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- PDB-8htd: Crystal structure of an effector from Chromobacterium violaceum i... -

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Basic information

Entry
Database: PDB / ID: 8htd
TitleCrystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin
Components
  • NAD(+)--protein-threonine ADP-ribosyltransferase
  • Ubiquitin
KeywordsTRANSFERASE / ubiquitination
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / host cell / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation ...glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / host cell / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40A fusion protein / NAD(+)--protein-threonine ADP-ribosyltransferase
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
Saccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 Å
AuthorsTan, J. / Wang, X. / Zhou, Y. / Zhu, Y.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81530068 China
National Natural Science Foundation of China (NSFC)81322024 China
National Natural Science Foundation of China (NSFC)31370722 China
National Natural Science Foundation of China (NSFC)81561130162 China
National Natural Science Foundation of China (NSFC)81501717 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Molecular basis of threonine ADP-ribosylation of ubiquitin by bacterial ARTs.
Authors: Tan, J. / Xu, Y. / Wang, X. / Yan, F. / Xian, W. / Liu, X. / Chen, Y. / Zhu, Y. / Zhou, Y.
History
DepositionDec 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(+)--protein-threonine ADP-ribosyltransferase
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)34,6482
Polymers34,6482
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.520, 74.644, 50.358
Angle α, β, γ (deg.)90.000, 99.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD(+)--protein-threonine ADP-ribosyltransferase / Adenosine diphosphate-ribosyltransferase / ADP-ribosyltransferase / Type III effector CteC


Mass: 26078.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: cteC, CV_1467 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7NY09, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein Ubiquitin


Mass: 8568.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: RPL40A, UBI1, YIL148W / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CH08
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, pH 6.5, 200 mM sodium acetate, 28% to 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.848→50 Å / Num. obs: 22527 / % possible obs: 93.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.05 / Rrim(I) all: 0.098 / Χ2: 1.742 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.883.60.26111670.9010.1580.3060.93497.4
1.88-1.923.60.25311330.930.1520.2960.92293.6
1.92-1.953.60.23211540.9360.140.2721.02996.5
1.95-1.993.60.20211370.9340.1230.2371.07395.5
1.99-2.043.60.18511250.9470.1120.2171.21893.4
2.04-2.083.60.18611130.9620.1120.2181.2994.4
2.08-2.143.60.17411030.9620.1040.2031.49590
2.14-2.193.60.16910180.9630.1020.1981.54584.6
2.19-2.263.70.14311490.970.0850.1671.61194.8
2.26-2.333.70.13311570.9720.0790.1551.6397.6
2.33-2.413.70.12611730.9730.0770.1481.75694.7
2.41-2.513.70.11711250.9720.0710.1371.83396.1
2.51-2.633.70.10611250.9820.0630.1241.93192.8
2.63-2.763.60.09810860.9830.0590.1151.99389.8
2.76-2.943.70.09610810.980.0580.1122.28989.6
2.94-3.163.70.08611680.9850.0520.1012.39296.4
3.16-3.483.70.07711460.9830.0470.0912.54994.9
3.48-3.993.60.06910970.9890.0420.0812.65990.4
3.99-5.023.70.06111080.9910.0370.0722.43890.4
5.02-503.70.06311620.9930.0370.0732.15593.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.848→41.373 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 25.86
RfactorNum. reflection% reflection
Rfree0.2253 1126 5 %
Rwork0.1881 --
obs0.19 22505 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.49 Å2 / Biso mean: 29.1709 Å2 / Biso min: 7.16 Å2
Refinement stepCycle: final / Resolution: 1.848→41.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 0 274 2553
Biso mean---36.01 -
Num. residues----293
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.848-1.9320.33191420.2424270595
1.932-2.03390.30341430.2306270295
2.0339-2.16130.28961360.2226260491
2.1613-2.32810.24271410.202265793
2.3281-2.56240.25811430.2022272895
2.5624-2.93310.24761360.201259091
2.9331-3.6950.19831450.1734273195
3.695-41.3730.17611400.1617266291
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)
11.04990.85310.02480.5241-0.2524-0.051-0.1292-0.1504-0.1069-0.228-0.0102-0.0612-0.05320.0013-0.02130.15830.06390.01450.1246-0.00370.139819.79713.613614.905
20.47760.2216-0.03770.26250.15541.1273-0.1283-0.0265-0.08920.17080.3237-0.09271.2570.8710.09380.30720.3225-0.02630.3949-0.0780.14536.8719.18-9.9125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 44:276)A44 - 276
2X-RAY DIFFRACTION2(chain B and resseq 1:75)B1 - 75

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