[English] 日本語
Yorodumi
- PDB-3ugb: UbcH5c~Ubiquitin Conjugate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ugb
TitleUbcH5c~Ubiquitin Conjugate
Components
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 D3
KeywordsLIGASE/PROTEIN BINDING / E2 ubiquitin-conjugating enzyme / ubiquitin / Ubl conjugation pathway / oxyester bond / ubiquitin-protein ligase activity / LIGASE-PROTEIN BINDING complex
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination ...(E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / 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 / Peroxisomal protein import / Termination of translesion DNA synthesis / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPage, R.C. / Pruneda, J.N. / Klevit, R.E. / Misra, S.
CitationJournal: Biochemistry / Year: 2012
Title: Structural insights into the conformation and oligomerization of E2~ubiquitin conjugates.
Authors: Page, R.C. / Pruneda, J.N. / Amick, J. / Klevit, R.E. / Misra, S.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D3
B: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4514
Polymers25,2672
Non-polymers1842
Water2,306128
1
A: Ubiquitin-conjugating enzyme E2 D3
B: Polyubiquitin-C
hetero molecules

A: Ubiquitin-conjugating enzyme E2 D3
B: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9028
Polymers50,5344
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Unit cell
Length a, b, c (Å)42.027, 52.510, 53.114
Angle α, β, γ (deg.)90.00, 101.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating ...Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 16690.068 Da / Num. of mol.: 1 / Fragment: unp residues 1-147 / Mutation: C85S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC5C, UBCH5C, UBE2D2, UBE2D3 / Plasmid: pET28N / Production host: Escherichia coli (E. coli) / References: UniProt: P61077, ubiquitin-protein ligase
#2: Protein Polyubiquitin-C / Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: unp residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M tri-potassium citrate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 9, 2011 / Details: mirrors
RadiationMonochromator: VariMax confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→52.51 Å / Num. all: 9319 / Num. obs: 9319 / % possible obs: 97.1 % / Redundancy: 4.89 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 5 / % possible all: 78.2

-
Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix 1.7.2_869)model building
PHENIX(phenix.refine: 1.7.2_869)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIX1.7.2_869phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3TGD AND 1UBQ

3tgd

1ubq


Resolution: 2.35→29.618 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 467 5.02 %
Rwork0.2108 --
obs0.213 9298 96.95 %
all-9298 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.985 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8773 Å20 Å23.1039 Å2
2--3.4703 Å20 Å2
3---0.407 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 12 128 1907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141819
X-RAY DIFFRACTIONf_angle_d1.0712466
X-RAY DIFFRACTIONf_dihedral_angle_d14.97696
X-RAY DIFFRACTIONf_chiral_restr0.089274
X-RAY DIFFRACTIONf_plane_restr0.012320
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)
16.54713.23380.90083.9464-0.0444.465-0.0814-0.0414-1.0833-0.31970.0609-0.86880.2180.69010.10540.1840.02340.00340.36930.03030.32117.2229-0.8634-35.8991
23.79682.8299-1.20383.4229-0.2782.2792-0.08270.3466-0.1317-0.39850.001-0.1624-0.0015-0.01940.10160.10720.0813-0.01340.2544-0.00380.1396-2.95810.8857-32.5569
33.75440.5645-2.23275.9118-3.02067.1510.39750.24360.32760.0273-0.29220.4697-0.2389-0.1844-0.11350.0896-0.00620.00680.1716-0.00920.1498-12.89190.6069-25.6323
47.84376.63980.09796.89810.7892.0924-0.04750.0034-0.01140.0761-0.3957-0.3117-0.260.30030.17770.1341-0.0413-0.0820.26270.10670.18450.79431.139-22.7659
52.2101-0.4857-2.24216.5462-4.64768.5021-0.0384-0.27860.1360.6649-0.03230.3149-0.28120.19630.11550.2617-0.02630.03670.1314-0.030.2194-14.8559-3.6068-12.6993
63.01151.2910.49362.83980.81612.0611-0.12640.3533-0.10890.0486-0.14220.50360.0681-0.3173-0.31880.1048-0.0458-0.03650.1724-0.12490.4373-18.8259-11.7882-23.4024
74.24781.15690.0845.99092.17334.36080.0105-0.0368-0.2206-0.02730.02050.61140.0515-0.65040.06880.2585-0.0519-0.01750.27020.03660.2641-33.80188.0583-5.8649
83.2583-2.92-0.7353.14930.25123.3699-0.0757-0.4144-0.07710.20750.24720.02960.1384-0.1141-0.0810.3077-0.0653-0.04150.20310.00020.1286-24.406210.558-4.9984
92.2801-0.5409-0.97812.47250.09862.2832-0.05120.21370.03850.39380.06370.33880.0251-0.34910.06140.1823-0.0797-0.00550.08070.03320.0889-28.268814.1792-7.2435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:25)
2X-RAY DIFFRACTION2chain 'A' and (resseq 26:65)
3X-RAY DIFFRACTION3chain 'A' and (resseq 66:84)
4X-RAY DIFFRACTION4chain 'A' and (resseq 85:111)
5X-RAY DIFFRACTION5chain 'A' and (resseq 112:130)
6X-RAY DIFFRACTION6chain 'A' and (resseq 131:147)
7X-RAY DIFFRACTION7chain 'B' and (resseq 1:22)
8X-RAY DIFFRACTION8chain 'B' and (resseq 23:54)
9X-RAY DIFFRACTION9chain 'B' and (resseq 55:76)

+
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