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- PDB-7r71: Crystal Structure of the UbArk2C-UbcH5b~Ub complex -

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Basic information

Entry
Database: PDB / ID: 7r71
TitleCrystal Structure of the UbArk2C-UbcH5b~Ub complex
Components
  • Ubiquitin
  • Ubiquitin,E3 ubiquitin-protein ligase RNF165
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsTRANSFERASE / RING E3 ligase Ubiquitin PTM / LIGASE / E2~Ub conjugate
Function / homology
Function and homology information


muscle structure development / forelimb morphogenesis / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / motor neuron axon guidance / innervation / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination ...muscle structure development / forelimb morphogenesis / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / motor neuron axon guidance / innervation / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / 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 / Prevention of phagosomal-lysosomal fusion / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / protein modification process / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / protein catabolic process / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Ubiquitin-dependent degradation of Cyclin D / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / SCF-beta-TrCP mediated degradation of Emi1 / Deactivation of the beta-catenin transactivating complex / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Stabilization of p53 / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Termination of translesion DNA synthesis / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / Regulation of TNFR1 signaling / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function
E3 ubiquitin-protein ligase MBR1/2-like / Zinc finger, RING-CH-type / The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...E3 ubiquitin-protein ligase MBR1/2-like / Zinc finger, RING-CH-type / The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase ARK2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPaluda, A. / Middleton, A.J. / Mace, P.D. / Day, C.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: Nat Commun / Year: 2022
Title: Ubiquitin and a charged loop regulate the ubiquitin E3 ligase activity of Ark2C.
Authors: Paluda, A. / Middleton, A.J. / Rossig, C. / Mace, P.D. / Day, C.L.
History
DepositionJun 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin,E3 ubiquitin-protein ligase RNF165
D: Ubiquitin
C: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2595
Polymers46,1293
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.330, 75.668, 99.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Ubiquitin,E3 ubiquitin-protein ligase RNF165 / Ark2C fused to Ubiquitin


Mass: 20337.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GPLGS remained after the tag cleavage. Followed by a fusion of Ubiquitin and Ark2C dN254 proteins with a 10 residue linker GESGSGGSG
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC, RNF165 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0CG48, UniProt: Q6ZSG1, RING-type E3 ubiquitin transferase
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WT Ubiquitin, untagged / Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48
#3: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 17214.643 Da / Num. of mol.: 1 / Mutation: C21S, S22R, C85K, C107S, C111S
Source method: isolated from a genetically manipulated source
Details: GPLGS remained after the tag removal, followed by the UbcH5b with 5 mutations. C21S, S22R, C85K, C107S, C111S
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MMT pH 6.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.796→46.99 Å / Num. obs: 10462 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 57.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.046 / Rrim(I) all: 0.169 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.9513.71.1082039314850.9340.3071.152.699
8.84-46.9910.70.04641553880.9980.0140.04837.799.5

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V3L

4v3l


Resolution: 2.8→43.591 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 986 9.48 %
Rwork0.2261 9419 -
obs0.2305 10405 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.94 Å2 / Biso mean: 75.6127 Å2 / Biso min: 38.71 Å2
Refinement stepCycle: final / Resolution: 2.8→43.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 2 0 2969
Biso mean--54.26 --
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023038
X-RAY DIFFRACTIONf_angle_d0.5534109
X-RAY DIFFRACTIONf_dihedral_angle_d12.7121885
X-RAY DIFFRACTIONf_chiral_restr0.042462
X-RAY DIFFRACTIONf_plane_restr0.004530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.796-2.94290.38941480.3312128699
2.9429-3.12720.33261410.29651324100
3.1272-3.36860.34411320.25711328100
3.3686-3.70740.31551400.2461320100
3.7074-4.24350.26911460.20691334100
4.2435-5.34480.24921330.19441381100
5.3448-43.5910.20611460.20561446100
Refinement TLS params.Method: refined / Origin x: -11.3022 Å / Origin y: -15.9579 Å / Origin z: 3.8552 Å
111213212223313233
T0.7104 Å2-0.0965 Å2-0.0186 Å2-0.4164 Å20.0114 Å2--0.4042 Å2
L0.0351 °2-0.2564 °2-0.2135 °2-1.8207 °21.0543 °2--1.9161 °2
S0.0212 Å °-0.0405 Å °0.0585 Å °0.3056 Å °-0.0513 Å °-0.0426 Å °0.3286 Å °-0.0738 Å °0.0356 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-3 - 341
2X-RAY DIFFRACTION1allD3 - 76
3X-RAY DIFFRACTION1allC0 - 147
4X-RAY DIFFRACTION1allB401 - 402

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