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- PDB-5fg1: Structure of the conserved yeast listerin (Ltn1) selenomethionine... -

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Basic information

Entry
Database: PDB / ID: 5fg1
TitleStructure of the conserved yeast listerin (Ltn1) selenomethionine-substituted N-terminal domain, TRIGONAL FORM
ComponentsE3 ubiquitin-protein ligase listerin
KeywordsLIGASE / ubiquitin ligase / protein quality control / ribosome
Function / homology
Function and homology information


RQC complex / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / proteasomal protein catabolic process / cytosolic ribosome / rescue of stalled ribosome / protein catabolic process / RING-type E3 ubiquitin transferase ...RQC complex / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / proteasomal protein catabolic process / cytosolic ribosome / rescue of stalled ribosome / protein catabolic process / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / chromatin organization / ubiquitin-dependent protein catabolic process / chromosome, telomeric region / protein ubiquitination / zinc ion binding / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase listerin / Listerin, zinc finger, RING-type / FANCL C-terminal domain / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase listerin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsDoamekpor, S.K. / Lima, C.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061906 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure and function of the yeast listerin (Ltn1) conserved N-terminal domain in binding to stalled 60S ribosomal subunits.
Authors: Doamekpor, S.K. / Lee, J.W. / Hepowit, N.L. / Wu, C. / Charenton, C. / Leonard, M. / Bengtson, M.H. / Rajashankar, K.R. / Sachs, M.S. / Lima, C.D. / Joazeiro, C.A.
History
DepositionDec 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase listerin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2352
Polymers48,1961
Non-polymers391
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint0 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.088, 58.088, 347.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein E3 ubiquitin-protein ligase listerin / RING domain mutant killed by rtf1 deletion protein 1


Mass: 48195.641 Da / Num. of mol.: 1 / Mutation: N-terminal SL cloning artifact
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Description: Methionine auxotroph / Gene: RKR1, LTN1, YMR247C, YM9408.09C, YM9920.01C / Plasmid: PSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3
References: UniProt: Q04781, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop
Details: 7.5% (w/v) PEG8000, 0.1 M potassium chloride, and 6% (v/v) glycerol
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→49.8 Å / Num. obs: 23371 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.5
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.5 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
PHASERphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→49.786 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.38 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 1152 4.88 %Random selection
Rwork0.2014 ---
obs0.2034 23326 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→49.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 1 31 3333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043370
X-RAY DIFFRACTIONf_angle_d0.6944560
X-RAY DIFFRACTIONf_dihedral_angle_d12.0111248
X-RAY DIFFRACTIONf_chiral_restr0.032524
X-RAY DIFFRACTIONf_plane_restr0.003567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5492-2.60840.2881630.29572583X-RAY DIFFRACTION96
2.6084-2.67370.2811060.26382711X-RAY DIFFRACTION100
2.6737-2.7460.26351540.27322731X-RAY DIFFRACTION100
2.746-2.82680.24581400.25092655X-RAY DIFFRACTION100
2.8268-2.9180.26161400.23842753X-RAY DIFFRACTION100
2.918-3.02230.28841880.2492658X-RAY DIFFRACTION100
3.0223-3.14330.2745860.23742722X-RAY DIFFRACTION100
3.1433-3.28630.32131660.25132673X-RAY DIFFRACTION100
3.2863-3.45950.2681100.22752758X-RAY DIFFRACTION100
3.4595-3.67620.23181300.21272727X-RAY DIFFRACTION100
3.6762-3.95990.2399980.18942720X-RAY DIFFRACTION100
3.9599-4.35820.24471470.17462727X-RAY DIFFRACTION100
4.3582-4.98830.17311560.16272680X-RAY DIFFRACTION100
4.9883-6.28280.26861560.21212683X-RAY DIFFRACTION100
6.2828-49.79510.22941380.16712715X-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)
12.448-0.33930.74791.8829-0.72062.65170.19140.28790.0317-0.4696-0.2184-0.34230.23780.2888-0.02170.68560.29790.04870.44590.01620.641263.281741.8794392.457
21.7143-0.38682.8240.8945-1.97798.2602-0.0498-0.0175-0.0051-0.06810.11670.0373-0.0667-0.7943-0.05980.65260.264-0.06610.81220.01830.654435.270648.9409369.2878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 224 )
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 419 )

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