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- EMDB-49515: Structure of R2 retrotransposon protein from Platysternon megacep... -

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Basic information

Entry
Database: EMDB / ID: EMD-49515
TitleStructure of R2 retrotransposon protein from Platysternon megacephalum initiating target-primed reverse transcription
Map data
Sample
  • Complex: R2 retrotransposon protein in TPRT initiation stage
    • Protein or peptide: R2 retrotransposon protein
    • DNA: Bottom strand for target rDNA
    • DNA: Primer
    • RNA: 3'UTR RNA
    • DNA: Top strand for target rDNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
KeywordsRetrotransposon / Reverse transcriptase / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesPlatysternon megacephalum (big-headed turtle) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsThawani A / Collins K / Nogales E
Funding support United States, 2 items
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 NT / Adelson DA / Nogales E / Collins K
History
DepositionMar 2, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49515.png

Downloads & links

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Map

FileDownload / File: emd_49515.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 224 pix.
= 234.752 Å		1.05 Å/pix.
x 224 pix.
= 234.752 Å		1.05 Å/pix.
x 224 pix.
= 234.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0279
Minimum - Maximum-0.07532588 - 0.14386319
Average (Standard dev.)0.00031641885 (±0.00392945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 234.752 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49515_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49515_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : R2 retrotransposon protein in TPRT initiation stage

EntireName: R2 retrotransposon protein in TPRT initiation stage
Components
  • Complex: R2 retrotransposon protein in TPRT initiation stage
    • Protein or peptide: R2 retrotransposon protein
    • DNA: Bottom strand for target rDNA
    • DNA: Primer
    • RNA: 3'UTR RNA
    • DNA: Top strand for target rDNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE

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Supramolecule #1: R2 retrotransposon protein in TPRT initiation stage

SupramoleculeName: R2 retrotransposon protein in TPRT initiation stage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Platysternon megacephalum (big-headed turtle)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: R2 retrotransposon protein

MacromoleculeName: R2 retrotransposon protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Platysternon megacephalum (big-headed turtle)
Molecular weightTheoretical: 127.729367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QKTIIQLPND NPACPFCGDH VGKPSALNVH LKRNHGGREV EFQCSMCNKA DPKAHSILCH IPKCKGKVTE EPTGDWACET CNKQFNTKS GLSQHKRIAH PAIRNQERIA ASQPKPNSQR GKHNSCWTVE EEQLLAAFNN MFWGKKNINI LISDHIHMKT A KQISEKRR ...String:
QKTIIQLPND NPACPFCGDH VGKPSALNVH LKRNHGGREV EFQCSMCNKA DPKAHSILCH IPKCKGKVTE EPTGDWACET CNKQFNTKS GLSQHKRIAH PAIRNQERIA ASQPKPNSQR GKHNSCWTVE EEQLLAAFNN MFWGKKNINI LISDHIHMKT A KQISEKRR LLGLNKNATV TTTNPLPVSS TCHLKIRTDS PNTTTGLKDT YMCKINENIV NQGQIKFDSE VISAWMAGDS NI RSLVEST SLDILSTFLM ETPKPRKKGN NKITNKKSGK KKKWMEKRAV KKGFYKRYQH LFETDRCKLA SIILDGTERL QCQ IPLTEI LETYKSKWET LTPFEGLGQF KSHAVADNTA FEILLSAKEI MKNIKEMNKN SAPGPDKVSL RDLLLADPEC NALE KLFNT WLITGIIPNS IKECRSLLIP KTADPEALKE LGNWRPLTIG SIVLRLFSRI ITNRLAKACP INARQRGFIA TPGCS ENLK ILHTIVKQAK TSKKSLGVVF VDIAKAFDSV SHDHIMWVLQ ERGLDQHIVN IIEDSYKKIH TRMEVGTERT PPIEIK VGV KQGDPMSPLL FNLAIDPLIT ALEKANTGFS YGKNKITSLA FADDLVMLSD TWEGMNKNIQ ILETFCNLSG LKVQAKK CY GFFLSPTHDS YTINKCDAWK IDKDSLNMIQ PGESEKYLGL KVDPWIGFSK PVLAEKLTIW LKRLTEAPLK PSQKLTML N IYTIPRIIYL ADHTDTKKTL LSSLDDNIRT VVKGWLHLPP DTCNGFIYTK TRDGGLGVTR LASLIPSIQA RRLHRIATS EDETIRNIAM ANNIEEEFQN LWVTAGGKKE EIPRITDPVS IDYRLPRRIL ELLNEWEKPA PKKMYPIPCN WREAEMAHWK NLPCQGSGI EHFDNDTISN DWLQFHRGFS ERQFLMGLKI RANVYPTREY QGRGRTNKNV NCRNCTASYE SLSHILGQCP A VQGARIRR HNKLCSMLKR EAKELKWVVY EEPHLHTTEK ELRKPDLIFV KEEMALVVDV TVRFEYKEKV FEDAAAEKVR HY KDLTSQI KELTGAKEIE YFGFPLGARG KWPEINEKVL TALGMPDYQQ KRTAKRFSKR TLLYSIDVIN TFENIGKNNK NNV P

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Macromolecule #2: Bottom strand for target rDNA

MacromoleculeName: Bottom strand for target rDNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 21.507758 KDa
SequenceString: (DT)(DT)(DA)(DG)(DA)(DT)(DG)(DA)(DC)(DG) (DA)(DG)(DG)(DC)(DA)(DT)(DT)(DT)(DG)(DG) (DC)(DT)(DA)(DC)(DC)(DT)(DT)(DA)(DA) (DG)(DA)(DG)(DA)(DG)(DT)(DC)(DA)(DT)(DA) (DG) (DT)(DT)(DA)(DC)(DT)(DC) ...String:
(DT)(DT)(DA)(DG)(DA)(DT)(DG)(DA)(DC)(DG) (DA)(DG)(DG)(DC)(DA)(DT)(DT)(DT)(DG)(DG) (DC)(DT)(DA)(DC)(DC)(DT)(DT)(DA)(DA) (DG)(DA)(DG)(DA)(DG)(DT)(DC)(DA)(DT)(DA) (DG) (DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC) (DG)(DC)(DC)(DG)(DT)(DT)(DT)(DA)(DC)(DC) (DC)(DG) (DC)(DG)(DC)(DT)(DT)(DC)(DA) (DC)(DA)(DG)

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Macromolecule #3: Primer

MacromoleculeName: Primer / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.997607 KDa
SequenceString:
(DG)(DG)(DC)(DA)(DT)(DT)(DT)(DG)(DG)(DC) (DT)(DA)(DT)

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Macromolecule #5: Top strand for target rDNA

MacromoleculeName: Top strand for target rDNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 21.654875 KDa
SequenceString: (DC)(DT)(DG)(DT)(DG)(DA)(DA)(DG)(DC)(DG) (DC)(DG)(DG)(DG)(DT)(DA)(DA)(DA)(DC)(DG) (DG)(DC)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DT)(DC) (DT) (DC)(DT)(DT)(DA)(DA)(DG) ...String:
(DC)(DT)(DG)(DT)(DG)(DA)(DA)(DG)(DC)(DG) (DC)(DG)(DG)(DG)(DT)(DA)(DA)(DA)(DC)(DG) (DG)(DC)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DT)(DC) (DT) (DC)(DT)(DT)(DA)(DA)(DG)(DG)(DT) (DA)(DG)(DC)(DC)(DA)(DA)(DA)(DT)(DG)(DC) (DC)(DT) (DC)(DG)(DT)(DC)(DA)(DT)(DC) (DT)(DA)(DA)

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Macromolecule #4: 3'UTR RNA

MacromoleculeName: 3'UTR RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 95.589312 KDa
SequenceString: UAGGGUAGAU AAUCUUUGUA UAGUGGGGGG GGAUCUCAUG UACCGGGUUU CUUUUAUUUG AUUUUCAAUA AAACAGACGG UAGCUAGGU UCGCAAGGCA GCCACAAGCC AAAGAUAGGU AGGGUGCUCA UAGUGAGUAG GGACAGUGCC UUUUGAUUCA C AACGCGUC ...String:
UAGGGUAGAU AAUCUUUGUA UAGUGGGGGG GGAUCUCAUG UACCGGGUUU CUUUUAUUUG AUUUUCAAUA AAACAGACGG UAGCUAGGU UCGCAAGGCA GCCACAAGCC AAAGAUAGGU AGGGUGCUCA UAGUGAGUAG GGACAGUGCC UUUUGAUUCA C AACGCGUC AAUACCAUCU GACACGGAUA CCCUUACCGG ACUUGUCAUG AUCUCCCAGA CUUGUCCAAG GUGGACGGGC CA CCUUUAC UUAACCCGGA AAAGGAACAU AUAUUAAUUA UAUGUGUUCG GAAAAUAGCC

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 6425 / Average exposure time: 1.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: RELION SGD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 30692
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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