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- PDB-9kbr: Crystal structure of the methyltransferase-ribozyme 1 bound to DN... -

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Basic information

Entry
Database: PDB / ID: 9kbr
TitleCrystal structure of the methyltransferase-ribozyme 1 bound to DNA substrate (with 1-methyl-adenosine)
Components
  • DNA (5'-D(*CP*CP*AP*CP*TP*GP*(MA7)P*GP*AP*GP*CP*TP*TP*C)-3')
  • RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3')
  • RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3')
KeywordsDNA-RNA HYBRID / Ribozyme / Methyltransferase / MTR1 / O6-methylguanine
Function / homologyGUANINE / DNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHe, Y. / Yan, K. / Lilley, D.M.J. / Huang, L.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
Cancer Research UKA18604 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the methyltransferase ribozyme MTR1 bound to DNA substrate
Authors: He, Y. / Yan, K. / Lilley, D.M.J. / Huang, L.
History
DepositionOct 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*CP*TP*GP*(MA7)P*GP*AP*GP*CP*TP*TP*C)-3')
B: RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3')
C: RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8968
Polymers19,6533
Non-polymers2435
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-35 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.196, 69.196, 65.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain DNA (5'-D(*CP*CP*AP*CP*TP*GP*(MA7)P*GP*AP*GP*CP*TP*TP*C)-3')


Mass: 4255.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3')


Mass: 7641.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3')


Mass: 7755.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 6 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 4 Å3/Da / Density % sol: 69.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM NaCl, 100mM LiCl, 10mM MgCl2, 34% MPD

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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 S 9M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→48.93 Å / Num. obs: 9120 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 88.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Net I/σ(I): 15.4
Reflection shellResolution: 2.65→2.79 Å / Rmerge(I) obs: 5.85 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1315 / CC1/2: 0.389 / Rpim(I) all: 2.303 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→34.6 Å / SU ML: 0.3966 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2231 455 5.12 %
Rwork0.1887 8438 -
obs0.1905 8893 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.23 Å2
Refinement stepCycle: LAST / Resolution: 2.65→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1301 15 1 1317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081466
X-RAY DIFFRACTIONf_angle_d1.20362273
X-RAY DIFFRACTIONf_chiral_restr0.0452292
X-RAY DIFFRACTIONf_plane_restr0.005763
X-RAY DIFFRACTIONf_dihedral_angle_d13.9165700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-3.030.37041540.35352648X-RAY DIFFRACTION92.9
3.03-3.820.26971540.22992876X-RAY DIFFRACTION99.93
3.82-34.60.18631470.1582914X-RAY DIFFRACTION99.87
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)
11.06588128564-0.6494574320920.7442670191031.28120786469-1.701540868492.00551725377-1.23225905026-0.785790185169-2.01928133945-0.407460745022-0.2269463759581.055603010551.25281468412-0.1439928797660.0033566576631.47158387417-0.3548941007470.2044826132661.43846914245-0.2267190897161.5871998823216.577474679218.4477518993-5.57000248704
27.435999764171.52123914256-0.2040219270382.389069925150.3268028462455.17314314085-0.22968157908-0.126931526766-0.646122363305-0.59090540469-0.2188191138440.23107161016-0.299441847713-0.407201715865-0.008056977873970.807772273580.0830511402362-0.08504839908240.5827370628590.03191563138330.64319045538627.392332880132.6973346792-2.80052767527
34.42799665568-0.0909214749137-2.380988550992.81723523488-0.8127550900144.21636026002-0.4066664830090.160135232867-0.550966826059-0.0771357104388-0.05525634019880.8306325721330.146423747827-1.036150436930.000115406346220.7134294853290.143780922176-0.09830176672980.923837268909-0.1459048793430.86406132126917.835991128732.23135232881.87865042126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:14)AA1 - 14
2X-RAY DIFFRACTION2(chain B and resseq 1:24)BB1 - 24
3X-RAY DIFFRACTION3(chain C and resseq 25:48)CC25 - 48

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