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- PDB-3qd6: Crystal structure of the CD40 and CD154 (CD40L) complex -

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Basic information

Entry
Database: PDB / ID: 3qd6
TitleCrystal structure of the CD40 and CD154 (CD40L) complex
Components
  • CD40 ligand
  • Tumor necrosis factor receptor superfamily member 5
KeywordsCYTOKINE/CYTOKINE RECEPTOR / Immune regulator / receptor / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


CD154 receptor binding / cellular response to erythropoietin / CD40 receptor binding / 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 ...CD154 receptor binding / cellular response to erythropoietin / CD40 receptor binding / 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 / isotype switching / tumor necrosis factor receptor binding / regulation of immunoglobulin production / leukocyte cell-cell adhesion / B cell activation / response to cobalamin / positive regulation of interleukin-4 production / B cell proliferation / defense response to protozoan / response to type II interferon / positive regulation of interleukin-10 production / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-1 / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / T cell costimulation / positive regulation of interleukin-12 production / protein serine/threonine kinase activator activity / B cell differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of GTPase activity / cytokine activity / TNFR2 non-canonical NF-kB pathway / integrin-mediated signaling pathway / antigen binding / positive regulation of MAP kinase activity / 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 / integrin binding / cellular response to tumor necrosis factor / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / protein-containing complex assembly / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / 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 / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
CD40 ligand / 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 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain ...CD40 ligand / 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 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 5 / CD40 ligand
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsLee, J.-O. / Kim, Y.J. / Song, D.H. / Kim, H.M. / Park, B.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystallographic and mutational analysis of the CD40-CD154 complex and its implications for receptor activation
Authors: An, H.-J. / Kim, Y.J. / Song, D.H. / Park, B.S. / Kim, H.M. / Lee, J.D. / Paik, S.-G. / Lee, J.-O. / Lee, H.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: CD40 ligand
B: CD40 ligand
C: CD40 ligand
D: CD40 ligand
E: CD40 ligand
F: CD40 ligand
R: Tumor necrosis factor receptor superfamily member 5
S: Tumor necrosis factor receptor superfamily member 5
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)176,01516
Polymers174,68810
Non-polymers1,3276
Water00
1
A: CD40 ligand
B: CD40 ligand
C: CD40 ligand
R: Tumor necrosis factor receptor superfamily member 5
S: Tumor necrosis factor receptor superfamily member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0088
Polymers87,3445
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: CD40 ligand
E: CD40 ligand
F: CD40 ligand
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)88,0088
Polymers87,3445
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.212, 133.212, 211.151
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
CD40 ligand / CD40-L


Mass: 16096.100 Da / Num. of mol.: 6 / Fragment: secreted form, soluble form
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD154, CD40L / Plasmid: pAcGP67A / Cell line (production host): HIGH FIVE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29965
#2: Protein
Tumor necrosis factor receptor superfamily member 5 / CD40L receptor


Mass: 19527.826 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD40 / Plasmid: pVL1393 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P25942
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.1 Å3/Da / Density % sol: 60.27 % / Mosaicity: 1.133 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG6000, 0.1M MOPS, 10% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 3.2→114.961 Å / Num. all: 24906 / Num. obs: 24906 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.5-3.692.50.5060.3512940937960.3080.5060.3512.297.6
3.69-3.912.50.3510.2473.1880335230.2110.3510.2473.296.9
3.91-4.182.50.2130.1445.2840333320.1270.2130.1445.296.4
4.18-4.522.50.1560.1067.2770330450.0920.1560.1067.595.2
4.52-4.952.60.1260.0849709027550.0740.1260.0849.693.4
4.95-5.532.60.1320.0928.1640624900.0760.1320.0929.692.7
5.53-6.392.60.1540.1036.3561921550.0890.1540.1031091.2
6.39-7.832.60.1320.0897.1456317590.0760.1320.08915.788.3
7.83-11.072.70.0760.0415.9359413310.0430.0760.0428.585.7
11.07-114.9612.80.1140.0464.520197200.0720.1140.04635.182.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.77 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å114.96 Å
Translation3.5 Å114.96 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER2.1.1phasing
CNS1.3refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ALY

1aly


Resolution: 3.5→114.961 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 3313622 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1209 4.9 %RANDOM
Rwork0.245 ---
obs0.245 24857 92.9 %-
all-26756 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5494 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 119.06 Å2 / Biso mean: 68.3904 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å20 Å20 Å2
2---2.61 Å20 Å2
3---5.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.5→114.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9812 0 84 0 9896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 220 5.3 %
Rwork0.265 3962 -
all-4182 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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