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- PDB-5ihl: STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 5ihl
TitleSTRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH 3H56-5 DAB
Components
  • 3H56-5 domain antibody (dAb)
  • Tumor necrosis factor receptor superfamily member 5
KeywordsIMMUNE SYSTEM/SIGNALING PROTEIN / CELL SURFACE RECEPTOR / DOMAIN ANTIBODY / ANTITUMOR / PROTEIN/PROTEIN INTERACTION / IMMUNE SYSTEM-SIGNALING PROTEIN complex
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 / 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 ...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 / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSheriff, S.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Functional Antagonism of Human CD40 Achieved by Targeting a Unique Species-Specific Epitope.
Authors: Yamniuk, A.P. / Suri, A. / Krystek, S.R. / Tamura, J. / Ramamurthy, V. / Kuhn, R. / Carroll, K. / Fleener, C. / Ryseck, R. / Cheng, L. / An, Y. / Drew, P. / Grant, S. / Suchard, S.J. / ...Authors: Yamniuk, A.P. / Suri, A. / Krystek, S.R. / Tamura, J. / Ramamurthy, V. / Kuhn, R. / Carroll, K. / Fleener, C. / Ryseck, R. / Cheng, L. / An, Y. / Drew, P. / Grant, S. / Suchard, S.J. / Nadler, S.G. / Bryson, J.W. / Sheriff, S.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Mar 24, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_cell_line ..._citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 5
B: 3H56-5 domain antibody (dAb)
D: Tumor necrosis factor receptor superfamily member 5
E: 3H56-5 domain antibody (dAb)
F: Tumor necrosis factor receptor superfamily member 5
G: 3H56-5 domain antibody (dAb)
H: Tumor necrosis factor receptor superfamily member 5
I: 3H56-5 domain antibody (dAb)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,81312
Polymers133,4298
Non-polymers3844
Water0
1
A: Tumor necrosis factor receptor superfamily member 5
B: 3H56-5 domain antibody (dAb)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6455
Polymers33,3572
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-11 kcal/mol
Surface area15340 Å2
MethodPISA
2
D: Tumor necrosis factor receptor superfamily member 5
E: 3H56-5 domain antibody (dAb)


Theoretical massNumber of molelcules
Total (without water)33,3572
Polymers33,3572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-12 kcal/mol
Surface area15230 Å2
MethodPISA
3
F: Tumor necrosis factor receptor superfamily member 5
G: 3H56-5 domain antibody (dAb)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4533
Polymers33,3572
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-11 kcal/mol
Surface area15070 Å2
MethodPISA
4
H: Tumor necrosis factor receptor superfamily member 5
I: 3H56-5 domain antibody (dAb)


Theoretical massNumber of molelcules
Total (without water)33,3572
Polymers33,3572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-12 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.600, 158.300, 200.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Tumor necrosis factor receptor superfamily member 5 / B-cell surface antigen CD40 / Bp50 / CD40L receptor / CDw40


Mass: 20084.449 Da / Num. of mol.: 4 / Fragment: Extra Cellular Domain (UNP residues 23-193)
Mutation: Protein produced with Asn 153 & Asn 180, but deglycosylated with PNGase F, which leaves Asp at those positions
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
#2: Antibody
3H56-5 domain antibody (dAb)


Mass: 13272.805 Da / Num. of mol.: 4 / Fragment: 3H56-5 dAb
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PDOM13 / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Sequence detailsTHE AUTHOR STATES THAT THE PROTEIN WAS EXPRESSED WITH ASN153 AND ASN180 (AND POST-TRANSLATIONAL ...THE AUTHOR STATES THAT THE PROTEIN WAS EXPRESSED WITH ASN153 AND ASN180 (AND POST-TRANSLATIONAL CARBOHYDRATE) AND THEN SUBJECTED TO PNGASE F CLEAVAGE WHICH REMOVES THE CARBOHYDRATE AND LEAVES ASP153 AND ASP180 RATHER THAN ASN.

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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: 4.66 Å3/Da / Density % sol: 73.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 80mM Tris-HCl, pH 8.5, 1.6M Ammonium dihydrogen phosphate, 20% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 4, 2009 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 37772 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 42.5 % / Biso Wilson estimate: 53.11 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 33.7
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 43.6 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 12.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF

1jma

2uwi

2aw2

1ncf


Resolution: 3.3→29.04 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.836 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 2.443 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.045 / SU Rfree Blow DPI: 0.486 / SU Rfree Cruickshank DPI: 0.496
RfactorNum. reflection% reflectionSelection details
Rfree0.298 953 2.78 %RANDOM
Rwork0.268 33355 --
obs0.269 34308 90.8 %-
Displacement parametersBiso mean: 79.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.3656 Å20 Å20 Å2
2---7.672 Å20 Å2
3---9.0375 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8271 0 20 0 8291
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018512HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.4311633HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2697SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes197HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1280HARMONIC5
X-RAY DIFFRACTIONt_it8512HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion23.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1149SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9756SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.4 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.454 82 2.6 %
Rwork0.3337 3076 -
all0.3366 3158 -
obs--90.8 %
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)
11.21721.10252.65760.43190.80311.4118-0.0822-0.1475-0.0456-0.01730.0291-0.06410.1074-0.39650.05310.0327-0.179-0.01020.345-0.3040.0243-22.354211.5121105.668
22.05880.6133-0.31414.4318-1.38366.39660.00180.3420.3745-0.0605-0.33450.1465-1.0885-0.00640.33270.1530.0248-0.3040.0521-0.2212-0.1679-5.388837.2118112.644
31.9092.4003-2.99130-1.94264.40430.1083-0.1320.37170.32840.06630.0540.0931-0.3241-0.17470.1019-0.15620.1970.2390.0176-0.0149-59.8421-19.3939101.194
44.41411.565-0.10814.94670.64839.6070.11-0.0876-0.2645-0.2527-0.2545-0.31540.31720.4550.14440.2601-0.1730.06160.43840.1563-0.439-72.781-46.6857112.328
50.23982.467-2.0071.8463-4.43643.5119-0.0973-0.01810.0407-0.3535-0.02930.35310.26650.09490.12660.1411-0.29060.05060.43840.1756-0.0523-22.95312.019445.9209
64.67851.50762.22893.2989-1.96511.8301-0.30510.1209-0.2720.06660.1448-0.51440.64240.29690.1603-0.03020.01390.00350.24230.2612-0.27342.154529.650638.0689
71.0332.2792.37461.31992.66185.3508-0.08280.13170.0152-0.35810.1101-0.05360.5537-0.156-0.02730.0579-0.304-0.25950.3336-0.1853-0.0749-52.784-26.225649.0339
85.00731.8698-1.34123.7121-0.06087.3325-0.0986-0.19950.25590.1855-0.25330.2236-1.08850.43750.35190.1778-0.2024-0.3040.064-0.3038-0.2461-80.2172-38.665138.0997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ E|* }
5X-RAY DIFFRACTION5{ F|* }
6X-RAY DIFFRACTION6{ G|* }
7X-RAY DIFFRACTION7{ H|* }
8X-RAY DIFFRACTION8{ I|* }

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