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- PDB-3cl3: Crystal Structure of a vFLIP-IKKgamma complex: Insights into vira... -

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Basic information

Entry
Database: PDB / ID: 3cl3
TitleCrystal Structure of a vFLIP-IKKgamma complex: Insights into viral activation of the IKK signalosome
Components
  • NF-kappa-B essential modulator
  • ORF K13
Keywordsviral protein/signaling protein / Death effector domain / coiled-coil / Coiled coil / Cytoplasm / Disease mutation / Ectodermal dysplasia / Host-virus interaction / Nucleus / Transcription / Transcription regulation / viral protein-signaling protein COMPLEX
Function / homology
Function and homology information


IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / Caspase activation via Death Receptors in the presence of ligand / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / Caspase activation via Death Receptors in the presence of ligand / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / signaling adaptor activity / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / mitotic spindle / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / spindle pole / Interleukin-1 signaling / Ovarian tumor domain proteases / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / protein-containing complex assembly / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / defense response to bacterium / inflammatory response / immune response / protein heterodimerization activity / protein domain specific binding / cysteine-type endopeptidase activity / innate immune response / apoptotic process / ubiquitin protein ligase binding / DNA damage response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
L1 transposable element, trimerization domain / Peptidase C14 family / C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / Death effector domain ...L1 transposable element, trimerization domain / Peptidase C14 family / C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death Domain, Fas / Death Domain, Fas / Death-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ORF K13 / FLICE inhibitory protein / NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHuman gammaherpesvirus 8
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsBagneris, C. / Ageichik, A.V. / Cronin, N. / Boshoff, C. / Waksman, G. / Barrett, T.
CitationJournal: Mol.Cell / Year: 2008
Title: Crystal structure of a vFlip-IKKgamma complex: insights into viral activation of the IKK signalosome.
Authors: Bagneris, C. / Ageichik, A.V. / Cronin, N. / Wallace, B. / Collins, M. / Boshoff, C. / Waksman, G. / Barrett, T.
History
DepositionMar 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.3Feb 21, 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: ORF K13
B: ORF K13
D: NF-kappa-B essential modulator
E: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)70,8474
Polymers70,8474
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-40.4 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.670, 145.670, 101.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ORF K13 / ks-vFLIP


Mass: 20670.133 Da / Num. of mol.: 2 / Fragment: residues 1-178
Source method: isolated from a genetically manipulated source
Details: Derived from pET44b(+) (Novogen) / Source: (gene. exp.) Human gammaherpesvirus 8 / Gene: vFLIP / Plasmid: pETM442 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P88961, UniProt: Q76RF1*PLUS
#2: Protein NF-kappa-B essential modulator / NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / ...NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / IkB kinase subunit gamma / I-kappa-B kinase gamma / IKK-gamma / IKKG / IkB kinase-associated protein 1 / IKKAP1 / FIP-3


Mass: 14753.303 Da / Num. of mol.: 2 / Fragment: residues 150-272
Source method: isolated from a genetically manipulated source
Details: Derived from pET44b(+) (Novogen) / Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / Plasmid: pETM6T1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9Y6K9

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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: 4.52 Å3/Da / Density % sol: 72.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 225mM Tris pH 7.5, 4% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2006 / Details: Wiggler
RadiationMonochromator: Channel cut ESRF monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→125 Å / Num. all: 20877 / Num. obs: 20877 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 93.9 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 16.1
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1530 / Rsym value: 0.543 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: Used a maximum likelihood target
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 1065 -Random
Rwork0.2608 ---
all-20830 --
obs-20830 100 %-
Displacement parametersBiso mean: 69.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.62 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 0 0 3477
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010003
X-RAY DIFFRACTIONc_angle_deg1.28824
X-RAY DIFFRACTIONc_mcbond_it1.436
X-RAY DIFFRACTIONc_mcangle_it2.564
LS refinement shellResolution: 3.2→3.25 Å
RfactorNum. reflection% reflection
Rfree0.337 55 -
Rwork0.36 --
obs-920 100 %

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