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- PDB-4bwn: NEMO CC2-LZ DOMAIN -

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Basic information

Entry
Database: PDB / ID: 4bwn
TitleNEMO CC2-LZ DOMAIN
ComponentsNF-KAPPA-B ESSENTIAL MODULATOR
KeywordsSIGNALING PROTEIN / NEMO - IKK GAMMA / NFKB PATHWAY / UBL CONJUGATTION / TRANSCRIPTION REGULATION
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
Nemo cc2-lz domain - 1d5 darpin complex / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDubosclard, V. / Duquerroy, S. / Fontan, E. / Agou, F.
Citation
Journal: To be Published
Title: High-Resolution of Crystal Structure of the Human Cc2-Lz Domain of Nemo by Protein Engineering
Authors: Dubosclard, V. / Duquerroy, S. / Fontan, E. / Agou, F.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Darpin-Assisted Crystallography of the Cc2-Lz Domain of Nemo Reveals a Coupling between Dimerization and Ubiquitin Binding.
Authors: Grubisha, O. / Kaminska, M. / Duquerroy, S. / Fontan, E. / Cordier, F. / Haouz, A. / Raynal, B. / Chiaravalli, J. / Delepierre, M. / Israel, A. / Veron, M. / Agou, F.
History
DepositionJul 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Refinement description
Revision 1.2Apr 28, 2021Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_redundancy
Revision 1.3Dec 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,6192
Polymers25,6192
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-57.3 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.353, 70.353, 78.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein NF-KAPPA-B ESSENTIAL MODULATOR / NEMO / FIP-3 / IKB KINASE-ASSOCIATED PROTEIN 1 / IKKAP1 / INHIB ITOR OF NUCLEAR FACTOR KAPPA-B ...NEMO / FIP-3 / IKB KINASE-ASSOCIATED PROTEIN 1 / IKKAP1 / INHIB ITOR OF NUCLEAR FACTOR KAPPA-B KINASE SUBUNIT GAMMA / I-KAPPA-B KIN ASE SUBUNIT GAMMA / IKK-GAMMA / IKKG / IKB KINASE SUBUNIT GAMMA / NF-K APPA-B ESSENTIAL MODIFIER / NEMO


Mass: 12809.521 Da / Num. of mol.: 2 / Fragment: CC2-LZ DOMAIN, RESIDUES 258-344 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6K9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.4 Å3/Da / Density % sol: 12 % / Description: NONE
Crystal growpH: 7.5
Details: 100 MM LITHIUM CHLORIDE, 10MM HEPES PH 7,5 AND 25% PEG 6000

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→35.18 Å / Num. obs: 9976 / % possible obs: 96.8 % / Observed criterion σ(I): 7.47 / Biso Wilson estimate: 45.07 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.47
Reflection shellResolution: 2.27→2.35 Å / Mean I/σ(I) obs: 4.34 / % possible all: 87

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
PHASERRMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V4H

2v4h


Resolution: 2.27→35.18 Å / Cor.coef. Fo:Fc: 0.9411 / Cor.coef. Fo:Fc free: 0.9449 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.275 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.215
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 482 4.83 %RANDOM
Rwork0.2152 ---
obs0.2165 9976 96.84 %-
Displacement parametersBiso mean: 79.97 Å2
Baniso -1Baniso -2Baniso -3
1-4.915 Å20 Å20 Å2
2--4.915 Å20 Å2
3----9.8299 Å2
Refine analyzeLuzzati coordinate error obs: 0.417 Å
Refinement stepCycle: LAST / Resolution: 2.27→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 0 25 1449
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011432HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.171914HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d578SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes184HARMONIC5
X-RAY DIFFRACTIONt_it1432HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion20.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion180SEMIHARMONIC5
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_contact1643SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.54 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2939 139 5.39 %
Rwork0.2568 2442 -
all0.2588 2581 -
obs--96.84 %
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)
11.80430.32350.37035.3004-3.14683.546-0.1401-0.1615-0.2918-0.2481-0.0974-0.20310.30770.11960.23750.19720.03250.0556-0.19130.20760.1068-1.4131-38.527821.7743
23.8566-1.40760.35453.5482-1.20852.39690.13360.01630.24340.2626-0.16150.03840.1802-0.07610.028-0.117-0.01560.0369-0.1320.0238-0.1896-8.0757-3.0622-1.6559
31.6185-2.95431.22547.1365-2.65320.3733-0.1119-0.1447-0.13350.0599-0.0776-0.7055-0.0814-0.13090.1895-0.00590.0971-0.0412-0.20620.15170.0253-19.968427.18-18.5559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A|259 - A|294 AND B|259 - B|294
2X-RAY DIFFRACTION2A|295 - A|315 AND B|295 - B|315
3X-RAY DIFFRACTION3A|316 - A|344 AND B|316 - B|344

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