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- EMDB-30123: Structure of HSV2 viron capsid portal vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-30123
TitleStructure of HSV2 viron capsid portal vertex
Map data
SampleHuman alphaherpesvirus 2 != Human herpesvirus 2

Human alphaherpesvirus 2

  • 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: coiled coils
    • Protein or peptide: Coiled coils
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase
KeywordsHSV2 / Portal vertex / Complex / VIRAL PROTEIN
Function / homology
Function and homology information


viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / viral penetration into host nucleus / viral capsid ...viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / DNA binding
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 / Herpesvirus UL25 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 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Capsid triplex subunit 2 / Small capsomere-interacting protein / Capsid triplex subunit 1 / Capsid vertex component 1 / Major capsid protein / Capsid vertex component 2 / Large tegument protein deneddylase
Similarity search - Component
Biological speciesHuman herpesvirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 5.39 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 24, 2021-
Map releaseMar 24, 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: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m6g
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6m6g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30123.png

Downloads & links

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Map

FileDownload / File: emd_30123.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 350 pix.
= 472.5 Å		1.35 Å/pix.
x 350 pix.
= 472.5 Å		1.35 Å/pix.
x 350 pix.
= 472.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.009
Minimum - Maximum-0.024774332 - 0.03486511
Average (Standard dev.)0.0003303116 (±0.0033459745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-174-174-174
Dimensions350350350
Spacing350350350
CellA=B=C: 472.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z472.500472.500472.500
α/β/γ90.00090.00090.000
start NX/NY/NZ1219875
NX/NY/NZ141223232
MAP C/R/S123
start NC/NR/NS-174-174-174
NC/NR/NS350350350
D min/max/mean-0.0250.0350.000

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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 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: coiled coils
    • Protein or peptide: Coiled coils
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase

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Supramolecule #1: Human herpesvirus 2

SupramoleculeName: Human herpesvirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10310 / Sci species name: Human herpesvirus 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: 149.398422 KDa
SequenceString: MAAPARDPPG YRYAAAMVPT GSILSTIEVA SHRRLFDFFA AVRSDENSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPVEQPVHNY MTKVIDRRAL NAAFSLATEA IALLTGEALD GTGISLHRQL R AIQQLARN ...String:
MAAPARDPPG YRYAAAMVPT 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 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 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 ALRDLARHVP 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: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 12.117615 KDa
SequenceString:
MAAPQFHRPS TITADNVRAL GTRGLVLATN NAQFIMDNSY PHPHGTQGAV REFLRGQAAA LTDLGVTHAN NTFAPQPMFA GDAAAEWLR PSFGLKRTYS PFVVRDPKTP STP

UniProtKB: Small capsomere-interacting protein

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Macromolecule #3: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 3 / 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 #4: coiled coils

MacromoleculeName: coiled coils / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 7.166825 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)(UNK)

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Macromolecule #5: Coiled coils

MacromoleculeName: Coiled coils / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 7.42214 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)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #6: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 6 / 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 #7: Capsid vertex component 1

MacromoleculeName: Capsid vertex component 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 74.793859 KDa
SequenceString: MNAHFANEVQ YDLTRDPSSP ASLIHVIISS ECLAAAGVPL SALVRGRPDG GAAANFRVET QTRAHATGDC TPWRSAFAAY VPADAVGAI LAPVIPAHPD LLPRVPSAGG LFVSLPVACD AQGVYDPYTV AALRLAWGPW ATCARVLLFS YDELVPPNTR Y AADGARLM ...String:
MNAHFANEVQ YDLTRDPSSP ASLIHVIISS ECLAAAGVPL SALVRGRPDG GAAANFRVET QTRAHATGDC TPWRSAFAAY VPADAVGAI LAPVIPAHPD LLPRVPSAGG LFVSLPVACD AQGVYDPYTV AALRLAWGPW ATCARVLLFS YDELVPPNTR Y AADGARLM RLCRHFCRYV ARLGAAAPAA ATEAAAHLSL GMGESGTPTP QASSVSGGAG PAVVGTPDPP ISPEEQLTAP GG DTATAED VSITQENEEI LALVQRAVQD VTRRHPVRAR PKHAASGVAS GLRQGALVHQ AVSGGALGAS DAEAVLAGLE PPG GGRFAS RGGPRAAGED VLNDVLTLVP GTAKPRSLVE WLDRGWEALA GGDRPDWLWS RRSISVVLRH HYGTKQRFVV VSYE NSVAW GGRRARPPRL SSELATALTE ACAAERVVRP HQLSPAAQTA LLRRFPALEG PLRHPRPVLQ PFDIAAEVAF VARIQ IACL RALGHSIRAA LQGGPRIFQR LRYDFGPHQS EWLGEVTRRF PVLLENLMRA LEGTAPDAFF HTAYALAVLA HLGGQG GRG RRRRLVPLSD DIPARFADSD AHYAFDYYST SGDTLRLTNR PIAVVIDGDV NGREQSKCRF MEGSPSTAPH RVCEQYL PG ESYAYLCLGF NRRLCGLVVF PGGFAFTINT AAYLSLADPV ARAVGLRFCR GAATGPGLVR

UniProtKB: Capsid vertex component 1

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Macromolecule #8: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 63.63782 KDa
SequenceString: MDPYYPFDAL DVWEHRRFIV ADSRSFITPE FPRDFWMLPV FNIPRETAAE RAAVLQAQRT AAAAALENAA LQAAELPVDI ERRIRPIEQ QVHHIADALE ALETAAAAAE EADAARDAEA RGEGAADGAA PSPTAGPAAA EMEVQIVRND PPLRYDTNLP V DLLHMVYA ...String:
MDPYYPFDAL DVWEHRRFIV ADSRSFITPE FPRDFWMLPV FNIPRETAAE RAAVLQAQRT AAAAALENAA LQAAELPVDI ERRIRPIEQ QVHHIADALE ALETAAAAAE EADAARDAEA RGEGAADGAA PSPTAGPAAA EMEVQIVRND PPLRYDTNLP V DLLHMVYA GRGAAGSSGV VFGTWYRTIQ ERTIADFPLT TRSADFRDGR MSKTFMTALV LSLQSCGRLY VGQRHYSAFE CA VLCLYLL YRTTHESSPD RDRAPVAFGD LLARLPRYLA RLAAVIGDES GRPQYRYRDD KLPKAQFAAA GGRYEHGALA THV VIATLV RHGVLPAAPG DVPRDTSTRV NPDDVAHRDD VNRAAAAFLA RGHNLFLWED QTLLRATANT ITALAVLRRL LANG NVYAD RLDNRLQLGM LIPGAVPAEA IARGASGLDS GAIKSGDNNL EALCVNYVLP LYQADPTVEL TQLFPGLAAL CLDAQ AGRP LASTRRVVDM SSGARQAALV RLTALELINR TRTNTTPVGE IINAHDALGI QYEQGPGLLA QQARIGLASN TKRFAT FNV GSDYDLLYFL CLGFIPQYLS VA

UniProtKB: Capsid vertex component 2

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Macromolecule #9: Large tegument protein deneddylase

MacromoleculeName: Large tegument protein deneddylase / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 330.425906 KDa
SequenceString: MIPAALPHPT MKRQGDRDIV VTGVRNQFAT DLEPGGSVSC MRSSLSFLSL LFDVGPRDVL SAEAIEGCLV EGGEWTRAAA GSGPPRMCS IIELPNFLEY PAARGGLRCV FSRVYGEVGF FGEPTAGLLE TQCPAHTFFA GPWAMRPLSY TLLTIGPLGM G LYRDGDTA ...String:
MIPAALPHPT MKRQGDRDIV VTGVRNQFAT DLEPGGSVSC MRSSLSFLSL LFDVGPRDVL SAEAIEGCLV EGGEWTRAAA GSGPPRMCS IIELPNFLEY PAARGGLRCV FSRVYGEVGF FGEPTAGLLE TQCPAHTFFA GPWAMRPLSY TLLTIGPLGM G LYRDGDTA YLFDPHGLPA GTPAFIAKVR AGDVYPYLTY YAHDRPKVRW AGAMVFFVPS GPGAVAPADL TAAALHLYGA SE TYLQDEP FVERRVAITH PLRGEIGGLG ALFVGVVPRG DGEGSGPVVP ALPAPTHVQT PGADRPPEAP RGASGPPDTP QAG HPNRPP DDVWAAALEG TPPAKPSAPD AAASGPPHAA PPPQTPAGDA AEEAEDLRVL EVGAVPVGRH RARYSTGLPK RRRP TWTPP SSVEDLTSGE RPAPKAPPAK AKKKSAPKKK APVAAEVPAS SPTPIAATVP PAPDTPPQSG QGGGDDGPAS PSSPS VLET LGARRPPEPP GADLAQLFEV HPNVAATAVR LAARDAALAR EVAACSQLTI NALRSPYPAH PGLLELCVIF FFERVL AFL IENGARTHTQ AGVAGPAAAL LDFTLRMLPR KTAVGDFLAS TRMSLADVAA HRPLIQHVLD ENSQIGRLAL AKLVLVA RD VIRETDAFYG DLADLDLQLR AAPPANLYAR LGEWLLERSR AHPNTLFAPA TPTHPEPLLH RIQALAQFAR GEEMRVEA E AREMREALDA LARGVDSVSQ RAGPLTVMPV PAAPGAGGRA PCPPALGPEA IQARLEDVRI QARRAIESAV KEYFHRGAV YSAKALQASD SHDCRFHVAS AAVVPMVQLL ESLPAFDQHT RDVAQRAALP PPPPLATSPQ AILLRDLLQR GQPLDAPEDL AAWLSVLTD AATQGLIERK PLEELARSIH GINDQQARRS SGLAELQRFD ALDAALAQQL DSDAAFVPAT GPAPYVDGGG L SPEATRMA EDALRQARAM EAAKMTAELA PEARSRLRER AHALEAMLND ARERAKVAHD AREKFLHKLQ GVLRPLPDFV GL KACPAVL ATLRASLPAG WTDLADAVRG PPPEVTAALR ADLWGLLGQY REALEHPTPD TATALAGLHP AFVVVLKTLF ADA PETPVL VQFFSDHAPT IAKAVSNAIN AGSAAVATAS PAATVDAAVR AHGALADAVS ALGAAARDPA SPLSFLAVLA DSAA GYVKA TRLALEARGA IDELTTLGSA AADLVVQARR ACAQPEGDHA ALIDAAARAT TAARESLAGH EAGFGGLLHA EGTAG DHSP SGRALQELGK VIGATRRRAD ELEAAVADLT AKMAAQRARG SSERWAAGVE AALDRVENRA EFDVVELRRL QALAGT HGY NPRDFRKRAE QALAANAEAV TLALDTAFAF NPYTPENQRH PMLPPLAAIH RLGWSAAFHA AAETYADMFR VDAEPLA RL LRIAEGLLEM AQAGDGFIDY HEAVGRLADD MTSVPGLRRY VPFFQHGYAD YVELRDRLDA IRADVHRALG GVPLDLAA A AEQISAARND PEATAELVRT GVTLPCPSED ALVACAAALE RVDQSPVKNT AYAEYVAFVT RQDTAETKDA VVRAKQQRA EATERVMAGL REALAARERR AQIEAEGLAN LKTMLKVVAV PATVAKTLDQ ARSVAEIADQ VEVLLDQTEK TRELDVPAVI WLEHAQRTF ETHPLSAARG DGPGPLARHA GRLGALFDTR RRVDALRRSL EEAEAEWDEV WGRFGRVRGG AWKSPEGFRA M HEQLRALQ DTTNTVSGLR AQPAYERLSA RYQGVLGAKG AERAEAVEEL GARVTKHTAL CARLRDEVVR RVPWEMNFDA LG GLLAEFD AAAADLAPWA VEEFRGAREL IQYRMGLYSA YARAGGQTGA GAESAPAPLL VDLRALDARA RASSSPEGHE VDP QLLRRR GEAYLRAGGD PGPLVLREAV SALDLPFATS FLAPDGTPLQ YALCFPAVTD KLGALLMRPE AACVRPPLPT DVLE SAPTV TAMYVLTVVN RLQLALSDAQ AANFQLFGRF VRHRQATWGA SMDAAAELYV ALVATTLTRE FGCRWAQLGW ASGAA APRP PPGPRGSQRH CVAFNENDVL VALVAGVPEH IYNFWRLDLV RQHEYMHLTL ERAFEDAAES MLFVQRLTPH PDARIR VLP TFLDGGPPTR GLLFGTRLAD WRRGKLSETD PLAPWRSALE LGTQRRDVPA LGKLSPAQAL AAVSVLGRMC LPSAALA AL WTCMFPDDYT EYDSFDALLA ARLESGQTLG PAGGREASLP EAPHALYRPT GQHVAVLAAA THRTPAARVT AMDLVLAA V LLGAPVVVAL RNTTAFSRES ELELCLTLFD SRPGGPDAAL RDVVSSDIET WAVGLLHTDL NPIENACLAA QLPRLSALI AERPLADGPP CLVLVDISMT PVAVLWEAPE PPGPPDVRFV GSEATEELPF VATAGDVLAA SAADADPFFA RAILGRPFDA SLLTGELFP GHPVYQRPLA DEAGPSAPTA ARDPRDLAGG DGGSGPEDPA APPARQADPG VLAPTLLTDA TTGEPVPPRM W AWIHGLEE LASDDAGGPT PNPAPALLPP PATDQSVPTS QYAPRPIGPA ATARETRPSV PPQQNTGRVP VAPRDDPRPS PP TPSPPAD AALPPPAFSG SAAAFSAAVP RVRRSRRTRA KSRAPRASAP PEGWRPPALP APVAPVAASA RPPDQPPTPE SAP PAWVSA LPLPPGPASA RGAFPAPTLA PIPPPPAEGA VVPGGDRRRG RRQTTAGPSP TPPRGPAAGP PRRLTRPAVA SLSA SLNSL PSPRDPADHA AAVSAAAAAV PPSPGLAPPT SAVQTSPPPL APGPVAPSEP LCGWVVPGGP VARRPPPQSP ATKPA ARTR IRARSVPQPP LPQPPLPQPP LPQPPLPQPP LPQPPLPQPP LPQPPLPQPP LPQPPLPQPP LPPVTRTLTP QSRDSV PTP ESPTHTNTHL PVSAVTSWAS SLALHVDSAP PPASLLQTLH ISSDDEHSDA DSLRFSDSDD TEALDPLPPE PHLPPAD EP PGPLAADHLQ SPHSQFGPLP VQANAVLSRR YVRSTGRSAL AVLIRACRRI QQQLQRTRRA LFQRSNAVLT SLHHVRML L G

UniProtKB: Large tegument protein deneddylase

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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: 5.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12001
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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