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- PDB-8vyd: A novel synthase generates m4(2)C to stabilize the archaeal ribosome -

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Basic information

Entry
Database: PDB / ID: 8vyd
TitleA novel synthase generates m4(2)C to stabilize the archaeal ribosome
ComponentsSAM-dependent methyltransferase, UPF0020 family
KeywordsRNA BINDING PROTEIN / N4 / N4-dimethylcytidine / synthase / RNA modifications / hyperthermophile
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / SAM-dependent methyltransferase, UPF0020 family
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHo, P.S. / Santangelo, T.J. / Fluke, K.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2022065 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM143963 United States
National Science Foundation (NSF, United States)2124202 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM132057 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A novel N 4, N 4-dimethylcytidine in the archaeal ribosome enhances hyperthermophily.
Authors: Fluke, K.A. / Dai, N. / Wolf, E.J. / Fuchs, R.T. / Ho, P.S. / Talbott, V. / Elkins, L. / Tsai, Y.L. / Schiltz, J. / Febvre, H.P. / Czarny, R. / Robb, G.B. / Correa Jr., I.R. / Santangelo, T.J.
History
DepositionFeb 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAM-dependent methyltransferase, UPF0020 family
B: SAM-dependent methyltransferase, UPF0020 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0328
Polymers65,8942
Non-polymers1386
Water3,279182
1
A: SAM-dependent methyltransferase, UPF0020 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0857
Polymers32,9471
Non-polymers1386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SAM-dependent methyltransferase, UPF0020 family


Theoretical massNumber of molelcules
Total (without water)32,9471
Polymers32,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.670, 97.280, 89.020
Angle α, β, γ (deg.)90.000, 99.642, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein SAM-dependent methyltransferase, UPF0020 family


Mass: 32947.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK2045 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2 / References: UniProt: Q5JDR0
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris-HCL, NaCl, DTT / PH range: 9.2 - 9.3

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Data collection

DiffractionMean temperature: 77 K / Ambient temp details: Lq N2 stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→42.54 Å / Num. obs: 44882 / % possible obs: 84.53 % / Redundancy: 12.4 % / Biso Wilson estimate: 32.12 Å2 / CC1/2: 0.942 / CC star: 0.985 / Rmerge(I) obs: 0.1891 / Rpim(I) all: 0.06204 / Rrim(I) all: 0.2001 / Net I/σ(I): 14.28
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 12.5 % / Num. unique obs: 56908 / CC1/2: 0.518 / CC star: 0.826 / % possible all: 40.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→42.54 Å / SU ML: 0.3837 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.6604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2871 1598 4.1 %
Rwork0.2383 37417 -
obs0.2404 39015 84.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.82 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 6 182 4411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084384
X-RAY DIFFRACTIONf_angle_d1.12585923
X-RAY DIFFRACTIONf_chiral_restr0.0586657
X-RAY DIFFRACTIONf_plane_restr0.0111775
X-RAY DIFFRACTIONf_dihedral_angle_d6.77608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.3074800.3551750X-RAY DIFFRACTION58.6
2.02-2.090.59421240.51312790X-RAY DIFFRACTION76.74
2.09-2.170.39971150.33962831X-RAY DIFFRACTION71.07
2.17-2.270.52951420.4253385X-RAY DIFFRACTION84.34
2.27-2.390.28861430.26873379X-RAY DIFFRACTION84.12
2.39-2.540.29261740.26774003X-RAY DIFFRACTION99.9
2.54-2.730.44071430.32993422X-RAY DIFFRACTION85.19
2.73-3.010.27361700.263995X-RAY DIFFRACTION99.98
3.01-3.440.31691640.23743970X-RAY DIFFRACTION98.01
3.44-4.340.2341610.19093808X-RAY DIFFRACTION94.84
4.34-42.540.20521820.16894084X-RAY DIFFRACTION99.77
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)
14.355006456910.9086282031240.456806127723.571982841450.9420751891246.975394382210.21857334389-0.2673105045070.5161820551770.539837336123-0.0580718576375-0.165464223111-0.8818049924830.172767449475-0.07736646131630.628048201705-0.02860833369730.07324741718340.262998698776-0.0292925046770.2979897861768.35512.56634.461
27.70155887383-6.01590902524-2.754576711765.922838156911.698169734781.15407061578-0.369367016254-1.125826048180.02148862233231.335370667850.135457418640.5862911498190.0227616123588-0.5632673183380.4992317780580.4775686180310.04193585767840.04015916428350.468309936741-0.1298675821760.3808854043352.116-6.11419.871
33.013158045770.8023234470360.6066182125953.088691287011.262773611183.94874181757-0.1244297744630.6332387510830.0591010975605-0.01101281404950.1124379758680.158889495572-0.250554497880.0288837313073-0.002195126335240.1036523112050.03043607454040.02698345994170.3128209357540.02116951778460.192529091151-1.4521.2877.751
44.55265518706-1.161324193980.764324342855.711301819310.3344735940037.20375956484-0.09530540794470.684762831573-1.413130321020.407263529535-0.05838143884120.4102911807670.0718763015669-0.5396428797780.2600324976880.223085166776-0.04434730790270.06451067484120.319098107324-0.1947072439080.501415941236-7.743-14.5115.083
56.499269355072.40163194658-0.02043638098926.65160360775-1.227273865918.294535663680.114722567685-0.04922976989280.51408329880.0408275490074-0.144960674782-0.268752203826-0.3984247478960.451229875238-0.01221438265530.2508030288340.04950102882560.04489930597290.2339462356470.05216997188780.241048313602-0.35816.44182.09
62.531826809821.21695265004-1.038042041164.443579025922.624351784037.08809053186-0.115063706153-0.121920475130.004723709861940.209296565746-0.4057024270670.5119834501050.866491829925-0.6189486415740.4310811182560.344374791163-0.03106726439780.08255353568850.422238872583-0.0456081754230.262985995823-9.4246.58371.564
72.42273980509-0.755704552519-0.06154599392114.34089283151.762588734584.63133486520.0949313014898-0.0492908890843-0.3733085848330.1420843949930.0242036400080.08635443379930.7841449694630.408228971614-0.1177309098620.4505969849970.09849814863690.003766323197580.300271414887-0.001107502542510.2269777515981.087-5.61551.945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:99 )A2 - 99
2X-RAY DIFFRACTION2( CHAIN A AND RESID 100:123 )A100 - 123
3X-RAY DIFFRACTION3( CHAIN A AND RESID 124:248 )A124 - 248
4X-RAY DIFFRACTION4( CHAIN A AND RESID 249:282 )A249 - 282
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:61 )B2 - 61
6X-RAY DIFFRACTION6( CHAIN B AND RESID 62:111 )B62 - 111
7X-RAY DIFFRACTION7( CHAIN B AND RESID 112:281 )B112 - 281

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