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- EMDB-9565: EM Structure of VP1A and VP1B -

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Basic information

Entry
Database: EMDB / ID: EMD-9565
TitleEM Structure of VP1A and VP1B
Map datathe structure of a cypovirus capsid of 750-%u212B diameter at 3.3-%u212B resolution using a 200 kV TEM
Sample
  • Complex: Cypovirus
    • Protein or peptide: VP1
Function / homology: / : / CPV Capsid shell protein VP1, small protrusion domain / Inner layer core protein VP1-like, C-terminal / T=2 icosahedral viral capsid / viral inner capsid / VP1 / Capsid protein VP1
Function and homology information
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi X / Zhou N / Xu B / Chen W / Zhu B / Wang X / Wang J / Liu H / Cheng L
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 28, 2016-
Header (metadata) releaseNov 2, 2016-
Map releaseJan 25, 2017-
UpdateJan 25, 2017-
Current statusJan 25, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 17
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5h0s
  • Surface level: 12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5h0s
  • Surface level: 17
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5h0s
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_9565.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe structure of a cypovirus capsid of 750-%u212B diameter at 3.3-%u212B resolution using a 200 kV TEM
Voxel sizeX=Y=Z: 0.932 Å
Density
Contour LevelBy AUTHOR: 17. / Movie #1: 17
Minimum - Maximum-40.258704999999999 - 53.433050000000001
Average (Standard dev.)0.6247966 (±5.606705)
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-40.25953.4330.625

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Supplemental data

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Sample components

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Entire : Cypovirus

EntireName: Cypovirus (cytoplasmic polyhedrosis viruses)
Components
  • Complex: Cypovirus
    • Protein or peptide: VP1

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Supramolecule #1: Cypovirus

SupramoleculeName: Cypovirus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori cypovirus 1
Molecular weightTheoretical: 148.696062 KDa
Recombinant expressionOrganism: Cypovirus (cytoplasmic polyhedrosis viruses)
SequenceString: MHSTNNNSNK RNNEEKHKQP EIDSSANNGE GTSGTRAQTV GDTATEAGVR NETKAGASTR RQTDGTGLSG TNAKIATASS ARQTDVEKP ADVTFTIENV DDVGIMQQKK PPTVVQSRTD VFNEQFANEA LHPMTKVIFN GLDVNTEVQP LSDDFKQISD P KGYLTYSV ...String:
MHSTNNNSNK RNNEEKHKQP EIDSSANNGE GTSGTRAQTV GDTATEAGVR NETKAGASTR RQTDGTGLSG TNAKIATASS ARQTDVEKP ADVTFTIENV DDVGIMQQKK PPTVVQSRTD VFNEQFANEA LHPMTKVIFN GLDVNTEVQP LSDDFKQISD P KGYLTYSV KYEDQFTKKD KLRASEADDR IVGPTVNLFK YGAAVVNIDL NRDFFDTATG IDLTKGIPLV QDLLVPIGVT AG AEQSAEY VSGLLMVLFK VMTDNRLVIV GETTTPMSNT LSTVVNNVLR TTYHNNVGVN PALLRDFTQV NWLNRDITNM LQQ AGTKYG LGLTETRLDY VRLVKTIVGH ALNIDHFAAS VLNINLRALM EANVTADDRI KALQAHSMIS TQFHGPNQGA LRPE LAFDH DHIIRCLMLA AANYPRLEGI IVQINTGYVA SANVIRPVSE KRYFPENLEQ NQSAARLVSA VKARASEADI SSIHL AIAR EVSPMFNVHE LKKIAESFED PSSIVVVLEF ILFALFFPTE FNRIKGDIQN VLLLFFSRWY PVEYGIFIQR GATYTI NAA GEFEFSGRNE KWDQSLYLSE HFPALFSDVP LAGANTIIAI MRLFTPQGFL RTDDLAIAAN FPRASRNPQT YIPYTNQ RG TVTNEFASRF RTIVATLANV VNERAVQDDM QKATRSCTKQ WLRHLETQFD NIAVAHTDHL SVVYATMSNF MLNFTNNF S GNHATFKPDQ YVITSPEGSY KPIIERQGET VDGLTIIDTS IVWPILCQCT YPLVRQSGKG VDAVSIMEEI VYPDPSTTL SQSLSVAQVL SKLTLPDAFI NMILSGGDSV VMRTYQTEAD DDLDEGIRMT TYDQYLSHIR ERLHITNVPD PIYITGASTP DQIAASVQA THVAVVLYQS GVINGSASTY LRENEVLVVM PDYYDVVSRF ANANLQMNNN RYHESVLEIA DIFDQADFIQ T SDAVRQLR ALMPTLSTSQ IRHAIERIAQ ITDVDSTDYG KLTLRFLGTL TRSLKMQNAQ IRRIRPDGTV LRYDDQIDIE AF RWSRYFL DELRLRRLSV GLRLITNPRI ARRFDGVRIM YLTDDDPDPD FVPDVPEGYV AVQYAHRLFS SSLANKRNRV TYT HPPTGM AYPSPTGRPH VHMTINERAG MSKLVADNII ASVIKSNWVV DIHDIEYTAE VMTPSEGYTQ HVDAESIMTA PKGK LFHLQ FMDGLLRPEP SAFDPPASGE DMRLIYPLQP ISVARSMRAI VNHNEVDRPR GAVAPSSYEM DTGTLSRNGD LLYSP VANG QVGIPKLEVD HISFSNVVSM MTANIRTGDD MAVERVNPDD VRAINIRNA

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

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Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27000

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