[English] 日本語
Yorodumi
- PDB-6qk9: A dimeric ubiquitin formed by a single amino acid substitution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qk9
TitleA dimeric ubiquitin formed by a single amino acid substitution
ComponentsPolyubiquitin-B
KeywordsSIGNALING PROTEIN / Ubiquitin / dimerisation / dimer
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 / energy homeostasis ...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 / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic 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 / 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 / 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 / neuron projection morphogenesis / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells
Similarity search - Function
Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.231 Å
AuthorsGabrielsen, M. / Kowalczyk, D. / Buetow, L. / Huang, D.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKA23278 United Kingdom
European Research Council647849 United Kingdom
CitationJournal: Structure / Year: 2019
Title: Identification and Characterization of Mutations in Ubiquitin Required for Non-covalent Dimer Formation.
Authors: Gabrielsen, M. / Buetow, L. / Kowalczyk, D. / Zhang, W. / Sidhu, S.S. / Huang, D.T.
History
DepositionJan 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyubiquitin-B
B: Polyubiquitin-B
C: Polyubiquitin-B
D: Polyubiquitin-B
E: Polyubiquitin-B
F: Polyubiquitin-B
G: Polyubiquitin-B
H: Polyubiquitin-B
I: Polyubiquitin-B
J: Polyubiquitin-B
K: Polyubiquitin-B
L: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)106,20112
Polymers106,20112
Non-polymers00
Water3,657203
1
A: Polyubiquitin-B
B: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)17,7002
Polymers17,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-25 kcal/mol
Surface area8590 Å2
MethodPISA
2
C: Polyubiquitin-B
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)17,7002
Polymers17,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-26 kcal/mol
Surface area8440 Å2
MethodPISA
3
E: Polyubiquitin-B
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)17,7002
Polymers17,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-26 kcal/mol
Surface area8580 Å2
MethodPISA
4
G: Polyubiquitin-B
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)17,7002
Polymers17,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-21 kcal/mol
Surface area8740 Å2
MethodPISA
5
I: Polyubiquitin-B
J: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)17,7002
Polymers17,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-23 kcal/mol
Surface area8660 Å2
MethodPISA
6
K: Polyubiquitin-B
L: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)17,7002
Polymers17,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-26 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.934, 87.262, 109.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Polyubiquitin-B / Ubiquitin


Mass: 8850.115 Da / Num. of mol.: 12 / Mutation: G10V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG47
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.23→29.16 Å / Num. obs: 39807 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.058 / Net I/σ(I): 13.2
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2 / Num. unique obs: 2718 / CC1/2: 0.763 / Rpim(I) all: 0.485 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZNZ

3znz


Resolution: 2.231→29.16 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.42
RfactorNum. reflection% reflection
Rfree0.2814 1995 5.02 %
Rwork0.239 --
obs0.2411 39732 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.231→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6875 0 0 204 7079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016947
X-RAY DIFFRACTIONf_angle_d1.3219410
X-RAY DIFFRACTIONf_dihedral_angle_d14.4444341
X-RAY DIFFRACTIONf_chiral_restr0.0641180
X-RAY DIFFRACTIONf_plane_restr0.0081199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2306-2.28640.30561230.28612475X-RAY DIFFRACTION93
2.2864-2.34820.36221480.29042652X-RAY DIFFRACTION100
2.3482-2.41720.33311390.28242689X-RAY DIFFRACTION100
2.4172-2.49520.33311400.28982667X-RAY DIFFRACTION100
2.4952-2.58440.33161460.27452667X-RAY DIFFRACTION100
2.5844-2.68780.29741470.26932678X-RAY DIFFRACTION100
2.6878-2.810.32831300.27362716X-RAY DIFFRACTION100
2.81-2.9580.37261470.28082687X-RAY DIFFRACTION100
2.958-3.14310.35751480.27272688X-RAY DIFFRACTION100
3.1431-3.38550.28781410.24562701X-RAY DIFFRACTION100
3.3855-3.72560.28191420.22952717X-RAY DIFFRACTION100
3.7256-4.26320.26061460.20862736X-RAY DIFFRACTION100
4.2632-5.36570.20621460.18932767X-RAY DIFFRACTION100
5.3657-29.16340.24291520.22912897X-RAY DIFFRACTION100

+
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