[English] 日本語
Yorodumi
- PDB-8ic9: Lys48-linked K48C-diubiquitin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ic9
TitleLys48-linked K48C-diubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin
KeywordsSIGNALING PROTEIN / UBIQUITIN / ISOPEPTIDE BOND
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: 1.25 Å
AuthorsHiranyakorn, M. / Yagi-Utsumi, M. / Yanaka, S. / Ohtsuka, N. / Momiyama, N. / Satoh, T. / Kato, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18H05229 Japan
Japan Science and TechnologyJPMJPR22AC Japan
CitationJournal: Int J Mol Sci / Year: 2023
Title: Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains.
Authors: Hiranyakorn, M. / Yagi-Utsumi, M. / Yanaka, S. / Ohtsuka, N. / Momiyama, N. / Satoh, T. / Kato, K.
History
DepositionFeb 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyubiquitin-B
B: Ubiquitin
C: Polyubiquitin-B
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)34,2554
Polymers34,2554
Non-polymers00
Water3,135174
1
A: Polyubiquitin-B
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1282
Polymers17,1282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area7750 Å2
MethodPISA
2
C: Polyubiquitin-B
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1282
Polymers17,1282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-6 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.790, 31.191, 25.272
Angle α, β, γ (deg.)90.000, 106.929, 88.650
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Polyubiquitin-B


Mass: 8550.794 Da / Num. of mol.: 2 / Mutation: K48C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
PH range: 4.0-4.5

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2021
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.25→19.641 Å / Num. obs: 66682 / % possible obs: 95.1 % / Redundancy: 3.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.7
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 11849 / CC1/2: 0.911 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→19.641 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.222 / SU B: 2.28 / SU ML: 0.041 / Average fsc free: 0.9412 / Average fsc work: 0.9488 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2188 3360 5.039 %
Rwork0.1861 63320 -
all0.188 --
obs-66680 95.071 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.291 Å2
Baniso -1Baniso -2Baniso -3
1--1.427 Å20.758 Å2-0.568 Å2
2--1.236 Å20.399 Å2
3---0.491 Å2
Refinement stepCycle: LAST / Resolution: 1.25→19.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 0 174 2574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152468
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6573282
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5915710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01923.548124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33615498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0181516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.2120.2357
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22266
X-RAY DIFFRACTIONr_nbtor_refined0.160.21145
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2133
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.228
X-RAY DIFFRACTIONr_nbd_other0.2170.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.230
X-RAY DIFFRACTIONr_mcbond_it3.8361.9631216
X-RAY DIFFRACTIONr_mcbond_other3.8241.9571214
X-RAY DIFFRACTIONr_mcangle_it4.6072.931514
X-RAY DIFFRACTIONr_mcangle_other4.5912.931514
X-RAY DIFFRACTIONr_scbond_it3.9582.4661224
X-RAY DIFFRACTIONr_scbond_other3.9592.4661224
X-RAY DIFFRACTIONr_scangle_it4.6313.4791766
X-RAY DIFFRACTIONr_scangle_other4.6293.4791766
X-RAY DIFFRACTIONr_lrange_it5.08723.3412465
X-RAY DIFFRACTIONr_lrange_other5.08823.3352463
X-RAY DIFFRACTIONr_rigid_bond_restr3.19634908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.3722880.3924487X-RAY DIFFRACTION93.2253
1.282-1.3170.3572500.3574478X-RAY DIFFRACTION93.1259
1.317-1.3550.3432470.3444357X-RAY DIFFRACTION93.806
1.355-1.3970.3862160.3144230X-RAY DIFFRACTION94.1351
1.397-1.4420.3122120.3044110X-RAY DIFFRACTION93.7527
1.442-1.4930.2831970.2624104X-RAY DIFFRACTION94.6106
1.493-1.5490.2751680.2213864X-RAY DIFFRACTION94.4262
1.549-1.6120.2441970.2123734X-RAY DIFFRACTION94.4498
1.612-1.6830.2441960.1963614X-RAY DIFFRACTION95.3931
1.683-1.7640.2321990.1623382X-RAY DIFFRACTION95.1887
1.764-1.8590.2161990.1543276X-RAY DIFFRACTION96.1007
1.859-1.9710.241620.1263169X-RAY DIFFRACTION96.4948
1.971-2.1050.1711370.1393006X-RAY DIFFRACTION96.8269
2.105-2.2720.1751450.1422722X-RAY DIFFRACTION96.8581
2.272-2.4860.1941460.1482553X-RAY DIFFRACTION97.2613
2.486-2.7740.2231120.1612312X-RAY DIFFRACTION97.2713
2.774-3.1920.228940.1562064X-RAY DIFFRACTION97.4266
3.192-3.8850.175920.1721727X-RAY DIFFRACTION97.4812
3.885-5.3940.167370.1671397X-RAY DIFFRACTION97.551
5.394-19.6410.172660.258734X-RAY DIFFRACTION93.5673

+
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