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

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Basic information

Entry
Database: PDB / ID: 5dmi
TitleStructure of the extracellular domain of the CD40 in complex with CHI220 FAB
Components
  • Chi220 Fab heavy chain
  • Chi220 Fab light chain
  • Tumor necrosis factor receptor superfamily member 5
KeywordsIMMUNE SYSTEM/SIGNALING PROTEIN / CELL SURFACE RECEPTOR / ANTIBODY-ANTIGEN COMPLEX / ANTITUMOR / IMMUNE SYSTEM-SIGNALING PROTEIN 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 / : / 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 / Immunoglobulins / Immunoglobulin-like ...Tumour necrosis factor receptor 5 / Tumour necrosis factor receptor 5, N-terminal / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 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
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
Revision 1.4Oct 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: Tumor necrosis factor receptor superfamily member 5
H: Chi220 Fab heavy chain
L: Chi220 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5475
Polymers67,3553
Non-polymers1922
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-47 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.152, 201.152, 63.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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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.: 1 / Fragment: Extracellular domain residues 23-193
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 Chi220 Fab heavy chain


Mass: 23908.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Chi220 Fab light chain


Mass: 23361.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 4.8 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 80mM sodiym acetate, pH 4.6, 1.6 M ammonium sulfate, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.69→201.15 Å / Num. obs: 14668 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 11.33 Å2 / Rsym value: 0.249 / Net I/σ(I): 13.2
Reflection shellResolution: 3.69→3.89 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 6.8 / Rejects: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X

1jma

2uwi

2aw2

1ncf

1tnr

2hev

2hey

3d85

2zpk

2o5x


Resolution: 3.69→32.64 Å / Cor.coef. Fo:Fc: 0.9002 / Cor.coef. Fo:Fc free: 0.8676 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.397
RfactorNum. reflection% reflectionSelection details
Rfree0.207 734 5.03 %RANDOM
Rwork0.1683 ---
obs0.1702 14605 99.77 %-
Displacement parametersBiso max: 121.46 Å2 / Biso mean: 42.89 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--8.9003 Å20 Å20 Å2
2---8.9003 Å20 Å2
3---17.8005 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: final / Resolution: 3.69→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 0 10 1 4012
Biso mean--103.29 16.25 -
Num. residues----534
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1329SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes604HARMONIC5
X-RAY DIFFRACTIONt_it4115HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion554SEMIHARMONIC5
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_contact4626SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4115HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5615HARMONIC21.39
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion25.24
LS refinement shellResolution: 3.69→3.98 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2283 152 5.18 %
Rwork0.172 2785 -
all0.175 2937 -
obs--98.89 %

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