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- PDB-6fax: Complex of Human CD40 Ectodomain with Lob 7.4 Fab -

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Basic information

Entry
Database: PDB / ID: 6fax
TitleComplex of Human CD40 Ectodomain with Lob 7.4 Fab
Components
  • Lob 7.4 heavy chain
  • Lob 7.4 light chain
  • Tumor necrosis factor receptor superfamily member 5
KeywordsIMMUNE SYSTEM / CD40 / engineered Fab / agonist / mAb
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 / : / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 ...Tumour necrosis factor receptor 5 / Tumour necrosis factor receptor 5, N-terminal / : / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.99 Å
AuthorsOrr, C.M. / Tews, I. / Pearson, A.R.
Funding support Germany, United Kingdom, 6items
OrganizationGrant numberCountry
German Research Foundation Germany
German Federal Excellence Cluste Germany
Institute for Life Sciences, University of Southampton United Kingdom
Antibody and Vaccine Group, United Kingdom
Cancer Research UK Antibody Programme United Kingdom
European Union602262-2
CitationJournal: Cancer Cell / Year: 2018
Title: Complex Interplay between Epitope Specificity and Isotype Dictates the Biological Activity of Anti-human CD40 Antibodies.
Authors: Yu, X. / Chan, H.T.C. / Orr, C.M. / Dadas, O. / Booth, S.G. / Dahal, L.N. / Penfold, C.A. / O'Brien, L. / Mockridge, C.I. / French, R.R. / Duriez, P. / Douglas, L.R. / Pearson, A.R. / Cragg, ...Authors: Yu, X. / Chan, H.T.C. / Orr, C.M. / Dadas, O. / Booth, S.G. / Dahal, L.N. / Penfold, C.A. / O'Brien, L. / Mockridge, C.I. / French, R.R. / Duriez, P. / Douglas, L.R. / Pearson, A.R. / Cragg, M.S. / Tews, I. / Glennie, M.J. / White, A.L.
History
DepositionDec 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Lob 7.4 light chain
H: Lob 7.4 heavy chain
R: Tumor necrosis factor receptor superfamily member 5


Theoretical massNumber of molelcules
Total (without water)68,5153
Polymers68,5153
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-30 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.753, 158.753, 93.622
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody Lob 7.4 light chain


Mass: 23463.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Lob 7.4 heavy chain


Mass: 25864.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 141 - 146 not visible in electron density. Pre crystallisation, construct was treated with pepsin, expected cleavage site ~ residue 240. Residues 227 onwards are not visible in the electron density.
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Tumor necrosis factor receptor superfamily member 5 / B-cell surface antigen CD40 / Bp50 / CD40L receptor / CDw40


Mass: 19187.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1 - 20 are post-translationally cleaved. Residues 124 - 194 are not visible in the electron density
Source: (gene. exp.) Homo sapiens (human) / Gene: CD40, TNFRSF5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P25942
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2745.86
22.2745.86
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting dropNA
2932vapor diffusion, hanging dropNA

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.976254
SYNCHROTRONESRF ID23-120.969995
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELApr 4, 2015
DECTRIS PILATUS 6M-F2PIXELApr 5, 2015
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2Si111SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9762541
20.9699951
ReflectionResolution: 2.99→52 Å / Num. obs: 27589 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.161 / Net I/σ(I): 13.7
Reflection shellResolution: 2.99→3.18 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.912 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia20.4.0.338-g7e19e23-dials-1.2data reduction
Aimless0.5.27data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U6A

1u6a


Resolution: 2.99→137.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.084 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.277 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23121 1319 4.8 %RANDOM
Rwork0.18482 ---
obs0.18707 26355 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 84.715 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å21.3 Å20 Å2
2--2.59 Å20 Å2
3----8.41 Å2
Refinement stepCycle: 1 / Resolution: 2.99→137.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 0 21 4078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024166
X-RAY DIFFRACTIONr_bond_other_d0.0020.023642
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.9485668
X-RAY DIFFRACTIONr_angle_other_deg1.15438546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7475.076529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45425.116172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.715682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5821512
X-RAY DIFFRACTIONr_chiral_restr0.1080.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214606
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02794
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.1488.4252109
X-RAY DIFFRACTIONr_mcbond_other7.1358.4222108
X-RAY DIFFRACTIONr_mcangle_it10.21712.6232631
X-RAY DIFFRACTIONr_mcangle_other10.21512.6272632
X-RAY DIFFRACTIONr_scbond_it8.258.9322057
X-RAY DIFFRACTIONr_scbond_other8.258.9352058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.56113.143038
X-RAY DIFFRACTIONr_long_range_B_refined14.05896.6024385
X-RAY DIFFRACTIONr_long_range_B_other14.05796.6284386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.992→3.069 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 78 -
Rwork0.362 1866 -
obs--95.81 %

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