[English] 日本語
Yorodumi
- PDB-4nqk: Structure of an Ubiquitin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nqk
TitleStructure of an Ubiquitin complex
Components
  • Probable ATP-dependent RNA helicase DDX58
  • Ubiquitin
KeywordsHydrolase/Apoptosis / CARD domain / Hydrolase-Apoptosis complex
Function / homology
Function and homology information


regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / cellular response to exogenous dsRNA ...regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / cellular response to exogenous dsRNA / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / RSV-host interactions / response to exogenous dsRNA / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / bicellular tight junction / positive regulation of defense response to virus by host / antiviral innate immune response / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / 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) / 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 / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / positive regulation of interferon-beta production / regulation of cell migration / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / positive regulation of interleukin-8 production / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function
RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. ...RIG-I, CARD domain repeat 2 / Death Domain, Fas / Death Domain, Fas / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / helicase superfamily c-terminal domain / Ubiquitin domain profile. / Ubiquitin-like domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Antiviral innate immune response receptor RIG-I / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsPeisley, A. / Wu, B. / Hur, S.
CitationJournal: Nature / Year: 2014
Title: Structural basis for ubiquitin-mediated antiviral signal activation by RIG-I.
Authors: Peisley, A. / Wu, B. / Xu, H. / Chen, Z.J. / Hur, S.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Feb 28, 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: Probable ATP-dependent RNA helicase DDX58
B: Probable ATP-dependent RNA helicase DDX58
C: Probable ATP-dependent RNA helicase DDX58
D: Probable ATP-dependent RNA helicase DDX58
E: Ubiquitin
F: Ubiquitin
G: Ubiquitin
H: Ubiquitin
I: Ubiquitin
J: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)148,21810
Polymers148,21810
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.539, 101.851, 88.151
Angle α, β, γ (deg.)90.00, 106.88, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Probable ATP-dependent RNA helicase DDX58 / DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG- ...DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 23872.389 Da / Num. of mol.: 4 / Fragment: N-terminal tandem CARD domain, UNP residues 1-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Production host: Escherichia coli (E. coli) / References: UniProt: O95786, RNA helicase
#2: Protein
Ubiquitin


Mass: 8788.049 Da / Num. of mol.: 6 / Fragment: UNP residues 76-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG3350, 0.2 M Tri-Li Citrate, 3% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→46 Å / Num. all: 30348 / Num. obs: 29885 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.164 / Net I/σ(I): 5.92
Reflection shellResolution: 3.7→3.93 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.55 / Rsym value: 0.617 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→46 Å / SU ML: 0.61 / σ(F): 1.12 / Phase error: 31.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2847 767 5.01 %
Rwork0.2217 --
obs0.2249 29885 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9555 0 0 0 9555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099719
X-RAY DIFFRACTIONf_angle_d1.60113114
X-RAY DIFFRACTIONf_dihedral_angle_d19.1993702
X-RAY DIFFRACTIONf_chiral_restr0.0611496
X-RAY DIFFRACTIONf_plane_restr0.0061661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.81940.38681380.33062559X-RAY DIFFRACTION98
3.8194-3.95580.3941290.32262554X-RAY DIFFRACTION98
3.9558-4.11410.36511400.28412600X-RAY DIFFRACTION99
4.1141-4.30120.32021430.24052592X-RAY DIFFRACTION99
4.3012-4.52780.31031260.22612617X-RAY DIFFRACTION99
4.5278-4.81120.29041340.21032584X-RAY DIFFRACTION99
4.8112-5.18230.26941380.21632583X-RAY DIFFRACTION99
5.1823-5.70290.29751340.21692569X-RAY DIFFRACTION99
5.7029-6.52610.32141410.23992591X-RAY DIFFRACTION99
6.5261-8.21470.26261350.2032582X-RAY DIFFRACTION98
8.2147-46.11670.17561390.14292557X-RAY DIFFRACTION97
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)
17.54120.3793-0.24425.87073.85137.48370.3929-0.2633-0.4470.3767-0.56541.05930.2286-0.52470.19580.3625-0.0927-0.01760.29380.07060.65931.2984-43.6745-36.4567
28.40371.1736-1.27576.461-2.75815.3728-0.1367-0.61920.07740.6453-0.2633-0.46880.1969-0.15160.25730.44810.0898-0.14110.4081-0.08480.441728.4673-34.3792-20.9275
35.3763-5.3547-0.45566.6823-2.15226.4626-0.0409-1.12810.51361.00750.2185-0.07510.25610.726-0.31370.77020.0550.00560.8938-0.14850.53626.3661-18.5259-2.0847
46.731.37210.27132.89582.02899.05150.2368-0.4549-0.42780.0656-0.17260.4830.0291-0.5999-0.02840.3694-0.00720.13970.31070.0120.8143-11.5253-21.7966-29.2046
57.99-3.21961.74257.2572-4.67484.54680.29460.6007-0.55120.1283-0.30970.58490.41110.2091-0.0430.474-0.02040.00360.419-0.14290.710142.3332-37.356-40.2675
66.81031.58172.0054.8816-1.55352.04240.4813-1.877-0.54692.6901-1.2097-1.90680.0911.23720.66131.8977-0.1843-0.40951.48630.21111.113441.5218-36.52162.7669
74.2124-3.29260.44933.8823-2.70814.103-0.49-1.812.13931.3061-0.3143-1.1965-0.78071.15040.49091.6693-0.0587-0.39462.7744-0.68250.820723.6537-8.016811.5027
85.3215-0.20514.84323.26661.91517.1163-0.2773-0.6881-0.49180.41870.30210.63060.2767-0.56280.07791.3414-0.00520.26741.33180.00220.5252-16.9941-20.212110.4588
93.56770.1231.81887.0590.69055.1084-0.2104-0.0759-0.43020.1449-0.47240.1656-0.3896-0.7760.61110.47470.08210.22520.8262-0.2461.1792-29.6386-8.4339-20.8643
107.6591-0.4859-0.17334.41370.50412.8461-0.02020.9842-0.5706-0.922-0.37280.2750.9687-0.1912-0.06320.1622-0.2199-0.38180.7964-0.24931.0171-18.8353-38.5817-48.5054
118.5549-1.14530.43068.90222.92995.9361-0.38060.15880.6619-0.13710.3777-0.2679-0.13050.62170.0470.3183-0.0693-0.02290.32960.02740.546318.2051-27.6352-42.4413
127.97741.19173.59392.04350.63546.5737-0.0186-1.33521.01870.15320.1355-0.43290.3116-0.10310.09440.58610.0484-0.30730.7145-0.22030.941227.4009-11.403-14.4623
139.34271.5381-1.39047.1562-0.04984.8736-0.0448-0.00360.47211.0316-0.24350.3518-0.1109-0.46920.20090.57330.0620.09320.4861-0.18820.6153-4.8804-2.2582-15.1499
146.35552.69790.96356.03482.51629.0460.3090.46620.36410.0728-0.18310.5089-0.0956-0.1074-0.12420.38770.0351-0.01970.28810.0140.6597-1-9.9267-47.4773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:91 )A1 - 91
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:91 )B1 - 91
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:91 )C1 - 91
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:91 )D1 - 91
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:72 )E1 - 72
6X-RAY DIFFRACTION6( CHAIN F AND RESID 1:73 )F1 - 73
7X-RAY DIFFRACTION7( CHAIN G AND RESID 1:71 )G1 - 71
8X-RAY DIFFRACTION8( CHAIN H AND RESID 1:75 )H1 - 75
9X-RAY DIFFRACTION9( CHAIN I AND RESID 1:71 )I1 - 71
10X-RAY DIFFRACTION10( CHAIN J AND RESID 1:73 )J1 - 73
11X-RAY DIFFRACTION11( CHAIN A AND RESID 94:188 )A94 - 188
12X-RAY DIFFRACTION12( CHAIN B AND RESID 94:188 )B94 - 188
13X-RAY DIFFRACTION13( CHAIN C AND RESID 94:188 )C94 - 188
14X-RAY DIFFRACTION14( CHAIN D AND RESID 94:188 )D94 - 188

+
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