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.043 / Net I/σ(I): 45.7
Reflection shellResolution: 2.01→2.05 Å / Rmerge(I) obs: 2.216 / Num. unique obs: 1053 / CC1/2: 0.756 / Rrim(I) all: 2.244

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MI2

6mi2


Resolution: 2.011→40.857 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: FREE R-VALUE / ESU R: 0.156 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.314 1070 4.984 %
Rwork0.2831 --
all0.285 --
obs-21467 99.851 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.013 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.011→40.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 42 30 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131139
X-RAY DIFFRACTIONr_bond_other_d0.0370.018965
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.6731530
X-RAY DIFFRACTIONr_angle_other_deg2.4641.5952269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0545142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.80322.24158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88115179
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg39.94153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.678157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021274
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02219
X-RAY DIFFRACTIONr_nbd_refined0.2310.2257
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2340.2950
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2545
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.25
X-RAY DIFFRACTIONr_nbd_other0.2780.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.22
X-RAY DIFFRACTIONr_mcbond_it6.0766.366578
X-RAY DIFFRACTIONr_mcbond_other6.076.365577
X-RAY DIFFRACTIONr_mcangle_it8.1649.517716
X-RAY DIFFRACTIONr_mcangle_other8.1589.517717
X-RAY DIFFRACTIONr_scbond_it7.127.129561
X-RAY DIFFRACTIONr_scbond_other7.1137.127562
X-RAY DIFFRACTIONr_scangle_it9.77310.485814
X-RAY DIFFRACTIONr_scangle_other9.76710.484815
X-RAY DIFFRACTIONr_lrange_it12.3677.3621217
X-RAY DIFFRACTIONr_lrange_other12.36677.3591215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.011-2.0630.438730.3831488X-RAY DIFFRACTION99.872
2.063-2.1190.46620.381435X-RAY DIFFRACTION99.9332
2.119-2.1810.434670.3771401X-RAY DIFFRACTION99.9319
2.181-2.2480.449590.4211372X-RAY DIFFRACTION99.7908
2.248-2.3220.427700.4411317X-RAY DIFFRACTION99.4978
2.322-2.4030.486680.4161282X-RAY DIFFRACTION99.926
2.403-2.4940.439670.3971224X-RAY DIFFRACTION99.8453
2.494-2.5950.444720.3771181X-RAY DIFFRACTION100
2.595-2.7110.524580.3861167X-RAY DIFFRACTION100
2.711-2.8430.419550.3631098X-RAY DIFFRACTION99.9133
2.843-2.9970.373520.3541048X-RAY DIFFRACTION99.6377
2.997-3.1780.4570.342994X-RAY DIFFRACTION99.9049
3.178-3.3980.327610.318939X-RAY DIFFRACTION99.9001
3.398-3.670.31550.284874X-RAY DIFFRACTION100
3.67-4.020.26480.264819X-RAY DIFFRACTION100
4.02-4.4930.238300.202756X-RAY DIFFRACTION100
4.493-5.1870.233390.188669X-RAY DIFFRACTION100
5.187-6.350.24400.215571X-RAY DIFFRACTION100
6.35-8.9690.238230.218469X-RAY DIFFRACTION100
8.969-40.8570.325140.297293X-RAY DIFFRACTION97.4603

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