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- PDB-7v9e: Crystal structure of a methyl transferase ribozyme -

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Basic information

Entry
Database: PDB / ID: 7v9e
TitleCrystal structure of a methyl transferase ribozyme
ComponentsRNA (68-MER)
KeywordsRNA / methyl transferase / ribozyme / riboswitch
Function / homology: / GUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDeng, J. / Lilley, D.M.J. / Huang, L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, China) United Kingdom
Cancer Research UKA18604 United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Structure and mechanism of a methyltransferase ribozyme.
Authors: Deng, J. / Wilson, T.J. / Wang, J. / Peng, X. / Li, M. / Lin, X. / Liao, W. / Lilley, D.M.J. / Huang, L.
History
DepositionAug 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 11, 2022Group: 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,31713
Polymers21,8841
Non-polymers1,43312
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-82 kcal/mol
Surface area11850 Å2
Unit cell
Length a, b, c (Å)50.381, 52.507, 99.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

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Components

#1: RNA chain RNA (68-MER)


Mass: 21884.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.08 M Potassium chloride, 0.02 M Barium chloride dihydrate, 0.04 M Sodium cacodylate trihydrate pH 6.8, 32% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50.38 Å / Num. obs: 21996 / % possible obs: 98.5 % / Observed criterion σ(I): 2.5 / Redundancy: 8.1 % / Biso Wilson estimate: 49.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.045 / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.622 / Num. unique obs: 1753 / CC1/2: 0.75 / Rpim(I) all: 0.42 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
ADDREFdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→24.43 Å / SU ML: 0.3698 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.6724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2706 1132 5.15 %
Rwork0.2437 20864 -
obs0.2452 21996 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1440 22 32 1494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391621
X-RAY DIFFRACTIONf_angle_d0.71522522
X-RAY DIFFRACTIONf_chiral_restr0.0316337
X-RAY DIFFRACTIONf_plane_restr0.005968
X-RAY DIFFRACTIONf_dihedral_angle_d12.638804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.410.35391710.33012632X-RAY DIFFRACTION98.63
2.41-2.530.371150.32242687X-RAY DIFFRACTION99.05
2.53-2.690.41941320.33742680X-RAY DIFFRACTION98.84
2.69-2.90.37651440.33492622X-RAY DIFFRACTION97.77
2.9-3.190.27181260.27672591X-RAY DIFFRACTION96.35
3.19-3.650.26561330.21862641X-RAY DIFFRACTION96.59
3.65-4.590.19821680.1932536X-RAY DIFFRACTION95.31
4.6-24.430.2631430.21852475X-RAY DIFFRACTION92.35
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)
12.40770296888-0.2423360091480.1568687914781.21524502899-0.5128776746352.95684087125-0.1874752769020.3853045302480.243357202488-0.121984808562-0.185428265694-0.270904441785-0.286533823080.3472724297720.3261666153360.355361159621-0.034657572586-0.03033494311520.3877750738910.0541108363370.41365000809733.49676855313.4771191574940.6796120763
26.06795888759-0.746152221689-3.214792320320.1167566533040.6813159880665.476661823240.1862602477341.054831291310.450429643348-0.747139424517-0.00569276443309-0.682126381349-0.4553824867080.383499371165-0.6357348730821.964279987370.08007967896151.556221587951.17881325212-0.3197932575951.9205531693745.0763331609-15.161590914520.7389759619
34.13710278708-0.365031900352-0.2145336487274.558957451860.9033815396343.80856955591-0.2849186552860.1623862343010.241175464091-0.3714720749220.0135438453763-0.462692110277-0.2245689557650.437370620390.1982490994530.3562716651060.01019969449450.02123067599720.477230119690.01523129004970.36691663786432.52889802473.3008978745435.9495192657
41.26155883180.198172348261-0.1027049800662.2389648755-0.9954395757421.04168390472-0.3094258111590.05532063610810.536561172680.201126300474-0.00432024177430.427907331679-0.216725216196-0.3646944335180.2910330662020.3902586448020.0948656952748-0.2140844740780.495359447542-0.01227463007880.59647231566715.763575108318.588418989339.0278653032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )AA2 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 26 )AA22 - 26
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 41 )AA27 - 41
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 69 )AA42 - 69

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