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- PDB-1rf3: Structurally Distinct Recognition Motifs in Lymphotoxin-B Recepto... -

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Basic information

Entry
Database: PDB / ID: 1rf3
TitleStructurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for TRAF-mediated Signaling
Components
  • 24-residue peptide from Lymphotoxin-B Receptor
  • TNF receptor associated factor 3
KeywordsSIGNALING PROTEIN / CD40 / NF-KB signaling / LTBR / TNF receptor / TRAF3 crystallography
Function / homology
Function and homology information


regulation of interferon-beta production / hematopoietic or lymphoid organ development / TRAF3 deficiency - HSE / Toll signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / serine/threonine protein kinase complex / CD40 receptor complex / myeloid dendritic cell differentiation / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway ...regulation of interferon-beta production / hematopoietic or lymphoid organ development / TRAF3 deficiency - HSE / Toll signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / serine/threonine protein kinase complex / CD40 receptor complex / myeloid dendritic cell differentiation / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / regulation of proteolysis / thioesterase binding / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / type I interferon-mediated signaling pathway / protein K63-linked ubiquitination / positive regulation of type I interferon production / ubiquitin ligase complex / regulation of cytokine production / TICAM1-dependent activation of IRF3/IRF7 / tumor necrosis factor-mediated signaling pathway / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / cellular response to mechanical stimulus / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / defense response to virus / protein phosphatase binding / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / endosome membrane / endosome / immune response / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / signal transduction / mitochondrion / zinc ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Tumour necrosis factor receptor 3 / Tumour necrosis factor receptor 3, N-terminal / : / TNF receptor-associated factor 2/3/5, RING domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. ...Tumour necrosis factor receptor 3 / Tumour necrosis factor receptor 3, N-terminal / : / TNF receptor-associated factor 2/3/5, RING domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / 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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 3 / TNF receptor-associated factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.5 Å
AuthorsLi, C. / Norris, P.S. / Ni, C.Z. / Havert, M.L. / Chiong, E.M. / Tran, B.R. / Cabezas, E. / Cheng, G. / Reed, J.C. / Satterthwait, A.C. ...Li, C. / Norris, P.S. / Ni, C.Z. / Havert, M.L. / Chiong, E.M. / Tran, B.R. / Cabezas, E. / Cheng, G. / Reed, J.C. / Satterthwait, A.C. / Ware, C.F. / Ely, K.R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structurally distinct recognition motifs in lymphotoxin-beta receptor and CD40 for tumor necrosis factor receptor-associated factor (TRAF)-mediated signaling.
Authors: Li, C. / Norris, P.S. / Ni, C.Z. / Havert, M.L. / Chiong, E.M. / Tran, B.R. / Cabezas, E. / Reed, J.C. / Satterthwait, A.C. / Ware, C.F. / Ely, K.R.
History
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TNF receptor associated factor 3
B: 24-residue peptide from Lymphotoxin-B Receptor


Theoretical massNumber of molelcules
Total (without water)25,4212
Polymers25,4212
Non-polymers00
Water0
1
A: TNF receptor associated factor 3
B: 24-residue peptide from Lymphotoxin-B Receptor

A: TNF receptor associated factor 3
B: 24-residue peptide from Lymphotoxin-B Receptor

A: TNF receptor associated factor 3
B: 24-residue peptide from Lymphotoxin-B Receptor


Theoretical massNumber of molelcules
Total (without water)76,2636
Polymers76,2636
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)83.700, 83.700, 79.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein TNF receptor associated factor 3 / / CD40 receptor associated factor 1 / CRAF1 / CD40 binding protein / CD40BP / LMP1 associated protein ...CD40 receptor associated factor 1 / CRAF1 / CD40 binding protein / CD40BP / LMP1 associated protein / LAP1 / CAP-1


Mass: 22904.287 Da / Num. of mol.: 1 / Fragment: Recognition motif (residues 377-568)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF3 OR CRAF1 OR CAP1 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q13114
#2: Protein/peptide 24-residue peptide from Lymphotoxin-B Receptor


Mass: 2516.669 Da / Num. of mol.: 1 / Fragment: Recognition motif (residues 385-408) / Source method: obtained synthetically
Details: The peptide was chemically synthesized, the sequence of the peptide occurs naturally in humans (Homo sapiens)
References: UniProt: P36941

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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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 18, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 4026 / Num. obs: 3177 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.43 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.12 / Net I/σ(I): 8
Reflection shellResolution: 3.5→3.63 Å / Mean I/σ(I) obs: 8 / Num. unique all: 390 / Rsym value: 0.38 / % possible all: 95

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1L0A

1l0a


Resolution: 3.5→8 Å / Isotropic thermal model: Engh & Huber / Cross valid method: Througout / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.315 163 -RANDOM
Rwork0.266 ---
all-3701 --
obs-3177 83 %-
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1-13.65 Å213.65 Å2-27.31 Å2
2---2.69 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 0 0 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_mcbond_it1.1291.5
X-RAY DIFFRACTIONc_mcangle_it1.9692
X-RAY DIFFRACTIONc_scbond_it1.5362
X-RAY DIFFRACTIONc_scangle_it2.5342.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
3.5-3.640.276190.262X-RAY DIFFRACTION4653
4.03-4.290.263460.236X-RAY DIFFRACTION6713
6-80.408380.307X-RAY DIFFRACTION6763
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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