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- PDB-5fg0: Structure of the conserved yeast listerin (Ltn1) N-terminal domai... -

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Basic information

Entry
Database: PDB / ID: 5fg0
TitleStructure of the conserved yeast listerin (Ltn1) N-terminal domain, MONOCLINIC FORM
ComponentsE3 ubiquitin-protein ligase listerin
KeywordsLIGASE / ubiquitin ligase / protein quality control / ribosome
Function / homology
Function and homology information


RQC complex / Antigen processing: Ubiquitination & Proteasome degradation / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / subtelomeric heterochromatin formation / rescue of stalled ribosome / cytosolic ribosome / proteasomal protein catabolic process / protein catabolic process / RING-type E3 ubiquitin transferase ...RQC complex / Antigen processing: Ubiquitination & Proteasome degradation / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / subtelomeric heterochromatin formation / rescue of stalled ribosome / cytosolic ribosome / proteasomal protein catabolic process / 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 / Resolution: 2.41 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
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,1877
Polymers95,9222
Non-polymers2645
Water3,045169
1
A: E3 ubiquitin-protein ligase listerin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0623
Polymers47,9611
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase listerin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1244
Polymers47,9611
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.514, 80.352, 97.325
Angle α, β, γ (deg.)90.00, 116.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 47961.164 Da / Num. of mol.: 2 / Mutation: N-terminal SL cloning artifact
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RKR1, LTN1, YMR247C, YM9408.09C, YM9920.01C / Plasmid: PSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIL
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.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 7% (w/v) PEG8000, 0.1 M potassium chloride, and 2.5% (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: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. obs: 46438 / % possible obs: 98 % / Redundancy: 3.2 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.6
Reflection shellResolution: 2.41→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.3 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.41→48.347 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 23.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 1880 4.05 %Random selection
Rwork0.1759 ---
obs0.1774 46411 97.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→48.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 14 169 6770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036740
X-RAY DIFFRACTIONf_angle_d0.6089099
X-RAY DIFFRACTIONf_dihedral_angle_d10.1112494
X-RAY DIFFRACTIONf_chiral_restr0.031050
X-RAY DIFFRACTIONf_plane_restr0.0031130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4083-2.47340.30031290.24663082X-RAY DIFFRACTION88
2.4734-2.54620.26371420.23163413X-RAY DIFFRACTION98
2.5462-2.62840.26561380.21423414X-RAY DIFFRACTION98
2.6284-2.72230.26471470.2173451X-RAY DIFFRACTION99
2.7223-2.83130.27471450.21893421X-RAY DIFFRACTION99
2.8313-2.96010.26041440.213486X-RAY DIFFRACTION99
2.9601-3.11620.25841470.21033402X-RAY DIFFRACTION98
3.1162-3.31140.2291460.21013461X-RAY DIFFRACTION99
3.3114-3.5670.23651480.19083447X-RAY DIFFRACTION99
3.567-3.92580.21111470.16613475X-RAY DIFFRACTION99
3.9258-4.49350.17181410.14563462X-RAY DIFFRACTION98
4.4935-5.65990.16541540.14733497X-RAY DIFFRACTION99
5.6599-48.35710.18971520.1513520X-RAY DIFFRACTION98
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)
11.81790.9755-0.81872.5064-0.23341.66310.0822-0.09520.0381-0.7195-0.1965-0.0364-0.25580.1052-0.03790.55110.0282-0.02990.2665-0.02160.2849204.391943.165718.2949
22.5867-0.2035-0.90340.906-0.03861.0130.0379-0.03120.04450.01020.06450.1806-0.074-0.20360.00020.28660.0147-0.01790.35230.02590.3617176.486935.881942.4506
31.9197-0.2997-0.36242.1028-0.26912.4595-0.00340.14740.0608-0.3269-0.0988-0.2408-0.07530.13350.00010.37920.01460.04850.30690.00780.2848204.79056.206412.836
42.84330.4399-0.96140.8815-0.34870.90740.0450.0059-0.03850.0090.02290.07590.1228-0.17070.00180.27960.0044-0.0250.2985-0.03180.3288178.8208-4.348536.9301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 225 )
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 420 )
3X-RAY DIFFRACTION3chain 'B' and (resid 14 through 224 )
4X-RAY DIFFRACTION4chain 'B' and (resid 225 through 420 )

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