[English] 日本語
Yorodumi
- PDB-3jsv: Crystal structure of mouse NEMO CoZi in complex with Lys63-linked... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jsv
TitleCrystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin
Components
  • (Ubiquitin) x 2
  • NF-kappa-B essential modulator
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / ubiquitin / coiled-coil / cellular signaling / Cytoplasm / Isopeptide bond / Nucleus / Phosphoprotein / Ubl conjugation / Coiled coil / Disulfide bond / Metal-binding / Transcription / Transcription regulation / Zinc / Zinc-finger / SIGNALING PROTEIN-TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation ...IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / TNFR1-induced NF-kappa-B signaling pathway / IKK complex recruitment mediated by RIP1 / RIP-mediated NFkB activation via ZBP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / protein modification process => GO:0036211 / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Ub-specific processing proteases / anoikis / peroxisome proliferator activated receptor binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / B cell homeostasis / Response of EIF2AK4 (GCN2) to amino acid deficiency / positive regulation of macroautophagy / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / canonical NF-kappaB signal transduction / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / cytosolic ribosome / signaling adaptor activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / 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 / 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 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / tumor necrosis factor-mediated signaling pathway / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / 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 / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / 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 / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell
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 / Ribosomal L40e family / Ribosomal_L40e ...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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / 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 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYoshikawa, A. / Sato, Y. / Mimura, H. / Yamashita, M. / Yamagata, A. / Fukai, S.
CitationJournal: Febs Lett. / Year: 2009
Title: Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin
Authors: Yoshikawa, A. / Sato, Y. / Yamashita, M. / Mimura, H. / Yamagata, A. / Fukai, S.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: NF-kappa-B essential modulator
D: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)39,5084
Polymers39,5084
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-68 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.380, 45.870, 83.290
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS
#2: Protein Ubiquitin


Mass: 8691.918 Da / Num. of mol.: 1 / Mutation: X77D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS
#3: 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: 11105.640 Da / Num. of mol.: 2 / Fragment: residues 250-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ikbkg, Nemo, NEMO(249-343) / Plasmid: pCold / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O88522
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 11492 / Num. obs: 11492 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 31 % / Biso Wilson estimate: 32.1 Å2 / Rsym value: 0.066 / Net I/σ(I): 14.2
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.216 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.5 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 110720.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.294 549 5.1 %RANDOM
Rwork0.25 ---
obs0.25 10739 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6733 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 82.1 Å2
Baniso -1Baniso -2Baniso -3
1--27.11 Å20 Å2-6.73 Å2
2---9.47 Å20 Å2
3---36.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 0 26 2652
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.662
X-RAY DIFFRACTIONc_scangle_it3.672.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 77 5.1 %
Rwork0.349 1439 -
obs--79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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://pdbjlvh1.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