[English] 日本語
Yorodumi
- PDB-2zvn: NEMO CoZi domain incomplex with diubiquitin in P212121 space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zvn
TitleNEMO CoZi domain incomplex with diubiquitin in P212121 space group
Components
  • NF-kappa-B essential modulator
  • UBC protein
KeywordsSIGNALING PROTEIN/Transcription / NF-kB signaling / Ubiquitin binding / Coiled coil / Cytoplasm / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / SIGNALING PROTEIN-Transcription COMPLEX
Function / homology
Function and homology information


SLC15A4:TASL-dependent IRF5 activation / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / Regulation of NF-kappa B signaling / TNFR1-induced NF-kappa-B signaling pathway / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation ...SLC15A4:TASL-dependent IRF5 activation / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / Regulation of NF-kappa B signaling / TNFR1-induced NF-kappa-B signaling pathway / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IKK complex recruitment mediated by RIP1 / IkappaB kinase complex / TRAF6 mediated NF-kB activation / Ovarian tumor domain proteases / PKR-mediated signaling / linear polyubiquitin binding / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Ub-specific processing proteases / peroxisome proliferator activated receptor binding / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / B cell homeostasis / positive regulation of macroautophagy / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / canonical NF-kappaB signal transduction / signaling adaptor activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / tumor necrosis factor-mediated signaling pathway / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D
Similarity search - Function
Nemo cc2-lz domain - 1d5 darpin complex / NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Nemo cc2-lz domain - 1d5 darpin complex / NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NF-kappa-B essential modulator / Polyubiquitin-C / UBC protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsRahighi, S. / Ikeda, F. / Kawasaki, M. / Akutsu, M. / Suzuki, N. / Kato, R. / Kensche, T. / Uejima, T. / Bloor, S. / Komander, D. ...Rahighi, S. / Ikeda, F. / Kawasaki, M. / Akutsu, M. / Suzuki, N. / Kato, R. / Kensche, T. / Uejima, T. / Bloor, S. / Komander, D. / Randow, F. / Wakatsuki, S. / Dikic, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation
Authors: Rahighi, S. / Ikeda, F. / Kawasaki, M. / Akutsu, M. / Suzuki, N. / Kato, R. / Kensche, T. / Uejima, T. / Bloor, S. / Komander, D. / Randow, F. / Wakatsuki, S. / Dikic, I.
History
DepositionNov 12, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBC protein
G: UBC protein
B: NF-kappa-B essential modulator
D: NF-kappa-B essential modulator
C: UBC protein
E: UBC protein
F: NF-kappa-B essential modulator
H: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)110,3988
Polymers110,3988
Non-polymers00
Water1,17165
1
A: UBC protein
G: UBC protein
B: NF-kappa-B essential modulator
D: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)55,1994
Polymers55,1994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-71 kcal/mol
Surface area25690 Å2
MethodPISA
2
C: UBC protein
E: UBC protein
F: NF-kappa-B essential modulator
H: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)55,1994
Polymers55,1994
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-74 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.195, 141.288, 144.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
UBC protein


Mass: 17279.785 Da / Num. of mol.: 4 / Fragment: Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q96C32, UniProt: P0CG48*PLUS
#2: Protein
NF-kappa-B essential modulator / NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / ...NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / IkB kinase subunit gamma / I-kappa-B kinase gamma / IKK-gamma / IKKG / IkB kinase-associated protein 1 / IKKAP1 / mFIP-3


Mass: 10319.728 Da / Num. of mol.: 4 / Fragment: CC2-LZ, CoZi domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O88522
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.96 % / Mosaicity: 0.654 °
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 24962 / Num. obs: 24893 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.097 / Χ2: 1.063 / Net I/σ(I): 19.934
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.116.20.60424120.88798.6
3.11-3.237.10.50624200.92799.9
3.23-3.387.30.34124530.95100
3.38-3.567.30.22624671.005100
3.56-3.787.30.15224561.024100
3.78-4.077.30.10224781.103100
4.07-4.487.30.07324981.208100
4.48-5.137.30.06124931.307100
5.13-6.467.20.06325431.231100
6.46-506.70.05726730.93899.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
MOLREPphasing
RefinementResolution: 3→45.75 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30274 1267 5.1 %RANDOM
Rwork0.26122 ---
obs0.26336 23571 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.53 Å2 / Biso mean: 77.39 Å2 / Biso min: 18.35 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å20 Å2
2--0.17 Å20 Å2
3---2.06 Å2
Refinement stepCycle: LAST / Resolution: 3→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7533 0 0 65 7598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227609
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.391.99110215
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.375923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.26126.296378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.411151602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.121542
X-RAY DIFFRACTIONr_chiral_restr0.1660.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2750.23815
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25226
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5021.54635
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.57127516
X-RAY DIFFRACTIONr_scbond_it1.72532974
X-RAY DIFFRACTIONr_scangle_it3.1564.52699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.001→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 84 -
Rwork0.361 1634 -
all-1723 -
obs--95.76 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more