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- PDB-6thh: Crystal structure of type I-D CRISPR-Cas nuclease Cas10d in compl... -

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Basic information

Entry
Database: PDB / ID: 6thh
TitleCrystal structure of type I-D CRISPR-Cas nuclease Cas10d in complex with the SIRV3 AcrID1 (gp02) anti-CRISPR protein
Components
  • CRISPR-associated protein, CscA
  • SIRV3 AcrID1 (gp02) anti-CRISPR protein
KeywordsIMMUNE SYSTEM / CRISPR / Cas / type I-D / Cas10 / Cas10d / complex / anti-CRISPR
Function / homologySulfolobus islandicus filamentous virus, Orf14 / Protein of unknown function (DUF1374) / PHOSPHATE ION / MafI family immunity protein / CRISPR-associated protein, CscA
Function and homology information
Biological speciesSulfolobus islandicus rudivirus 3
Sulfolobus islandicus LAL14/1 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.48 Å
AuthorsManav, M.C. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
LundbeckfondenR87-2018-1555 Denmark
Novo Nordisk Foundation Denmark
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for inhibition of an archaeal CRISPR-Cas type I-D large subunit by an anti-CRISPR protein.
Authors: Manav, M.C. / Van, L.B. / Lin, J. / Fuglsang, A. / Peng, X. / Brodersen, D.E.
History
DepositionNov 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jun 30, 2021Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIRV3 AcrID1 (gp02) anti-CRISPR protein
B: SIRV3 AcrID1 (gp02) anti-CRISPR protein
C: CRISPR-associated protein, CscA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,6665
Polymers124,5053
Non-polymers1602
Water0
1
A: SIRV3 AcrID1 (gp02) anti-CRISPR protein
B: SIRV3 AcrID1 (gp02) anti-CRISPR protein
C: CRISPR-associated protein, CscA
hetero molecules

A: SIRV3 AcrID1 (gp02) anti-CRISPR protein
B: SIRV3 AcrID1 (gp02) anti-CRISPR protein
C: CRISPR-associated protein, CscA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,33210
Polymers249,0116
Non-polymers3214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)157.990, 157.990, 130.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SIRV3 AcrID1 (gp02) anti-CRISPR protein


Mass: 13086.693 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus rudivirus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B3SN05
#2: Protein CRISPR-associated protein, CscA


Mass: 98332.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus LAL14/1 (acidophilic)
Gene: SiL_0609 / Production host: Escherichia coli (E. coli) / References: UniProt: M9U4Y8
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes 7.5, 2% (w/v) PEG 8000, 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.48→67.542 Å / Num. obs: 21713 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 137.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9
Reflection shellResolution: 3.48→3.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2139 / CC1/2: 0.6 / % possible all: 99.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXDEphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.48→67.542 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 1841 8.49 %
Rwork0.2364 19855 -
obs0.2379 21696 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 282.81 Å2 / Biso mean: 137.0532 Å2 / Biso min: 61.23 Å2
Refinement stepCycle: final / Resolution: 3.48→67.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8238 0 6 0 8244
Biso mean--148.63 --
Num. residues----1008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
3.48-3.57410.35461121512X-RAY DIFFRACTION0100
3.5741-3.67920.30861541496X-RAY DIFFRACTION0100

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