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- PDB-6pe9: Crystal Structure of CD40 complexed to FAB516 -

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Basic information

Entry
Database: PDB / ID: 6pe9
TitleCrystal Structure of CD40 complexed to FAB516
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


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 / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / CD40 signaling pathway / CD40 receptor complex / positive regulation of isotype switching to IgG isotypes / response to cobalamin ...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 / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / CD40 signaling pathway / CD40 receptor complex / positive regulation of isotype switching to IgG isotypes / response to cobalamin / positive regulation of protein kinase C signaling / defense response to protozoan / B cell activation / B cell proliferation / positive regulation of endothelial cell apoptotic process / cellular response to interleukin-1 / positive regulation of blood vessel endothelial cell migration / cell surface receptor signaling pathway via JAK-STAT / response to type II interferon / 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 / cellular response to mechanical stimulus / platelet activation / positive regulation of angiogenesis / intracellular calcium ion homeostasis / 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: 3.13 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 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

Downloads & links

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Assembly

Deposited unit
A: FAB Heavy chain
B: FAB Light chain
C: FAB Heavy chain
D: FAB Light chain
E: FAB Heavy chain
F: FAB Light chain
G: Tumor necrosis factor receptor superfamily member 5
H: FAB Heavy chain
I: Tumor necrosis factor receptor superfamily member 5
J: Tumor necrosis factor receptor superfamily member 5
K: FAB Heavy chain
L: FAB Light chain
M: FAB Light chain
U: Tumor necrosis factor receptor superfamily member 5
V: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,55520
Polymers336,07515
Non-polymers4805
Water1,56787
1
A: FAB Heavy chain
B: FAB Light chain
hetero molecules

I: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4075
Polymers67,2153
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_757-x+5/2,y+1/2,-z+21
2
C: FAB Heavy chain
D: FAB Light chain
G: Tumor necrosis factor receptor superfamily member 5


Theoretical massNumber of molelcules
Total (without water)67,2153
Polymers67,2153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: FAB Heavy chain
F: FAB Light chain
U: Tumor necrosis factor receptor superfamily member 5


Theoretical massNumber of molelcules
Total (without water)67,2153
Polymers67,2153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: FAB Heavy chain
L: FAB Light chain
V: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5036
Polymers67,2153
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
J: Tumor necrosis factor receptor superfamily member 5
K: FAB Heavy chain
M: FAB Light chain


Theoretical massNumber of molelcules
Total (without water)67,2153
Polymers67,2153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)254.840, 224.035, 111.358
Angle α, β, γ (deg.)90.00, 98.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
FAB Heavy chain


Mass: 23780.588 Da / Num. of mol.: 5
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
FAB Light chain


Mass: 24246.926 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
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.: 5
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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.68 Å3/Da / Density % sol: 73.74 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion
Details: 1.6M Ammonium Sulfate 2% w/v PEG1000, 100 mM HEPES Sodium Salt pH 7.5

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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: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.13→167.5 Å / Num. obs: 108254 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.99 / Net I/σ(I): 11.2
Reflection shellResolution: 3.13→3.14 Å / Num. unique obs: 1044 / CC1/2: 0.76

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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: 6PE8

6pe8


Resolution: 3.13→35.338 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2552 5445 5.05 %
Rwork0.2162 --
obs0.2182 107879 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.13→35.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18506 0 25 87 18618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118980
X-RAY DIFFRACTIONf_angle_d1.13425872
X-RAY DIFFRACTIONf_dihedral_angle_d3.07511180
X-RAY DIFFRACTIONf_chiral_restr0.0612906
X-RAY DIFFRACTIONf_plane_restr0.0063323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.16560.37871700.31273452X-RAY DIFFRACTION100
3.1656-3.20280.3531580.29513451X-RAY DIFFRACTION100
3.2028-3.24180.32311870.28173350X-RAY DIFFRACTION100
3.2418-3.28280.3232060.27383443X-RAY DIFFRACTION100
3.2828-3.3260.32091960.26693415X-RAY DIFFRACTION100
3.326-3.37150.29441910.2693423X-RAY DIFFRACTION100
3.3715-3.41960.34591760.25483387X-RAY DIFFRACTION100
3.4196-3.47060.30462000.2543445X-RAY DIFFRACTION100
3.4706-3.52480.2931940.23533368X-RAY DIFFRACTION100
3.5248-3.58260.27361950.22533443X-RAY DIFFRACTION100
3.5826-3.64430.24911740.22893403X-RAY DIFFRACTION100
3.6443-3.71050.28171700.22343457X-RAY DIFFRACTION100
3.7105-3.78180.26851650.21773415X-RAY DIFFRACTION100
3.7818-3.85890.25381930.21293442X-RAY DIFFRACTION100
3.8589-3.94270.22632020.20083393X-RAY DIFFRACTION100
3.9427-4.03420.23061990.19463387X-RAY DIFFRACTION100
4.0342-4.1350.22051730.19323411X-RAY DIFFRACTION100
4.135-4.24660.19941680.18663436X-RAY DIFFRACTION99
4.2466-4.37130.2271710.17853405X-RAY DIFFRACTION99
4.3713-4.51220.21231690.17113421X-RAY DIFFRACTION99
4.5122-4.67310.21661850.17763412X-RAY DIFFRACTION99
4.6731-4.85970.20552010.17313420X-RAY DIFFRACTION99
4.8597-5.08030.23691720.1743425X-RAY DIFFRACTION99
5.0803-5.34730.22481910.18683413X-RAY DIFFRACTION100
5.3473-5.6810.20591460.1923452X-RAY DIFFRACTION99
5.681-6.11760.25451770.21433407X-RAY DIFFRACTION99
6.1176-6.72940.25561850.21923409X-RAY DIFFRACTION99
6.7294-7.69440.26821540.23223455X-RAY DIFFRACTION99
7.6944-9.66120.23151810.21363377X-RAY DIFFRACTION98
9.6612-35.34030.30171960.26933317X-RAY DIFFRACTION95

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