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- PDB-7yxu: Crystal structure of agonistic antibody 1618 fab domain bound to ... -

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Basic information

Entry
Database: PDB / ID: 7yxu
TitleCrystal structure of agonistic antibody 1618 fab domain bound to human 4-1BB.
Components
  • Tumor necrosis factor receptor superfamily member 9
  • heavy chain of Fab
  • light chain of Fab
KeywordsIMMUNE SYSTEM / complex / Fab / tumor necrosis factor
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
: / trimethylamine oxide / Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsHakansson, M. / Rose, N. / Petersson, J. / Enell Smith, K. / Thorolfsson, M. / von Schantz, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol.Cancer Ther. / Year: 2023
Title: The Bispecific Tumor Antigen-Conditional 4-1BB x 5T4 Agonist, ALG.APV-527, Mediates Strong T-Cell Activation and Potent Antitumor Activity in Preclinical Studies.
Authors: Nelson, M.H. / Fritzell, S. / Miller, R. / Werchau, D. / Van Citters, D. / Nilsson, A. / Misher, L. / Ljung, L. / Bader, R. / Deronic, A. / Chunyk, A.G. / Schultz, L. / Varas, L.A. / Rose, N. ...Authors: Nelson, M.H. / Fritzell, S. / Miller, R. / Werchau, D. / Van Citters, D. / Nilsson, A. / Misher, L. / Ljung, L. / Bader, R. / Deronic, A. / Chunyk, A.G. / Schultz, L. / Varas, L.A. / Rose, N. / Hakansson, M. / Gross, J. / Furebring, C. / Pavlik, P. / Sundstedt, A. / Veitonmaki, N. / Ramos, H.J. / Sall, A. / Dahlman, A. / Bienvenue, D. / von Schantz, L. / McMahan, C.J. / Askmyr, M. / Hernandez-Hoyos, G. / Ellmark, P.
History
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: Tumor necrosis factor receptor superfamily member 9
H: heavy chain of Fab
L: light chain of Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9015
Polymers62,7713
Non-polymers1302
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-34 kcal/mol
Surface area26810 Å2
Unit cell
Length a, b, c (Å)65.064, 213.465, 54.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11H-577-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 15118.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA / Cell (production host): 293-6E / Cell line (production host): HEK / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q07011

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Antibody , 2 types, 2 molecules HL

#2: Antibody heavy chain of Fab


Mass: 24221.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Variant (production host): 293-6E
#3: Antibody light chain of Fab


Mass: 23430.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Variant (production host): 293-6E

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Non-polymers , 3 types, 280 molecules

#4: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl pH 8.5, 0.2 M trimethyloxide (TMAO), 20% (w/v) PEG 2000 monomethylether (MME) and 20 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.31→54.01 Å / Num. obs: 34026 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.97 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.9
Reflection shellResolution: 2.31→2.37 Å / Num. unique obs: 2403 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NNP, 6A3W

4nnp

6a3w


Resolution: 2.31→41.56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.274 / SU Rfree Blow DPI: 0.218 / SU Rfree Cruickshank DPI: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1721 5.07 %RANDOM
Rwork0.205 ---
obs0.208 33952 99.8 %-
Displacement parametersBiso max: 141.38 Å2 / Biso mean: 58.75 Å2 / Biso min: 32.44 Å2
Baniso -1Baniso -2Baniso -3
1--7.4579 Å20 Å20 Å2
2--7.8189 Å20 Å2
3----0.361 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.31→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 6 278 4551
Biso mean--68.14 56.2 -
Num. residues----566
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1474SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes743HARMONIC5
X-RAY DIFFRACTIONt_it4398HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion576SEMIHARMONIC5
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_contact4929SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4398HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5972HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion18.38
LS refinement shellResolution: 2.31→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.246 25 3.68 %
Rwork0.2434 655 -
all0.2435 680 -
obs--92.3 %
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)
11.05510.6916-0.46231.7666-0.678300.0056-0.007-0.0428-0.06370.0132-0.12430.06210.0531-0.01880.0115-0.0878-0.0058-0.027-0.0475-0.0826-14.5901-4.25-29.5566
21.81051.8803-1.01914.3909-2.61811.67260.3535-0.27690.37070.6514-0.27490.3119-0.4197-0.0477-0.07850.0514-0.10150.0656-0.0946-0.1117-0.0943-15.11439.964-18.7301
30.3678-2.7788-1.24244.68142.20560.0584-0.19890.0834-0.06980.54550.1602-0.21470.3616-0.03060.03870.13460.04180.0074-0.0043-0.00630.1757-4.3042-51.6884-14.6538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|1 - H|223 }H1 - 223
2X-RAY DIFFRACTION2{ L|1 - L|213 }L1 - 213
3X-RAY DIFFRACTION3{ A|26 - A|160 }A26 - 160

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