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- PDB-9n1f: Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex -

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Basic information

Entry
Database: PDB / ID: 9n1f
TitleCrystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex
Components
  • (Ubiquitin-conjugating enzyme E2 ...) x 2
  • E3 ubiquitin-protein ligase ARK2C
  • Ubiquitin
KeywordsTRANSFERASE / RING E3 ligase Ubiquitin PTM / LIGASE / E2~Ub conjugate
Function / homology
Function and homology information


muscle structure development / forelimb morphogenesis / error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / positive regulation of BMP signaling pathway / motor neuron axon guidance ...muscle structure development / forelimb morphogenesis / error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / positive regulation of BMP signaling pathway / motor neuron axon guidance / innervation / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / regulation of DNA repair / negative regulation of TORC1 signaling / 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 / antiviral innate immune response / 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 / positive regulation of DNA repair / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / ubiquitin binding / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / 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 / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / 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 / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / 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
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, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues ...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, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / 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
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 2 / E3 ubiquitin-protein ligase ARK2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPaluda, A. / Middleton, A.J. / Day, C.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes.
Authors: Rossig, C. / Paluda, A. / Chen, R. / Middleton, A.J. / Day, C.L.
History
DepositionJan 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase ARK2C
B: Ubiquitin-conjugating enzyme E2 N
C: Ubiquitin-conjugating enzyme E2 variant 2
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4986
Polymers52,3674
Non-polymers1312
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.735, 100.415, 142.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein E3 ubiquitin-protein ligase ARK2C / RING finger protein 165 / RNF165


Mass: 9859.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GPLGS residues remained after the N-terminal tag cleavage. N-terminal residues 1-254 were truncated. Deletion of residues 273-282. Two zinc ions coordinated.
Source: (gene. exp.) Homo sapiens (human) / Gene: ARK2C, RNF165 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6ZSG1, RING-type E3 ubiquitin transferase
#4: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal Gly76 is linked to the Lys87 of Ubc13 (chain B) via a isopeptide bond.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48

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Ubiquitin-conjugating enzyme E2 ... , 2 types, 2 molecules BC

#2: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17566.135 Da / Num. of mol.: 1 / Mutation: C87K, K92T, K94Q
Source method: isolated from a genetically manipulated source
Details: GPLGS remained after the tag N-terminal removal. Lys87 is covalently connected to the C terminal Gly76 of chain D via an isopeptide bond.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: Protein Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein


Mass: 16364.731 Da / Num. of mol.: 1 / Mutation: S32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V2, MMS2, UEV2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15819

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Non-polymers , 2 types, 66 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium Malonate and 18% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→41 Å / Num. obs: 31139 / % possible obs: 99.93 % / Redundancy: 14.5 % / Biso Wilson estimate: 45.03 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09095 / Rpim(I) all: 0.02493 / Rrim(I) all: 0.09437 / Net I/σ(I): 18.16
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.459 / Num. unique obs: 3060 / CC1/2: 0.7 / CC star: 0.908 / Rpim(I) all: 0.3888 / Rrim(I) all: 1.51 / Net I/σ(I) obs: 2.12 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
Aimless0.6.2data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2786 1513 -
Rwork0.2285 --
obs-31134 99.93 %
Refinement stepCycle: LAST / Resolution: 2.1→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 2 64 3535
LS refinement shellResolution: 2.1→2.1751 Å / Cor.coef. Fo:Fc: 0.664 / Cor.coef. Fo:Fc free: 0.498
RfactorNum. reflection
Rfree0.4395 164
Rwork0.3735 -
obs-3061

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