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- PDB-8z8u: Crystal structure of LINE-1 ribozyme mutant - C39U -

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Basic information

Entry
Database: PDB / ID: 8z8u
TitleCrystal structure of LINE-1 ribozyme mutant - C39U
ComponentsRNA (41-MER)
KeywordsRNA / ribozyme / LINE-1
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo (humans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsRen, Y. / Huang, L. / Lin, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: A general strategy for engineering GU base pairs to facilitate RNA crystallization.
Authors: Ren, Y. / Lin, X. / Liao, W. / Peng, X. / Deng, J. / Zhang, Z. / Zhan, J. / Zhou, Y. / Westhof, E. / Lilley, D.M.J. / Wang, J. / Huang, L.
History
DepositionApr 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 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: RNA (41-MER)
B: RNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9448
Polymers26,5142
Non-polymers4306
Water36020
1
A: RNA (41-MER)
B: RNA (41-MER)
hetero molecules

A: RNA (41-MER)
B: RNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,88816
Polymers53,0284
Non-polymers86012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5620 Å2
ΔGint-105 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.871, 94.871, 261.635
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-102-

SO4

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Components

#1: RNA chain RNA (41-MER)


Mass: 13256.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo (humans)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 6.41 Å3/Da / Density % sol: 80.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Magnesium Chloride 0.05 M MES pH 5.6 2.0 M Lithium Sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979137 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979137 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. obs: 19754 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC1/2: 0.992 / Net I/σ(I): 5.8
Reflection shellResolution: 2.72→2.87 Å / Num. unique obs: 2792 / CC1/2: 0.464

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→44.59 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 955 4.88 %
Rwork0.219 --
obs0.2203 19571 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1762 22 20 1804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041984
X-RAY DIFFRACTIONf_angle_d0.9153091
X-RAY DIFFRACTIONf_dihedral_angle_d12.039978
X-RAY DIFFRACTIONf_chiral_restr0.044410
X-RAY DIFFRACTIONf_plane_restr0.00782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.860.39961250.40132590X-RAY DIFFRACTION99
2.86-3.030.37821210.34662589X-RAY DIFFRACTION99
3.03-3.270.27831370.28172606X-RAY DIFFRACTION99
3.27-3.60.2471450.22312598X-RAY DIFFRACTION99
3.6-4.120.24011410.1952654X-RAY DIFFRACTION99
4.12-5.190.19391400.17972689X-RAY DIFFRACTION100
5.19-44.590.21781460.17572890X-RAY DIFFRACTION99
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)
10.6162-0.65320.42121.1941-0.1590.46260.41330.9606-0.0989-0.0065-0.23250.6146-0.7521-0.3687-0.08180.6370.2032-0.10520.75840.13040.6863-43.019717.9502-37.2353
20.3830.8833-1.22552.0001-2.82233.9336-0.16670.40910.0545-0.26840.38480.01450.0191-0.0274-0.4690.5619-0.0843-0.08180.72720.06030.5556-28.1116.2171-49.1031
30.77660.8351-1.24680.7957-1.12733.28380.00050.23520.1626-0.10050.3280.05720.24780.0269-0.37110.5913-0.1494-0.04510.63470.08050.4669-26.552819.6689-50.4057
46.0161-3.5072-0.19266.8971-0.38534.8713-0.22590.17090.1661-0.41580.14040.8769-0.6188-1.20770.09280.60440.0719-0.21350.72020.01750.6744-50.292613.7138-39.3915
52.4326-0.0354-0.3161.3883-0.60511.66590.08070.0405-0.28820.10110.00260.21990.33150.11230.00630.5509-0.0426-0.05860.3360.02460.4349-36.15241.7539-23.2529
63.2836-0.84930.00046.75143.60691.99740.13590.5519-0.49160.0506-0.02770.36480.8024-0.2495-0.01310.7668-0.0798-0.03030.583-0.03560.5663-38.7165-6.9724-38.5734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 30 )
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 41 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 41 )

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