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- PDB-8yx1: CD40 in complex with Bleselumab Fab -

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Basic information

Entry
Database: PDB / ID: 8yx1
TitleCD40 in complex with Bleselumab Fab
Components
  • Bleselumab, heavy chain
  • Bleselumab, 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


CD154 receptor binding / cellular response to erythropoietin / response to peptide / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / positive regulation of protein kinase C signaling / CD40 signaling pathway / varicosity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of isotype switching to IgG isotypes ...CD154 receptor binding / cellular response to erythropoietin / response to peptide / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / positive regulation of protein kinase C signaling / CD40 signaling pathway / varicosity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of isotype switching to IgG isotypes / CD40 receptor complex / TRIF-dependent toll-like receptor signaling pathway / positive regulation of endothelial cell apoptotic process / B cell activation / response to cobalamin / B cell proliferation / response to type II interferon / defense response to protozoan / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-1 / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / antigen binding / TNFR2 non-canonical NF-kB pathway / positive regulation of MAP kinase activity / platelet activation / positive regulation of GTPase activity / intracellular calcium ion homeostasis / cellular response to mechanical stimulus / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / cellular response to lipopolysaccharide / inflammatory response / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / intracellular membrane-bounded organelle / neuronal cell body / 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: 2.7 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 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Bleselumab, heavy chain
L: Bleselumab, light chain
R: Tumor necrosis factor receptor superfamily member 5
A: Bleselumab, heavy chain
B: Bleselumab, light chain
C: Tumor necrosis factor receptor superfamily member 5


Theoretical massNumber of molelcules
Total (without water)134,9456
Polymers134,9456
Non-polymers00
Water45025
1
H: Bleselumab, heavy chain
L: Bleselumab, light chain
R: Tumor necrosis factor receptor superfamily member 5


Theoretical massNumber of molelcules
Total (without water)67,4723
Polymers67,4723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bleselumab, heavy chain
B: Bleselumab, light chain
C: Tumor necrosis factor receptor superfamily member 5


Theoretical massNumber of molelcules
Total (without water)67,4723
Polymers67,4723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.565, 116.002, 121.651
Angle α, β, γ (deg.)90.000, 91.713, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Bleselumab, heavy chain


Mass: 24351.355 Da / Num. of mol.: 2
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 Bleselumab, light chain


Mass: 23104.572 Da / Num. of mol.: 2
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.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium chloride 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: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.56 Å / Num. obs: 37822 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.059 / Net I/σ(I): 12.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4604 / CC1/2: 0.824 / Rpim(I) all: 0.537 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDS20210323data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.56 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU B: 37.372 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R: 2.158 / ESU R Free: 0.361
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2651 1858 4.915 %
Rwork0.204 35944 -
all0.207 --
obs-37802 99.865 %
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: 52.149 Å2
Baniso -1Baniso -2Baniso -3
1--1.872 Å20 Å2-1.951 Å2
2--2.942 Å20 Å2
3----0.952 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8812 0 0 25 8837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0129042
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168165
X-RAY DIFFRACTIONr_angle_refined_deg1.561.80712317
X-RAY DIFFRACTIONr_angle_other_deg0.5371.73618992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.50251154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.349528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.614101442
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.88610349
X-RAY DIFFRACTIONr_chiral_restr0.0690.21390
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021952
X-RAY DIFFRACTIONr_nbd_refined0.2020.21508
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.27486
X-RAY DIFFRACTIONr_nbtor_refined0.1810.24344
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.24851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2190
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.219
X-RAY DIFFRACTIONr_nbd_other0.2310.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0930.25
X-RAY DIFFRACTIONr_mcbond_it2.0143.1424646
X-RAY DIFFRACTIONr_mcbond_other2.0133.1424646
X-RAY DIFFRACTIONr_mcangle_it3.2625.6395790
X-RAY DIFFRACTIONr_mcangle_other3.2625.6395791
X-RAY DIFFRACTIONr_scbond_it2.1583.2844396
X-RAY DIFFRACTIONr_scbond_other2.1583.2844397
X-RAY DIFFRACTIONr_scangle_it3.5385.9656527
X-RAY DIFFRACTIONr_scangle_other3.5385.9656528
X-RAY DIFFRACTIONr_lrange_it5.08830.4349323
X-RAY DIFFRACTIONr_lrange_other5.08930.4369323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.3941420.3282665X-RAY DIFFRACTION100
2.77-2.8460.3621300.3052543X-RAY DIFFRACTION99.9252
2.846-2.9280.3621480.2842519X-RAY DIFFRACTION100
2.928-3.0170.351340.2722370X-RAY DIFFRACTION99.8803
3.017-3.1160.371280.2692401X-RAY DIFFRACTION100
3.116-3.2250.3351170.2472247X-RAY DIFFRACTION99.9577
3.225-3.3460.2911200.2372202X-RAY DIFFRACTION99.957
3.346-3.4820.2971120.2222133X-RAY DIFFRACTION99.9555
3.482-3.6360.29910.2162042X-RAY DIFFRACTION100
3.636-3.8120.251840.2122001X-RAY DIFFRACTION99.9521
3.812-4.0160.2491170.1951803X-RAY DIFFRACTION100
4.016-4.2580.191670.1541766X-RAY DIFFRACTION100
4.258-4.5490.227980.1371654X-RAY DIFFRACTION100
4.549-4.910.1881040.1381527X-RAY DIFFRACTION100
4.91-5.3720.204520.1431434X-RAY DIFFRACTION99.9327
5.372-5.9960.23610.1621297X-RAY DIFFRACTION100
5.996-6.9030.198570.1811153X-RAY DIFFRACTION100
6.903-8.4070.295470.187986X-RAY DIFFRACTION99.9033
8.407-11.6920.161350.167761X-RAY DIFFRACTION99.7494
11.692-45.560.22140.264440X-RAY DIFFRACTION93.8017
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)
10.9764-0.28220.4940.5211-0.31611.8666-0.0442-0.2562-0.02560.10440.0934-0.0498-0.1878-0.0899-0.04920.0330.0015-0.00220.1591-0.02980.022-12.1287-4.01076.4857
20.8058-0.07830.44110.8791-0.93392.5621-0.014-0.1048-0.14980.0702-0.0097-0.08280.15740.19790.02370.04520.0466-0.00670.2012-0.03230.05930.6094-17.30933.1815
31.4976-1.5661-1.92281.67652.05452.5798-0.113-0.1033-0.17460.0785-0.02730.20410.0069-0.01140.14030.26550.00470.03830.37490.02710.2127-32.458518.0663-10.7092
40.96290.0266-0.32850.6188-0.39382.0751-0.00890.2837-0.1155-0.1588-0.026-0.02570.1527-0.04250.03490.09420.0555-0.07360.262-0.11980.1388-34.8494-5.86-67.2428
51.15620.2185-0.010.4922-0.06932.4411-0.02230.27730.1891-0.1492-0.03370.08-0.3220.14980.0560.10820.0402-0.05630.2388-0.05120.1061-22.15517.7601-65.2113
62.75182.26683.06891.89082.50353.45960.0373-0.17350.1345-0.0449-0.16170.16540.144-0.2340.12440.2949-0.0048-0.08870.4749-0.05430.4035-57.8885-26.8963-50.466
Refinement TLS groupSelection: ALL

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