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- PDB-5lde: Crystal structure of a vFLIP-IKKgamma stapled peptide dimer -

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Basic information

Entry
Database: PDB / ID: 5lde
TitleCrystal structure of a vFLIP-IKKgamma stapled peptide dimer
Components
  • Immunoglobulin G-binding protein G,Viral FLICE protein
  • Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a
KeywordsVIRAL PROTEIN / vFLIP / NF-kB / Nemo
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 / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 ...: / : / 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 / 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 / IgG binding / 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 / kinase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / protein-containing complex assembly / 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 / extracellular region / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 ...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 / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Death-like domain superfamily
Similarity search - Domain/homology
Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a / Viral FLICE protein / Immunoglobulin G-binding protein G / NF-kappa-B essential modulator
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Human herpesvirus 8
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsBarrett, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC19746/A9867 United Kingdom
CitationJournal: J. Virol. / Year: 2017
Title: IKK gamma-Mimetic Peptides Block the Resistance to Apoptosis Associated with Kaposi's Sarcoma-Associated Herpesvirus Infection.
Authors: Briggs, L.C. / Chan, A.W.E. / Davis, C.A. / Whitelock, N. / Hotiana, H.A. / Baratchian, M. / Bagneris, C. / Selwood, D.L. / Collins, M.K. / Barrett, T.E.
History
DepositionJun 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 2.0Nov 22, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / database_PDB_caveat
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _chem_comp.name / _citation.journal_volume / _citation.title
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G,Viral FLICE protein
B: Immunoglobulin G-binding protein G,Viral FLICE protein
R: Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a
S: Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a


Theoretical massNumber of molelcules
Total (without water)65,1244
Polymers65,1244
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-20 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.510, 90.510, 134.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Antibody Immunoglobulin G-binding protein G,Viral FLICE protein / IgG-binding protein G / vFLIP


Mass: 30194.514 Da / Num. of mol.: 2 / Fragment: UNP residues 304-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Human herpesvirus 8
Gene: spg, ORF71 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909, UniProt: F5HEZ4
#2: Protein/peptide Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a


Mass: 2367.700 Da / Num. of mol.: 2 / Fragment: UNP residues 45-64 / Source method: obtained synthetically / Details: Synthesised 20mer peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: D3DWY2, UniProt: Q9Y6K9*PLUS

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop
Details: 1.2M Ammonium Sulphate, 0.05M tri-sodium citrate, 3% isopropanol, 0.1-0.2% vitamin B12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→78.5 Å / Num. obs: 9482 / % possible obs: 99.8 % / Redundancy: 9.4 % / Biso Wilson estimate: 115.42 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.3
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.773 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1954 / CC1/2: 0.498 / Rpim(I) all: 0.902

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CL3

3cl3


Resolution: 3.38→25 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.872 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.609
RfactorNum. reflection% reflectionSelection details
Rfree0.29 404 4.81 %RANDOM
Rwork0.255 ---
obs0.257 8407 95.7 %-
Displacement parametersBiso mean: 135.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.6495 Å20 Å20 Å2
2---0.6495 Å20 Å2
3---1.299 Å2
Refine analyzeLuzzati coordinate error obs: 0.6 Å
Refinement stepCycle: 1 / Resolution: 3.38→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 27 0 3464
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093514HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034814HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1079SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes536HARMONIC5
X-RAY DIFFRACTIONt_it3514HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.86
X-RAY DIFFRACTIONt_other_torsion21.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion505SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4022SEMIHARMONIC4
LS refinement shellResolution: 3.38→3.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.284 -3.73 %
Rwork0.239 2037 -
all0.241 2116 -
obs--85.15 %
Refinement TLS params.

Method: refined / 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)
15.1257-0.01411.48287.4863-1.104512.2532-0.22780.14650.30120.1039-0.3099-1.088-0.8402-0.22180.5377-0.27620.0543-0.15-0.9682-0.3508-0.4929-52.53728.3352-16.4395
26.580.5429-0.91834.58770.830913.0566-0.2917-0.0739-1.02590.0204-0.2455-0.2880.2583-1.00650.5372-0.8496-0.2975-0.2209-0.4848-0.2793-0.4871-33.254241.416932.0334
31.635-2.5940.31584.3423-0.89146.3308-0.02870.08610.1811-0.0451-0.03750.0623-0.3002-0.20370.0662-0.4466-0.35070.01-0.1279-0.4011-0.1567-28.606240.88838.0801
45.4257-1.6970.4072-1.8046-1.70335.3763-0.0403-0.0716-0.0240.1122-0.04220.12870-0.28730.08250.0807-0.1154-0.402-0.7833-0.1168-0.2001-49.80544.24317.6692
57.1328-0.0609-4.45974.0522-5.27329.49020.05930.2217-0.1442-0.34920.0831-0.7616-0.04720.4975-0.14240.2313-0.2830.2370.45040.3433-0.1136-16.21165.87824.4255
64.1795-0.4909-1.88479.5025-6.125510.02990.1416-0.2765-0.71940.1125-0.0473-0.44890.45210.1171-0.09430.8075-0.09670.06040.18710.43950.077-13.481310.6965-8.1862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|101-271}
2X-RAY DIFFRACTION2{ B|101-271}
3X-RAY DIFFRACTION3{ R|* }
4X-RAY DIFFRACTION4{ S|* }
5X-RAY DIFFRACTION5{ B|2-56 }
6X-RAY DIFFRACTION6{ A|2-56 }

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