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- PDB-7myh: Ubiquitin variant UbV.k.2 in complex with Ube2k -

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Basic information

Entry
Database: PDB / ID: 7myh
TitleUbiquitin variant UbV.k.2 in complex with Ube2k
Components
  • Ubiquitin variant UbV.k.2
  • Ubiquitin-conjugating enzyme E2 K
KeywordsTRANSFERASE/INHIBITOR / Ubiquitin conjugating enzyme / degradation / ubiquitin variant / inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of type I interferon-mediated signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / symbiont entry into host cell via disruption of host cell glycocalyx / positive regulation of peptidyl-threonine phosphorylation / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope ...free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of type I interferon-mediated signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / symbiont entry into host cell via disruption of host cell glycocalyx / positive regulation of peptidyl-threonine phosphorylation / ubiquitin-ubiquitin ligase activity / 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 / cellular response to interferon-beta / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Negative regulators of DDX58/IFIH1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / UBA/TS-N domain / Ubiquitin associated domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / UBA/TS-N domain / Ubiquitin associated domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / 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
Similarity search - Domain/homology
Tail fiber / Ubiquitin-conjugating enzyme E2 K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsMiddleton, A.J. / Day, C.L. / Teyra, J. / Sidhu, S.S.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandUOO1714 New Zealand
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Identification of Ubiquitin Variants That Inhibit the E2 Ubiquitin Conjugating Enzyme, Ube2k.
Authors: Middleton, A.J. / Teyra, J. / Zhu, J. / Sidhu, S.S. / Day, C.L.
History
DepositionMay 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 K
B: Ubiquitin variant UbV.k.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0563
Polymers32,9632
Non-polymers921
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-6 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.841, 76.088, 135.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 K / E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier ...E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier protein / Ubiquitin-conjugating enzyme E2-25 kDa / Ubiquitin-conjugating enzyme E2(25K) / Ubiquitin-conjugating enzyme E2-25K / Ubiquitin-protein ligase


Mass: 22501.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2K, HIP2, LIG / Production host: Escherichia coli (E. coli)
References: UniProt: P61086, E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin variant UbV.k.2


Mass: 10461.811 Da / Num. of mol.: 1
Mutation: K6S, L8F, T9V, K11L, T14M, K63N, E64D, T66I, H68R, L71I, G76L
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.04 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium citrate tribasic trihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20% PEG3350

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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: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.39→38.835 Å / Num. obs: 16440 / % possible obs: 99.1 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.099 / Net I/σ(I): 12.8
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.401 / Num. unique obs: 9474 / CC1/2: 0.551 / Rrim(I) all: 1.54 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DFL

5dfl


Resolution: 2.394→38.835 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 807 4.92 %
Rwork0.2063 15580 -
obs0.2084 16387 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.64 Å2 / Biso mean: 61.592 Å2 / Biso min: 27.64 Å2
Refinement stepCycle: final / Resolution: 2.394→38.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 6 24 2197
Biso mean--51.55 46.12 -
Num. residues----274
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3942-2.54410.37731360.3064250298
2.5441-2.74050.27841380.2836253999
2.7405-3.01620.31511420.2638254799
3.0162-3.45240.27141200.24372597100
3.4524-4.34880.24861400.19512627100
4.3488-38.8350.20011310.15992768100

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