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- PDB-6qk9: A dimeric ubiquitin formed by a single amino acid substitution -

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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 / fat pad development / mitochondrion transport along microtubule / 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 / fat pad development / mitochondrion transport along microtubule / 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 / neuron projection morphogenesis / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / 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 REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / regulation of mitochondrial membrane potential / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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