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- PDB-7pdj: R12E vFLIP mutant -

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Basic information

Entry
Database: PDB / ID: 7pdj
TitleR12E vFLIP mutant
ComponentsFLICE inhibitory protein
KeywordsVIRAL PROTEIN / KSHV virus / tandem DED protein / NF-kappaB activation / IKK kinase binding / IKKgamma
Function / homologyDeath effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Caspase activation via Death Receptors in the presence of ligand / Death-like domain superfamily / regulation of apoptotic process / FLICE inhibitory protein
Function and homology information
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsBarrett, T.E.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)LiDo London Consortium DTP United Kingdom
Wellcome Trust209250/Z/17/Z United Kingdom
Sarcoma UKSUK203.2017 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Mechanistic insights into the activation of the IKK kinase complex by the Kaposi's sarcoma herpes virus oncoprotein vFLIP.
Authors: Bagneris, C. / Senthil Kumar, S.L. / Baratchian, M. / Britt, H.M. / Assafa, T.E. / Thalassinos, K. / Collins, M.K. / Barrett, T.E.
History
DepositionAug 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLICE inhibitory protein
B: FLICE inhibitory protein
C: FLICE inhibitory protein
D: FLICE inhibitory protein
E: FLICE inhibitory protein
F: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)131,2646
Polymers131,2646
Non-polymers00
Water00
1
D: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.402, 69.324, 131.887
Angle α, β, γ (deg.)90, 89.85, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
FLICE inhibitory protein / K13 / ORF71 / ORF71 protein / ORF71/K13 / Putative apoptosis inhibitor protein


Mass: 21877.367 Da / Num. of mol.: 6 / Mutation: R12E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF71, HHV8GK18_gp80 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 star / References: UniProt: Q76RF1

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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 % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.125 M Na HEPES pH 7.0, 1 % PEG 8000 and 3% methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2019
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 4.2→132 Å / Num. obs: 8076 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 63 Å2 / CC1/2: 0.5 / Rpim(I) all: 0.59 / Net I/σ(I): 2.5
Reflection shellResolution: 4.2→4.7 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2287 / CC1/2: 0.21 / Rpim(I) all: 2.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CL3

3cl3


Resolution: 4.2→65.94 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.776 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 1.043
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 790 -RANDOM
Rwork0.2234 ---
obs0.228 8075 99.7 %-
Displacement parametersBiso mean: 74.93 Å2
Baniso -1Baniso -2Baniso -3
1--13.92 Å20 Å212.4755 Å2
2--0.2311 Å20 Å2
3---13.6889 Å2
Refine analyzeLuzzati coordinate error obs: 0.66 Å
Refinement stepCycle: LAST / Resolution: 4.2→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7092 0 0 0 7092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077213HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.919868HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2295SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1214HARMONIC5
X-RAY DIFFRACTIONt_it7213HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1010SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5130SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion20.45
LS refinement shellResolution: 4.2→4.23 Å
RfactorNum. reflection% reflection
Rfree0.3933 17 -
Rwork0.2269 --
obs0.2411 208 100 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.6999-0.0648-0.27162.7519-0.8331.72030.2654-0.15190.1577-0.1519-0.08490.19240.15770.1924-0.18050.11290.13820.01880.1448-0.0066-0.0581-4.114618.0498180.6616
24.569-2.91381.27623.5281-1.26824.7366-0.0482-0.16380.0854-0.1638-0.07050.32830.08540.32830.1188-0.04350.04440.1520.304-0.1085-0.034214.466847.7718157.1212
32.27251.5119-0.82284.7839-0.23253.0201-0.00010.0471-0.00250.04710.1651-0.0108-0.0025-0.0108-0.1649-0.1510.05020.10990.25840.0993-0.0789-17.584656.4922136.5431
43.53992.911-0.08965.60310.21993.95690.05110.1527-0.29880.15270.1336-0.3328-0.2988-0.3328-0.1848-0.0740.1040.12040.16790.10470.0357-21.846849.0027171.0786
56.77430.1555-1.4190.1994-0.80183.7603-0.36140.54430.43480.54430.1814-0.06090.4348-0.06090.180.21570.1139-0.04010.2754-0.0304-0.13831.156225.8246150.4765
61.4106-0.25181.08644.4629-0.38943.70150.10670.1296-0.17310.1296-0.26910.265-0.17310.2650.16230.0576-0.0530.11160.27040.0198-0.173113.347449.6265194.0053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 170
2X-RAY DIFFRACTION2{ B|* }B4 - 170
3X-RAY DIFFRACTION3{ C|* }C0 - 170
4X-RAY DIFFRACTION4{ D|* }D0 - 170
5X-RAY DIFFRACTION5{ E|* }E3 - 169
6X-RAY DIFFRACTION6{ F|* }F0 - 170

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