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- EMDB-62872: Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-62872
TitleType III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 1)
Map data
Sample
  • Complex: Archaeoglobus fulgidus type III-B CRISPR-Cas effector
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr4
    • Protein or peptide: CRISPR system Cmr subunit Cmr5
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr6
    • Protein or peptide: Cmr1 C-terminal domain-containing protein
    • Protein or peptide: GGDEF domain-containing protein
    • Protein or peptide: Type III-B CRISPR module-associated protein Cmr3
    • RNA: Pf7.01 crRNA
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
KeywordsCRISPR-Cas effector / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


defense response to virus / nucleotide binding / cytoplasm
Similarity search - Function
: / Cmr1, C-terminal domain / CRISPR-associated protein TM1795 / CRISPR-associated protein, TM1793 / 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 ...: / Cmr1, C-terminal domain / CRISPR-associated protein TM1795 / CRISPR-associated protein, TM1793 / 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 / GGDEF domain profile. / GGDEF domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Type III-B CRISPR module RAMP protein Cmr1 / GGDEF domain-containing protein / Type III-B CRISPR module-associated protein Cmr3 / CRISPR type III-associated protein domain-containing protein / CRISPR system Cmr subunit Cmr5 / CRISPR type III-associated protein domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea) / Pyrococcus furiosus DSM 3638 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsOuchi R / Numata T
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H04759 Japan
Japan Society for the Promotion of Science (JSPS)16KK0166 Japan
Japan Society for the Promotion of Science (JSPS)20H02916 Japan
Japan Society for the Promotion of Science (JSPS)24H00505 Japan
CitationJournal: To Be Published
Title: A new in vitro reconstitution system of type III-B CRISPR-Cas effector for functional and structural studies
Authors: Ouchi R / Numata T
History
DepositionDec 26, 2024-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62872.png

Downloads & links

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Map

FileDownload / File: emd_62872.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.)
0.75 Å/pix.
x 400 pix.
= 300.8 Å		0.75 Å/pix.
x 400 pix.
= 300.8 Å		0.75 Å/pix.
x 400 pix.
= 300.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.214
Minimum - Maximum-0.42265052 - 0.9858886
Average (Standard dev.)-0.0004252718 (±0.034764647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62872_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_62872_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62872_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_62872_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 : Archaeoglobus fulgidus type III-B CRISPR-Cas effector

EntireName: Archaeoglobus fulgidus type III-B CRISPR-Cas effector
Components
  • Complex: Archaeoglobus fulgidus type III-B CRISPR-Cas effector
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr4
    • Protein or peptide: CRISPR system Cmr subunit Cmr5
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr6
    • Protein or peptide: Cmr1 C-terminal domain-containing protein
    • Protein or peptide: GGDEF domain-containing protein
    • Protein or peptide: Type III-B CRISPR module-associated protein Cmr3
    • RNA: Pf7.01 crRNA
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Archaeoglobus fulgidus type III-B CRISPR-Cas effector

SupramoleculeName: Archaeoglobus fulgidus type III-B CRISPR-Cas effector / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 404 KDa

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Macromolecule #1: Type III-B CRISPR module RAMP protein Cmr4

MacromoleculeName: Type III-B CRISPR module RAMP protein Cmr4 / type: protein_or_peptide / ID: 1 / Details: His-tagged protein / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 41.252254 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPMFDMFE KAVVFGLYSI TPVHAGSGAE LSVIALPIQR ERHTGFPVIW GQSLKGVLRS RFRQLELDEK IEVESQKWK WKEKTKEVLK EKADEFIKKV EERKRDPLLT EIVFGPATDG ASEHAGAVSV GDAKILLFPV RSAKGVFAFV T SPIVIQRL ...String:
MGSSHHHHHH SQDPMFDMFE KAVVFGLYSI TPVHAGSGAE LSVIALPIQR ERHTGFPVIW GQSLKGVLRS RFRQLELDEK IEVESQKWK WKEKTKEVLK EKADEFIKKV EERKRDPLLT EIVFGPATDG ASEHAGAVSV GDAKILLFPV RSAKGVFAFV T SPIVIQRL KEDFELVSEI ENDIELKQIL SRFKVELSNN ETIAGNALIL NGENKVILED IVLKVKSDSN VIENLVEVLK TL FGDNFFG KPIESIKERI AIVSDDVFKS FTRFSTEIVA RVRIDAEKGT VARGGLWYEE FLPSDTLMYS LIAVGSPKKE NLP KEVDNT QKIVNVLKVT FNNAFLQIGG DETVGKGFVK VRAGVLTGGH KGN

UniProtKB: CRISPR type III-associated protein domain-containing protein

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Macromolecule #2: CRISPR system Cmr subunit Cmr5

MacromoleculeName: CRISPR system Cmr subunit Cmr5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 17.407707 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDIREIEQER ASFAFKVVSD IKDKYSQNKK VQGKYSSYAE KAPTIILNNG LGATLAFFLS KLEKPIDDVD YKSINPESFG NAENIAYAF LYKHLSTWLA EGNGKDSAFS GLTNGEDPLK YIMEKTAIDV AISTEEALSI LNWIKKFAKA MLEEEL

UniProtKB: CRISPR system Cmr subunit Cmr5

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Macromolecule #3: Type III-B CRISPR module RAMP protein Cmr6

MacromoleculeName: Type III-B CRISPR module RAMP protein Cmr6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 39.469902 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKSNVVVKYP VNSELANYAE KFWKKELAIY NLSLILNKMT PFVKRRSESY KSSLSAVKEI FKNVDDFQNF LNSVLRRSLD EYRVFFENY ERLFNSFSSK IFSMRTKSRL VVGLGDESVY ETSIRLHRNY GVPYIPGSAL KGVAKHYAFS ILARENGDEI L RIYESVKE ...String:
MKSNVVVKYP VNSELANYAE KFWKKELAIY NLSLILNKMT PFVKRRSESY KSSLSAVKEI FKNVDDFQNF LNSVLRRSLD EYRVFFENY ERLFNSFSSK IFSMRTKSRL VVGLGDESVY ETSIRLHRNY GVPYIPGSAL KGVAKHYAFS ILARENGDEI L RIYESVKE DLKARIAKRD KIKKNDVPED YYLTAAVIQE LFEKKFDELG AIRNTRVEIG DTVISVGDIV KIFGTQKEEG SV IFFDAFP TPEQLKDKPN LELDIMNPHY QPYYQHGEPP GDWHSPNPIF FLTVPAGVEF TFAVASRDLD DLAEKAEKLL KEA LKKFGV GAKTSLGYGR FDARDDR

UniProtKB: CRISPR type III-associated protein domain-containing protein

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Macromolecule #4: Cmr1 C-terminal domain-containing protein

MacromoleculeName: Cmr1 C-terminal domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 38.016969 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MCMYSATFTL EAITPVFMRG ANQSKAEIRA ASIKGLMRWW FRALSGSYFG NDVEGLRRVE EYVFGSTKRE SRVVVEVVKE HVEERFCPL PMVWKKKKGV TTRVSQRAIA PGSKFTLLLT SDDEEVLKLA CYSLIGLVYF GGIGFRCSRG AGSLKISSLK S DVQLIDLP ...String:
MCMYSATFTL EAITPVFMRG ANQSKAEIRA ASIKGLMRWW FRALSGSYFG NDVEGLRRVE EYVFGSTKRE SRVVVEVVKE HVEERFCPL PMVWKKKKGV TTRVSQRAIA PGSKFTLLLT SDDEEVLKLA CYSLIGLVYF GGIGFRCSRG AGSLKISSLK S DVQLIDLP KNKNQLGQMV NDLTVEIAKI LKKTFLCDHE NKNCTSYSSF WCFYLFLWGE KAELEEVYYR SNNLENERLT LL DLFEKEF KNKNNHLSNY GYRDFVFGLP RGTKKDRRAS PIKVGITELS EKYHVRVSVF KTKIFKPGMN VKWDNIFVFL ENI GAERIY PER

UniProtKB: Type III-B CRISPR module RAMP protein Cmr1

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Macromolecule #5: GGDEF domain-containing protein

MacromoleculeName: GGDEF domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 115.211852 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGQYFRVSGK YRGRENLPRE VNKMADNEFW LNKIRAFFHD PPDKSFELKT HERRASFILG ELKPSKSLKR IIKNADIQAS SLQRVDLEK SIHKKELKST FDRIHNTEKY EYIGQPIIRH PVTGEIKEYG TILANLPQTQ REVYDVDDEG KEDYEEQFQE I LSRILKIE ...String:
MGQYFRVSGK YRGRENLPRE VNKMADNEFW LNKIRAFFHD PPDKSFELKT HERRASFILG ELKPSKSLKR IIKNADIQAS SLQRVDLEK SIHKKELKST FDRIHNTEKY EYIGQPIIRH PVTGEIKEYG TILANLPQTQ REVYDVDDEG KEDYEEQFQE I LSRILKIE KKVFDDFKNR YSDPKDLYIS LWAFYAEKLK EALEEEFSAS FAEEFVNLPA YTLSPDHTLF DHADATSAIF GA EIDGKKP VLVLFKISPV QKFIADARKE KDLWAASHML STLTFKAISF IADKFGPDVV IYPHLRGNPF FHAWLHSKKI WEF SDSHSL KIASVPNKFL ALVGVSDEKE LNNLREGIRN EIESFLADLF DKLWNEVIVG ALEHSDALKH LGDKKEIHKE ILLK RFTLT LSSLKIHDVD VSGSKEEAYE KVKDFVRSLG LPNAIESKYL QWLDMLGSVE ASNNRPTKYD LYSLYYEILT VLNAI ESTH FDKPAEPAGY KCTLCGEHLA IGGESREMME NVWGKIHKRW PSHLRSNERL CAVCAVKRFY PKFIETLDIF EGVGKV VPD IESVSEVAMC RRTKHGITWK EVYDYLRGLK NVDDEKLLGK LENLKHSVQT LINNVKSELK SRKVYPEEFL EGLNRNF SN EILYSERLRD FNTLLDTLGF DAAKLGLDDV KNYETMISEL RERLSEVYKM LGEPPKYYAI LMMDGDEMGK LLSGEKLK T AEHYLHSAIL ERVSDALRVK AKTVRRLITP AAHSSISRAL KNFSVNHVPD VVRKGNGTLI YSGGDDVLVL LPVDTAFDV ATELAMTFST SWNGWEMLPG NKLSAGLLIV HYKHPLYDAL EKTRELLQKA KKLGRNAIAV GLLKRSGSYY ESVVNFETLE DAKAVANLL VKEQVSPRII YELLNFADVI SKEFLHQLVK YEAVRHSIDK NLAEEFQSVF ARGHQGVRVE LEGNDEEINK Y ISDGANLE TFLDKYEKAV DVIRKQVRGF LNLVKILYES IRGGAK

UniProtKB: GGDEF domain-containing protein

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Macromolecule #6: Type III-B CRISPR module-associated protein Cmr3

MacromoleculeName: Type III-B CRISPR module-associated protein Cmr3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 39.043328 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MILVMKPYDS LLFREPRPFD VNNHVARTIL PLPQTLAGAV RSAIYVKYGS KVKDLIGFGK EEPEFEILGH FFYRYDGKFE LLVESPHDV TQNLGLVKPH RIDKLGITIL MDSEGIKFRP FNGFLKFSGL IDYLQGRIAE DSVVERQKIF KKERRVGIAL T KAKVTKEE ...String:
MILVMKPYDS LLFREPRPFD VNNHVARTIL PLPQTLAGAV RSAIYVKYGS KVKDLIGFGK EEPEFEILGH FFYRYDGKFE LLVESPHDV TQNLGLVKPH RIDKLGITIL MDSEGIKFRP FNGFLKFSGL IDYLQGRIAE DSVVERQKIF KKERRVGIAL T KAKVTKEE HFYQVEMLRF SDDCGIAVWV EDGVDFDDEG ILGVGGERRF VKFEKREEPE CITNLRSKWK KIRDKINETG RL KIYLATP AILGAKGYSS KLDYDLLGDI GIERVRSVNF IGGKPVIFSG WDFVTRKPKP TRYAVPAGSV YFVEFEGEVK LDM PYLKLG KLTKLGYGLC FMGVW

UniProtKB: Type III-B CRISPR module-associated protein Cmr3

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Macromolecule #7: Pf7.01 crRNA

MacromoleculeName: Pf7.01 crRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 14.501589 KDa
SequenceString:
AUUGAAAGUU GUAGUAUGCG GUCCUUGCGG CUGAGAGCAC UUCAG

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.8 mg/mL
BufferpH: 7
Component:
ConcentrationName
20.0 mMTris-HCl
200.0 mMNaCl
1.0 mMDTT
2.0 mMMgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5500 / Average exposure time: 2.597 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 60000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold2 model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 80152
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: The initial model containing all protein subunits was constructed by AlphaFold2
Output model

PDB-9l7c:
Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 1)

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