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- EMDB-49591: Cryo-ET map of the VZV capsid vertex (5-fold axis). -

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Basic information

Entry
Database: EMDB / ID: EMD-49591
TitleCryo-ET map of the VZV capsid vertex (5-fold axis).
Map dataCryo-ET map of the VZV capsid vertex.
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: ORF40
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: ORF20
    • Protein or peptide: ORF41
    • Protein or peptide: ORF43
    • Protein or peptide: ORF34
    • Protein or peptide: Large tegument protein deneddylase
KeywordsVaricella-zoster virus / capsid / cryo-ET / cryo-FIB / VIRUS
Function / homology
Function and homology information


deNEDDylase activity / viral genome packaging / 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 ...deNEDDylase activity / viral genome packaging / 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 / cysteine-type deubiquitinase activity / host cell cytoplasm / 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 / DNA polymerase family B signature. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
ORF43 / ORF41 / ORF40 / ORF34 / Small capsomere-interacting protein / ORF20 / Large tegument protein deneddylase
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsubtomogram averaging / cryo EM / Resolution: 8.3 Å
AuthorsOliver SL / Chen M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: Cryogenic Electron Tomography Redefines Herpesvirus Capsid Assembly Intermediates Inside the Cell Nucleus.
Authors: Stefan L Oliver / Muyuan Chen / Leeya Engel / Corey W Hecksel / Xueting Zhou / Michael F Schmid / Ann M Arvin / Wah Chiu
Abstract: Herpesviruses encapsulate their double-stranded DNA (dsDNA) genomes within an icosahedral nucleocapsid formed in the infected cell nucleus. Four biochemically purified nucleocapsids have been ...Herpesviruses encapsulate their double-stranded DNA (dsDNA) genomes within an icosahedral nucleocapsid formed in the infected cell nucleus. Four biochemically purified nucleocapsids have been characterized, but their roles in herpesvirus replication remain controversial. The status of the capsid vertex-specific component (CVSC), essential for capsid stability and dsDNA packaging and retention, is also unclear. By integrating cryogenic focused ion beam milling with electron tomography and subtomogram averaging, we derived atomic models for all protein components, including the CVSC, across different herpesvirus capsid types within infected cell nuclei. Focused classification of pentonal vertex densities revealed differences in CVSC occupancy between genome-filled capsids and capsids lacking dsDNA, highlighting structural heterogeneity and providing insight into distinct capsid assembly stages . These intra-nuclear findings redefine the maturation model of herpesvirus capsid assembly, advancing the understanding of herpesvirus replication, and demonstrate the effectiveness of electron imaging by studying virus assembly within host cells.
History
DepositionMar 7, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49591.png

Downloads & links

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Map

FileDownload / File: emd_49591.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET map of the VZV capsid vertex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.44 Å/pix.
x 192 pix.
= 660.48 Å		3.44 Å/pix.
x 192 pix.
= 660.48 Å		3.44 Å/pix.
x 192 pix.
= 660.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.05
Minimum - Maximum-7.3818445 - 14.690272
Average (Standard dev.)0.032990295 (±0.42300716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 660.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49591_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-ET odd half map of the VZV capsid vertex.

Fileemd_49591_half_map_1.map
AnnotationCryo-ET odd half map of the VZV capsid vertex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-ET even half map of the VZV capsid vertex.

Fileemd_49591_half_map_2.map
AnnotationCryo-ET even half map of the VZV capsid vertex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human alphaherpesvirus 3

EntireName: Human alphaherpesvirus 3 (Varicella-zoster virus)
Components
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: ORF40
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: ORF20
    • Protein or peptide: ORF41
    • Protein or peptide: ORF43
    • Protein or peptide: ORF34
    • Protein or peptide: Large tegument protein deneddylase

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Supramolecule #1: Human alphaherpesvirus 3

SupramoleculeName: Human alphaherpesvirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10335 / Sci species name: Human alphaherpesvirus 3 / Sci species strain: pOka / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1250.0 Å / T number (triangulation number): 16

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Macromolecule #1: ORF40

MacromoleculeName: ORF40 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 155.145359 KDa
SequenceString: MTTVSCPANV ITTTESDRIA GLFNIPAGII PTGNVLSTIE VCAHRCIFDF FKQIRSDDNS LYSAQFDILL GTYCNTLNFV RFLELGLSV ACICTKFPEL AYVRDGVIQF EVQQPMIARD GPHPVDQPVH NYMVKRIHKR SLSAAFAIAS EALSLLSNTY V DGTEIDSS ...String:
MTTVSCPANV ITTTESDRIA GLFNIPAGII PTGNVLSTIE VCAHRCIFDF FKQIRSDDNS LYSAQFDILL GTYCNTLNFV RFLELGLSV ACICTKFPEL AYVRDGVIQF EVQQPMIARD GPHPVDQPVH NYMVKRIHKR SLSAAFAIAS EALSLLSNTY V DGTEIDSS LRIRAIQQMA RNLRTVLDSF ERGTADQLLG VLLEKAPPLS LLSPINKFQP EGHLNRVARA ALLSDLKRRV CA DMFFMTR HAREPRLISA YLSDMVSCTQ PSVMVSRITH TNTRGRQVDG VLVTTATLKR QLLQGILQID DTAADVPVTY GEM VLQGTN LVTALVMGKA VRGMDDVARH LLDITDPNTL NIPSIPPQSN SDSTTAGLPV NARVPADLVI VGDKLVFLEA LERR VYQAT RVAYPLIGNI DITFIMPMGV FQANSMDRYT RHAGDFSTVS EQDPRQFPPQ GIFFYNKDGI LTQLTLRDAM GTICH SSLL DVEATLVALR QQHLDRQCYF GVYVAEGTED TLDVQMGRFM ETWADMMPHH PHWVNEHLTI LQFIAPSNPR LRFELN PAF DFFVAPGDVD LPGPQRPPEA MPTVNATLRI INGNIPVPLC PISFRDCRGT QLGLGRHTMT PATIKAVKDT FEDRAYP TI FYMLEAVIHG NERNFCALLR LLTQCIRGYW EQSHRVAFVN NFHMLMYITT YLGNGELPEV CINIYRDLLQ HVRALRQT I TDFTIQGEGH NGETSEALNN ILTDDTFIAP ILWDCDALIY RDEAARDRLP AIRVSGRNGY QALHFVDMAG HNFQRRDNV LIHGRPVRGD TGQGIPITPH HDREWGILSK IYYYIVIPAF SRGSCCTMGV RYDRLYPALQ AVIVPEIPAD EEAPTTPEDP RHPLHAHQL VPNSLNVYFH NAHLTVDGDA LLTLQELMGD MAERTTAILV SSAPDAGAAT ATTRNMRIYD GALYHGLIMM A YQAYDETI ATGTFFYPVP VNPLFACPEH LASLRGMTNA RRVLAKMVPP IPPFLGANHH ATIRQPVAYH VTHSKSDFNT LT YSLLGGY FKFTPISLTH QLRTGFHPGI AFTVVRQDRF ATEQLLYAER ASESYFVGQI QVHHHDAIGG VNFTLTQPRA HVD LGVGYT AVCATAALRC PLTDMGNTAQ NLFFSRGGVP MLHDNVTESL RRITASGGRL NPTEPLPIFG GLRPATSAGI ARGQ ASVCE FVAMPVSTDL QYFRTACNPR GRASGMLYMG DRDADIEAIM FDHTQSDVAY TDRATLNPWA SQKHSYGDRL YNGTY NLTG ASPIYSPCFK FFTPAEVNTN CNTLDRLLME AKAVASQSST DTEYQFKRPP GSTEMTQDPC GLFQEAYPPL CSSDAA MLR TAHAGETGAD EVHLAQYLIR DASPLRGCLP LPR

UniProtKB: ORF40

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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 alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 24.440119 KDa
SequenceString: MTQPASSRVV FDPSNPTTFS VEAIAAYTPV ALIRLLNASG PLQPGHRVDI ADARSIYTVG AAASAARARA NHNANTIRRT AMFAETDPM TWLRPTVGLK RTFNPRIIRP QPPNPSMSLG ISGPTILPQK TQSADQSALQ QPAALAFSGS SPQHPPPQTT S ASVGQQQH ...String:
MTQPASSRVV FDPSNPTTFS VEAIAAYTPV ALIRLLNASG PLQPGHRVDI ADARSIYTVG AAASAARARA NHNANTIRRT AMFAETDPM TWLRPTVGLK RTFNPRIIRP QPPNPSMSLG ISGPTILPQK TQSADQSALQ QPAALAFSGS SPQHPPPQTT S ASVGQQQH VVSGSSGQQP QQGAQSSTVQ PTTGSPPAAQ GVPQSTPPPT QNTPQGGKGQ TLSHTGQSGN ASRSRRV

UniProtKB: Small capsomere-interacting protein

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Macromolecule #3: ORF20

MacromoleculeName: ORF20 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 54.02818 KDa
SequenceString: MGSQPTNSHF TLNEQTLCGT NISLLGNNRF IQIGNGLHMT YAPGFFGNWS RDLTIGPRFG GLNKQPIHVP PKRTETASIQ VTPRSIVIN RMNNIQINPT SIGNPQVTIR LPLNNFKSTT QLIQQVSLTD FFRPDIEHAG SIVLILRHPS DMIGEANTLT Q AGRDPDVL ...String:
MGSQPTNSHF TLNEQTLCGT NISLLGNNRF IQIGNGLHMT YAPGFFGNWS RDLTIGPRFG GLNKQPIHVP PKRTETASIQ VTPRSIVIN RMNNIQINPT SIGNPQVTIR LPLNNFKSTT QLIQQVSLTD FFRPDIEHAG SIVLILRHPS DMIGEANTLT Q AGRDPDVL LEGLRNLFNA CTAPWTVGEG GGLRAYVTSL SFIAACRAEE YTDKQAADAN RTAIVSAYGC SRMETRLIRF SE CLRAMVQ CHVFPHRFIS FFGSLLEYTI QDNLCNITAV AKGPQEAART DKTSTRRVTA NIPACVFWDV DKDLHLSADG LKH VFLVFV YTQRRQREGV RLHLALSQLN EQCFGRGIGF LLGRIRAENA AWGTEGVANT HQPYNTRALP LVQLSNDPTS PRCS IGEIT GVNWNLARQR LYQWTGDFRG LPTQLSCMYA AYTLIGTIPS ESVRYTRRME RFGGYNVPTI WLEGVVWGGT NTWNE CYY

UniProtKB: ORF20

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Macromolecule #4: ORF41

MacromoleculeName: ORF41 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 34.421914 KDa
SequenceString: MAMPFEIEVL LPGELSPAET SALQKCEGKI ITFSTLRHRA SLVDIALSSY YINGAPPDTL SLLEAYRMRF AAVITRVIPG KLLAHAIGV GTPTPGLFIQ NTSPVDLCNG DYICLLPPVF GSADSIRLDS VGLEIVFPLT IPQTLMREII AKVVARAVER T AAGAQILP ...String:
MAMPFEIEVL LPGELSPAET SALQKCEGKI ITFSTLRHRA SLVDIALSSY YINGAPPDTL SLLEAYRMRF AAVITRVIPG KLLAHAIGV GTPTPGLFIQ NTSPVDLCNG DYICLLPPVF GSADSIRLDS VGLEIVFPLT IPQTLMREII AKVVARAVER T AAGAQILP HEVLRGADVI CYNGRRYELE TNLQHRDGSD AAIRTLVLNL MFSINEGCLL LLALIPTLLV QGAHDGYVNL LI QTANCVR ETGQLINIPP MPRIQDGHRR FPIYETISSW ISTSSRLGDT LGTRAILRVC VFDGPSTVHP GDRTAVIQV

UniProtKB: ORF41

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Macromolecule #5: ORF43

MacromoleculeName: ORF43 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 73.97843 KDa
SequenceString: MEAHLANETK HALWHNDHTK GLLHVVIPNA GLIAAGIDPA LLILKKPGQR FKVEVQTRYH ATGQCEPWCQ VFAAYIPDNA LTNLLIPKT EPFVSHVFSA THNSGGLILS LPVYLSPGLF FDAFNVVAIR INTGNRKHRD ICIMYAELIP NGTRYFADGQ R VLLLCKQL ...String:
MEAHLANETK HALWHNDHTK GLLHVVIPNA GLIAAGIDPA LLILKKPGQR FKVEVQTRYH ATGQCEPWCQ VFAAYIPDNA LTNLLIPKT EPFVSHVFSA THNSGGLILS LPVYLSPGLF FDAFNVVAIR INTGNRKHRD ICIMYAELIP NGTRYFADGQ R VLLLCKQL IAYIRCTPRL ASSIKIYAEH MVAAMGESHT SNGDNIGPVS SIIDLDRQLT SGGIDDSPAE TRIQENNRDV LE LIKRAVN IVNSRHPVRP SSSRVASGLL QSAKGHGAQT SNTDPINNGS FDGVLEPPGQ GRFTGKKNNS SASIPPLQDV LLF TPASTE PQSLMEWFDI CYAQLVSGDT PADFWKRRPL SIVPRHYAES PSPLIVVSYN GSSAWGGRIT GSPILYHSAQ AIID AACIN ARVDNPQSLH VTARQELVAR LPFLANVLNN QTPLPAFKPG AEMFLNQVFK QACVTSLTQG LITELQTNPT LQQLM EYDI ADSSQTVIDE IVARTPDLIQ TIVSVLTEMS MDAFYNSSLM YAVLAYLSSV YTRPQGGGYI PYLHASFPCW LGNRSI YLF DYYNSGGEIL KLSKVPVPVA LEKVGIGNST QLRGKFIRSA DIVDIGICSK YLPGQCYAYI CLGFNQQLQS ILVLPGG FA ACFCITDTLQ AALPASLIGP ILDRFCFSIP NPHK

UniProtKB: ORF43

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Macromolecule #6: ORF34

MacromoleculeName: ORF34 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 65.253941 KDa
SequenceString: MTARYGFGSI SFPNKCGIFL STTKNFIAPN FPIHYWTAPA FELRGRMNPD LEKNTLTLKN AAAVAALDNL RGETITLPTE IDRRLKPLE EQLTRMAKVL DSLETAAAEA EEADAQSEEC TRTEIIRNES IHPEVQIAKN DAPLQYDTNF QVDFITLVYL G RARGNNSP ...String:
MTARYGFGSI SFPNKCGIFL STTKNFIAPN FPIHYWTAPA FELRGRMNPD LEKNTLTLKN AAAVAALDNL RGETITLPTE IDRRLKPLE EQLTRMAKVL DSLETAAAEA EEADAQSEEC TRTEIIRNES IHPEVQIAKN DAPLQYDTNF QVDFITLVYL G RARGNNSP GIVFGPWYRT LQERLVLDRP VAARGVDCKD GRISRTFMNT TVTCLQSAGR MYVGDRAYSA FECAVLCLYL MY RTSNSVH EPQVSSFGNL IEHLPEYTET FVNYMTTHEN KNSYQFCYDR LPRDQFHARG GRYDQGALTS HSVMDALIRL QVL PPAPGQ FNPGVNDIID RNHTAYVDKI QQAAAAYLER AQNVFLMEDQ TLLRLTIDTI TALLLLRRLL WNGNVYGDKL KNNF QLGLI VSEATGTPTN NVILRGATGF DGKFKSGNNN FQFLCERYIA PLYTLNRTTE LTEMFPGLVA LCLDAHTQLS RGSLG RTVI DISSGQYQDR LISLIALELE HRRQNVTSLP IAAVVSIHDS VMLQYERGLG MLMHQPRVRA ALEESRRLAQ FNVNSD YDL LYFVCLGVIP QFASTP

UniProtKB: ORF34

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Macromolecule #7: Large tegument protein deneddylase

MacromoleculeName: Large tegument protein deneddylase / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 306.666938 KDa
SequenceString: MDIIPPIAVT VAGVGSRNQF DGALGPASGL SCLRTSLSFL HMTYAHGINA TLSSDMIDGC LQEGAAWTTD LSNMGRGVPD MCALVDLPN RISYIKLGDT TSTCCVLSRI YGDSHFFTVP DEGFMCTQIP ARAFFDDVWM GREESYTIIT VDSTGMAIYR Q GNISFIFD ...String:
MDIIPPIAVT VAGVGSRNQF DGALGPASGL SCLRTSLSFL HMTYAHGINA TLSSDMIDGC LQEGAAWTTD LSNMGRGVPD MCALVDLPN RISYIKLGDT TSTCCVLSRI YGDSHFFTVP DEGFMCTQIP ARAFFDDVWM GREESYTIIT VDSTGMAIYR Q GNISFIFD PHGHGTIGQA VVVRVNTTDV YSYIASEYTH RPDNVESQWA AALVFFVTAN DGPVSEEALS SAVTLIYGSC DT YFTDEQY CEKLVTAQHP LLLSPPNSTT IVLNKSSIVP LHQNVGESVS LEATLHSTLT NTVALDPRCS YSEVDPWHAV LET TSTGSG VLDCRRRRRP SWTPPSSEEN LACIDDGLVN NTHSTDNLHK PAKKVLKFKP TVDVPDKTQV AHVLPRLREV ANTP DVVLN VSNVDTPESS PTFSRNMNVG SSLKDRKPFL FEQSGDVNMV VEKLLQHGHE ISNGYVQNAV GTLDTVITGH TNVPI WVTR PLVMPDEKDP LELFINLTIL RLTGFVVENG TRTHHGATSV VSDFIGPLGE ILTGFPSAAE LIRVTSLILT NMPGAE YAI KTVLRKKCTI GMLIIAKFGL VAMRVQDTTG ALHAELDVLE ADLGGSSPID LYSRLSTGLI SILNSPIISH PGLFAEL IP TRTGSLSERI RLLCELVSAR ETRYMREHTA LVSSVKALEN ALRSTRNKID AIQIPEVPQE PPEETDIPPE ELIRRVYE I RSEVTMLLTS AVTEYFTRGV LYSTRALIAE QSPRRFRVAT ASTAPIQRLL DSLPEFDAKL TAIISSLSIH PPPETIQNL PVVSLLKELI KEGEDLNTDT ALVSWLSVVG EAQTAGYLSR REFDELSRTI KTINTRATQR ASAEAELSCF NTLSAAVDQA VKDYETYNN GEVKYPEITR DDLLATIVRA TDDLVRQIKI LSDPMIQSGL QPSIKRRLET RLKEVQTYAN EARTTQDTIK S RKQAAYNK LGGLLRPVTG FVGLRAAVDL LPELASELDV QGALVNLRTK VLEAPVEIRS QLTGDFWALF NQYRDILEHP GN ARTSVLG GLGACFTAII EIVPIPTEYR PSLLAFFGDV ADVLASDIAT VSTNPESESA INAVVATLSK ATLVSSTVPA LSF VLSLYK KYQALQQEIT NTHKLTELQK QLGDDFSTLA VSSGHLKFIS SSNVDDYEIN DAILSIQTNV HALMDTVKLV EVEL QKLPP HCIAGTSTLS RVVKDLHKLV TMAHEKKEQA KVLITDCERA HKQQTTRVLY ERWTRDIIAC LEAMETRHVF NGTEL ARLR DMAAAGGFDI HAVYPQARQV VAACETTAVT ALDTVFRHNP HTPENTNIPP PLALLRGLTW FDDFSITAPV FTVMFP GVS IEGLLLLMRI RAVVLLSADT SINGIPNYRD MILRTSGDLL QIPALAGYVD FYTRSYDQFI TESVTLSELR ADIRQAA GA KLTEANKALE EVTHVRAHET AKLALKEGVF ITLPSEGLLI RAIEYFTTFD HKRFIGTAYE RVLQTMVDRD LKEANAEL A QFRMVCQATK NRAIQILQNI VDTANATEQQ EDVDFTNLKT LLKLTPPPKT IALAIDRSTS VQDIVTQFAL LLGRLEEET GTLDIQAVDW MYQARNIIDS HPLSVRIDGT GPLHTYKDRV DKLYALRTKL DLLRRRIETG EVTWDDAWTT FKRETGDMLA SGDTYATSV DSIKALQASA SVVDMLCSEP EFFLLPVETK NRLQKKQQER KTALDVVLQK QRQFEETASR LRALIERIPT E SDHDVLRM LLHDFDQFTH LPIWIKTQYM TFRNLLMVRL GLYASYAEIF PPASPNGVFA PIPAMSGVCL EDQSRCIRAR VA AFMGEAS VVQTFREARS SIDALFGKNL TFYLDTDGVP LRYRVCYKSV GVKLGTMLCS QGGLSLRPAL PDEGIVEETT LSA LRVANE VNELRIEYES AIKSGFSAFS TFVRHRHAEW GKTNARRAIA EIYAGLITTT LTRQYGVHWD KLIYSFEKHH LTSV MGNGL TKPIQRRGDV RVLELTLSDI VTILVATTPV HLLNFARLDL IKQHEYMART LRPVIEAAFR GRLLVRSLDG DPKGN ARAF FNAAPSKHKL PLALGSNQDP TGGRIFAFRM ADWKLVKMPQ KITDPFAPWQ LSPPPGVKAN VDAVTRIMAT DRLATI TVL GRMCLPPISL VSMWNTLQPE EFAYRTQDDV DIIVDARLDL SSTLNARFDT APSNTTLEWN TDRKVITDAY IQTGATT VF TVTGAAPTHV SNVTAFDIAT TAILFGAPLV IAMELTSVFS QNSGLTLGLK LFDSRHMATD SGISSAVSPD IVSWGLRL L HMDPHPIENA CLIVQLEKLS ALIANKPLTN NPPCLLLLDE HMNPSYVLWE RKDSIPAPDY VVFWGPESLI DLPYIDSDE DSFPSCPDDP FYSQIIAGYA PQGPPNLDTT DFYPTEPLFK SPVQVVRSSK CKKMPVQPVQ PAQPVQPAQP AQPVQPAQPI EPGTQIVVQ NFKKPQSVKT TLSQKDIPLY VETESETAVL IPKQLTTSIK TTVCKSITPP NNQLSDWKNN PQQNQTLNQA F NKPILEIT SIPTDDSISY RTWIEKSNQT QKRHQNDPRM YNSKTVFHPV NNQLPSWVDT AADAPQTDLL TNYKTRQPSP NF PRDVHTW GVSSNPFNSP NRDLYESDFS EPSDGYSSES ENSIVLSLDE HRSCRVPRHV RVVNADVVTG RRYVRGTALG ALA LLSQAC RRMIDNVRYT RKLLMDHTED IFQGLGYVKL LLDGTYI

UniProtKB: Large tegument protein deneddylase

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 0.974 sec. / Average electron dose: 1.577 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 3804
ExtractionNumber tomograms: 69 / Number images used: 3804
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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