[English] 日本語
Yorodumi
- EMDB-10196: Cryo-EM structure of the Type III-B Cmr-beta bound to cognate tar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10196
TitleCryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP, state 2, in the presence of ssDNA
Map data
Sample
  • Complex: Type III-B Cmr-beta ternary complex, cognate target RNA and AMPPnP bound, in the presence of ssDNA
    • Complex: CRISPR-associated RAMP protein, Cmr4 family
      • Protein or peptide: x 1 types
    • Complex: CRISPR-associated RAMP protein, Cmr6 family
      • Protein or peptide: x 1 types
    • Complex: crRNA
      • RNA: x 1 types
    • Complex: CRISPR-associated protein, Cmr5 family
      • Protein or peptide: x 1 types
    • Complex: CRISPR-associated protein, Cmr3 family
      • Protein or peptide: x 1 types
    • Complex: Cmr1,CRISPR-associated RAMP protein, Cmr1 family
      • Protein or peptide: x 1 types
    • Complex: CRISPR-associated protein, Cmr2 family
      • Protein or peptide: x 1 types
    • Complex: CRISPR-associated protein Cmrx
      • Protein or peptide: x 1 types
    • Complex: Cognate target RNA
      • RNA: x 1 types
  • Ligand: x 3 types
Function / homology
Function and homology information


CRISPR-cas system / defense response to virus / membrane / cytoplasm
Similarity search - Function
CRISPR system CMR subunit Cmr7 1 / CRISPR system CMR subunit Cmr7 1 / CRISPR-associated protein, TM1793 / CRISPR-associated protein, TM1791 / CRISPR-associated protein TM1795 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily ...CRISPR system CMR subunit Cmr7 1 / CRISPR system CMR subunit Cmr7 1 / CRISPR-associated protein, TM1793 / CRISPR-associated protein, TM1791 / CRISPR-associated protein TM1795 / 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 / CRISPR type III-associated protein / RAMP superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
CRISPR-associated protein, Cmr3 family / CRISPR-associated protein, Cmr2 family / CRISPR-associated RAMP protein, Cmr6 family / CRISPR-associated RAMP protein, Cmr1 family / CRISPR type III-B/RAMP module-associated protein Cmr5 / CRISPR-associated RAMP protein, Cmr4 family / CRISPR-associated protein Cmrx
Similarity search - Component
Biological speciesSulfolobus islandicus REY15A (acidophilic) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsSofos N / Montoya G
Funding support Denmark, 3 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF17SA0030214 Denmark
Novo Nordisk FoundationNNF0024386 Denmark
Citation
Journal: Mol Cell / Year: 2020
Title: Structures of the Cmr-β Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas.
Authors: Nicholas Sofos / Mingxia Feng / Stefano Stella / Tillmann Pape / Anders Fuglsang / Jinzhong Lin / Qihong Huang / Yingjun Li / Qunxin She / Guillermo Montoya /
Abstract: Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) ...Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) cleavage, cyclic oligoadenylate synthesis, and also a unique UA-specific single-stranded RNA (ssRNA) hydrolysis by the Cmr2 subunit. Here, we present the structure-function relationship of Cmr-β, unveiling how binding of the target RNA regulates the Cmr2 activities. Cryoelectron microscopy (cryo-EM) analysis revealed the unique subunit architecture of Cmr-β and captured the complex in different conformational stages of the immune response, including the non-cognate and cognate target-RNA-bound complexes. The binding of the target RNA induces a conformational change of Cmr2, which together with the complementation between the 5' tag in the CRISPR RNAs (crRNA) and the 3' antitag of the target RNA activate different configurations in a unique loop of the Cmr3 subunit, which acts as an allosteric sensor signaling the self- versus non-self-recognition. These findings highlight the diverse defense strategies of type III complexes.
#1: Journal: Biorxiv / Year: 2020
Title: Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas
Authors: Sofos N / Feng M / Stella S / Pape T / Fuglsang A / Lin J / Huang Q / Li Y / She Q / Montoya G
History
DepositionAug 6, 2019-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6sh8
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10196.png

Downloads & links

-
Map

FileDownload / File: emd_10196.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 1.8 / Movie #1: 2
Minimum - Maximum-13.125933 - 23.571354
Average (Standard dev.)0.00032796155 (±0.60951185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-13.12623.5710.000

-
Supplemental data

-
Additional map: None

Fileemd_10196_additional.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_10196_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_10196_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Type III-B Cmr-beta ternary complex, cognate target RNA and AMPPn...

EntireName: Type III-B Cmr-beta ternary complex, cognate target RNA and AMPPnP bound, in the presence of ssDNA
Components
  • Complex: Type III-B Cmr-beta ternary complex, cognate target RNA and AMPPnP bound, in the presence of ssDNA
    • Complex: CRISPR-associated RAMP protein, Cmr4 family
      • Protein or peptide: CRISPR-associated RAMP protein, Cmr4 family
    • Complex: CRISPR-associated RAMP protein, Cmr6 family
      • Protein or peptide: CRISPR-associated RAMP protein, Cmr6 family
    • Complex: crRNA
      • RNA: crRNA
    • Complex: CRISPR-associated protein, Cmr5 family
      • Protein or peptide: CRISPR-associated protein, Cmr5 family
    • Complex: CRISPR-associated protein, Cmr3 family
      • Protein or peptide: CRISPR-associated protein, Cmr3 family
    • Complex: Cmr1,CRISPR-associated RAMP protein, Cmr1 family
      • Protein or peptide: Cmr1,CRISPR-associated RAMP protein, Cmr1 family
    • Complex: CRISPR-associated protein, Cmr2 family
      • Protein or peptide: CRISPR-associated protein, Cmr2 family
    • Complex: CRISPR-associated protein Cmrx
      • Protein or peptide: CRISPR-associated protein Cmrx
    • Complex: Cognate target RNA
      • RNA: Cognate target RNA
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MANGANESE (II) ION

+
Supramolecule #1: Type III-B Cmr-beta ternary complex, cognate target RNA and AMPPn...

SupramoleculeName: Type III-B Cmr-beta ternary complex, cognate target RNA and AMPPnP bound, in the presence of ssDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: Cognate target RNA, AMPPnP, and ssDNA added to the sample
Molecular weightExperimental: 900 KDa

+
Supramolecule #2: CRISPR-associated RAMP protein, Cmr4 family

SupramoleculeName: CRISPR-associated RAMP protein, Cmr4 family / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Recombinant expressionOrganism: Sulfolobus islandicus REY15A (acidophilic)

+
Supramolecule #3: CRISPR-associated RAMP protein, Cmr6 family

SupramoleculeName: CRISPR-associated RAMP protein, Cmr6 family / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Recombinant expressionOrganism: Sulfolobus islandicus REY15A (acidophilic)

+
Supramolecule #4: crRNA

SupramoleculeName: crRNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #9
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Recombinant expressionOrganism: Sulfolobus islandicus REY15A (acidophilic)

+
Supramolecule #5: CRISPR-associated protein, Cmr5 family

SupramoleculeName: CRISPR-associated protein, Cmr5 family / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)

+
Supramolecule #6: CRISPR-associated protein, Cmr3 family

SupramoleculeName: CRISPR-associated protein, Cmr3 family / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)

+
Supramolecule #7: Cmr1,CRISPR-associated RAMP protein, Cmr1 family

SupramoleculeName: Cmr1,CRISPR-associated RAMP protein, Cmr1 family / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)

+
Supramolecule #8: CRISPR-associated protein, Cmr2 family

SupramoleculeName: CRISPR-associated protein, Cmr2 family / type: complex / ID: 8 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)

+
Supramolecule #9: CRISPR-associated protein Cmrx

SupramoleculeName: CRISPR-associated protein Cmrx / type: complex / ID: 9 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)

+
Supramolecule #10: Cognate target RNA

SupramoleculeName: Cognate target RNA / type: complex / ID: 10 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: synthetic construct (others)

+
Macromolecule #1: CRISPR-associated protein, Cmr5 family

MacromoleculeName: CRISPR-associated protein, Cmr5 family / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 17.961834 KDa
SequenceString:
MLYEEDYKLA LEAFKKVFNA LTHYGAKQAF RSRARDLVEE IYNSGFIPTF FYIISKAELN SDSLDSLISL FSSDNAILRG SDENVSYSA YLFIILYYLI KRGIIEQKFL IQALRCEKTR LDLIDKLYNL APIISAKIRT YLLAIKRLSE ALIEAR

+
Macromolecule #2: CRISPR-associated RAMP protein, Cmr4 family

MacromoleculeName: CRISPR-associated RAMP protein, Cmr4 family / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 32.322359 KDa
Recombinant expressionOrganism: Sulfolobus islandicus REY15A (acidophilic)
SequenceString: MPYYAFAEPF FIHAITHLHV GSGSSVEEEI ALPFQRDELG YPTIYASSLK GAIKSFLLKE FPDKRDVIYK VLGEDENPEE ASLGTFLDA ILFAIPSRII EIDSAKPYVW VYVTTYELLK KVKLYLDSIS QLSNASFSNL KNKIDTILAK EGKNITLDSD L KSAILNED ...String:
MPYYAFAEPF FIHAITHLHV GSGSSVEEEI ALPFQRDELG YPTIYASSLK GAIKSFLLKE FPDKRDVIYK VLGEDENPEE ASLGTFLDA ILFAIPSRII EIDSAKPYVW VYVTTYELLK KVKLYLDSIS QLSNASFSNL KNKIDTILAK EGKNITLDSD L KSAILNED FYVELEALNN KIPSIINAGV PLLVLEDSIG REVINRSLIR VRRIRIDRDK KVVETGGLWS EEYVPMKTIF FS VLLGKES KESAIFASCI LRNLRYVILG GKETIGKGIV ELRWVKDVI

+
Macromolecule #3: CRISPR-associated protein, Cmr3 family

MacromoleculeName: CRISPR-associated protein, Cmr3 family / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 36.008547 KDa
SequenceString: MKRVLIKPLE PLMFRSQGEF EPLITGSHTA AQSLIIPRPS TIAGMLGYIL FNKSSGTGDW LSDLTNLLAT IYGTFIETNG EYLFPLRMG NHLALVDQQH LINLPTLLEK EYERREKGIY ELFYDKNKLF QIINHQDRIG ISIDKSTRTV KEHYLYSARY L AFKKEVNY ...String:
MKRVLIKPLE PLMFRSQGEF EPLITGSHTA AQSLIIPRPS TIAGMLGYIL FNKSSGTGDW LSDLTNLLAT IYGTFIETNG EYLFPLRMG NHLALVDQQH LINLPTLLEK EYERREKGIY ELFYDKNKLF QIINHQDRIG ISIDKSTRTV KEHYLYSARY L AFKKEVNY VIFIDNDAIS DKINGKIVNF GGENRIAKLE VDDYKVDTSI EEEYYLALSP ILIPDEALDN FLDNISDYVA MG KVDKISL GFDIANTKRK EMLTAILEGS IVKRSIIDFI KNEIKNDLRY RFSKYEKIGY NTLMSLCKLA LRKILS

+
Macromolecule #4: CRISPR-associated RAMP protein, Cmr6 family

MacromoleculeName: CRISPR-associated RAMP protein, Cmr6 family / type: protein_or_peptide / ID: 4
Details: C-terminal histidine-tag for co-purification of the complex.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 33.945914 KDa
Recombinant expressionOrganism: Sulfolobus islandicus REY15A (acidophilic)
SequenceString: MAIDFLVNIL ELIKEKQCNI NLFSAISLTS IVYNNFGEFL SNNQSYSTNN PLLKYHIIIL NDKNKTKDVE EKRNIFKREV AELISRNFK LDGEKVRNYF DSLKEVLKSL KYTIVDVEIT TRTRALIGVS TSLGKLIFGS GISFDPYMNL PYIPASEIKG I VRSYIEGK ...String:
MAIDFLVNIL ELIKEKQCNI NLFSAISLTS IVYNNFGEFL SNNQSYSTNN PLLKYHIIIL NDKNKTKDVE EKRNIFKREV AELISRNFK LDGEKVRNYF DSLKEVLKSL KYTIVDVEIT TRTRALIGVS TSLGKLIFGS GISFDPYMNL PYIPASEIKG I VRSYIEGK LGEQEAEEIF GNEEREGNVN FTDAYPTRSK DFLFVPDVIT PHYNGKKSEA DAEPRPVIHL TIAPKVTFRF LI YYKREDV GKPICDSMPI ILIRGLGARS SVGYSLFELR KIEVIKAAAH HHHHHHHHH

+
Macromolecule #5: Cmr1,CRISPR-associated RAMP protein, Cmr1 family

MacromoleculeName: Cmr1,CRISPR-associated RAMP protein, Cmr1 family / type: protein_or_peptide / ID: 5
Details: The N-terminal "MEEELL" sequence is not part of the annotated sequence (F0NDX4) due to an annotation mistake.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 55.388965 KDa
SequenceString: MEELLMSLKL KALYPLTGGY NRHSINPFYE ELVRPTEIKG LWRWWNRVLF NTLAYSTKGK LYTYESIDRL FEDVFGSENK KSAVRLEVI TDEGNDNRFE LSYVELDKVI DCLRNYKRKV SLDFIDNTLI AEIEGSTKIP ISFKSNLDID KIIKDLVHNN K LLSFELLG ...String:
MEELLMSLKL KALYPLTGGY NRHSINPFYE ELVRPTEIKG LWRWWNRVLF NTLAYSTKGK LYTYESIDRL FEDVFGSENK KSAVRLEVI TDEGNDNRFE LSYVELDKVI DCLRNYKRKV SLDFIDNTLI AEIEGSTKIP ISFKSNLDID KIIKDLVHNN K LLSFELLG FKSVEIDATK ISDKKILKEI LRDLITNYLE YFNIKQEVTF TLNIYLDKSR EHKQNFEDKL KFALYSLLVF IL LGGIGRK TSRGFGSLSI IDVKCYDNSI CKKIEDLAKN FLKISSGNEL KSKIESILDC IKNSCIDTLY IENNILSEID PKK NVVYFI NSDLFEVKRI NDKEKVLANI YKAVSSEGCC IKSIITDKYV RKSFLIAFGG YRKVEKDKGL DIGFIKNYLC ETCE TVSSF NIVDFLLSEG SFMSDYILQY EHRNSLLRFK LISDNSNNSY LIGYILHSSY FKKIDIKYVR CILEKLTYCV I

+
Macromolecule #6: CRISPR-associated protein, Cmr2 family

MacromoleculeName: CRISPR-associated protein, Cmr2 family / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 120.856453 KDa
SequenceString: MSIDNVLREF LDYKIIALLH DPPNKAWVIT GRARNLTQQL SNIRASRKHE KVAKYIINQL FGKNYSEKVD NADKLASSID RYLGSIVYK ERSLFENRSI FLKNILLSNI QRDIGNLFPK DKSKLDNLIL EYKKLLNVIN KTNLILKYQL FYLIYELVWI D SKYENTPS ...String:
MSIDNVLREF LDYKIIALLH DPPNKAWVIT GRARNLTQQL SNIRASRKHE KVAKYIINQL FGKNYSEKVD NADKLASSID RYLGSIVYK ERSLFENRSI FLKNILLSNI QRDIGNLFPK DKSKLDNLIL EYKKLLNVIN KTNLILKYQL FYLIYELVWI D SKYENTPS DTRNPTHTIF DHLYATAAMM NWILSLEKEA KGYLLGIDTI GVADFISKGR KTRDLWISSY LVSALLWYVI TW FIEEYGP DVILFPSLRF NQFYAFYLLE KLRKEGVSED VIDEIKELIT KYIFNGDDLF ENLKIPPYPI IPGRITLILP GLI REGEEY KKVQDDNCFI SKVKERYNEG WRKLIEGLRC YSERKREDGF WNLVCRVLKL TEDLLQTTPL NIRVKQVSVT EDEI FNNNK LRSDSWKIYD NKYRQLVSEF KKSKLVKVTP ESRLKLFELT KFDKLPQIGE KSKRGYEFCT SCGVLPAVVI MPKED ELEK KLIDLGIARD EKDVRSIKNM ISPGERLCPW CLVKRALGAE PRLMRILLLG DLYSVEKIVN EIVSRDVKIE IPSTSD IAS IKTFEEMIEK KNEICEDLKE EEVCEKPSES VLSMWQWFNK NYYNGINLTI DPEEYWFSEK RRRYYFSVFR RHRITFP SP YYALVRADSD YLGDLLEGKL TPYLAGIIDS GDYANISEKK EEVNKLLEEY LVNAGSGSIV DYVKTVLKCI RENLNKCS C AEKIYSNEVA KVMFRVNVEK ANVEEEVKNS LEYFETILNE GRIIVTPAWH VSISSALNRG LLVELELVNK HKGFVIYAG GDDLLAMLPV DEVLDFIKES RRAFAGFGTE KLGNMCLENG FVRINNAYYP SLPIVGRSYS VIIAHYADPL FFVINDSYNL LEEGKEIIR YRVMYNGEYK DAKKDVAIFR YQGLTSVIPL SLKRPIVSSV SDFNEIASII DVILELKKRI DEGRISVSLL Y DYEKYKHL IVASDEKYLT EFLVKDWIKR NSLRKHVEFT IDEKLYGVRL TIENYPIKIP NDLISNIVYT LRIIYGGEK

+
Macromolecule #7: CRISPR-associated protein Cmrx

MacromoleculeName: CRISPR-associated protein Cmrx / type: protein_or_peptide / ID: 7 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 19.705607 KDa
SequenceString:
MSTQREYVFI PITNSITIDV KITIGGSDHI TNIDERGIHN VLVITGYAVD EKNGRLVPTL DPCDYVKGIL VAGTPQQAQS NDFLTLKLP ANKLYLIRKK GNISDDLKIY IPYSSPDARN SMKTKPVSIS DDTIVNNIIK EVFDKIYNIT QKEKVKIEKV K EDIKELFS YYALEQ

+
Macromolecule #8: Cognate target RNA

MacromoleculeName: Cognate target RNA / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.704712 KDa
SequenceString:
UGUUAAGUCU GGUUUCCCUC CAGGGUAUCU AAGCUUUGAA AAAAAA

+
Macromolecule #9: crRNA

MacromoleculeName: crRNA / type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 16.409871 KDa
SequenceString:
AUUGAAAGUU CAAAGCUUAG AUACCCUGGA GGGAAACCAG ACUUAACACC A

+
Macromolecule #10: ZINC ION

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

+
Macromolecule #11: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 11 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

+
Macromolecule #12: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 12 / Number of copies: 3 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
0.15 MNaClSodium chloridesodium chloride
0.01 MMES
1.0 mMCaCl2Calcium Chloride
GridModel: Quantifoil, UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 5 mA (Leica EM ACE200)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3-4 s blotting before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.1 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5298 / Average exposure time: 40.0 sec. / Average electron dose: 41.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 429000
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER
Details: Model generated ab initio with cisTEM using a dataset of a similar sample.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Software - details: beta
Final 3D classificationNumber classes: 3 / Avg.num./class: 45000 / Software - Name: cisTEM (ver. 1.0) / Software - details: beta
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0) / Software - details: beta
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0) / Software - details: beta / Number images used: 50409
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-6sh8:
Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP, state 2, in the presence of ssDNA

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more