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- EMDB-33686: Structure of Cas7-11-crRNA-tgRNA in complex with TPR-CHAT -

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Basic information

Entry
Database: EMDB / ID: EMD-33686
TitleStructure of Cas7-11-crRNA-tgRNA in complex with TPR-CHAT
Map data
Sample
  • Complex: type III-E CRISPR-Cas effector
    • Complex: TPR-CHAT
      • Protein or peptide: CHAT domain protein
      • Protein or peptide: RAMP superfamily protein
    • Complex: RNA
      • RNA: RNA (37-MER)
      • RNA: RNA (5'-R(P*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*C)-3')
  • Ligand: ZINC ION
KeywordsImmune / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homologyCHAT domain / CHAT domain / : / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RNA binding / RAMP superfamily protein / CHAT domain protein
Function and homology information
Biological speciesCandidatus Scalindua brodae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang S / Guo M / Zhu Y / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31422014 China
CitationJournal: Cell Res / Year: 2022
Title: Cryo-EM structure of the type III-E CRISPR-Cas effector gRAMP in complex with TPR-CHAT.
Authors: Shuo Wang / Minghui Guo / Yuwei Zhu / Zhiying Lin / Zhiwei Huang /
History
DepositionJun 24, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33686.png

Downloads & links

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Map

FileDownload / File: emd_33686.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.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-3.3754616 - 6.1060867
Average (Standard dev.)-0.000514802 (±0.084703386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33686_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_33686_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 : type III-E CRISPR-Cas effector

EntireName: type III-E CRISPR-Cas effector
Components
  • Complex: type III-E CRISPR-Cas effector
    • Complex: TPR-CHAT
      • Protein or peptide: CHAT domain protein
      • Protein or peptide: RAMP superfamily protein
    • Complex: RNA
      • RNA: RNA (37-MER)
      • RNA: RNA (5'-R(P*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*C)-3')
  • Ligand: ZINC ION

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Supramolecule #1: type III-E CRISPR-Cas effector

SupramoleculeName: type III-E CRISPR-Cas effector / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: TPR-CHAT

SupramoleculeName: TPR-CHAT / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4

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Macromolecule #1: CHAT domain protein

MacromoleculeName: CHAT domain protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 82.549992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNTEENIDR IQEPTREDID RKEAERLLDE AFNPRTKPVD RKKIINSALK ILIGLYKEKK DDLTSASFIS IARAYYLVSI TILPKGTTI PEKKKEALRK GIEFIDRAIN KFNGSILDSQ RAFRIKSVLS IEFNRIDREK CDNIKLKNLL NEAVDKGCTD F DTYEWDIQ ...String:
MNNTEENIDR IQEPTREDID RKEAERLLDE AFNPRTKPVD RKKIINSALK ILIGLYKEKK DDLTSASFIS IARAYYLVSI TILPKGTTI PEKKKEALRK GIEFIDRAIN KFNGSILDSQ RAFRIKSVLS IEFNRIDREK CDNIKLKNLL NEAVDKGCTD F DTYEWDIQ IAIRLCELGV DMEGHFDNLI KSNKANDLQK AKAYYFIKKD DHKAKEHMDK CTASLKYTPC SHRLWDETVG FI ERLKGDS STLWRDFAIK TYRSCRVQEK ETGTLRLRWY WSRHRVLYDM AFLAVKEQAD DEEPDVNVKQ AKIKKLAEIS DSL KSRFSL RLSDMEKMPK SDDESNHEFK KFLDKCVTAY QDGYVINRSE DKEGQGENKS TTSKQPEPRP QAKLLELTQV PEGW VVVHF YLNKLEGMGN AIVFDKCANS WQYKEFQYKE LFEVFLTWQA NYNLYKENAA EHLVTLCKKI GETMPFLFCD NFIPN GKDV LFVPHDFLHR LPLHGSIENK TNGKLFLENH SCCYLPAWSF ASEKEASTSD EYVLLKNFDQ GHFETLQNNQ IWGTQS VKD GASSDDLENI RNNPRLLTIL CHGEANMSNP FRSMLKLANG GITYLEILNS VKGLKGSQVI LGACETDLVP PLSDVMD EH YSVATALLLI GAAGVVGTMW KVRSNKTKSL IEWKLENIEY KLNEWQKETG GAAYKDHPPT FYRSIAFRSI GFPL

UniProtKB: CHAT domain protein

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Macromolecule #2: RAMP superfamily protein

MacromoleculeName: RAMP superfamily protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 197.823797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSNDMNITV ELTFFEPYRL VEWFDWDARK KSHSAMRGQA FAQWTWKGKG RTAGKSFITG TLVRSAVIKA VEELLSLNNG KWEGVPCCN GSFQTDESKG KKPSFLRKRH TLQWQANNKN ICDKEEACPF CILLGRFDNA GKVHERNKDY DIHFSNFDLD H KQEKNDLR ...String:
MKSNDMNITV ELTFFEPYRL VEWFDWDARK KSHSAMRGQA FAQWTWKGKG RTAGKSFITG TLVRSAVIKA VEELLSLNNG KWEGVPCCN GSFQTDESKG KKPSFLRKRH TLQWQANNKN ICDKEEACPF CILLGRFDNA GKVHERNKDY DIHFSNFDLD H KQEKNDLR LVDIASGRIL NRVDFDTGKA KDYFRTWEAD YETYGTYTGR ITLRNEHAKK LLLASLGFVD KLCGALCRIE VI KKSESPL PSDTKEQSYT KDDTVEVLSE DHNDELRKQA EVIVEAFKQN DKLEKIRILA DAIRTLRLHG EGVIEKDELP DGK EERDKG HHLWDIKVQG TALRTKLKEL WQSNKDIGWR KFTEMLGSNL YLIYKKETGG VSTRFRILGD TEYYSKAHDS EGSD LFIPV TPPEGIETKE WIIVGRLKAA TPFYFGVQQP SDSIPGKEKK SEDSLVINEH TSFNILLDKE NRYRIPRSAL RGALR RDLR TAFGSGCNVS LGGQILCNCK VCIEMRRITL KDSVSDFSEP PEIRYRIAKN PGTATVEDGS LFDIEVGPEG LTFPFV LRY RGHKFPEQLS SVIRYWEEND GKNGMAWLGG LDSTGKGRFA LKDIKIFEWD LNQKINEYIK ERGMRGKEKE LLEMGES SL PDGLIPYKFF EERECLFPYK ENLKPQWSEV QYTIEVGSPL LTADTISALT EPGNRDAIAY KKRVYNDGNN AIEPEPRF A VKSETHRGIF RTAVGRRTGD LGKEDHEDCT CDMCIIFGNE HESSKIRFED LELINGNEFE KLEKHIDHVA IDRFTGGAL DKAKFDTYPL AGSPKKPLKL KGRFWIKKGF SGDHKLLITT ALSDIRDGLY PLGSKGGVGY GWVAGISIDD NVPDDFKEMI NKTEMPLPE EVEESNNGPI NNDYVHPGHQ SPKQDHKNKN IYYPHYFLDS GSKVYREKDI ITHEEFTEEL LSGKINCKLE T LTPLIIPD TSDENGLKLQ GNKPGHKNYK FFNINGELMI PGSELRGMLR THFEALTKSC FAIFGEDSTL SWRMNADEKD YK IDSNSIR KMESQRNPKY RIPDELQKEL RNSGNGLFNR LYTSERRFWS DVSNKFENSI DYKREILRCA GRPKNYKGGI IRQ RKDSLM AEELKVHRLP LYDNFDIPDS AYKANDHCRK SATCSTSRGC RERFTCGIKV RDKNRVFLNA ANNNRQYLNN IKKS NHDLY LQYLKGEKKI RFNSKVITGS ERSPIDVIAE LNERGRQTGF IKLSGLNNSN KSQGNTGTTF NSGWDRFELN ILLDD LETR PSKSDYPRPR LLFTKDQYEY NITKRCERVF EIDKGNKTGY PVDDQIKKNY EDILDSYDGI KDQEVAERFD TFTRGS KLK VGDLVYFHID GDNKIDSLIP VRISRKCASK TLGGKLDKAL HPCTGLSDGL CPGCHLFGTT DYKGRVKFGF AKYENGP EW LITRGNNPER SLTLGVLESP RPAFSIPDDE SEIPGRKFYL HHNGWRIIRQ KQLEIRETVQ PERNVTTEVM DKGNVFSF D VRFENLREWE LGLLLQSLDP GKNIAHKLGK GKPYGFGSVK IKIDSLHTFK INSNNDKIKR VPQSDIREYI NKGYQKLIE WSGNNSIQKG NVLPQWHVIP HIDKLYKLLW VPFLNDSKLE PDVRYPVLNE ESKGYIEGSD YTYKKLGDKD NLPYKTRVKG LTTPWSPWN PFQVIAEHEE QEVNVTGSRP SVTDKIERDG KMV

UniProtKB: RAMP superfamily protein

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Macromolecule #3: RNA (37-MER)

MacromoleculeName: RNA (37-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 11.768993 KDa
SequenceString:
GGACUUAAUG UCACGGUACC CAAUUUUCUG CCCCGGA

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Macromolecule #4: RNA (5'-R(P*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*C)-3')

MacromoleculeName: RNA (5'-R(P*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*C)-3')
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 5.874595 KDa
SequenceString:
CGGGGCAGAA AAUUGGAC

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / 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

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87226
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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