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- PDB-5d0m: Structure of UbE2D2:RNF165:Ub complex -

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Basic information

Entry
Database: PDB / ID: 5d0m
TitleStructure of UbE2D2:RNF165:Ub complex
Components
  • Polyubiquitin-B
  • RING finger protein 165
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / complex / ubiquitin
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 / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / virus tail ...muscle structure development / forelimb morphogenesis / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / motor neuron axon guidance / innervation / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein catabolic process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein modification process / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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 / Pectin lyase fold / Pectin lyase fold/virulence factor / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tail fiber / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase ARK2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.913 Å
AuthorsWright, J.D. / Day, C.L. / Mace, P.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity.
Authors: Wright, J.D. / Mace, P.D. / Day, C.L.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
C: RING finger protein 165
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8166
Polymers35,5913
Non-polymers2263
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.620, 62.620, 82.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 3 types, 3 molecules ACB

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...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
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein RING finger protein 165


Mass: 9799.096 Da / Num. of mol.: 1 / Fragment: UNP residues 255-346 / Mutation: del273-282, M313A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF165 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZSG1
#3: Protein Polyubiquitin-B


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: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 3 types, 103 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: SPG buffer, PEG 1500 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→31.31 Å / Num. obs: 24549 / % possible obs: 100 % / Redundancy: 6.6 % / Net I/σ(I): 19.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.913→28.005 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 1282 5.23 %Random selection
Rwork0.1787 ---
obs0.1805 24511 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.913→28.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 7 100 2304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092265
X-RAY DIFFRACTIONf_angle_d1.083069
X-RAY DIFFRACTIONf_dihedral_angle_d14.529837
X-RAY DIFFRACTIONf_chiral_restr0.047347
X-RAY DIFFRACTIONf_plane_restr0.006397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.913-1.98960.33361390.27052533X-RAY DIFFRACTION100
1.9896-2.08010.25811090.21282631X-RAY DIFFRACTION100
2.0801-2.18980.23161490.19512550X-RAY DIFFRACTION100
2.1898-2.32690.24041580.19332576X-RAY DIFFRACTION100
2.3269-2.50640.21321300.18912591X-RAY DIFFRACTION100
2.5064-2.75850.2741390.19692557X-RAY DIFFRACTION100
2.7585-3.15720.24611290.19142616X-RAY DIFFRACTION100
3.1572-3.97590.22551570.1732578X-RAY DIFFRACTION100
3.9759-28.00750.16491720.15512597X-RAY DIFFRACTION100
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)
12.8924-0.40220.95882.7031-1.39624.3294-0.0310.2227-0.13630.0497-0.1823-0.08230.07390.12740.18370.2161-0.0328-0.00470.2269-0.03770.2012-34.613181.681-14.0616
22.58460.37990.25433.5085-1.7524.62710.0787-0.7464-0.34430.7351-0.4128-0.76660.30080.46810.310.6549-0.044-0.10660.42720.14410.4693-27.580765.21639.0927
33.12891.0358-0.40163.4933-1.13632.6399-0.02140.329-0.2308-0.06540.1280.7450.3464-0.5672-0.09950.3726-0.0832-0.02970.3749-0.05250.4734-49.726565.142-6.9659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:147)
2X-RAY DIFFRACTION2(chain C and resseq 258:339)
3X-RAY DIFFRACTION3(chain B and resseq 1:76)

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