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- PDB-6mi4: Structure of the I65M mutant of NEMO(51-112) with N- and C-termin... -

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Basic information

Entry
Database: PDB / ID: 6mi4
TitleStructure of the I65M mutant of NEMO(51-112) with N- and C-terminal coiled-coil adaptors.
ComponentsNF-kB ESSENTIAL MODULATOR
KeywordsTRANSCRIPTION / coiled coil / scaffolding / NF-kB pathway
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 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process ...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 / 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 / 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 / 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
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
Similarity search - Domain/homology
NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50009425402 Å
AuthorsPellegrini, M. / Barczewski, A.H. / Mierke, D.F. / Ragusa, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R03 AR066130 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM113132 United States
CitationJournal: Sci Rep / Year: 2019
Title: The IKK-binding domain of NEMO is an irregular coiled coil with a dynamic binding interface.
Authors: Barczewski, A.H. / Ragusa, M.J. / Mierke, D.F. / Pellegrini, M.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NF-kB ESSENTIAL MODULATOR
B: NF-kB ESSENTIAL MODULATOR


Theoretical massNumber of molelcules
Total (without water)29,5072
Polymers29,5072
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer by gel filtration and SDS-PAGE Analysis. Circular dichroism shows coiled coil character as indicated by the 222 nm to 208 nm ratio.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-66 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.407, 34.124, 77.416
Angle α, β, γ (deg.)90.000, 113.890, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein NF-kB ESSENTIAL MODULATOR


Mass: 14753.613 Da / Num. of mol.: 2 / Mutation: C76A C95S E56A E57A I65M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Rosetta 2 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6K9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8.0, 5.8% PGA-LM, 5.45% PEG 20,000 mother liquor in MRC2 96 well sitting drop plates.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979329 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979329 Å / Relative weight: 1
ReflectionResolution: 2.50009425402→38.2856809844 Å / Num. obs: 10941 / % possible obs: 98.43 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1237 / Rpim(I) all: 0.05388 / Rrim(I) all: 0.1353 / Net I/σ(I): 11.64
Reflection shellResolution: 2.50009425402→2.589 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7702 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 1068 / CC1/2: 0.875 / Rpim(I) all: 0.3543 / Rrim(I) all: 0.8505 / % possible all: 97.42

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BRV

3brv


Resolution: 2.50009425402→38.2856809844 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.54
RfactorNum. reflection% reflection
Rfree0.2948 542 5.01 %
Rwork0.252 --
obs0.2542 10821 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.74 Å2 / Biso mean: 57.5741 Å2 / Biso min: 27.57 Å2
Refinement stepCycle: final / Resolution: 2.50009425402→38.2856809844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 0 59 2096
Biso mean---51.25 -
Num. residues----246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.75160.3851330.31622505263898
2.7516-3.14960.38011340.29192567270199
3.1496-3.96750.32191340.25522554268899
3.9675-38.29020.22111410.21522653279498

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