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- PDB-1zms: LMP1 Protein binds to TRAF3 as a structural CD40 -

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Basic information

Entry
Database: PDB / ID: 1zms
TitleLMP1 Protein binds to TRAF3 as a structural CD40
Components
  • Latent membrane protein 1
  • TNF receptor associated factor 3
KeywordsSIGNALING PROTEIN / CD40 / NF-kB signaling / LMP1 / TNF receptor / TRAF3
Function / homology
Function and homology information


: / regulation of interferon-beta production / TRAF3 deficiency - HSE / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / Toll signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / serine/threonine protein kinase complex / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway ...: / regulation of interferon-beta production / TRAF3 deficiency - HSE / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / Toll signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / serine/threonine protein kinase complex / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / regulation of proteolysis / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / transformation of host cell by virus / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / protein K63-linked ubiquitination / positive regulation of type I interferon production / ubiquitin ligase complex / regulation of cytokine production / tumor necrosis factor-mediated signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / 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 / regulation of apoptotic process / protein phosphatase binding / defense response to virus / membrane => GO:0016020 / endosome membrane / endosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / signal transduction / mitochondrion / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Herpesvirus latent membrane 1 / Herpesvirus latent membrane protein 1 (LMP1) / : / 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. ...Herpesvirus latent membrane 1 / Herpesvirus latent membrane protein 1 (LMP1) / : / 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 / 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
Latent membrane protein 1 / TNF receptor-associated factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWu, S.D. / Xie, P. / Welsh, K. / Li, C. / Ni, C.-Z. / Zhu, X. / Reed, J.C. / Satterthwait, A.C. / Bishop, G.A. / Ely, K.R.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: LMP1 protein from the Epstein Barr virus is a structural CD40 decoy in B lymphocytes fro binding to TRAF3
Authors: Wu, S.D. / Xie, P. / Welsh, K. / Li, C. / Ni, C.-Z. / Zhu, X. / Reed, J.C. / Satterthwait, A.C. / Bishop, G.A. / Ely, K.R.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: TNF receptor associated factor 3
B: Latent membrane protein 1


Theoretical massNumber of molelcules
Total (without water)22,7452
Polymers22,7452
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-3 kcal/mol
Surface area11830 Å2
MethodPISA
2
A: TNF receptor associated factor 3
B: Latent membrane protein 1

A: TNF receptor associated factor 3
B: Latent membrane protein 1

A: TNF receptor associated factor 3
B: Latent membrane protein 1


Theoretical massNumber of molelcules
Total (without water)68,2356
Polymers68,2356
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
Buried area10110 Å2
ΔGint-54 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.670, 83.670, 77.960
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: 21833.135 Da / Num. of mol.: 1 / Fragment: Sequence database residues 377-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF3, CAP1, CRAF1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13114
#2: Protein/peptide Latent membrane protein 1 / LMP-1 / Protein p63


Mass: 911.892 Da / Num. of mol.: 1 / Fragment: Residues 203-210 / Source method: obtained synthetically
Details: This sequence occurs naturally in the Latent Membrane Protein I of Epstein Barr Virus
References: UniProt: P13198

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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: 3.44 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 4000, 0.1 M MES, pH 6.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-3 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→39 Å / Num. all: 8103 / Num. obs: 7836 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 47.3 Å2 / Rsym value: 0.079 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4 / Num. unique all: 784 / Rsym value: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→32.86 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 104805.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 389 5.4 %RANDOM
Rwork0.206 ---
obs0.206 7167 88.7 %-
all-8103 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.8989 Å2 / ksol: 0.388601 e/Å3
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.8→32.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 0 0 1586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 45 4.7 %
Rwork0.266 907 -
obs-907 73.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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