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- EMDB-6907: Atomic structure of the herpes simplex virus type 2 B-capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-6907
TitleAtomic structure of the herpes simplex virus type 2 B-capsid
Map data
Sample
  • Virus: Human herpesvirus 2
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Triplex capsid protein 1
Keywordsherpesvirus / capsid / cryo-em / atomic structure / VIRUS
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral capsid assembly / viral process / virion component / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus UL35 / Herpesvirus UL35 family / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Capsid triplex subunit 1 / Capsid triplex subunit 2 / Major capsid protein / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman herpesvirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYuan S / Wang JL / Zhu DJ / Wang N / Gao Q / Chen WY / Tang H / Wang JZ / Zhang XZ / Liu HR ...Yuan S / Wang JL / Zhu DJ / Wang N / Gao Q / Chen WY / Tang H / Wang JZ / Zhang XZ / Liu HR / Rao ZH / Wang XX
CitationJournal: Nat Commun / Year: 2018
Title: Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions.
Authors: Dongjie Zhu / Xiangxi Wang / Qianglin Fang / James L Van Etten / Michael G Rossmann / Zihe Rao / Xinzheng Zhang /
Abstract: The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a ...The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a "block-based" reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes.
History
DepositionFeb 8, 2018-
Header (metadata) releaseApr 18, 2018-
Map releaseApr 18, 2018-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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

emd_6907.png

Downloads & links

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Map

FileDownload / File: emd_6907.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 1200 pix.
= 1656. Å		1.38 Å/pix.
x 1200 pix.
= 1656. Å		1.38 Å/pix.
x 1200 pix.
= 1656. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0 / Movie #1: 12
Minimum - Maximum-84.361335999999994 - 121.638626000000002
Average (Standard dev.)0.0014450494 (±3.2395287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120012001200
Spacing120012001200
CellA=B=C: 1656.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z120012001200
origin x/y/z0.0000.0000.000
length x/y/z1656.0001656.0001656.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120012001200
D min/max/mean-84.361121.6390.001

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Supplemental data

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Sample components

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Entire : Human herpesvirus 2

EntireName: Human herpesvirus 2
Components
  • Virus: Human herpesvirus 2
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Triplex capsid protein 1

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Supramolecule #1: Human herpesvirus 2

SupramoleculeName: Human herpesvirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1, #4, #2-#3 / NCBI-ID: 10310 / Sci species name: Human herpesvirus 2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Human herpesvirus 2

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 149.370359 KDa
SequenceString: MAAPARDPPG YRYAAAMVPT GSILSTIEVA SHRRLFDFFA RVRSDENSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPVEQPVHNY MTKVIDRRAL NAAFSLATEA IALLTGEALD GTGISLHRQL R AIQQLARN ...String:
MAAPARDPPG YRYAAAMVPT GSILSTIEVA SHRRLFDFFA RVRSDENSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPVEQPVHNY MTKVIDRRAL NAAFSLATEA IALLTGEALD GTGISLHRQL R AIQQLARN VQAVLGAFER GTADQMLHVL LEKAPPLALL LPMQRYLDNG RLATRVARAT LVAELKRSFC DTSFFLGKAG HR REAIEAW LVDLTTATQP SVAVPRLTHA DTRGRPVDGV LVTTAAIKQR LLQSFLKVED TEADVPVTYG EMVLNGANLV TAL VMGKAV RSLDDVGRHL LDMQEEQLEA NRETLDELES APQTTRVRAD LVAIGDRLVF LEALEKRIYA ATNVPYPLVG AMDL TFVLP LGLFNPAMER FAAHAGDLVP APGHPEPRAF PPRQLFFWGK DHQVLRLSME NAVGTVCHPS LMNIDAAVGG VNHDP VEAA NPYGAYVAAP AGPGADMQQR FLNAWRQRLA HGRVRWVAEC QMTAEQFMQP DNANLALELH PAFDFFAGVA DVELPG GEV PPAGPGAIQA TWRVVNGNLP LALCPVAFRD ARGLELGVGR HAMAPATIAA VRGAFEDRSY PAVFYLLQAA IHGSEHV FC ALARLVTQCI TSYWNNTRCA AFVNDYSLVS YIVTYLGGDL PEECMAVYRD LVAHVEALAQ LVDDFTLPGP ELGGQAQA E LNHLMRDPAL LPPLVWDCDG LMRHAALDRH RDCRIDAGGH EPVYAAACNV ATADFNRNDG RLLHNTQARA ADAADDRPH RPADWTVHHK IYYYVLVPAF SRGRCCTAGV RFDRVYATLQ NMVVPEIAPG EECPSDPVTD PAHPLHPANL VANTVNAMFH NGRVVVDGP AMLTLQVLAH NMAERTTALL CSAAPDAGAN TASTANMRIF DGALHAGVLL MAPQHLDHTI QNGEYFYVLP V HALFAGAD HVANAPNFPP ALRDLARHVP LVPPALGANY FSSIRQPVVQ HARESAAGEN ALTYALMAGY FKMSPVALYH QL KTGLHPG FGFTVVRQDR FVTENVLFSE RASEAYFLGQ LQVARHETGG GVNFTLTQPR GNVDLGVGYT AVAATATVRN PVT DMGNLP QNFYLGRGAP PLLDNAAAVY LRNAVVAGNR LGPAQPLPVF GCAQVPRRAG MDHGQDAVCE FIATPVATDI NYFR RPCNP RGRAAGGVYA GDKEGDVIAL MYDHGQSDPA RPFAATANPW ASQRFSYGDL LYNGAYHLNG ASPVLSPCFK FFTAA DITA KHRCLERLIV ETGSAVSTAT AASDVQFKRP PGCRELVEDP CGLFQEAYPI TCASDPALLR SARDGEAHAR ETHFTQ YLI YDASPLKGLS L

UniProtKB: Major capsid protein

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Macromolecule #2: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 34.373785 KDa
SequenceString: MITDCFEADI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LALADVAHES FVSGGVSPDT LGLLLAYRRR FPAVITRVLP TRIVACPVD LGLTHAGTVN LRNTSPVDLC NGDPVSLVPP VFEGQATDVR LESLDLTLRF PVPLPTPLAR EIVARLVARG I RDLNPDPR ...String:
MITDCFEADI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LALADVAHES FVSGGVSPDT LGLLLAYRRR FPAVITRVLP TRIVACPVD LGLTHAGTVN LRNTSPVDLC NGDPVSLVPP VFEGQATDVR LESLDLTLRF PVPLPTPLAR EIVARLVARG I RDLNPDPR TPGELPDLNV LYYNGARLSL VADVQQLASV NTELRSLVLN MVYSITEGTT LILTLIPRLL ALSAQDGYVN AL LQMQSVT REAAQLIHPE APMLMQDGER RLPLYEALVA WLAHAGQLGD ILALAPAVRV CTFDGAAVVQ SGDMAPVIRY P

UniProtKB: Capsid triplex subunit 2

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Macromolecule #3: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 50.542617 KDa
SequenceString: MKTKPLPTAP MAWAESAVET TTSPRELAGH APLRRVLRPP IARRDGPVLL GDRAPRRTAS TMWLLGIDPA ESSPGTRATR DDTEQAVDK ILRGARRAGG LTVPGAPRYH LTRQVTLTDL CQPNAERAGA LLLALRHPTD LPHLARHRAP PGRQTERLAE A WGQLLEAS ...String:
MKTKPLPTAP MAWAESAVET TTSPRELAGH APLRRVLRPP IARRDGPVLL GDRAPRRTAS TMWLLGIDPA ESSPGTRATR DDTEQAVDK ILRGARRAGG LTVPGAPRYH LTRQVTLTDL CQPNAERAGA LLLALRHPTD LPHLARHRAP PGRQTERLAE A WGQLLEAS ALGSGRAESG CARAGLVSFN FLVAACTAAY DARDAAEAVR AHITTNYGGT RAGARLDRFS ECLRAMVHTH VF PHEVMRF FGGLVSWVTQ DELASVTAVC SGPQEATHTG HPGRPCSAVT IPACAFVDLD AELCLGGPGA AFLYLVFTYR QCR DQELCC VYVVKSQLPP RGLEAALERL FGRLRITNTI HGAEDMTPPP PNRNVDFPLA VLAASSQSPR CSASQVTNPQ FVDR LYRWQ PDLRGRPTAR TCTYAAFAEL GVMPDDSPRC LHRTERFGAV GVPVVILEGV VWRPGGWRAC A

UniProtKB: Capsid triplex subunit 1

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Macromolecule #4: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 4 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 12.147707 KDa
SequenceString:
MAAPQFHRPS TITADNVRAL GMRGLVLATN NAQFIMDNSY PHPHGTQGAV REFLRGQAAA LTDLGVTHAN NTFAPQPMFA GDAAAEWLR PSFGLKRTYS PFVVRDPKTP STP

UniProtKB: Small capsomere-interacting protein

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: COMMON LINE

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