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- PDB-5dmj: Structure of the extracellular domain of the CD40 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5dmj
TitleStructure of the extracellular domain of the CD40 in complex with 3H56-5 DAB
Components
  • 3H65-5 domain antibody (dAb)
  • Tumor necrosis factor receptor superfamily member 5
KeywordsIMMUNE SYSTEM/SIGNALING PROTEIN / CELL SURFACE RECEPTOR / DOMAIN ANTIBODY / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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
DepositionSep 8, 2015Deposition 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 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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: 3H65-5 domain antibody (dAb)
D: Tumor necrosis factor receptor superfamily member 5
E: 3H65-5 domain antibody (dAb)
F: Tumor necrosis factor receptor superfamily member 5
G: 3H65-5 domain antibody (dAb)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1899
Polymers100,0726
Non-polymers1173
Water23413
1
A: Tumor necrosis factor receptor superfamily member 5
B: 3H65-5 domain antibody (dAb)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3963
Polymers33,3572
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-10 kcal/mol
Surface area14670 Å2
MethodPISA
2
D: Tumor necrosis factor receptor superfamily member 5
E: 3H65-5 domain antibody (dAb)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3963
Polymers33,3572
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-8 kcal/mol
Surface area14980 Å2
MethodPISA
3
F: Tumor necrosis factor receptor superfamily member 5
G: 3H65-5 domain antibody (dAb)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3963
Polymers33,3572
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.300, 48.700, 138.800
Angle α, β, γ (deg.)90.000, 118.200, 90.000
Int Tables number5
Space group name H-MC121

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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.: 3 / Mutation: D153, D180
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 3H65-5 domain antibody (dAb)


Mass: 13272.805 Da / Num. of mol.: 3
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 100mM Citric Acid, pH 3.5, 20% (w/v) PEG 4000, 200 mM potassium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 29303 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 66.59 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.4 / Rejects: 0 / % possible all: 98

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; DAB FROM 2VYR

1jma

2uwi

2aw2

1ncf

1tnr

2hev

2hey

2vyr


Resolution: 2.79→46.26 Å / Cor.coef. Fo:Fc: 0.8641 / Cor.coef. Fo:Fc free: 0.8508 / SU R Cruickshank DPI: 0.734 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.698 / SU Rfree Blow DPI: 0.324 / SU Rfree Cruickshank DPI: 0.33
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 1036 3.54 %RANDOM
Rwork0.2288 28263 --
obs0.2299 29299 98.1 %-
Displacement parametersBiso max: 151.62 Å2 / Biso mean: 56.91 Å2 / Biso min: 6.06 Å2
Baniso -1Baniso -2Baniso -3
1--9.7752 Å20 Å2-20.4608 Å2
2---1.4444 Å20 Å2
3---11.2196 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.79→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6137 0 3 13 6153
Biso mean--50.7 29.29 -
Num. residues----844
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1993SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes138HARMONIC2
X-RAY DIFFRACTIONt_gen_planes955HARMONIC5
X-RAY DIFFRACTIONt_it6315HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion858SEMIHARMONIC5
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_contact6927SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6315HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8637HARMONIC21.36
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion22.05
LS refinement shellResolution: 2.79→2.89 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3047 107 3.94 %
Rwork0.2827 2610 -
all0.2835 2717 -
obs--92.74 %

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