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- PDB-8yx9: CD40 in complex with Dacetuzumab Fab -

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Basic information

Entry
Database: PDB / ID: 8yx9
TitleCD40 in complex with Dacetuzumab Fab
Components
  • Dacetuzumab, Heavy chain
  • Dacetuzumab, light chain
  • Tumor necrosis factor receptor superfamily member 5
KeywordsIMMUNE SYSTEM / CD40 / Dacetuzumab / Bleselumab / agonist activity / tumor necrosis factor
Function / homology
Function and homology information


positive regulation of protein kinase C signaling / cellular response to erythropoietin / varicosity / B cell mediated immunity / positive regulation of interleukin-4-mediated signaling pathway / immune response-regulating cell surface receptor signaling pathway / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / CD40 receptor complex / positive regulation of isotype switching to IgG isotypes ...positive regulation of protein kinase C signaling / cellular response to erythropoietin / varicosity / B cell mediated immunity / positive regulation of interleukin-4-mediated signaling pathway / immune response-regulating cell surface receptor signaling pathway / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / CD40 receptor complex / positive regulation of isotype switching to IgG isotypes / defense response to protozoan / response to cobalamin / B cell activation / B cell proliferation / cellular response to interleukin-1 / response to type II interferon / positive regulation of endothelial cell apoptotic process / cell surface receptor signaling pathway via JAK-STAT / positive regulation of blood vessel endothelial cell migration / antigen binding / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / TNFR2 non-canonical NF-kB pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / platelet activation / intracellular calcium ion homeostasis / cellular response to mechanical stimulus / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cellular response to tumor necrosis factor / signaling receptor activity / cellular response to lipopolysaccharide / protein-containing complex assembly / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / inflammatory response / protein domain specific binding / external side of plasma membrane / neuronal cell body / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / enzyme binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 5 / Tumour necrosis factor receptor 5, 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
Tumor necrosis factor receptor superfamily member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCaaveiro, J.M.M. / Fernandez-Perez, J. / Tsumoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05090, 20H03228, 19H05766, 20H02531 Japan
Japan Agency for Medical Research and Development (AMED)JP20mk0101170, JP223fa627001, JP223fa727002 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab.
Authors: Asano, R. / Nakakido, M. / Perez, J.F. / Ise, T. / Caaveiro, J.M.M. / Nagata, S. / Tsumoto, K.
History
DepositionApr 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 16, 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
H: Dacetuzumab, Heavy chain
L: Dacetuzumab, light chain
B: Dacetuzumab, Heavy chain
C: Dacetuzumab, light chain
E: Dacetuzumab, Heavy chain
F: Dacetuzumab, light chain
G: Dacetuzumab, Heavy chain
I: Dacetuzumab, light chain
A: Tumor necrosis factor receptor superfamily member 5
D: Tumor necrosis factor receptor superfamily member 5
J: Tumor necrosis factor receptor superfamily member 5
K: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,24819
Polymers271,60312
Non-polymers6457
Water1,04558
1
H: Dacetuzumab, Heavy chain
L: Dacetuzumab, light chain
A: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0855
Polymers67,9013
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dacetuzumab, Heavy chain
C: Dacetuzumab, light chain
J: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0855
Polymers67,9013
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Dacetuzumab, Heavy chain
F: Dacetuzumab, light chain
D: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0855
Polymers67,9013
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Dacetuzumab, Heavy chain
I: Dacetuzumab, light chain
K: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9934
Polymers67,9013
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.194, 208.172, 198.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody
Dacetuzumab, Heavy chain


Mass: 23858.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Antibody / Cell line (production host): EXPI293 / Production host: Homo sapiens (human)
#2: Antibody
Dacetuzumab, light chain


Mass: 24025.658 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Antibody / Cell line (production host): EXPI293 / Production host: Homo sapiens (human)
#3: Protein
Tumor necrosis factor receptor superfamily member 5 / B-cell surface antigen CD40 / Bp50 / CD40L receptor / CDw40


Mass: 20016.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD40, TNFRSF5 / Cell line (production host): EXPI293 / Production host: Homo sapiens (human) / References: UniProt: P25942
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.78 Å3/Da / Density % sol: 67.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate tribasic pH 7.0 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.8 Å / Num. obs: 101033 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.042 / Net I/σ(I): 17.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4996 / CC1/2: 0.813 / Rpim(I) all: 0.375 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDS20220120data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.889 / SU B: 13.346 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.459 / ESU R Free: 0.313
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2617 4995 4.946 %
Rwork0.209 96004 -
all0.212 --
obs-100999 99.974 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 67.037 Å2
Baniso -1Baniso -2Baniso -3
1-3.065 Å20 Å2-0 Å2
2---4.423 Å20 Å2
3---1.359 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16768 0 42 58 16868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01217264
X-RAY DIFFRACTIONr_bond_other_d0.0020.01615549
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.80823488
X-RAY DIFFRACTIONr_angle_other_deg0.4751.73936072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.86652186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.196565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.748102735
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.79610703
X-RAY DIFFRACTIONr_chiral_restr0.0610.22629
X-RAY DIFFRACTIONr_chiral_restr_other0.0540.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023863
X-RAY DIFFRACTIONr_nbd_refined0.2040.22969
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.214137
X-RAY DIFFRACTIONr_nbtor_refined0.1790.28213
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.29130
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2354
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1120.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.233
X-RAY DIFFRACTIONr_nbd_other0.1580.2236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1020.227
X-RAY DIFFRACTIONr_mcbond_it4.7696.7198783
X-RAY DIFFRACTIONr_mcbond_other4.7676.7198783
X-RAY DIFFRACTIONr_mcangle_it7.38312.05610947
X-RAY DIFFRACTIONr_mcangle_other7.38312.05610948
X-RAY DIFFRACTIONr_scbond_it4.4946.8988481
X-RAY DIFFRACTIONr_scbond_other4.4936.8988482
X-RAY DIFFRACTIONr_scangle_it7.04812.58712538
X-RAY DIFFRACTIONr_scangle_other7.04812.58712539
X-RAY DIFFRACTIONr_lrange_it9.78662.7217851
X-RAY DIFFRACTIONr_lrange_other9.78562.7217852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.3624040.3297025X-RAY DIFFRACTION100
2.873-2.9510.363800.3226806X-RAY DIFFRACTION100
2.951-3.0360.3573600.2886612X-RAY DIFFRACTION99.9857
3.036-3.1290.333350.2646499X-RAY DIFFRACTION100
3.129-3.2310.2883060.2516269X-RAY DIFFRACTION100
3.231-3.3440.2922850.2446137X-RAY DIFFRACTION100
3.344-3.470.2912870.2415862X-RAY DIFFRACTION100
3.47-3.6110.2913060.2435657X-RAY DIFFRACTION100
3.611-3.7710.2652750.2245424X-RAY DIFFRACTION100
3.771-3.9540.2572870.25183X-RAY DIFFRACTION100
3.954-4.1660.2262440.1914968X-RAY DIFFRACTION100
4.166-4.4170.2182370.1634676X-RAY DIFFRACTION100
4.417-4.7190.1972210.1444458X-RAY DIFFRACTION100
4.719-5.0930.1922130.1424107X-RAY DIFFRACTION100
5.093-5.5740.2062080.1523813X-RAY DIFFRACTION100
5.574-6.2220.2711770.1863462X-RAY DIFFRACTION100
6.222-7.1660.2941750.1993063X-RAY DIFFRACTION100
7.166-8.7310.2191290.182634X-RAY DIFFRACTION100
8.731-12.1630.2221110.1792074X-RAY DIFFRACTION100
12.163-49.80.366550.3091275X-RAY DIFFRACTION99.9249

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