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- PDB-9nl4: Structure of R2 retrotransposon protein from Platysternon megacep... -

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Basic information

Entry
Database: PDB / ID: 9nl4
TitleStructure of R2 retrotransposon protein from Platysternon megacephalum after second strand nicking
Components
  • 3'UTR RNA
  • Bottom strand of target rDNA
  • R2 retrotransposon protein
  • Top strand for target rDNA
  • complementary DNA
KeywordsRNA BINDING PROTEIN/RNA/DNA / Retrotransposon / Reverse transcriptase / RNA BINDING PROTEIN-RNA-DNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesPlatysternon megacephalum (big-headed turtle)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsThawani, A. / Collins, K. / Nogales, E.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP1 HL156819 United States
CitationJournal: To Be Published
Title: Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second strand nicking
Authors: Thawani, A. / Rodriguez-Vargas, A. / Van Treeck, B. / Hassan, N.T. / Adelson, D.A. / Nogales, E. / Collins, K.
History
DepositionMar 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R2 retrotransposon protein
B: Bottom strand of target rDNA
P: complementary DNA
R: 3'UTR RNA
T: Top strand for target rDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,7139
Polymers217,4525
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 3 types, 3 molecules BPT

#2: DNA chain Bottom strand of target rDNA


Mass: 21507.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain complementary DNA


Mass: 22722.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain Top strand for target rDNA


Mass: 21654.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / RNA chain / Non-polymers , 3 types, 6 molecules AR

#1: Protein R2 retrotransposon protein


Mass: 127729.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Platysternon megacephalum (big-headed turtle)
Production host: Escherichia coli (E. coli)
#4: RNA chain 3'UTR RNA


Mass: 23837.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: R2 retrotransposon protein after second strand nicking
Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)Organism: Platysternon megacephalum (big-headed turtle)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9195
Image scansWidth: 11520 / Height: 8184

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32239 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00511180
ELECTRON MICROSCOPYf_angle_d0.94915509
ELECTRON MICROSCOPYf_dihedral_angle_d24.4012118
ELECTRON MICROSCOPYf_chiral_restr0.0631743
ELECTRON MICROSCOPYf_plane_restr0.0061654

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