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- EMDB-37859: SpCas9-MMLV RT-pegRNA-target DNA complex (initiation) -

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Entry
Database: EMDB / ID: EMD-37859
TitleSpCas9-MMLV RT-pegRNA-target DNA complex (initiation)
Map data
Sample
  • Complex: SpCas9-MMLV RT-pegRNA-target DNA complex
    • Protein or peptide: CRISPR-associated endonuclease Cas9/Csn1
    • Protein or peptide: Gag-Pol polyprotein
    • DNA: DNA (51-MER)
    • DNA: DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3')
    • RNA: RNA (115-MER)
    • Other: DNA/RNA (35-MER)
KeywordsCRISPR-Cas / RNA BINDING PROTEIN
Function / homology
Function and homology information


host cell late endosome membrane / maintenance of CRISPR repeat elements / virion assembly / 3'-5' exonuclease activity / DNA endonuclease activity / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity ...host cell late endosome membrane / maintenance of CRISPR repeat elements / virion assembly / 3'-5' exonuclease activity / DNA endonuclease activity / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / defense response to virus / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / metal ion binding / plasma membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / : / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / : / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, bridge helix / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / Bridge helix of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / Cas9 RuvC domain / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Gag-Pol polyprotein / CRISPR-associated endonuclease Cas9/Csn1
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria) / Streptococcus pyogenes serotype M1 (bacteria) / Moloney murine leukemia virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsShuto Y / Nakagawa R / Hoki M / Omura SN / Hirano H / Itoh Y / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121012 Japan
CitationJournal: Nature / Year: 2024
Title: Structural basis for pegRNA-guided reverse transcription by a prime editor.
Authors: Yutaro Shuto / Ryoya Nakagawa / Shiyou Zhu / Mizuki Hoki / Satoshi N Omura / Hisato Hirano / Yuzuru Itoh / Feng Zhang / Osamu Nureki /
Abstract: The prime editor system composed of Streptococcus pyogenes Cas9 nickase (nSpCas9) and engineered Moloney murine leukaemia virus reverse transcriptase (M-MLV RT) collaborates with a prime editing ...The prime editor system composed of Streptococcus pyogenes Cas9 nickase (nSpCas9) and engineered Moloney murine leukaemia virus reverse transcriptase (M-MLV RT) collaborates with a prime editing guide RNA (pegRNA) to facilitate a wide variety of precise genome edits in living cells. However, owing to a lack of structural information, the molecular mechanism of pegRNA-guided reverse transcription by the prime editor remains poorly understood. Here we present cryo-electron microscopy structures of the SpCas9-M-MLV RTΔRNaseH-pegRNA-target DNA complex in multiple states. The termination structure, along with our functional analysis, reveals that M-MLV RT extends reverse transcription beyond the expected site, resulting in scaffold-derived incorporations that cause undesired edits at the target loci. Furthermore, structural comparisons among the pre-initiation, initiation and elongation states show that M-MLV RT remains in a consistent position relative to SpCas9 during reverse transcription, whereas the pegRNA-synthesized DNA heteroduplex builds up along the surface of SpCas9. On the basis of our structural insights, we rationally engineered pegRNA variants and prime-editor variants in which M-MLV RT is fused within SpCas9. Collectively, our findings provide structural insights into the stepwise mechanism of prime editing, and will pave the way for the development of a versatile prime editing toolbox.
History
DepositionOct 21, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37859.png

Downloads & links

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Map

FileDownload / File: emd_37859.map.gz / Format: CCP4 / Size: 19.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 172 pix.
= 223.067 Å		1.3 Å/pix.
x 172 pix.
= 223.067 Å		1.3 Å/pix.
x 172 pix.
= 223.067 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2969 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.393
Minimum - Maximum-0.22723447 - 2.031961
Average (Standard dev.)0.0028424745 (±0.084183015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin424242
Dimensions172172172
Spacing172172172
CellA=B=C: 223.0668 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37859_msk_1.map
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Half map: #2

Fileemd_37859_half_map_1.map
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Half map: #1

Fileemd_37859_half_map_2.map
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Sample components

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Entire : SpCas9-MMLV RT-pegRNA-target DNA complex

EntireName: SpCas9-MMLV RT-pegRNA-target DNA complex
Components
  • Complex: SpCas9-MMLV RT-pegRNA-target DNA complex
    • Protein or peptide: CRISPR-associated endonuclease Cas9/Csn1
    • Protein or peptide: Gag-Pol polyprotein
    • DNA: DNA (51-MER)
    • DNA: DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3')
    • RNA: RNA (115-MER)
    • Other: DNA/RNA (35-MER)

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Supramolecule #1: SpCas9-MMLV RT-pegRNA-target DNA complex

SupramoleculeName: SpCas9-MMLV RT-pegRNA-target DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pyogenes (bacteria)

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Macromolecule #1: CRISPR-associated endonuclease Cas9/Csn1

MacromoleculeName: CRISPR-associated endonuclease Cas9/Csn1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes serotype M1 (bacteria)
Molecular weightTheoretical: 158.457578 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: DKKYSIGLAI GTNSVGWAVI TDEYKVPSKK FKVLGNTDRH SIKKNLIGAL LFDSGETAEA TRLKRTARRR YTRRKNRICY LQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH M IKFRGHFL ...String:
DKKYSIGLAI GTNSVGWAVI TDEYKVPSKK FKVLGNTDRH SIKKNLIGAL LFDSGETAEA TRLKRTARRR YTRRKNRICY LQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH M IKFRGHFL IEGDLNPDNS DVDKLFIQLV QTYNQLFEEN PINASGVDAK AILSARLSKS RRLENLIAQL PGEKKNGLFG NL IALSLGL TPNFKSNFDL AEDAKLQLSK DTYDDDLDNL LAQIGDQYAD LFLAAKNLSD AILLSDILRV NTEITKAPLS ASM IKRYDE HHQDLTLLKA LVRQQLPEKY KEIFFDQSKN GYAGYIDGGA SQEEFYKFIK PILEKMDGTE ELLVKLNRED LLRK QRTFD NGSIPHQIHL GELHAILRRQ EDFYPFLKDN REKIEKILTF RIPYYVGPLA RGNSRFAWMT RKSEETITPW NFEEV VDKG ASAQSFIERM TNFDKNLPNE KVLPKHSLLY EYFTVYNELT KVKYVTEGMR KPAFLSGEQK KAIVDLLFKT NRKVTV KQL KEDYFKKIEC FDSVEISGVE DRFNASLGTY HDLLKIIKDK DFLDNEENED ILEDIVLTLT LFEDREMIEE RLKTYAH LF DDKVMKQLKR RRYTGWGRLS RKLINGIRDK QSGKTILDFL KSDGFANRNF MQLIHDDSLT FKEDIQKAQV SGQGDSLH E HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK GQKNSRERMK RIEEGIKELG SQILKEHPV ENTQLQNEKL YLYYLQNGRD MYVDQELDIN RLSDYDVDAI VPQSFLKDDS IDNKVLTRSD KNRGKSDNVP SEEVVKKMKN YWRQLLNAK LITQRKFDNL TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS K LVSDFRKD FQFYKVREIN NYHHAHDAYL NAVVGTALIK KYPKLESEFV YGDYKVYDVR KMIAKSEQEI GKATAKYFFY SN IMNFFKT EITLANGEIR KRPLIETNGE TGEIVWDKGR DFATVRKVLS MPQVNIVKKT EVQTGGFSKE SILPKRNSDK LIA RKKDWD PKKYGGFDSP TVAYSVLVVA KVEKGKSKKL KSVKELLGIT IMERSSFEKN PIDFLEAKGY KEVKKDLIIK LPKY SLFEL ENGRKRMLAS AGELQKGNEL ALPSKYVNFL YLASHYEKLK GSPEDNEQKQ LFVEQHKHYL DEIIEQISEF SKRVI LADA NLDKVLSAYN KHRDKPIREQ AENIIHLFTL TNLGAPAAFK YFDTTIDRKR YTSTKEVLDA TLIHQSITGL YETRID LSQ LGGD

UniProtKB: CRISPR-associated endonuclease Cas9/Csn1

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Macromolecule #2: Gag-Pol polyprotein

MacromoleculeName: Gag-Pol polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moloney murine leukemia virus
Molecular weightTheoretical: 55.656242 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: TLNIEDEYRL HETSKEPDVS LGSTWLSDFP QAWAETGGMG LAVRQAPLII PLKATSTPVS IKQYPMSQEA RLGIKPHIQR LLDQGILVP CQSPWNTPLL PVKKPGTNDY RPVQDLREVN KRVEDIHPTV PNPYNLLSGL PPSHQWYTVL DLKDAFFCLR L HPTSQPLF ...String:
TLNIEDEYRL HETSKEPDVS LGSTWLSDFP QAWAETGGMG LAVRQAPLII PLKATSTPVS IKQYPMSQEA RLGIKPHIQR LLDQGILVP CQSPWNTPLL PVKKPGTNDY RPVQDLREVN KRVEDIHPTV PNPYNLLSGL PPSHQWYTVL DLKDAFFCLR L HPTSQPLF AFEWRDPEMG ISGQLTWTRL PQGFKNSPTL FNEALHRDLA DFRIQHPDLI LLQYVDDLLL AATSELDCQQ GT RALLQTL GNLGYRASAK KAQICQKQVK YLGYLLKEGQ RWLTEARKET VMGQPTPKTP RQLREFLGKA GFCRLFIPGF AEM AAPLYP LTKPGTLFNW GPDQQKAYQE IKQALLTAPA LGLPDLTKPF ELFVDEKQGY AKGVLTQKLG PWRRPVAYLS KKLD PVAAG WPPCLRMVAA IAVLTKDAGK LTMGQPLVIL APHAVEALVK QPPDRWLSNA RMTHYQALLL DTDRVQFGPV VALNP ATLL PLPEEGLQHN CL

UniProtKB: Gag-Pol polyprotein

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Macromolecule #3: DNA (51-MER)

MacromoleculeName: DNA (51-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 15.636033 KDa
SequenceString:
(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DC)(DT) (DG)(DC)(DC)(DA)(DT)(DC)(DA)(DG)(DA)(DG) (DC)(DA)(DA)(DG)(DC)(DA)(DC)(DT)(DA) (DC)(DG)(DG)(DC)(DC)(DG)(DA)(DT)(DT)(DG) (DC) (DT)(DC)(DT)(DA)(DA)(DG)(DT)(DG) (DA)(DT)(DC)

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Macromolecule #4: DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3')

MacromoleculeName: DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 5.291446 KDa
SequenceString:
(DT)(DG)(DA)(DT)(DG)(DG)(DC)(DA)(DG)(DA) (DG)(DT)(DA)(DC)(DT)(DA)(DG)

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Macromolecule #5: RNA (115-MER)

MacromoleculeName: RNA (115-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 37.065949 KDa
SequenceString:
GGCCGUAGUG CUUGCUCUGA GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU GGCACCGAG UCGGUGCGCA CAUCGUGCUC AGUCUG

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Macromolecule #6: DNA/RNA (35-MER)

MacromoleculeName: DNA/RNA (35-MER) / type: other / ID: 6 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 10.75995 KDa
SequenceString:
(DG)(DA)(DT)(DC)(DA)(DC)(DT)(DT)(DA)(DG) (DA)(DG)(DC)(DA)(DA)(DT)(DC)(DG)(DG)(DC) (DC)(DC)(DA)(DG)(DA)(DC)(DT)(DG)(DA) (DG)(DC)(DA)(DC)(DG)(2DA)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118125
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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