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- EMDB-30125: Structure of HSV2 B-capsid portal vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-30125
TitleStructure of HSV2 B-capsid portal vertex
Map data
Sample
  • Virus: Human alphaherpesvirus 2
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Coiled coils chain 1
    • Protein or peptide: Coiled coils chain 2
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Small capsomere-interacting protein
KeywordsHSV2 / Portal vertex / Complex / VIRAL PROTEIN
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 2 / Small capsomere-interacting protein / Capsid triplex subunit 1 / Major capsid protein
Similarity search - Component
Biological speciesHuman herpesvirus 2 / Human alphaherpesvirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsWang XX / Wang N
CitationJournal: Protein Cell / Year: 2020
Title: Structures of the portal vertex reveal essential protein-protein interactions for Herpesvirus assembly and maturation.
Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong ...Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong Liu / Zihe Rao / Xiangxi Wang /
History
DepositionMar 14, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m6i
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6m6i
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30125.png

Downloads & links

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Map

FileDownload / File: emd_30125.map.gz / Format: CCP4 / Size: 103 MB / 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 300 pix.
= 414. Å		1.38 Å/pix.
x 300 pix.
= 414. Å		1.38 Å/pix.
x 300 pix.
= 414. 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: 0.03 / Movie #1: 0.04
Minimum - Maximum-0.13736576 - 0.23177262
Average (Standard dev.)0.00022576634 (±0.019204533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-149-149-149
Dimensions300300300
Spacing300300300
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z414.000414.000414.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ296296296
MAP C/R/S123
start NC/NR/NS-149-149-149
NC/NR/NS300300300
D min/max/mean-0.1370.2320.000

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Supplemental data

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Sample components

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Entire : Human alphaherpesvirus 2

EntireName: Human alphaherpesvirus 2
Components
  • Virus: Human alphaherpesvirus 2
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Coiled coils chain 1
    • Protein or peptide: Coiled coils chain 2
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Small capsomere-interacting protein

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Supramolecule #1: Human alphaherpesvirus 2

SupramoleculeName: Human alphaherpesvirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10310 / Sci species name: Human alphaherpesvirus 2 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 149.399359 KDa
SequenceString: MAAPARDPPG YRYAAAILPT GSILSTIEVA SHRRLFDFFA AVRSDENSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPVEQPVHNY MTKVIDRRAL NAAFSLATEA IALLTGEALD GTGISLHRQL R AIQQLARN ...String:
MAAPARDPPG YRYAAAILPT GSILSTIEVA SHRRLFDFFA AVRSDENSLY 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 LEALERRIYA 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 IHGNEHV 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 VANTVKRMFH NGRVVVDGP AMLTLQVLAH NMAERTTALL CSAAPDAGAN TASTANMRIF DGALHAGVLL MAPQHLDHTI QNGEYFYVLP V HALFAGAD HVANAPNFPP ALRDLARDVP LVPPALGANY FSSIRQPVVQ HARESAAGEN ALTYALMAGY FKMSPVALYH QL KTGLHPG FGFTVVRQDR FVTENVLFSE RASEAYFLGQ LQVARHETGG GVNFTLTQPR GNVDLGVGYT AVAATGTVRN 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: Coiled coils chain 1

MacromoleculeName: Coiled coils chain 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 6.911511 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #3: Coiled coils chain 2

MacromoleculeName: Coiled coils chain 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 7.08172 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #4: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / 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 #5: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 50.566648 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 FLVAACAAAY DARDAAEAVR AHITTNYGGT RAGARLDRFS ECLRAMVHTH VF PHEVMRF FGGLVSWVTQ DELASVTAVC SGPQEATHTG HPGRPRSAVT 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 #6: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 6 / Number of copies: 6 / 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 recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON II (4k x 4k) / #0 - Average electron dose: 30.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON II (4k x 4k) / #1 - Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22158
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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