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- EMDB-29243: Golden Shiner Reovirus Core Polar Vertex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-29243
TitleGolden Shiner Reovirus Core Polar Vertex
Map data
Sample
  • Virus: Golden shiner reovirus
    • Protein or peptide: x 6 types
    • RNA: x 6 types
  • Ligand: x 1 types
KeywordsdsRNA / virus / RNA-dependent / RNA-polymerase
Function / homology
Function and homology information


viral intermediate capsid / T=2 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / 7-methylguanosine mRNA capping / viral genome replication / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase ...viral intermediate capsid / T=2 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / 7-methylguanosine mRNA capping / viral genome replication / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / hydrolase activity / RNA helicase / RNA-directed RNA polymerase / nucleotide binding / RNA-dependent RNA polymerase activity / GTP binding / structural molecule activity / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / : / : / : / : / : / : / : / : ...Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / : / : / : / : / : / : / : / : / Reovirus core-spike protein lambda-2 (L2), 6th domain / Reovirus core-spike protein lambda-2 (L2), 7th domain / Reovirus core-spike protein lambda-2 (L2), ferredoxin-like domain / Reovirus core-spike protein lambda-2 (L2), GTase domain / Reovirus core-spike protein lambda-2 (L2), N-terminal / Reovirus core-spike protein lambda-2 (L2), methyltransferase-1 / Reovirus core-spike protein lambda-2 (L2), methyltransferase-2 / Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / Reovirus core-spike lambda-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Reovirus RNA-dependent RNA polymerase lambda 3 / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Clamp protein VP6 / Microtubule-associated protein VP5 / Major inner capsid protein VP3 / RNA-directed RNA polymerase VP2 / Outer capsid protein VP1
Similarity search - Component
Biological speciesGolden shiner reovirus / AQRV-C (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsStevens AS / Zhou ZH
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007323 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
CitationJournal: Protein Cell / Year: 2023
Title: Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation.
Authors: Alexander Stevens / Yanxiang Cui / Sakar Shivakoti / Z Hong Zhou /
History
DepositionDec 19, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29243.png

Downloads & links

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Map

FileDownload / File: emd_29243.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.00665
Minimum - Maximum-0.017798452 - 0.039396122
Average (Standard dev.)0.0005335958 (±0.0030573301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29243_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_29243_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 : Golden shiner reovirus

EntireName: Golden shiner reovirus
Components
  • Virus: Golden shiner reovirus
    • Protein or peptide: RNA-directed RNA polymerase VP2
    • Protein or peptide: Microtubule-associated protein VP5
    • Protein or peptide: Major inner capsid protein VP3
    • Protein or peptide: Major inner capsid protein VP3
    • Protein or peptide: Clamp protein VP6
    • Protein or peptide: Outer capsid protein VP1
    • RNA: RNA (52-MER)
    • RNA: RNA (60-MER)
    • RNA: RNA (40-MER)
    • RNA: RNA (18-MER)
    • RNA: RNA (38-MER)
    • RNA: RNA (30-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Golden shiner reovirus

SupramoleculeName: Golden shiner reovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Details: cultured in Fat Head minnow cellsfrom ATCC "CCL-42"
NCBI-ID: 185783 / Sci species name: Golden shiner reovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Notemigonus crysoleucas (golden shiner)
Molecular weightTheoretical: 47 MDa
Virus shellShell ID: 1 / Name: inner capsid shell

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Macromolecule #1: RNA-directed RNA polymerase VP2

MacromoleculeName: RNA-directed RNA polymerase VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 141.605281 KDa
SequenceString: EELFNALPQP LQQLSLALAG EIPLTDHIFE QAASTWHVQP RSLTYKLLDH IPFSTPVVVP PSIYHSLDWS KCFAVNQDRV ERVPTIDDP DDVYVPNSDI GPLLTSLHTI PDYGFLHPAI ENDATTLRAE RARCASTFYK IASSQARQVK LDPIRMLGFL L LVQARPRV ...String:
EELFNALPQP LQQLSLALAG EIPLTDHIFE QAASTWHVQP RSLTYKLLDH IPFSTPVVVP PSIYHSLDWS KCFAVNQDRV ERVPTIDDP DDVYVPNSDI GPLLTSLHTI PDYGFLHPAI ENDATTLRAE RARCASTFYK IASSQARQVK LDPIRMLGFL L LVQARPRV PSGLVTDQPT RRDPTQSPAL HAIWQVMQYY KVAGVYYAPA LVVPSGAIWW IPPPGKRNVV SVQYLLTDLI NL AILAHMT DMSPTLELTG VLMYLRAASS HSHAYTLLQM KSVFPALSLR SMYRNKGFGG KAPAIEWTEP RSKYKFRWTG VTQ LHDGLR PRSPSMDVPT LEVLTKYELV DIGHIIIRER NAHPRHNHDS VRFVRDVMAL TSGMYLVRQP TMSVLREYSQ VPDI KDPIP PSAWTGPIGN VRYLLPSVQG PARHLYDTWR AAARQIAQDP QWHDPLNQAI MRAQYVTARG GSSASLKFAL KVTGI VLPE YDDSKVKKSS KIYQAAQIAR IAFMLLIAAI HAEVTMGIRN QVQRRARSIM PLNVIQQAIS APHTLVANYI NKHMNL STT SGSVVTDKVI PLILYASTPP NTVVNVDIKA CDASITYNYF LSVICGAMHE GFEVGNADAA FMGVPSTIVS DRRSSVA PY SRPISGLQTM VQHLADLYAA GFRYSVSDAF SSGNKFSFPT STFPSGSTAT STEHTANNST MMEYFLNVHA PSHVKSAS L KRILTDMTIQ RNYVCQGDDG ILLLPHEAAS KISADDMNEL LTCLRDYGQL FGWNYDIDWS DTAEYLKLYA LMGCRIPNT SRHPPVGKEY AAPQTDEIWP SLIDIVIGHH LNGVTDVLNW REWLRFSWAF ACYSSRGGYT NPKGQSFSAQ YPWWTFVYLG IPPILLPGQ TPFIHSCYMP PGDQGMFSIL NGWRDWLISH ASTTLPPLRH NHPVWGLSDV PSLLSQFGVY AGYHAAQHYR R PKPAPETA SSDSINQITS DLTEYLFYDS ALKARVMKGR YNWERLSSSL SLNVGSRVPS LFDVPGKWVA AGRDAEKPPP SS VEDMFTS LNRCIRRPTH SFSRLLELYL RVHVTLGESI PLAIDPDVPQ VAGADPANDD HWFKYTCLGD IPSATRNYFG ESL FVGRVV SGLDVEAVDA TLLRLKILGA PPEAFIAVLN GIGMSDSEAH QIAGRISLAN AQLVQIARVV HLSIPSSWMT LNTG PYIHH HAYDFKPGIT QPSAKSRDKS IWMSPILKLL CTSYAMTVAG PVRTSIVTEI DGSAAALSGN LRVWMRDV

UniProtKB: RNA-directed RNA polymerase VP2

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Macromolecule #2: Microtubule-associated protein VP5

MacromoleculeName: Microtubule-associated protein VP5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 79.347359 KDa
SequenceString: MITIVVIPTA HFSWTDTNFL NSVDYRLTSQ PKIRDRFAVY APGWLRRQLD EFSASLTASE LLQALQTIPI PVKARCLLLP KPKRFAQWL LDVPSANIWH IPVTTLRATV ASKHPSSDVY NYIPDHVPPS AEFDTVTRRV AAGRDIYVRS TKVLGAPLCL A APAKYYAG ...String:
MITIVVIPTA HFSWTDTNFL NSVDYRLTSQ PKIRDRFAVY APGWLRRQLD EFSASLTASE LLQALQTIPI PVKARCLLLP KPKRFAQWL LDVPSANIWH IPVTTLRATV ASKHPSSDVY NYIPDHVPPS AEFDTVTRRV AAGRDIYVRS TKVLGAPLCL A APAKYYAG YLSTHQLDGV YPDNWAPDNF HKREFCLTIL PSLLGPRTFL LDVDADRDAS YPLSVLWPQL RVLALKSRLL LP PVALLRR VVDPGLKPTW SADSDAAFRA LRLSRPSSAS KPTGFDFSAL PVVDIICLFE SEPDDHGRVA PGTRLTIHSV PTD LLTSLS IQEGVRYPLR QESGMFVPWV LLALLMSDDV TISGTRRSVK LETAHASARP FVHITVERCA SARVVDVRGS PAMY ANAVC LTLPKGSYKS TIIDTLPAMF SDLSILEQAA VIDSDALGDS LRPSFETQFL ERLENLDPKL LDRAVASILS PASDT SDDA VTTVLDVFNA LYREVMTPAQ RSRLPLLTQQ GRVLAFAHSD YELLSANIPI QVVRGSIPID HVVNLLARRN RVGGTA LQV LLDYCYRTQA SPLAPTPAGR LYKQLFGPWL MVPRLSDPLI KLRLVASAPA KVLRAAGWTI DGDPPLEVSC LCAYVTD RA MAAALIERRL DSRALVNVGG DQLMFVEYAP PLPLVSIPRT FLLPVTYVVH WVSPQRVLLN GGNVSFTSGL EWTFDD

UniProtKB: Microtubule-associated protein VP5

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Macromolecule #3: Major inner capsid protein VP3

MacromoleculeName: Major inner capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 124.694531 KDa
SequenceString: DIITRPTSDS IAAVANATKP AAVVSDPQSM KVTPIVNPSS YVCNVCNARF STMSALSEHL RSDHRDDAST LLATPMINNA IRSFLTAWD GIRILSPDVS SKHLSAYLDS AVANGPELIV EDTGLCTSFM LLDNIPSAHL TKELIGFTWF MQMYQMTPPL P EGAVNRIV ...String:
DIITRPTSDS IAAVANATKP AAVVSDPQSM KVTPIVNPSS YVCNVCNARF STMSALSEHL RSDHRDDAST LLATPMINNA IRSFLTAWD GIRILSPDVS SKHLSAYLDS AVANGPELIV EDTGLCTSFM LLDNIPSAHL TKELIGFTWF MQMYQMTPPL P EGAVNRIV CMTNWASLGD EGRGLEVRLP PPTDSSVHAY KTVLSRGYID NAQFNPLALR SNVLLMLLQF TLSNLKINKS ST FTSDVTT ITSGRMIRAF EGRPELLALA YPGRAVLPTQ TKNAQFLSTA IADRIGRLDR ANLIGGEVSA MVECMELCDA LTL HIRETY VMLLRSMHQD PTQIVQIVNE CANNLLNSTI PISLRPTILC PWFASSEDLR LQQVMHLVNI SSNTAAALPL VEAL STLLR SVTPLVLDPT VLTNAITTIS ESTTQTISPI SEILRLLQPM GNDYAAFWKC IASWAYNGLV TTVLSEDAFP DSSQS ITHL PSMWKCLFLT LAGPMTSDPH SPVKVFMALA NLLAQPEPIA IGVPGMHQTT PASQFSHPGV WPPGFLNPQL INPQQA PLL RAFAEHIRAN WPQPSEFGYG STLQGSANLF IPPNRMVYPW PNQPLPRLTV APTYDSAMSN WISTTIAFFI RVVNSVN MT ATVNDLTRRT MTGVMTAMRQ VKTMTPFYIQ HMCPTELSVL ASVTVTPPFQ VPFTRLVQND VITNVLVARV DPAQRGDA A VDIRATHATF AAALPVDPAA IVVAMLCGQT ETNLIPSHHY GKAFAPLFAS NAMFTRNQRA VITREAFVCA RSAVAQCQD AGFLVPRPLD ALRQFDVTSA AAAEIMHAVN DAFKTAFDLD GALLDGLALY GDPRIADLSA AYLQYGGNVV REHVPPGPSH IHRTLQQVE STFMAEMNLF NVARGNLYLV QTATNGNWSP MAPVAAPPFV RGGPNVRVVG RFGTIVPRPD GLEPQLIDDG N VPRDIAGD WVYPSDVLQV SVAVFCDYVW PMVKAGRTRV LVELGHYVYT LHYYDPQISL DEAPILEEWL SKINPAGIPP VP FCIPIPQ VYPCITARRV HYAFTSENNN DSLFSTNAAS IDTAFGENAA VSPLRWPGLV DPNYRVGTND LPNRITLYNS LYR YNFTYP TLDGIMYVRS AT

UniProtKB: Major inner capsid protein VP3

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Macromolecule #4: Major inner capsid protein VP3

MacromoleculeName: Major inner capsid protein VP3 / type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: AQRV-C (virus)
Molecular weightTheoretical: 9.147655 KDa
SequenceString:
TASPADTNVV PAKDAPTTNS PPSTTSPNQA AADANQQQAG IVSSQSGPNA VGDSAPSTSV NNDGDIITRP TSDSIAAVAN ATKPAAVVS DPQSM

UniProtKB: Major inner capsid protein VP3

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Macromolecule #5: Clamp protein VP6

MacromoleculeName: Clamp protein VP6 / type: protein_or_peptide / ID: 5 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: AQRV-C (virus)
Molecular weightTheoretical: 44.489391 KDa
SequenceString: AQRQFFGLTY NFYGQPAPLF DLNDLQELAG CYARPWTSRF SHLAISTGSL PVWSARYPSV ASRNIIVNTL LGAHLNPFAG GQVTSHQGI TWRDPVLSSL APVPAIQPPP VWAVAENVPL DSNNYPTYVL NLSSMWPINQ DVHIMTMWAL SDQGPIYHLE V PVDPMPAA ...String:
AQRQFFGLTY NFYGQPAPLF DLNDLQELAG CYARPWTSRF SHLAISTGSL PVWSARYPSV ASRNIIVNTL LGAHLNPFAG GQVTSHQGI TWRDPVLSSL APVPAIQPPP VWAVAENVPL DSNNYPTYVL NLSSMWPINQ DVHIMTMWAL SDQGPIYHLE V PVDPMPAA TTAALMAYIG VPIAHLAQTA YRFAGQLPQS PDSTMVSTIR WLSAIWFGSL TGRLNRSRTC NGFYFEFAKP AL NPDQAVL KWNDGARAAP PAAAQSSYMR CISPHWQHQI VEVAGALMSQ SVTAVTGLPA LIDEATLPAW SQGVANLTGN GQG VVPCLD YNPVPMAAAR HLQWRQDGLI TAAQEAQLNN DYTAYALTIE RHLTAMLVAN PIAAGRMPIQ PFNAADFGQA GQTA AAVAL AQAMFV

UniProtKB: Clamp protein VP6

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Macromolecule #6: Outer capsid protein VP1

MacromoleculeName: Outer capsid protein VP1 / type: protein_or_peptide / ID: 6 / Number of copies: 5 / Enantiomer: LEVO / EC number: mRNA guanylyltransferase
Source (natural)Organism: AQRV-C (virus)
Molecular weightTheoretical: 141.10975 KDa
SequenceString: AAVFGIQLVP KLNTSTTRRT FLPLRFDLLL DRLQSTNLHG VLYRALDFNP VDRSATVIQT YPPLNAWSPH PAFIENPLDY RDWTEFIHD RALAFVGVLT QRYPLTQNAQ RYTNPLVLGA AFGDFLNARS IDIFLDRLFY GPTQESPITS ITKFPYQWTI D FNVTADSV ...String:
AAVFGIQLVP KLNTSTTRRT FLPLRFDLLL DRLQSTNLHG VLYRALDFNP VDRSATVIQT YPPLNAWSPH PAFIENPLDY RDWTEFIHD RALAFVGVLT QRYPLTQNAQ RYTNPLVLGA AFGDFLNARS IDIFLDRLFY GPTQESPITS ITKFPYQWTI D FNVTADSV RTPAGCKYIT LYGYDPSRPS TPATYGKHRP TYATVFYYST LPARSRLLAN LAAGPTVLEH FDSPTYGPHL LL PQTGDVL GYSSSLISQA ALLMVESVMD ALRDNANASA STAVTRLDQS YHPVTSFDPS TFNTLLQRAT NLALLAVQGV QSE SAIPAI PTMSDVRSFV ARLMAEGDPQ QWFPYRVDQI LYWPESPFVP PIGPFYAPFR PVNFPFTTGS YTVVPDASRP LRLL PQYRN ATITVQQADD AYEDTALSPL ITTHGFCVTG GVSTSIYDIS GDPTAYPPAQ LVDTPNDYFD RERMARRDLF RRLRA PADR SAIKDRAVFD FLASLVNPTT ANPVLDTSFS MAYLGASSAH ANADEPVILA DIRSGSIPGL PIPRRIVQFG YDVVHG SLL DLSRAVPTGT FGLVYADLDQ VEDAGTDMPA ANRAAIAMLG TALQMTTAGG VSVLKVNFPT RAFWTQVFNL YATHATT LH LVKPTIVNSS EVFLVFGGRQ SNGALRSTTA LQRALLSLYA RNAAIDRAVT HIPFFGVPDD GTSDLGIDAV RLFDPMFS D AVANLPSNAL ASLVSRVVPS SIMFTRVPSN GPVSTTIYGK RTFLSNRRRA RLRDVPMLIT TTLVHQRRFT TPPTFTLFS SEAVPVTTLV AAGYNSFISE QTRNPNLAHL LDLGTGPECR ILSLIPPTLQ VTMSDARPCA ELMASFDPAL TAYVQGDYST AAFWNGIRC DSATAIFTLG AAAAAAGTDL IAFVQQLIPR IVAAGGTRMW LQLNTPLYEV SSLPDLIDID LRDRVYRFNG G ERVEPYAD PVPLQQAIAA LLPAAALSWH TLSPTCDWLP YIIGVGSPLN LSDINTAISY SRLTPILHID TTTPPLRVNP VP TPLNQQC AIRITSLDPA AVLSVQHNGV EVIGGTPGNV ISVAGAAALQ YILANQEFLL QFTPTLPGIF DVFLTTLGQP PVP RGSFTI TPPPTTVVLN MPPPGQLDFT DVGNDARITC DPYYQLAVCI FKDGQYVRVN PEKASVVTNA PNRDLHFVLD LADN HVLLY LCDVTPSGLG DRIAFPIVDI YRIAFPRNTP VRASLPYTGG GAHLTSGGNP FMSLTTPPAV LPAGVALAAL STSVA TQYP TYTLPAGVYE YVI

UniProtKB: Outer capsid protein VP1

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Macromolecule #7: RNA (52-MER)

MacromoleculeName: RNA (52-MER) / type: rna / ID: 7 / Number of copies: 2
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 16.474699 KDa
SequenceString:
UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA UA

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Macromolecule #8: RNA (60-MER)

MacromoleculeName: RNA (60-MER) / type: rna / ID: 8 / Number of copies: 2
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 19.016188 KDa
SequenceString:
UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA

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Macromolecule #9: RNA (40-MER)

MacromoleculeName: RNA (40-MER) / type: rna / ID: 9 / Number of copies: 2
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 12.662472 KDa
SequenceString:
UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA

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Macromolecule #10: RNA (18-MER)

MacromoleculeName: RNA (18-MER) / type: rna / ID: 10 / Number of copies: 2
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 5.673388 KDa
SequenceString:
UAUAUAUAUA UAUAUAUA

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Macromolecule #11: RNA (38-MER)

MacromoleculeName: RNA (38-MER) / type: rna / ID: 11 / Number of copies: 2
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 12.027101 KDa
SequenceString:
UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA UAUAUAUA

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Macromolecule #12: RNA (30-MER)

MacromoleculeName: RNA (30-MER) / type: rna / ID: 12 / Number of copies: 2
Source (natural)Organism: Golden shiner reovirus
Molecular weightTheoretical: 9.485617 KDa
SequenceString:
UAUAUAUAUA UAUAUAUAUA UAUAUAUAUA

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / 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: 7.4 / Details: Phosphate buffered saline
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was acquired from the media of infected cell culture

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6m99

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119182
FSC plot (resolution estimation)

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