[English] 日本語
Yorodumi
- PDB-6k9p: Structure of Deubiquitinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k9p
TitleStructure of Deubiquitinase
Components
  • Ubiquitin thioesterase
  • Ubiquitin
KeywordsHYDROLASE / In complex with ubiquitin
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of proteasomal protein catabolic process ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling
Similarity search - Function
Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Papain-like cysteine peptidase superfamily ...Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Phosphorylase Kinase; domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ubiquitinyl hydrolase 1 / Polyubiquitin-B
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.047 Å
AuthorsLu, L.N. / Liu, L. / Wang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Nat Commun / Year: 2022
Title: Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains
Authors: Lu, L. / Zhai, X. / Li, X. / Wang, S. / Zhang, L. / Wang, L. / Jin, X. / Liang, L. / Deng, Z. / Li, Z. / Wang, Y. / Fu, X. / Hu, H. / Wang, J. / Mei, Z. / He, Z. / Wang, F.
History
DepositionJun 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ubiquitin thioesterase
G: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)37,2622
Polymers37,2622
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-10 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.897, 75.342, 50.520
Angle α, β, γ (deg.)90.00, 92.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquitin thioesterase


Mass: 28685.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: OsJ_28104 / Production host: Escherichia coli (E. coli) / References: UniProt: B9G207, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9873 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 44853 / % possible obs: 99.8 % / Redundancy: 6 % / Rpim(I) all: 0.052 / Net I/σ(I): 16.13
Reflection shellResolution: 1.62→1.65 Å / Num. unique obs: 2207 / Rpim(I) all: 0.596

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2828:V1.0)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZFY, 1UBQ

2zfy

1ubq


Resolution: 2.047→41.93 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.19
RfactorNum. reflection% reflection
Rfree0.2101 1107 4.81 %
Rwork0.1724 --
obs0.1742 23032 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.047→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 0 138 2680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072591
X-RAY DIFFRACTIONf_angle_d0.8933493
X-RAY DIFFRACTIONf_dihedral_angle_d19.2451572
X-RAY DIFFRACTIONf_chiral_restr0.056387
X-RAY DIFFRACTIONf_plane_restr0.005454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0471-2.14030.27181370.2322634X-RAY DIFFRACTION96
2.1403-2.25310.2271320.20182746X-RAY DIFFRACTION100
2.2531-2.39420.25181300.20272755X-RAY DIFFRACTION100
2.3942-2.57910.21951430.19962737X-RAY DIFFRACTION100
2.5791-2.83860.27321330.19542753X-RAY DIFFRACTION100
2.8386-3.24920.26661630.18782742X-RAY DIFFRACTION100
3.2492-4.09310.21731350.16252748X-RAY DIFFRACTION100
4.0931-41.93830.14421340.14462810X-RAY DIFFRACTION100
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)
10.2454-0.30170.13390.2292-0.09170.21460.14590.08760.3086-0.6222-0.0446-0.2363-0.4595-0.0564-0.00030.52-0.05990.04950.36930.04010.57649.610720.14312.1862
21.2606-0.6719-0.64341.2042-0.54550.81460.259-0.02660.24710.04440.0064-0.6766-0.52670.13780.00610.4017-0.0823-0.00830.2531-0.03280.41239.391418.73239.9607
30.206-0.1881-0.22170.51920.6830.58460.0947-0.24530.3363-0.0111-0.0115-0.3907-0.15480.0063-0.00030.2126-0.0366-0.01550.2930.01270.40615.16962.09365.9385
40.3406-0.2301-0.14020.14810.22910.26140.0847-0.2161-0.5560.2055-0.0175-0.37790.49710.06860.00130.32160.0763-0.04140.31750.06130.438211.6563-13.35399.4267
50.21230.10380.21680.33930.12230.0955-0.17190.1553-0.3234-0.2370.0937-0.44060.24880.0144-0.00010.36670.02930.05620.2668-0.01120.39478.9964-11.6154-1.1089
60.2919-0.0719-0.16460.3345-0.20180.48810.29280.07240.4219-0.6595-0.2811-0.5980.07150.63310.00060.3870.0140.12780.51890.02640.536522.29110.1354-3.8575
70.27920.3012-0.59050.72780.22760.4046-0.06140.0714-0.1527-0.15330.0942-0.16830.1067-0.1058-0.00020.2731-0.00110.010.26850.00710.28173.6569-5.49391.8632
80.20810.28250.32360.55230.43460.3451-0.1801-0.77130.24720.4482-0.0895-0.2496-0.0507-0.4430.00130.37530.03650.00070.46130.07110.3581-9.3936-4.764116.2466
90.21150.140.18180.14930.06850.20780.13640.14710.0079-0.0624-0.0830.57750.1012-0.0721-0.00050.3085-0.0383-0.05030.40520.01270.3956-11.0194-5.24816.7912
100.840.4795-0.24270.59730.10110.29510.0014-0.07750.06950.17170.00630.0677-0.0719-0.05450.00020.3130.0034-0.02840.28610.02250.2634-0.1684-0.69928.3221
110.94410.5486-0.67350.4876-0.35891.16910.2473-0.24880.39320.6922-0.0635-0.0688-0.33140.08090.00060.543-0.062-0.04280.4116-0.08270.35564.203516.281119.2215
120.12080.0678-0.1873-0.0085-0.03440.09920.0028-0.23620.07810.86170.1686-0.89830.17980.2488-0.0010.52620.0205-0.15330.5328-0.03730.37379.73955.223219.7347
130.16980.0430.09510.81060.11240.29990.1502-0.0920.10520.3961-0.093-0.10590.0429-0.03230.00010.2953-0.0363-0.01440.2686-0.01280.31858.706212.2819.6644
140.43590.09840.17680.42020.60570.95590.0642-1.1357-0.30721.7230.14290.26020.15480.62260.50490.9909-0.04010.24480.69650.03050.2791-8.60471.937230.7811
150.0174-0.03160.00940.0357-0.01780.01930.3174-0.2144-0.31580.1843-0.17540.0415-0.09140.102200.87020.28720.41491.12760.15191.3227-19.08512.00133.5145
160.32620.1523-0.13640.215-0.05940.0688-0.4343-0.77590.37091.1424-0.01050.246-0.89610.1679-0.00460.7908-0.09130.10250.6948-0.14210.3918-8.248712.640129.1966
170.16540.0199-0.28360.2538-0.06150.3294-0.0783-0.16010.13730.41630.00970.6458-0.3899-0.35240.00070.5280.0350.05290.4955-0.08880.3573-10.60948.612320.5951
180.0164-0.01570.00230.2121-0.04780.02170.28240.45611.4048-1.15180.88951.2538-0.80240.014600.67060.06260.1170.8664-0.09050.9713-19.299113.223421.1998
190.06950.1335-0.06720.1832-0.12080.1140.472-0.70330.43061.1309-0.62271.57810.6557-0.4712-0.00970.9752-0.01620.36940.99950.10811.0419-21.63845.074629.5765
200.39380.01280.28490.66570.3530.3036-0.42650.31290.21720.27660.31130.34910.2853-0.5345-0.00060.4253-0.00750.06260.41250.03050.3149-7.16315.81417.1385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 73 through 95 )
2X-RAY DIFFRACTION2chain 'B' and (resid 96 through 120 )
3X-RAY DIFFRACTION3chain 'B' and (resid 121 through 139 )
4X-RAY DIFFRACTION4chain 'B' and (resid 140 through 159 )
5X-RAY DIFFRACTION5chain 'B' and (resid 160 through 181 )
6X-RAY DIFFRACTION6chain 'B' and (resid 182 through 200 )
7X-RAY DIFFRACTION7chain 'B' and (resid 201 through 221 )
8X-RAY DIFFRACTION8chain 'B' and (resid 222 through 234 )
9X-RAY DIFFRACTION9chain 'B' and (resid 235 through 245 )
10X-RAY DIFFRACTION10chain 'B' and (resid 246 through 265 )
11X-RAY DIFFRACTION11chain 'B' and (resid 266 through 286 )
12X-RAY DIFFRACTION12chain 'B' and (resid 287 through 308 )
13X-RAY DIFFRACTION13chain 'B' and (resid 309 through 324 )
14X-RAY DIFFRACTION14chain 'G' and (resid 1 through 16 )
15X-RAY DIFFRACTION15chain 'G' and (resid 17 through 22 )
16X-RAY DIFFRACTION16chain 'G' and (resid 23 through 34 )
17X-RAY DIFFRACTION17chain 'G' and (resid 35 through 49 )
18X-RAY DIFFRACTION18chain 'G' and (resid 50 through 54 )
19X-RAY DIFFRACTION19chain 'G' and (resid 55 through 65 )
20X-RAY DIFFRACTION20chain 'G' and (resid 66 through 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