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- EMDB-68883: anti-Crispr protein in apo form -

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Basic information

Entry
Database: EMDB / ID: EMD-68883
Titleanti-Crispr protein in apo form
Map data
Sample
  • Complex: anti-Crispr protein in apo form
    • Protein or peptide: anti-Crispr protein in apo form
  • Ligand: NICKEL (II) ION
Keywordsanti-Crispr protein in apo form / CELL INVASION
Biological speciesPectobacterium araliae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsWang WH / Xie YC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400565 China
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for dual mechanism of Cas2/3 nuclease inhibition by anti-CRISPR protein AcrIF19.
Authors: Yuanshuo Sa / Chunlei Liu / Lingguang Yang / Ling Yue / Limin Zhu / Ying Guo / Ruimei Wang / Yafei Wang / Yue Feng / Yong Wang / Yi Zhang / Wenhe Wang / Yongchao Xie /
Abstract: CRISPR-Cas systems are prokaryotic immune mechanisms often targeted by phage-encoded anti-CRISPR (Acr) proteins. This study characterizes AcrIF19, a potent inhibitor of the type I-F system in ...CRISPR-Cas systems are prokaryotic immune mechanisms often targeted by phage-encoded anti-CRISPR (Acr) proteins. This study characterizes AcrIF19, a potent inhibitor of the type I-F system in Pectobacterium atrosepticum. The cryo-EM structure of the apo Cas2/3 and Cas2/3-AcrIF19 complex reveals a dual inhibitory mechanism. AcrIF19 employs a negatively charged β-β loop to sterically occlude the non-target DNA strand entry channel, acting as a competitive inhibitor to disrupt Cas2/3 recruitment. Concurrently, this steric occlusion impedes ssDNA-mediated allosteric activation, which locks the critical helix-like loop motif in an inhibitory conformation and thereby abrogates DNA cleavage activity. AcrIF19 represents an anti-CRISPR protein inhibiting Cas2/3 via two different mechanisms, integrating a competitive ssDNA inhibitor with an allosteric blockade to suppress both target recruitment and DNA cleavage.
History
DepositionFeb 1, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68883.png

Downloads & links

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Map

FileDownload / File: emd_68883.map.gz / Format: CCP4 / Size: 64 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.)
0.84 Å/pix.
x 256 pix.
= 216.064 Å		0.84 Å/pix.
x 256 pix.
= 216.064 Å		0.84 Å/pix.
x 256 pix.
= 216.064 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.1631644 - 1.7474427
Average (Standard dev.)-0.000876738 (±0.053019956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.064 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68883_msk_1.map
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Half map: #2

Fileemd_68883_half_map_1.map
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Half map: #1

Fileemd_68883_half_map_2.map
Projections & Slices
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Sample components

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Entire : anti-Crispr protein in apo form

EntireName: anti-Crispr protein in apo form
Components
  • Complex: anti-Crispr protein in apo form
    • Protein or peptide: anti-Crispr protein in apo form
  • Ligand: NICKEL (II) ION

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Supramolecule #1: anti-Crispr protein in apo form

SupramoleculeName: anti-Crispr protein in apo form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pectobacterium araliae (bacteria)

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Macromolecule #1: anti-Crispr protein in apo form

MacromoleculeName: anti-Crispr protein in apo form / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium araliae (bacteria)
Molecular weightTheoretical: 125.099453 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNILLISECN KRALVETRRI LDQFAERKGE RSWQTAITQE GLNTLRKLLR KTARRNTAVA CHWVRSTNHT ELLWVVGNLR RFNAQGSVP TNTTSRDVLR TKDENPWHSA EVFSLLAAIA GLFHDVGKAN MLFQAGLSGT GPRSQPYRHE WVSLRLFQAF V GEQDDKAW ...String:
MNILLISECN KRALVETRRI LDQFAERKGE RSWQTAITQE GLNTLRKLLR KTARRNTAVA CHWVRSTNHT ELLWVVGNLR RFNAQGSVP TNTTSRDVLR TKDENPWHSA EVFSLLAAIA GLFHDVGKAN MLFQAGLSGT GPRSQPYRHE WVSLRLFQAF V GEQDDKAW LTTLSTITSE AEVALLATLQ QDKPTFSDSP FRTLPPLAQT IAWLIVSHHR LPVFNKSTEL APNSRPPQLD YA ETWLTDH LSPQWNALNH CQTNCLPSER EQNWQFPNGT PLRSTVWREK ARKFAGRALK LPSFMHFSQL EQRLTVHLAR LAL MLADHH YSAGAATVGW QDITYPVWAN TDRKTGEYKQ RLDEHCVGVG QNALLLGRSL PHLRDTLPAI TRHKGFRQRS THPR FRWQD RAFDLACSIR DASKQHGFFG INMASTGRGK TFANARIMYG LSDESIGCRF SVALGLRTLT LQTGDALRQR LKLDE DDLA VLIGSQAVQD LHEMRQENEA RQQNTPQTGS ESADPLFSEH QYVRYDGSLD DGRLKAWLER SPTLHQLLSA PVLITT IDH LMPATEGLRG GHQIAPMLRL LTSDLVLDEP DDFGLEDLPA LCRLVNWAGM LGSRVLLSSA TLPPALIRAL FDAYLDG RA AWQQAYGTPN TPLNVCCGWF DEFDCQHEQY GDVKDFMVSH DAFVHQRLKN LTKDELPLRF ATIVPVSSSS KNKDDVHL A VAQAIHPRMF DLHSQHHQQH ENGKTVSLGL VRMANIDPLV AIARQLIAIP SPPDTCIHYC IYHSQHPLAM RSHIEQRLD AALMRNDINA LWQVEEIRQA IENSPQQHHV FVVLATSVAE VGRDHDYDWA IVEPSSMRSL IQLAGRILRH RQDKQYVPKA PNIYLLSHN IRALRGKDIA YCKPGFESQD DSLDTHDLHQ LLQEKEYRHL SAAPRIVQPT SFAKPLSLVA LEHAVLGKTL L GLKNQKLD DLKRPPAAFW WRAHPHWNGE LQRRTPFRQS AKDEAYYLWI ADDDEEPVFM VQDDGPSGWK QSDIARPVTL DM AEGVSAW IEQDYHALYQ RLAEEKQWEL SWVSARFGEI RLREEEDWYW HPLLGVFGAL S

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Macromolecule #2: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 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: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 115474
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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