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- PDB-6mi3: Structure of NEMO(51-112) with N- and C-terminal coiled-coil adaptors. -

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Basic information

Entry
Database: PDB / ID: 6mi3
TitleStructure of NEMO(51-112) with N- and C-terminal coiled-coil adaptors.
ComponentsNF-kB ESSENTIAL MODULATOR,NF-kappa-B essential modulator,NF-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: 1.783 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 1.0Jul 31, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NF-kB ESSENTIAL MODULATOR,NF-kappa-B essential modulator,NF-kB ESSENTIAL MODULATOR
B: NF-kB ESSENTIAL MODULATOR,NF-kappa-B essential modulator,NF-kB ESSENTIAL MODULATOR


Theoretical massNumber of molelcules
Total (without water)29,2842
Polymers29,2842
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer by SEC and by SDS-PAGE analysis. Circular dichroism also supports coiled coil in solution through observation of 222 nm and 208 nm ratio
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-66 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.480, 33.620, 76.870
Angle α, β, γ (deg.)90.000, 115.040, 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,NF-kappa-B essential modulator,NF-kB ESSENTIAL MODULATOR / NEMO / FIP-3 / IkB kinase-associated protein 1 / IKKAP1 / Inhibitor of nuclear factor kappa-B ...NEMO / FIP-3 / IkB kinase-associated protein 1 / IKKAP1 / Inhibitor of nuclear factor kappa-B kinase subunit gamma / IkB kinase subunit gamma / NF-kappa-B essential modifier


Mass: 14641.783 Da / Num. of mol.: 2 / Mutation: E56A, E57A, C76A, C95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / Cell line (production host): Rosetta 2 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6K9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919774 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919774 Å / Relative weight: 1
ReflectionResolution: 1.783→37.754 Å / Num. obs: 28586 / % possible obs: 67.52 % / Redundancy: 3.3 % / Biso Wilson estimate: 48.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08025 / Rpim(I) all: 0.05212 / Rrim(I) all: 0.09603 / Net I/σ(I): 5.71
Reflection shellResolution: 1.783→1.847 Å / Redundancy: 3.4 % / Rmerge(I) obs: 5.483 / Mean I/σ(I) obs: 0.24 / Num. unique obs: 431 / CC1/2: 0.0894 / Rpim(I) all: 3.444 / Rrim(I) all: 6.493 / % possible all: 15.12

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Processing

Software
NameVersionClassification
PHENIXdev_2849refinement
XDSdata reduction
STARANISOv3.000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DMD

4dmd


Resolution: 1.783→37.754 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 992 5.06 %431
Rwork0.2428 ---
obs0.2441 19587 67.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.13 Å2 / Biso mean: 48.8741 Å2 / Biso min: 15.52 Å2
Refinement stepCycle: final / Resolution: 1.783→37.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 0 183 2220
Biso mean---47.31 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122060
X-RAY DIFFRACTIONf_angle_d1.1412745
X-RAY DIFFRACTIONf_chiral_restr0.055306
X-RAY DIFFRACTIONf_plane_restr0.006359
X-RAY DIFFRACTIONf_dihedral_angle_d28.337841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7835-1.87750.5533320.429264067216
1.8775-1.99510.4294620.39771152121430
1.9951-2.14910.34581040.33651921202549
2.1491-2.36540.31711740.3123158333281
2.3654-2.70760.33481940.27993863405798
2.7076-3.41090.27422080.25223909411799
3.4109-37.76260.21392180.19133952417098

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