[English] 日本語
Yorodumi
- EMDB-9564: RNA dependent RNA polymerase ,vp4,dsRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9564
TitleRNA dependent RNA polymerase ,vp4,dsRNA
Map datathe structure of RNA-dependent RNA polymerase (RdRp) complexes within the capsid at 3.9-%u212B resolution using a 200 kV TEM
Sample
  • Complex: RNA dependent RNA polymerase ,VP4,dsRNA
    • Complex: RNA dependent RNA polymerase
      • Protein or peptide: RNA-dependent RNA polymerase
    • Complex: VP4
      • Protein or peptide: VP4 protein
    • Complex: dsRNA
      • RNA: RNA (42-MER)
    • Complex: dsRNA
      • RNA: RNA (42-MER)
Keywordsstructural classification / TRANSFERASE-RNA complex
Function / homology
Function and homology information


viral genome replication / RNA-dependent RNA polymerase activity / RNA binding
Similarity search - Function
: / : / CPV, RNA-directed RNA polymerase, N-terminal / CPV, RNA-directed RNA polymerase, central polymerase domain / CPV, RNA-directed RNA polymerase, C-terminal / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile.
Similarity search - Domain/homology
RNA-dependent RNA polymerase / VP4 protein
Similarity search - Component
Biological speciesBombyx mori cytoplasmic polyhedrosis virus / Dendrolimus punctatus cypovirus 1 / Cypovirus (cytoplasmic polyhedrosis viruses)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLi X / Zhou N
Funding support China, 5 items
OrganizationGrant numberCountry
the National Research and Development Program of China2016YFA0501103 China
he National Research and Development Program of China2015CB910104 China
the National Natural Science Foundation of China91530321 China
the National Natural Science Foundation of China31570727 China
the National Natural Science Foundation of China31570742 China
CitationJournal: J Mol Biol / Year: 2017
Title: Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200kV.
Authors: Xiaowu Li / Niyun Zhou / Wenyuan Chen / Bin Zhu / Xurong Wang / Bin Xu / Jiawei Wang / Hongrong Liu / Lingpeng Cheng /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) allows the high-resolution structural determination of biological assemblies in a near-native environment. However, all high-resolution (better than ...Single-particle cryo-electron microscopy (cryo-EM) allows the high-resolution structural determination of biological assemblies in a near-native environment. However, all high-resolution (better than 3.5Å) cryo-EM structures reported to date were obtained by using 300kV transmission electron microscopes (TEMs). We report here the structures of a cypovirus capsid of 750-Å diameter at 3.3-Å resolution and of RNA-dependent RNA polymerase (RdRp) complexes within the capsid at 3.9-Å resolution using a 200-kV TEM. The newly resolved structure revealed conformational changes of two subdomains in the RdRp. These conformational changes, which were involved in RdRp's switch from non-transcribing to transcribing mode, suggest that the RdRp may facilitate the unwinding of genomic double-stranded RNA. The possibility of 3-Å resolution structural determinations for biological assemblies of relatively small sizes using cryo-EM at 200kV was discussed.
History
DepositionOct 27, 2016-
Header (metadata) releaseNov 2, 2016-
Map releaseJan 25, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5h0r
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5h0r
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5h0r
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9564.png

Downloads & links

-
Map

FileDownload / File: emd_9564.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe structure of RNA-dependent RNA polymerase (RdRp) complexes within the capsid at 3.9-%u212B resolution using a 200 kV TEM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 700 pix.
= 652.4 Å		0.93 Å/pix.
x 700 pix.
= 652.4 Å		0.93 Å/pix.
x 700 pix.
= 652.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0 / Movie #1: 12
Minimum - Maximum-27.507093000000001 - 45.616573000000002
Average (Standard dev.)0.6388262 (±4.628242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-937-937-937
Dimensions700700700
Spacing700700700
CellA=B=C: 652.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9320.9320.932
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z652.400652.400652.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS-937-937-937
NC/NR/NS700700700
D min/max/mean-27.50745.6170.639

-
Supplemental data

-
Sample components

-
Entire : RNA dependent RNA polymerase ,VP4,dsRNA

EntireName: RNA dependent RNA polymerase ,VP4,dsRNA
Components
  • Complex: RNA dependent RNA polymerase ,VP4,dsRNA
    • Complex: RNA dependent RNA polymerase
      • Protein or peptide: RNA-dependent RNA polymerase
    • Complex: VP4
      • Protein or peptide: VP4 protein
    • Complex: dsRNA
      • RNA: RNA (42-MER)
    • Complex: dsRNA
      • RNA: RNA (42-MER)

-
Supramolecule #1: RNA dependent RNA polymerase ,VP4,dsRNA

SupramoleculeName: RNA dependent RNA polymerase ,VP4,dsRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: RNA dependent RNA polymerase

SupramoleculeName: RNA dependent RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

-
Supramolecule #3: VP4

SupramoleculeName: VP4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

-
Supramolecule #4: dsRNA

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

-
Supramolecule #5: dsRNA

SupramoleculeName: dsRNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4

-
Macromolecule #1: RNA-dependent RNA polymerase

MacromoleculeName: RNA-dependent RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori cytoplasmic polyhedrosis virus
Molecular weightTheoretical: 139.077281 KDa
Recombinant expressionOrganism: Cypovirus (cytoplasmic polyhedrosis viruses)
SequenceString: MLPNTKLHNT IFSETRKFTR ESFKEIEHLT ARLANDSVAR HDFLFNTSIA LISDYSGEDS NGNQLQATIT IPNEIINPKE YDPSDYPLA EDESFFKQGH KYDYLVTFRA GSLTNTYEPK TKMYKLHAAL DKLMHVRQRK SRFADLWREL CAVIASLDVW Y QTTNYPLR ...String:
MLPNTKLHNT IFSETRKFTR ESFKEIEHLT ARLANDSVAR HDFLFNTSIA LISDYSGEDS NGNQLQATIT IPNEIINPKE YDPSDYPLA EDESFFKQGH KYDYLVTFRA GSLTNTYEPK TKMYKLHAAL DKLMHVRQRK SRFADLWREL CAVIASLDVW Y QTTNYPLR TYVKLLFHRG DEFPFYESPS QDRIIFNDKS VASILPTFVY TCCQVGTAIM SGILTHVESI VAMNHFLHCA KD SYIDEKL KIKGIGRSWY QEALHNVGQA TVPVWSQFNE VIGHRRKSTS EPHFVSSTFI SLRAKRAELL YPEFNAYINR AIQ LSKTQN DVANYYAACR AMTNDGTFLA TLTELSLDAA VFPRIEQRLV TRPAVLMSNT RHESLKQKYT NGVGSIAQSY LSSF TDEIA KRVNGIHHDE AWLNFLTTSS PGRKLTEIEK LEVGGDVAAW SNSRIVMQAV FAREYRTPER IFKSLKAPIK LVERQ QSDR RQRAISGLDN DRLFLSFMPY TIGKQIYELN DNAAQGKQAG NAFDIGEMLY WTSQRNVLLS SIDVAGMDAS VTTNTK DIY NTFVLDVASK CTVPRFGPYY AKNMEVFEVG KRQSQVRYVN AAWQACALEA ADSQTSTSYE SEIFGQVKNA EGTYPSG RA DTSTHHTVLL QGLVRGNELK RASDGKNSCL ATIKILGDDI MEIFQGSESD TYDHAMSNAN ILNESGFATT AELSQNSI V LLQQLVVNGT FWGFADRISL WTREDTKDIG RLNLAMMELN ALIDDLVFRV RRPEGLKMLG FFCGAICLRR FTLSVDNKL YDSTYNNLSK YMTLIKYDKN PDFDSTLMSL ILPLAWLFMP RGGEYPAYPF ERRDGTFTED ESMFTARGAY KRRLLYDVSN IREMIQQNS MALDDDLLHE YGFTGALLLI DLNILDLIDE VKKEDISPVK VSELATSLEQ LGKLGEREKS RRAASDLKIR G HALSNDIV YGYGLQEKIQ KSAMATKETT VQSKRVSSRL HDVIVAKTRD YKISTIPADA LRLHEFEVED VTVDLLPHAK HT SYSSLAY NMSFGSDGWF AFALLGGLDR SANLLRLDVA SIRGNYHKFS YDDPVFKQGY KIYKSDATLL NDFFTAISAG PKE QGILLR AFAYYSLYGN VEYHYVLSPR QLFFLSDNPV SAERLVRIPP KYYVSTQCRA LYNIFSYLHI LRSIANNWGK RLKM VLHPG LIAYVRGTSQ GAILPEADNV

UniProtKB: RNA-dependent RNA polymerase

-
Macromolecule #2: VP4 protein

MacromoleculeName: VP4 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dendrolimus punctatus cypovirus 1
Molecular weightTheoretical: 63.734707 KDa
Recombinant expressionOrganism: Cypovirus (cytoplasmic polyhedrosis viruses)
SequenceString: MFAIDPLKHP KLYEEYGLYL RPHQINQEIK PTTIKKKELA PTIRSIKYAS LIHSMLAKHA ARHNGTLINP RMYADMITLG NTKVTVTKG TPKAQIDTLK MNGLTVVSKS RRNNKKKPVS DTTASTDETT DDVVTYKALT EMSTLVESFR LPSGLTLIVF D DEKYQSLI ...String:
MFAIDPLKHP KLYEEYGLYL RPHQINQEIK PTTIKKKELA PTIRSIKYAS LIHSMLAKHA ARHNGTLINP RMYADMITLG NTKVTVTKG TPKAQIDTLK MNGLTVVSKS RRNNKKKPVS DTTASTDETT DDVVTYKALT EMSTLVESFR LPSGLTLIVF D DEKYQSLI PDYINQLITY TQPHIIPTWQ GITDFSDTYL RSYFKRPFEL TASNLAVPQK HNLSPITRSI FNNTGREDAI IR KLYGYGE YVFIKYEGCL ITWTGLYGAV TMMVNLPKRD LGLDVGDDFL KEYKKLLFHG VITDAIPSGI SAKSTVMRIS PHK MMNPSG GALAVLSKYI EAVVSTNVIN ATLVVYAEKG AGKTSFLSTY AQQLSLASGQ IVGHLSSDAY GRWLAKNKDV EEPS FEYDY VLSLDTDDNE SYYEQKASEL LTSHGISELS QYELLSVRRK VKMMNEMDEI LIAQLDNANT HSERNFYYMV STGKN TPRT LIVEGHFNAQ DATIARTDTT ILLRTINDTT QAMRDRQRSG VVQLFLRDTY YRLLPSLHTT VYPFEMLESI KRWKWV H

UniProtKB: VP4 protein

-
Macromolecule #3: RNA (42-MER)

MacromoleculeName: RNA (42-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Cypovirus (cytoplasmic polyhedrosis viruses)
Molecular weightTheoretical: 13.781683 KDa
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AA

-
Macromolecule #4: RNA (42-MER)

MacromoleculeName: RNA (42-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Cypovirus (cytoplasmic polyhedrosis viruses)
Molecular weightTheoretical: 12.814002 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UU

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27000
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
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