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- EMDB-38189: P-hexon capsomer of the VZV C-Capsid -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38189
TitleP-hexon capsomer of the VZV C-Capsid
Map data
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: x 11 types
KeywordsVZV / capsid structure / VIRUS
Function / homology
Function and homology information


nuclear capsid assembly / viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / viral process / viral penetration into host nucleus ...nuclear capsid assembly / viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / viral process / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / 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 large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / 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 major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Major capsid protein / Capsid vertex component 2 / Large tegument protein deneddylase / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNan W / Lei C / Xiangxi W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Hlife / Year: 2024
Title: Insights into varicella-zoster virus assembly from the B- and C-capsid at near-atomic resolution structures
Authors: Cao L / Wang N / Lv Z / Chen W / Chen Z / Song L / Sha X / Wang G / Hu Y / Lian X / Cui G / Fan J / Quan Y / Liu H / Hou H / Wang X
History
DepositionDec 1, 2023-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38189.png

Downloads & links

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Map

FileDownload / File: emd_38189.map.gz / Format: CCP4 / Size: 83.7 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 280 pix.
= 378. Å		1.35 Å/pix.
x 280 pix.
= 378. Å		1.35 Å/pix.
x 280 pix.
= 378. 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: 0.004
Minimum - Maximum-0.038671143 - 0.063336454
Average (Standard dev.)0.000103866725 (±0.0042153043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38189_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38189_half_map_2.map
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: Tri2A
    • Protein or peptide: Tri1
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: CVC1
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Capsid vertex component 2
    • Protein or peptide: Large tegument protein deneddylase
    • Protein or peptide: Tri2A

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Supramolecule #1: Human alphaherpesvirus 3

SupramoleculeName: Human alphaherpesvirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #10-#11, #1-#9 / NCBI-ID: 10335 / Sci species name: Human alphaherpesvirus 3 / Virus type: VIRION / Virus isolate: OTHER / 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: 5 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 152.267125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PAGIIPTGNV LSTIEVCAHR CIFDFFKQIR SDDNSLYSAQ FDILLGTYCN TLNFVRFLEL GLSVACICTK FPELAYVRDG VIQFEVQQP MIARDGPHPV DQPVHNYMVK RIHKRSLSAA FAIASEALSL LSNTYVDGTE IDSSLRIRAI QQMARNLRTV L DSFERGTA ...String:
PAGIIPTGNV LSTIEVCAHR CIFDFFKQIR SDDNSLYSAQ FDILLGTYCN TLNFVRFLEL GLSVACICTK FPELAYVRDG VIQFEVQQP MIARDGPHPV DQPVHNYMVK RIHKRSLSAA FAIASEALSL LSNTYVDGTE IDSSLRIRAI QQMARNLRTV L DSFERGTA DQLLGVLLEK APPLSLLSPI NKFQPEGHLN RVARAALLSD LKRRVCADMF FMTRHAREPR LISAYLSDMV SC TQPSVMV SRITHTNTRG RQVDGVLVTT ATLKRQLLQG ILQIDDTAAD VPVTYGEMVL QGTNLVTALV MGKAVRGMDD VAR HLLDIT DPNTLNIPSI PPQSNSDSTT AGLPVNARVP ADLVIVGDKL VFLEALERRV YQATRVAYPL IGNIDITFIM PMGV FQANS MDRYTRHAGD FSTVSEQDPR QFPPQGIFFY NKDGILTQLT LRDAMGTICH SSLLDVEATL VALRQQHLDR QCYFG VYVA EGTEDTLDVQ MGRFMETWAD MMPHHPHWVN EHLTILQFIA PSNPRLRFEL NPAFDFFVAP GDVDLPGPQR PPEAMP TVN ATLRIINGNI PVPLCPISFR DCRGTQLGLG RHTMTPATIK AVKDTFEDRA YPTIFYMLEA VIHGNERNFC ALLRLLT QC IRGYWEQSHR VAFVNNFHML MYITTYLGNG ELPEVCINIY RDLLQHVRAL RQTITDFTIQ GEGHNGETSE ALNNILTD D TFIAPILWDC DALIYRDEAA RDRLPAIRVS GRNGYQALHF VDMAGHNFQR RDNVLIHGRP VRGDTGQAIP ITPHHDREW GILSKIYYYI VIPAFSRGSC CTMGVRYDRL YPALQAVIVP EIPADEEAPT TPEDPRHPLH AHQLVPNSLN VYFHNAHLTV DGDALLTLQ ELMGDMAERT TAILVSSAPD AGAATATTRN MRIYDGALYH GLIMMAYQAY DETIATGTFF YPVPVNPLFA C PEHLASLR GMTNARRVLA KMVPPIPPFL GANHHATIRQ PVAYHVTHSK SDFNTLTYSL LGGYFKFTPI SLTHQLRTGF HP GIAFTVV RQDRFATEQL LYAERASESY FVGQIQVHHH DAIGGVNFTL TQPRAHVDLG VGYTAVCATA ALRCPLTDMG NTA QNLFFS RGGVPMLHDN VTESLRRITA SGGRLNPTEP LPIFGGLRPA TSAGIARGQA SVCEFVAMPV STDLQYFRTA CNPR GRASG MLYMGDRDAD IEAIMFDHTQ SDVAYTDRAT LNPWASQKHS YGDRLYNGTY NLTGASPIYS PCFKFFTPAE VNTNC NTLD RLLMEAKAVA SQSSTDTEYQ FKRPPGSTEM TQDPCGLFQE AYPPLCSSDA AMLRTAHAGE TGADEVHLAQ YLIRDA SPL RGCLPL

UniProtKB: Major capsid protein

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 152.354203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IPAGIIPTGN VLSTIEVCAH RCIFDFFKQI RSDDNSLYSA QFDILLGTYC NTLNFVRFLE LGLSVACICT KFPELAYVRD GVIQFEVQQ PMIARDGPHP VDQPVHNYMV KRIHKRSLSA AFAIASEALS LLSNTYVDGT EIDSSLRIRA IQQMARNLRT V SDSFERGT ...String:
IPAGIIPTGN VLSTIEVCAH RCIFDFFKQI RSDDNSLYSA QFDILLGTYC NTLNFVRFLE LGLSVACICT KFPELAYVRD GVIQFEVQQ PMIARDGPHP VDQPVHNYMV KRIHKRSLSA AFAIASEALS LLSNTYVDGT EIDSSLRIRA IQQMARNLRT V SDSFERGT ADQLLGVLLE KAPPLSLLSP INKFQPEGHL NRVARAALLS DLKRRVCADM FFMTRHAREP RLISAYLSDM VS CTQPSVM VSRITHTNTR GRQVDGVLVT TATLKRQLLQ GILQIDDTAA DVPVTYGEMV LQGTNLVTAL VMGKAVRGMD DVA RHLLDI TDPNTLNIPS IPPQSNSDST TAGLPVNARV PADLVIVGDK LVFLEALERR VYQATRVAYP LIGNIDITFI MPMG VFQAN SMDRYTRHAG DFSTVSEQDP RQFPPQGIFF YNKDGILTQL TLRDAMGTIC HSSLLDVEAT LVALRQQHLD RQCYF GVYV AEGTEDTLDV QMGRFMETWA DMMPHHPHWV NEHLTILQFI APSNPRLRFE LNPAFDFFVA PGDVDLPGPQ RPPEAM PTV NATLRIINGN IPVPLCPISF RDCRGTQLGL GRHTMTPATI KAVKDTFEDR AYPTIFYMLE AVIHGNERNF CALLRLL TQ CIRGYWEQSH RVAFVNNFHM LMYITTYLGN GELPEVCINI YRDLLQHVRA LRQTITDFTI QGEGHNGETS EALNNILT D DTFIAPILWD CDALIYRDEA ARDRLPAIRV SGRNGYQALH FVDMAGHNFQ RRDNVLIHGR PVRGDTGQAI PITPHHDRE WGILSKIYYY IVIPAFSRGS CCTMGVRYDR LYPALQAVIV PEIPADEEAP TTPEDPRHPL HAHQLVPNSL NVYFHNAHLT VDGDALLTL QELMGDMAER TTAILVSSAP DAGAATATTR NMRIYDGALY HGLIMMAYQA YDETIATGTF FYPVPVNPLF A CPEHLASL RGMTNARRVL AKMVPPIPPF LGANHHATIR QPVAYHVTHS KSDFNTLTYS LLGGYFKFTP ISLTHQLRTG FH PGIAFTV VRQDRFATEQ LLYAERASES YFVGQIQVHH HDAIGGVNFT LTQPRAHVDL GVGYTAVCAT AALRCPLTDM GNT AQNLFF SRGGVPMLHD NVTESLRRIT ASGGRLNPTE PLPIFGGLRP ATSAGIARGQ ASVCEFVAMP VSTDLQYFRT ACNP RGRAS GMLYMGDRDA DIEAIMFDHT QSDVAYTDRA TLNPWASQKH SYGDRLYNGT YNLTGASPIY SPCFKFFTPA EVNTN CNTL DRLLMEAKAV ASQSSTDTEY QFKRPPGSTE MTQDPCGLFQ EAYPPLCSSD AAMLRTAHAG ETGADEVHLA QYLIRD ASP LRGCLPL

UniProtKB: Major capsid protein

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Macromolecule #3: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 152.468312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NIPAGIIPTG NVLSTIEVCA HRCIFDFFKQ IRSDDNSLYS AQFDILLGTY CNTLNFVRFL ELGLSVACIC TKFPELAYVR DGVIQFEVQ QPMIARDGPH PVDQPVHNYM VKRIHKRSLS AAFAIASEAL SLLSNTYVDG TEIDSSLRIR AIQQMARNLR T VSDSFERG ...String:
NIPAGIIPTG NVLSTIEVCA HRCIFDFFKQ IRSDDNSLYS AQFDILLGTY CNTLNFVRFL ELGLSVACIC TKFPELAYVR DGVIQFEVQ QPMIARDGPH PVDQPVHNYM VKRIHKRSLS AAFAIASEAL SLLSNTYVDG TEIDSSLRIR AIQQMARNLR T VSDSFERG TADQLLGVLL EKAPPLSLLS PINKFQPEGH LNRVARAALL SDLKRRVCAD MFFMTRHARE PRLISAYLSD MV SCTQPSV MVSRITHTNT RGRQVDGVLV TTATLKRQLL QGILQIDDTA ADVPVTYGEM VLQGTNLVTA LVMGKAVRGM DDV ARHLLD ITDPNTLNIP SIPPQSNSDS TTAGLPVNAR VPADLVIVGD KLVFLEALER RVYQATRVAY PLIGNIDITF IMPM GVFQA NSMDRYTRHA GDFSTVSEQD PRQFPPQGIF FYNKDGILTQ LTLRDAMGTI CHSSLLDVEA TLVALRQQHL DRQCY FGVY VAEGTEDTLD VQMGRFMETW ADMMPHHPHW VNEHLTILQF IAPSNPRLRF ELNPAFDFFV APGDVDLPGP QRPPEA MPT VNATLRIING NIPVPLCPIS FRDCRGTQLG LGRHTMTPAT IKAVKDTFED RAYPTIFYML EAVIHGNERN FCALLRL LT QCIRGYWEQS HRVAFVNNFH MLMYITTYLG NGELPEVCIN IYRDLLQHVR ALRQTITDFT IQGEGHNGET SEALNNIL T DDTFIAPILW DCDALIYRDE AARDRLPAIR VSGRNGYQAL HFVDMAGHNF QRRDNVLIHG RPVRGDTGQA IPITPHHDR EWGILSKIYY YIVIPAFSRG SCCTMGVRYD RLYPALQAVI VPEIPADEEA PTTPEDPRHP LHAHQLVPNS LNVYFHNAHL TVDGDALLT LQELMGDMAE RTTAILVSSA PDAGAATATT RNMRIYDGAL YHGLIMMAYQ AYDETIATGT FFYPVPVNPL F ACPEHLAS LRGMTNARRV LAKMVPPIPP FLGANHHATI RQPVAYHVTH SKSDFNTLTY SLLGGYFKFT PISLTHQLRT GF HPGIAFT VVRQDRFATE QLLYAERASE SYFVGQIQVH HHDAIGGVNF TLTQPRAHVD LGVGYTAVCA TAALRCPLTD MGN TAQNLF FSRGGVPMLH DNVTESLRRI TASGGRLNPT EPLPIFGGLR PATSAGIARG QASVCEFVAM PVSTDLQYFR TACN PRGRA SGMLYMGDRD ADIEAIMFDH TQSDVAYTDR ATLNPWASQK HSYGDRLYNG TYNLTGASPI YSPCFKFFTP AEVNT NCNT LDRLLMEAKA VASQSSTDTE YQFKRPPGST EMTQDPCGLF QEAYPPLCSS DAAMLRTAHA GETGADEVHL AQYLIR DAS PLRGCLPL

UniProtKB: Major capsid protein

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Macromolecule #4: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 10.185611 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SNPTTFSVEA IAAYTPVALI RLLNASGPLQ PGHRVDIADA RSIYTVGAAA SAARARANHN ANTIRRTAMF AETDPMTWLR PTVGLRRTF NPRII

UniProtKB: Small capsomere-interacting protein

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Macromolecule #5: CVC1

MacromoleculeName: CVC1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 59.751445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNAHLANEVQ YDLGHPSSLV HVIISSECLA AAGIPLAALM RANFQVEIQT RAHATGDCTP WCTAFAAYVP ADAVGELLAP VVPAHPGLL PRASSAGGLF VSLPVVCDAQ GVYDPYAVAA LRLAWGSGAS CARVILFSYD ELVPPNTRYA ADSTRIMRVC R HLCRYVAL ...String:
MNAHLANEVQ YDLGHPSSLV HVIISSECLA AAGIPLAALM RANFQVEIQT RAHATGDCTP WCTAFAAYVP ADAVGELLAP VVPAHPGLL PRASSAGGLF VSLPVVCDAQ GVYDPYAVAA LRLAWGSGAS CARVILFSYD ELVPPNTRYA ADSTRIMRVC R HLCRYVAL LGAAAPPAAK EAAAHLSMGL PPISPEEQLT APGGDTTAAQ DVSIAQENEE ILALVQRRSL VEWLDRGWEA LA GGDRPDW LWSRRSISVV LRHHYGTKQR FVVVSYENSV AWGGRRARPP LLSSALATAL TEACAAERVV RPHQLSPAGQ AEL LLRFPA LEVPLRHPRP VLPPFDIAAE VAFTARIHLA CLRALGQAIR AALQGGPRIS QRLRYDFGPD QRAWLGEVTR RFPI LLENL MRAVEGTAPD AFFHTAYALA VLAHLGGRVV PLGDDLPARF ADSDGHYVFD YYSTSGDTLR LNNRPIAVAM DEQSK CRFM EAPRRVCEQY LPGESYAYLC LGFNRRLCGI VVFPGGFAFT INIAAYLSLS DPVARAAVLR FCRKVS

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Macromolecule #6: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 10.890343 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDPYCPFDAL DVWEHRRFIV ADSRNFITPE FPRDFWMSPV FNLPRETAAE QVVVLQAQRT AAAAALENAA MQAAELPVDI ERRLRPIER NVHEI

UniProtKB: Capsid vertex component 2

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Macromolecule #7: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 9.280526 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
WEHRRFIVAD SRNFITPEFP RDFWMSPVFN LPRETAAEQV VVLQAQRTAA AAALENAAMQ AAELPVDIER RLRPIERNVH

UniProtKB: Capsid vertex component 2

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Macromolecule #8: Large tegument protein deneddylase

MacromoleculeName: Large tegument protein deneddylase / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 5.50051 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QRTGRSALAV LIRACYRLQQ QLQRTRRALL HHSDAVLTSL HHVRMLL

UniProtKB: Large tegument protein deneddylase

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Macromolecule #9: Tri2A

MacromoleculeName: Tri2A / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 27.729641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AMPFEIEVLL PGELSPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVYG SADSIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVEDL N LMFSINEG ...String:
AMPFEIEVLL PGELSPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVYG SADSIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVEDL N LMFSINEG CLLILALIPR LLALLIPRLL ALVTREAAQL IHPEAPMLML PIYETISSWI STSSRLGDTL GTRAILRVCV FD GPSTVHP GDRTAVIQV

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Macromolecule #10: Tri2A

MacromoleculeName: Tri2A / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 28.721295 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AMPFEIEVLL PGEISPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVFG SADEIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVERT A ADVICYNG ...String:
AMPFEIEVLL PGEISPAETS ALQKCEGKII TFSTLRHRAS LVDIALSSYY INGAPPDTLS LLEAYRMRFA AVITRVIPGK LLAHAIGVG TPTPGLFIQN TSPVDLCNGD YICLLPPVFG SADEIRLDSV GLEIVFPLTI PQTLMREIIA KVVARAVERT A ADVICYNG RRYELETNLQ HRDGSDAAIR TLVLNLMFSI NEGTTLILTL ITRLLRFPIY EAISSWISTS SRLGDTLGTR AI LRVCVFD GPSTVHPGDR TAVIQV

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Macromolecule #11: Tri1

MacromoleculeName: Tri1 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 32.26891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FKSTTQLIQQ VSLTDFFRPD IEHAGSTVLI LRHPTDLPAL ARHRAPPGRQ TERLAEAWGQ LLEASRAYVT SLSFIAACRA EEYTDKQAA EANRTAIVSA YGCSRMGARL IRFSECLRAM VQCHVFPHRF ISFFGSLLEY TIQDNLCNIT AVAKGPQEAA R TDKTSTRR ...String:
FKSTTQLIQQ VSLTDFFRPD IEHAGSTVLI LRHPTDLPAL ARHRAPPGRQ TERLAEAWGQ LLEASRAYVT SLSFIAACRA EEYTDKQAA EANRTAIVSA YGCSRMGARL IRFSECLRAM VQCHVFPHRF ISFFGSLLEY TIQDNLCNIT AVAKGPQEAA R TDKTSTRR VTANIPACVF WDVDKDLHLS ADGLKHVFLV FVYTQRRQRE GVRLHLALSQ LNEQCFGRGI GFLLGARICM YA AYTLIGT IPSESVRYTR RMERFGGYNV PTIWLEGVVW GGTNTWNEC

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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: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1671456
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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