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- EMDB-62471: Cryo-EM structure of PsCas9-sgRNA binary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62471
TitleCryo-EM structure of PsCas9-sgRNA binary complex
Map data
Sample
  • Complex: type II CRISPR RNA-guided endonuclease Cas9
    • Protein or peptide: CRISPR-associated endonuclease Cas9
    • RNA: RNA (131-MER)
KeywordsCRISPR-Cas9 / RNA / binary complex / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
Biological speciesParasutterella secunda (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsShen PP / Lu XY / Huang J-W / Chen C-C / Gut R-T
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2025
Title: Structural and Mechanistic Investigations of a High-Fidelity Cas9 from Parasutterella secunda
Authors: Shen P / Lu X / Wang C / Huang JW / Min J / Luo J / Sun Y / Chen CC / Guo RT
History
DepositionNov 20, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62471.png

Downloads & links

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Map

FileDownload / File: emd_62471.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 360 pix.
= 334.8 Å		0.93 Å/pix.
x 360 pix.
= 334.8 Å		0.93 Å/pix.
x 360 pix.
= 334.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.2979262 - 3.2679324
Average (Standard dev.)0.00035685528 (±0.049669184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 334.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62471_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_62471_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 : type II CRISPR RNA-guided endonuclease Cas9

EntireName: type II CRISPR RNA-guided endonuclease Cas9
Components
  • Complex: type II CRISPR RNA-guided endonuclease Cas9
    • Protein or peptide: CRISPR-associated endonuclease Cas9
    • RNA: RNA (131-MER)

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Supramolecule #1: type II CRISPR RNA-guided endonuclease Cas9

SupramoleculeName: type II CRISPR RNA-guided endonuclease Cas9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Parasutterella secunda (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: CRISPR-associated endonuclease Cas9

MacromoleculeName: CRISPR-associated endonuclease Cas9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Parasutterella secunda (bacteria)
Molecular weightTheoretical: 165.211922 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHVAGA GAGENLYFQG MTVKSTLAVD MGGRYTGIFS YTTDSGFPKA KEARAYVLNM PDNDALTYSM AARTQTRHRI RSQQRFVLA RRLTYILIEG KLKRKLSPRE KEAISSLLRR RGYSRLESEL DLSVLQGVES GFFKCFLPNF DEDENLLTQW T SLTDGYLQ ...String:
HHHHHHVAGA GAGENLYFQG MTVKSTLAVD MGGRYTGIFS YTTDSGFPKA KEARAYVLNM PDNDALTYSM AARTQTRHRI RSQQRFVLA RRLTYILIEG KLKRKLSPRE KEAISSLLRR RGYSRLESEL DLSVLQGVES GFFKCFLPNF DEDENLLTQW T SLTDGYLQ NNSDSRRQIQ IFLESSKDSK EFLTVVKSQH QDTKEYKNAL KVMRDDAESM IEQSMFGHKH RRLYLEAIAQ DI PRDSRLK PIIEAFSGVE KFHHFIGNLS NLQLRALRWY FNDPSMKNNV FDKERLKSVL VRAYQFFHYP KDLTQQRAEV LNA YEGATD ILETLQTLNP ELTIPPYEDQ NNRRPPLDQT LWLSPRLLDQ RYGDTWEIWV QNLLRSPLSK GIDENLDTIL ITTD RKARL LERQSGRLIH YTSQKLYHSY VLQRLLDRTV ENDAYLLKTL VSSNRGNSNE IHQAQERLTR DLGSQHIKKF LDFVR QYYD EVDKAKRGLW FIVEKPLMER ADIHPPMKND SVILRLVGNI LCVSDLVDLS FWTRKVKGQS TVRSLCTAIE KTRKEY GNS FNYLYQRALY LQSKGKKLSA EDKDFIKLQS NVLLVSDVIA EALDIKEEQK KKFANPFSLA QLYNIIETEK SGFISTT LA AVDENAWRNN LQGKARCVQL CADTVRPFDG ALRNILDRQA YEIAKLKAEE LLSTELKNQT IDLVVLLESN QFAFSASL A EVKKSANTAA IRQKVAKAQK RQQDRWLSKD ERIKSASRGL CPYTGKNLGD KGEVDHIIPR SLSMNYMGSI LNSEANLIY CSQEGNQLKL NGRKKLSDLA DNYLKVVFGT ADRGTICKYI EKSVSELTDA KIVQFELLDR SQQDAVRHAL FLEDFSEARR RIIRLLGKI NTARVNGTQA WFAKSFITKL RELTKEWCAN NQITLAFDLY RLDAQTVSQD YRKKFALINK DWAKPDDKKQ P IASHAIDA FCVFAAAKDK RNIANVLGVF DEVAEEQNLK TIAQLMPSEV NLISPKRKSI LDKNEVGSRA LMKEGIFAEH FL PILVRGD DCRIGFDWSE SGSVKVKDAD KLFGVLDGLL KQSQKRSVNG FETYTVDRIK AFELLHDVFI RPCSQKMLEQ AEV LEKLHY ITQNISVTSV YDAVNRQFKC REEILKDKDF DIKVDLGNRF GSAKGKITLP AKREWEKLVN RSELKNLIKD KLSD KGSEK TPDGETLIYD IFRSIPVQKL SHKATRRVWS LPKIPSISSG VRIKRKDSNG NDIYQLYMLN DTKCKGFVVN EKGVI DWSS DLVADLYKQP TLTILNGRYL KADQYVRMDQ WYEVDCGRDD VIVKMCPGTS GRRYIEITQS KKQFEDWTGY ISGSFW NYP VTIKLSSQQI ANFVKNSQMP LLGKPRSGQI TVITLGNTLK YWYCVESKNS MMNEAYQKAY LVHFNQKRPA AT

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Macromolecule #2: RNA (131-MER)

MacromoleculeName: RNA (131-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Parasutterella secunda (bacteria)
Molecular weightTheoretical: 42.108891 KDa
SequenceString:
GUGGGGCCAC UAGGGACAGG AUGUUUCAGU UAUUCGUGAA AACGAAUGAA GUCACUCUUA AAGUGAGCUG AAAUCACUAA AAAUUAAGA UUGAACCCGG CUACUGACUC UGUCAUCCGG GUUUACUUAU UU

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 270781
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9ko9:
Cryo-EM structure of PsCas9-sgRNA binary complex

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