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- EMDB-61449: Structure of Cas12p-TrxA-guide RNA-target DNA complex(33-bp dsDNA) -

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Basic information

Entry
Database: EMDB / ID: EMD-61449
TitleStructure of Cas12p-TrxA-guide RNA-target DNA complex(33-bp dsDNA)
Map data
Sample
  • Complex: complex of Cas12p-TrxA-guide RNA-target DNA (33-bp dsDNA)
    • Protein or peptide: Cas12p
    • RNA: RNA (246-MER)
    • DNA: DNA (33-MER)
    • DNA: DNA (33-MER)
    • Protein or peptide: Thioredoxin
KeywordsCRISPR-Cas / nuclease / Heterodimer / RNA BINDING PROTEIN/RNA/DNA / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology:
Function and homology information
Biological speciesunidentified (others) / Escherichia coli BL21(DE3) (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang ZP / Wang YJ / Ji QJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22277078 China
CitationJournal: To Be Published
Title: Host thioredoxin is a CRISPR enhancer of phage-encoded miniature Cas12p nucleases
Authors: Wang ZP / Wang YJ / Ji QJ
History
DepositionSep 5, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61449.png

Downloads & links

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Map

FileDownload / File: emd_61449.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0036273177 - 1.8558934
Average (Standard dev.)0.0012432669 (±0.025742635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61449_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61449_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 : complex of Cas12p-TrxA-guide RNA-target DNA (33-bp dsDNA)

EntireName: complex of Cas12p-TrxA-guide RNA-target DNA (33-bp dsDNA)
Components
  • Complex: complex of Cas12p-TrxA-guide RNA-target DNA (33-bp dsDNA)
    • Protein or peptide: Cas12p
    • RNA: RNA (246-MER)
    • DNA: DNA (33-MER)
    • DNA: DNA (33-MER)
    • Protein or peptide: Thioredoxin

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Supramolecule #1: complex of Cas12p-TrxA-guide RNA-target DNA (33-bp dsDNA)

SupramoleculeName: complex of Cas12p-TrxA-guide RNA-target DNA (33-bp dsDNA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: unidentified (others)

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Macromolecule #1: Cas12p

MacromoleculeName: Cas12p / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 84.964945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSM SDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLMEA FAKRQGKEMD SLRFLYDGI RIQADQTPED LDMEDNDIIE AHREQIGGHS SLEVLFQGPM KTIKIKIKLT TDQVQLCDRY LEELTWLWNL T LSNQLHNH ...String:
MGSSHHHHHH SSGLVPRGSM SDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLMEA FAKRQGKEMD SLRFLYDGI RIQADQTPED LDMEDNDIIE AHREQIGGHS SLEVLFQGPM KTIKIKIKLT TDQVQLCDRY LEELTWLWNL T LSNQLHNH CVTWYAWAAK LSADLDKATE KLDKLKPEQQ QLVKDYYRTK DKPRLTKKEQ ELVAKFDIFA RWSSFSLDGI IP VPLRLGN SGYEGLSCQI ATGGNYWKRD ENINIPINTK KGIIHVKGYK LVKGDKLWQR IEIVPHKYRT FPGGKFEGRE LTT LEKLDN VNGLNTLRAF QNLPDLQVSS HYIGGLLAFF KESWSAFLDP KRMNSRKPKF KKDSDKITTL SNNQCAPNRI DVNK NIVTV TGFSPITIID KNWVKRLNLS QVLPRTYMLT QNPSGYYINI VIAHPLHEEK IALVKKLPKV KKEFGEDSQE YEDIK SKIK FLEQQIKESS IVKGKDLSVG IDPGVQAVVS TDHGALFLPN LTRERVSIHI EELQSRLDNA ELINDKKWKS LGNKTP RIK TKNETKLQEK ISRLHERGAN SSNAFNHKLS TRLSRTYEHI AWEDTQINNL LKQVEPKALP EGVGYAHNGA SAKRGLN WI MRQRCLSDLK AKTKQKTENR GGNFHEPPAN YSSQTCHCCG QKGERRSQHE FVCKNSDCKL FDIPQQADTN AARNHKQN G GFELGEVKYH NVKLVYQKPK

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Macromolecule #5: Thioredoxin

MacromoleculeName: Thioredoxin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 11.818582 KDa
SequenceString:
MSDKIIHLTD DSFDTDVLKA DGAILVDFWA EWCGPCKMIA PILDEIADEY QGKLTVAKLN IDQNPGTAPK YGIRGIPTLL LFKNGEVAA TKVGALSKGQ LKEFLDANLA

UniProtKB: UNIPROTKB: A0A140SSC0

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Macromolecule #2: RNA (246-MER)

MacromoleculeName: RNA (246-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 79.190891 KDa
SequenceString: AGAUUUAAGA AAAAACGCUU GACAAAGUAA UAAGAUUAGG CUAAUAUUAA AUUACCGCAG UUUGGGCGGG CAGCUAAUAA UAUUAGCUU AUGACUUCUA AGGCUUUUGC CUAAAAAGUA AGGGGGAAGG CGACAACCCC CAAAGACCAG CCGGAACUAU G GCUGGCAA ...String:
AGAUUUAAGA AAAAACGCUU GACAAAGUAA UAAGAUUAGG CUAAUAUUAA AUUACCGCAG UUUGGGCGGG CAGCUAAUAA UAUUAGCUU AUGACUUCUA AGGCUUUUGC CUAAAAAGUA AGGGGGAAGG CGACAACCCC CAAAGACCAG CCGGAACUAU G GCUGGCAA CUAUACCCUC UCUUUUGGAA ACUUGCAACU AAGACUGGGG ACUGAGGAUA GUUGAAACUG UCCUCUUCCU CU UUAGCG

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Macromolecule #3: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.325686 KDa
SequenceString:
(DT)(DG)(DA)(DG)(DC)(DG)(DC)(DT)(DA)(DA) (DA)(DG)(DA)(DG)(DG)(DA)(DA)(DG)(DA)(DG) (DG)(DA)(DC)(DA)(DT)(DA)(DC)(DA)(DG) (DT)(DT)(DG)(DA)

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Macromolecule #4: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.973404 KDa
SequenceString:
(DT)(DC)(DA)(DA)(DC)(DT)(DG)(DT)(DA)(DT) (DG)(DT)(DC)(DC)(DT)(DC)(DT)(DT)(DC)(DC) (DT)(DC)(DT)(DT)(DT)(DA)(DG)(DC)(DG) (DC)(DT)(DC)(DA)

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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

Concentration3.6 mg/mL
BufferpH: 7.5
GridModel: Homemade / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 66342
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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