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- PDB-6pe8: Crystal structure of CD40/ABBV-323 FAB complex -

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Basic information

Entry
Database: PDB / ID: 6pe8
TitleCrystal structure of CD40/ABBV-323 FAB complex
Components
  • FAB Heavy chain
  • FAB Light chain
  • Tumor necrosis factor receptor superfamily member 5
KeywordsIMMUNE SYSTEM / CD40 / FAB / complex
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: 2.84 Å
AuthorsArgiriadi, M.A.
CitationJournal: BMC Mol Cell Biol / Year: 2019
Title: CD40/anti-CD40 antibody complexes which illustrate agonist and antagonist structural switches.
Authors: Argiriadi, M.A. / Benatuil, L. / Dubrovska, I. / Egan, D.A. / Gao, L. / Greischar, A. / Hardman, J. / Harlan, J. / Iyer, R.B. / Judge, R.A. / Lake, M. / Perron, D.C. / Sadhukhan, R. / ...Authors: Argiriadi, M.A. / Benatuil, L. / Dubrovska, I. / Egan, D.A. / Gao, L. / Greischar, A. / Hardman, J. / Harlan, J. / Iyer, R.B. / Judge, R.A. / Lake, M. / Perron, D.C. / Sadhukhan, R. / Sielaff, B. / Sousa, S. / Wang, R. / McRae, B.L.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / software
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.2Oct 23, 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
A: FAB Heavy chain
B: FAB Light chain
H: FAB Heavy chain
L: FAB Light chain
T: Tumor necrosis factor receptor superfamily member 5
U: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,83810
Polymers134,4546
Non-polymers3844
Water2,720151
1
A: FAB Heavy chain
B: FAB Light chain
U: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4195
Polymers67,2273
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: FAB Heavy chain
L: FAB Light chain
T: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4195
Polymers67,2273
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.308, 75.959, 126.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody FAB Heavy chain


Mass: 23748.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody FAB Light chain


Mass: 24290.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD40, TNFRSF5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P25942
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion / Details: 2M ammonium sulfate, 0.1M phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→173.2 Å / Num. obs: 40335 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 15.8
Reflection shellResolution: 2.84→2.85 Å / Num. unique obs: 380 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PE7

6pe7


Resolution: 2.84→37.98 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 27.69 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2653 1925 4.8 %
Rwork0.2052 --
obs0.2081 40063 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8968 0 20 151 9139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019243
X-RAY DIFFRACTIONf_angle_d1.12512591
X-RAY DIFFRACTIONf_dihedral_angle_d3.3236279
X-RAY DIFFRACTIONf_chiral_restr0.0561405
X-RAY DIFFRACTIONf_plane_restr0.0061616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.9110.4421150.31352704X-RAY DIFFRACTION100
2.911-2.98970.35161350.27762671X-RAY DIFFRACTION100
2.9897-3.07760.37391420.25262686X-RAY DIFFRACTION100
3.0776-3.17690.32241540.23732662X-RAY DIFFRACTION100
3.1769-3.29040.32791590.23262698X-RAY DIFFRACTION100
3.2904-3.42210.31411250.23192679X-RAY DIFFRACTION100
3.4221-3.57770.29771450.20192680X-RAY DIFFRACTION100
3.5777-3.76620.25921190.1952733X-RAY DIFFRACTION100
3.7662-4.00190.24981330.18212721X-RAY DIFFRACTION100
4.0019-4.31050.19891390.16322710X-RAY DIFFRACTION100
4.3105-4.74350.19891360.15132749X-RAY DIFFRACTION100
4.7435-5.42820.20571600.16832731X-RAY DIFFRACTION100
5.4282-6.83250.2771280.21042787X-RAY DIFFRACTION100
6.8325-37.98290.2811350.24432927X-RAY DIFFRACTION100

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