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- PDB-8z9k: Crystal structure of LINE-1 ribozyme -

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Basic information

Entry
Database: PDB / ID: 8z9k
TitleCrystal structure of LINE-1 ribozyme
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: 3.86 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 23, 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)26,6277
Polymers26,5122
Non-polymers1155
Water724
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)53,25414
Polymers53,0244
Non-polymers23010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5630 Å2
ΔGint-113 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.247, 93.247, 262.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain RNA (41-MER)


Mass: 13256.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo (humans)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 6.22 Å3/Da / Density % sol: 80.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.02 M Calcium Chloride dihydrate 0.1 M Sodium Acetate trihydrate pH 4.6 30% v/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.86→80.75 Å / Num. obs: 6885 / % possible obs: 98.2 % / Redundancy: 18 % / CC1/2: 0.999 / Net I/σ(I): 22
Reflection shellResolution: 3.86→4.06 Å / Num. unique obs: 863 / CC1/2: 0.976

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.86→36.67 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 45.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3457 337 4.98 %
Rwork0.3136 --
obs0.3151 6768 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.86→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1762 5 4 1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041972
X-RAY DIFFRACTIONf_angle_d1.0053072
X-RAY DIFFRACTIONf_dihedral_angle_d14.756978
X-RAY DIFFRACTIONf_chiral_restr0.049410
X-RAY DIFFRACTIONf_plane_restr0.00782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.86-4.860.31530.28693048X-RAY DIFFRACTION95
4.86-36.670.3541840.31933383X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -36.6508 Å / Origin y: 7.9415 Å / Origin z: -36.6024 Å
111213212223313233
T1.1175 Å2-0.264 Å2-0.4059 Å2-1.4667 Å20.0521 Å2--1.1691 Å2
L4.1203 °22.2326 °2-1.9748 °2-3.0691 °2-0.7477 °2--6.6586 °2
S-0.3305 Å °1.0644 Å °0.3248 Å °-0.9754 Å °0.5906 Å °0.619 Å °1.553 Å °-1.4458 Å °-0.4083 Å °
Refinement TLS groupSelection details: all

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