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- EMDB-63293: Cryo-EM structure of Apo type III-B CRISPR-Cas effector complex -

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Entry
Database: EMDB / ID: EMD-63293
TitleCryo-EM structure of Apo type III-B CRISPR-Cas effector complex
Map data
Sample
  • Complex: Apo type III-B CRISPR-Cas effector complex
    • Protein or peptide: Cmr1
    • Protein or peptide: Type III-B CRISPR-associated protein Cas10/Cmr2
    • Protein or peptide: CRISPR-associated protein Cmr3
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr4
    • Protein or peptide: CRISPR type III-B/RAMP module-associated protein Cmr5
    • Protein or peptide: RAMP superfamily protein
    • RNA: crRNA
  • Ligand: MANGANESE (II) ION
KeywordsCRISPR-Cas complex / adaptive immunity / RNA degradation / second messenger / IMMUNE SYSTEM/RNA / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


defense response to virus / nucleotide binding / cytoplasm
Similarity search - Function
CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster ...CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / CRISPR-associated protein Cmr2, N-terminal / : / Cas10/Cmr2, second palm domain / CRISPR type III-associated protein / RAMP superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
CRISPR type III-B/RAMP module-associated protein Cmr5 / RAMP superfamily protein / Type III-B CRISPR-associated protein Cas10/Cmr2 / Uncharacterized protein / CRISPR-associated protein Cmr3 / Type III-B CRISPR module RAMP protein Cmr4
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsJin X / Chen Z / Zhao B
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2025
Title: Molecular basis of SAM-AMP synthesis and degradation in the type III-B CRISPR-Cas system.
Authors: Benzhen Duan / Xiaohui Jin / Xiaoman An / Yang Xiao / Qianxi Yang / Hongyu Zhao / Yunxiao Huang / Jingwen Wang / Qian Wang / Fenglei Du / Lu Lu / Lei Sun / Zhenguo Chen / Baoyu Zhao /
Abstract: Upon sensing nonself target RNA, the CorA-associated type III-B CRISPR-Cas system catalyzes S-adenosyl methionine (SAM) and ATP to synthesize SAM-AMP, which activates the effector CorA and triggers ...Upon sensing nonself target RNA, the CorA-associated type III-B CRISPR-Cas system catalyzes S-adenosyl methionine (SAM) and ATP to synthesize SAM-AMP, which activates the effector CorA and triggers immune responses. SAM-AMP can be degraded by NrN and SAM lyase, potentially deactivating the system. Here we find that the type III-B effector complex from Bacteroides fragilis uses a specific mechanism to recognize nonself target RNA and synthesize SAM-AMP. The 3' anti-tag of nonself target RNA induces conformational changes in the Cmr2 subunit, triggering SAM-AMP synthesis independently of the stalk loop of Cmr3 subunit. SAM-AMP binding induces NrN to transit from an open to a closed conformation, enabling hydrolysis of the 3'-5' phosphodiester bond. SAM lyase forms a triangular trimer that specifically degrades SAM-AMP into 5'-methylthioadenosine-AMP and homoserine lactone. These findings unveil unique mechanisms for SAM-AMP synthesis and degradation and provide deeper insights into the molecular basis of type III CRISPR-Cas signaling.
History
DepositionJan 27, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63293.png

Downloads & links

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Map

FileDownload / File: emd_63293.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 372.8 Å		0.93 Å/pix.
x 400 pix.
= 372.8 Å		0.93 Å/pix.
x 400 pix.
= 372.8 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.15386818 - 31.097486
Average (Standard dev.)-0.017243456 (±0.4698262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63293_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_63293_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Apo type III-B CRISPR-Cas effector complex

EntireName: Apo type III-B CRISPR-Cas effector complex
Components
  • Complex: Apo type III-B CRISPR-Cas effector complex
    • Protein or peptide: Cmr1
    • Protein or peptide: Type III-B CRISPR-associated protein Cas10/Cmr2
    • Protein or peptide: CRISPR-associated protein Cmr3
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr4
    • Protein or peptide: CRISPR type III-B/RAMP module-associated protein Cmr5
    • Protein or peptide: RAMP superfamily protein
    • RNA: crRNA
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Apo type III-B CRISPR-Cas effector complex

SupramoleculeName: Apo type III-B CRISPR-Cas effector complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Bacteroides fragilis (bacteria)

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Macromolecule #1: Cmr1

MacromoleculeName: Cmr1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 55.34025 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNQLTAILKQ HTPMIHFQHN ESGATLRASE VKPLLDKFIL TKLGNGDIRE GRLYAKKNNW LIDNEKNYAL NYKLSISLQK KSRLEYLIT SSTFPLPTER PSNFFTIQNS PYFAQEKCVG INTNSTIILK KSNSDPRKKE AEFKEKNWSQ IDKKGLEWQD F TIKIFSLK ...String:
MNQLTAILKQ HTPMIHFQHN ESGATLRASE VKPLLDKFIL TKLGNGDIRE GRLYAKKNNW LIDNEKNYAL NYKLSISLQK KSRLEYLIT SSTFPLPTER PSNFFTIQNS PYFAQEKCVG INTNSTIILK KSNSDPRKKE AEFKEKNWSQ IDKKGLEWQD F TIKIFSLK GDLINKIQTY LPAFFICHNF GTRNNKGFGS FTVEYINNQK NICNVEDTLK ENFAFVYKKK IALSRQSTLD FI YIYNQIF STIKKDYQIL KSGYNFRNEY IKSLLFCYFV SKYPNYRWEK RKMKQLIKAR GYELKGDHSP ISGIRENDNS WND PNPNGY NYAYIRAILG LAEQYEFQLE TPYQKAIVKI KSANNCISRY KSPLLFKIIN NSIYLVGNEI NTEILNKPFQ YSYI EQTKN KNMRTGKSEI TERTMHINEI EMNYKNRINY HYTPTSFSLI DFMQYAMSYK KNGKNILNYI PLKQ

UniProtKB: Uncharacterized protein

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Macromolecule #2: Type III-B CRISPR-associated protein Cas10/Cmr2

MacromoleculeName: Type III-B CRISPR-associated protein Cas10/Cmr2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 69.247078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKYIAITLGP ITRTIEMAES TKELWAASYF FSYLAKKIVE PFVKKNRTFQ LPLINEEMQK PHCGAGLFPD RYIFKSEPGD LELLKQHSD QVLIEIAGHI ASPSLPGTAK DVSQIYHYLK SYIKIYFIER TLESDDPHVV IPACEKYLNI IENQETFPEQ E ETMISHQK ...String:
MKYIAITLGP ITRTIEMAES TKELWAASYF FSYLAKKIVE PFVKKNRTFQ LPLINEEMQK PHCGAGLFPD RYIFKSEPGD LELLKQHSD QVLIEIAGHI ASPSLPGTAK DVSQIYHYLK SYIKIYFIER TLESDDPHVV IPACEKYLNI IENQETFPEQ E ETMISHQK SDFLKFLITN VNGKIYRKDK NSIPRFTGSF LTRDAFGDMN GERLFESILE ISASELNINI QQKALEVITA NE KNKGEKY SDQIWDAEEI ILNDNKAQLR PYHKYIAIIK SDGDSMGETI KSMGAYNIPI TQLSKALLSF NIESINEIVA YGG KPIFIG GDDLLCFAPV CCNGNNVFNL VEKLSTCFDQ CINQHLQQYI NACSEAQRPL PSLSFGISIT YHKYPMFEAL HTTD YLLEM VAKDNLFKYT LSNKNILNEN MKRFILKNKL AFSLQKHSGQ IYHTAMSKKG KSYVKFNMLL QKYILKNKDM SKTQE SEKF LSSVIQMIRA HAEILQIILQ NEDKRTEMLK NYFDNNFNES CHLGYTGLFE DIQTLLCLRY QENIQDYQNR NEIIQQ NTI LTSDEKEILI VSPAMDAIHT IFTALQFIHF INYNKDE

UniProtKB: Type III-B CRISPR-associated protein Cas10/Cmr2

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Macromolecule #3: CRISPR-associated protein Cmr3

MacromoleculeName: CRISPR-associated protein Cmr3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 49.059207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHHHHHHHH DGKPIPNPLL GLDSTGSDQT ENSGENLYFQ GANAMNRHYL ITLTPMDWFF FGGERTLDDG KSADYISHSN KFPQQSALL GMIRYQLLKQ HNLLSQFPYT ENKPTEKEIM KTLIGEQSFR MTERKAKSLG LGVIKQISPL MLIECKDDTS S RSIYFPLP ...String:
MSHHHHHHHH DGKPIPNPLL GLDSTGSDQT ENSGENLYFQ GANAMNRHYL ITLTPMDWFF FGGERTLDDG KSADYISHSN KFPQQSALL GMIRYQLLKQ HNLLSQFPYT ENKPTEKEIM KTLIGEQSFR MTERKAKSLG LGVIKQISPL MLIECKDDTS S RSIYFPLP LDDGYKVSFN ETSNEDKVFY NGIECPIPNV YPASEEQDSG NQKRKFFDHK TYNNYLFWCT QGNNQIKKLL SD EIWISKM QIGITKHVEE GEDNDKSFYK QEFLQLKKSF IYAFYITLSG ESELSSDIIQ LGGQRSVFRM EVESIEENSD IQE KYQTAA QFLTQSDRLL ILSPTYVDNL KELSALCNFM WSDSIVFRNI QTTNASNFYG KPIKSSSKYH FLKPGSVLYF KQGK RKEVE KLLMDYTYLR LSGYNIYI

UniProtKB: CRISPR-associated protein Cmr3

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Macromolecule #4: Type III-B CRISPR module RAMP protein Cmr4

MacromoleculeName: Type III-B CRISPR module RAMP protein Cmr4 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 31.581049 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTRMYVINT LSNMHVGSGE VNYGVIDNLI QRDSVTNLPN INSSGLKGAI REYFKENEDL VRELFGSAPR DEKTLPGKVR FFEANLLSM PVRSDKVPFL MAISDEVLQE LITKMKFFNC EEATQYISHL STLLDNIKTQ AQGTDFAYVF DPLLQGAIIE E VSIRATCP ...String:
MTTRMYVINT LSNMHVGSGE VNYGVIDNLI QRDSVTNLPN INSSGLKGAI REYFKENEDL VRELFGSAPR DEKTLPGKVR FFEANLLSM PVRSDKVPFL MAISDEVLQE LITKMKFFNC EEATQYISHL STLLDNIKTQ AQGTDFAYVF DPLLQGAIIE E VSIRATCP SHIPLQPSLK KLLGDRLVIL SHKYFSILSD DNHLPVLSRN NLENGQSANL WYEQVLPRYS RLYFMLMDGN AQ SEYLKKF RDTLCTPSTI IQIGANASIG YGYCQISELS PF

UniProtKB: Type III-B CRISPR module RAMP protein Cmr4

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Macromolecule #5: CRISPR type III-B/RAMP module-associated protein Cmr5

MacromoleculeName: CRISPR type III-B/RAMP module-associated protein Cmr5 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 15.273493 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKISKKQIEY AIEALRANNI ITNDNQYPKV FKGYISSFGA AVIQSGLIPA IIFFENEDND ANADRHKIIG VLKDIINAMR QQYTVTDAT ILVSSQIPAN YSMAQYIIEH GNTDQLLKEI TEAAVAMKLA LRMYKSE

UniProtKB: CRISPR type III-B/RAMP module-associated protein Cmr5

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Macromolecule #6: RAMP superfamily protein

MacromoleculeName: RAMP superfamily protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 35.951883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPKNYTLQNA SNLGWLFYKD YYRQEPNVDF ISTQGKESDT TADFFRKTNQ RITAYQLNSE SPLVAAFNNH FGTPLQLKTI YPGLITGSG LPHQTGSKGE FKLGFQFDYT TGLPYIPGSS IKGTLRSMFP FSLKDKGSTK RILPEYRKER MEYIRDLIIE V TNINEISD ...String:
MPKNYTLQNA SNLGWLFYKD YYRQEPNVDF ISTQGKESDT TADFFRKTNQ RITAYQLNSE SPLVAAFNNH FGTPLQLKTI YPGLITGSG LPHQTGSKGE FKLGFQFDYT TGLPYIPGSS IKGTLRSMFP FSLKDKGSTK RILPEYRKER MEYIRDLIIE V TNINEISD TEIQALEYAI FTNSTPSGKT IEFSLEEKDV FYDAFVADSK DGVMLSDDYI TPHGENPLKD PKPILFLKIR PD VTINFYF KLCTTHLYKE KVCSSKQIEE IKKQNDFSSS DYKMITAHQK RNLFEKILLC IGIGAKTNIG YGQLKKL

UniProtKB: RAMP superfamily protein

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Macromolecule #7: crRNA

MacromoleculeName: crRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 15.671214 KDa
SequenceString:
AUUAAGACAU UCGUGAGUGA UUUAUUUCCA UGAAGUGGCG UCCCUUGUG

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Macromolecule #8: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k 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: 3.0 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95862
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9lq5:
Cryo-EM structure of Apo type III-B CRISPR-Cas effector complex

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