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- EMDB-34704: One CVSC-binding penton vertex in HCMV B-capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-34704
TitleOne CVSC-binding penton vertex in HCMV B-capsid
Map data
Sample
  • Virus: Human betaherpesvirus 5
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2
KeywordsB-capsid / one CVSC-binding penton vertex / asymmetric reconstruction / VIRUS / VIRAL PROTEIN
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral genome packaging / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein ...Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / 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
Similarity search - Domain/homology
Major capsid protein / UL77 protein / Capsid vertex component 1 / Small capsomere-interacting protein / Capsid triplex subunit 2 / Capsid triplex subunit 1
Similarity search - Component
Biological speciesHuman betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLi Z / Yu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-electron microscopy structures of capsids and in situ portals of DNA-devoid capsids of human cytomegalovirus.
Authors: Zhihai Li / Jingjing Pang / Rongchao Gao / Qingxia Wang / Maoyan Zhang / Xuekui Yu /
Abstract: The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold ...The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold interaction and the conformational changes that occur to the portal during the different stages of capsid formation have yet to be elucidated structurally. Here we present high-resolution structures of the A- and B-capsids and in-situ portals of human cytomegalovirus. We show that scaffolds bind to the hydrophobic cavities formed by the dimerization and Johnson-fold domains of the major capsid proteins. We further show that 12 loop-helix-loop fragments-presumably from the scaffold domain-insert into the hydrophobic pocket of the portal crown domain. The portal also undergoes significant changes both positionally and conformationally as it accompanies DNA packaging. These findings unravel the mechanism by which the portal interacts with the scaffold to nucleate capsid assembly and further our understanding of scaffold expulsion and DNA incorporation.
History
DepositionNov 9, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34704.png

Downloads & links

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Map

FileDownload / File: emd_34704.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.625 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.043540534 - 0.08184645
Average (Standard dev.)0.0021870357 (±0.007300424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34704_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34704_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human betaherpesvirus 5

EntireName: Human betaherpesvirus 5
Components
  • Virus: Human betaherpesvirus 5
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Triplex capsid protein 2
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Capsid vertex component 1
    • Protein or peptide: Capsid vertex component 2

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Supramolecule #1: Human betaherpesvirus 5

SupramoleculeName: Human betaherpesvirus 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10359 / Sci species name: Human betaherpesvirus 5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 8.495924 KDa
SequenceString:
MSNTAPGPTV ANKRDEKHRH VVNVVLELPT EISEATHPVL ATMLSKYTRM SSLFNDKCAF KLDLLRMVAV SRTRR

UniProtKB: Small capsomere-interacting protein

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 154.048906 KDa
SequenceString: MENWSALELL PKVGIPTDFL THVKTSAGEE MFEALRIYYG DDPERYNIHF EAIFGTFCNR LEWVYFLTSG LAAAAHAIKF HDLNKLTTG KMLFHVQVPR VASGAGLPTS RQTTIMVTKY SEKSPITIPF ELSAACLTYL RETFEGTILD KILNVEAMHT V LRALKNTA ...String:
MENWSALELL PKVGIPTDFL THVKTSAGEE MFEALRIYYG DDPERYNIHF EAIFGTFCNR LEWVYFLTSG LAAAAHAIKF HDLNKLTTG KMLFHVQVPR VASGAGLPTS RQTTIMVTKY SEKSPITIPF ELSAACLTYL RETFEGTILD KILNVEAMHT V LRALKNTA DAMERGLIHS FLQTLLRKAP PYFVVQTLVE NATLARQALN RIQRSNILQS FKAKMLATLF LLNRTRDRDY VL KFLTRLA EAATDSILDN PTTYTTSSGA KISGVMVSTA NVMQIIMSLL SSHITKETVS APATYGNFVL SPENAVTAIS YHS ILADFN SYKAHLTSGQ PHLPNDSLSQ AGAHSLTPLS MDVIRLGEKT VIMENLRRVY KNTDTKDPLE RNVDLTFFFP VGLY LPEDR GYTTVESKVK LNDTVRNALP TTAYLLNRDR AVQKIDFVDA LKTLCHPVLH EPAPCLQTFT ERGPPSEPAM QRLLE CRFQ QEPMGGAARR IPHFYRVRRE VPRTVNEMKQ DFVVTDFYKV GNITLYTELH PFFDFTHCQE NSETVALCTP RIVIGN LPD GLAPGPFHEL RTWEIMEHMR LRPPPDYEET LRLFKTTVTS PNYPELCYLV DVLVHGNVDA FLLIRTFVAR CIVNMFH TR QLLVFAHSYA LVTLIAEHLA DGALPPQLLF HYRNLVAVLR LVTRISALPG LNNGQLAEEP LSAYVNALHD HRLWPPFV T HLPRNMEGVQ VVADRQPLNP ANIEARHHGV SDVPRLGAMD ADEPLFVDDY RATDDEWTLQ KVFYLCLMPA MTNNRACGL GLNLKTLLVD LFYRPAFLLM PAATAVSTSG TTSKESTSGV TPEDSIAAQR QAVGEMLTEL VEDVATDAHT PLLQACRELF LAVQFVGEH VKVLEVRAPL DHAQRQGLPD FISRQHVLYN GCCVVTAPKT LIEYSLPVPF HRFYSNPTIC AALSDDIKRY V TEFPHYHR HDGGFPLPTA FAHEYHNWLR SPFSRYSATC PNVLHSVMTL AAMLYKISPV SLVLQTKAHI HPGFALTAVR TD TFEVDML LYSGKSCTSV IINNPIVTKE ERDISTTYHV TQNINTVDMG LGYTSNTCVA YVNRVRTDMG VRVQDLFRVF PMN VYRHDE VDRWIRHAAG VERPQLLDTE TISMLTFGSM SERNAAATVH GQKAACELIL TPVTMDVNYF KIPNNPRGRA SCML AVDPY DTEAATKAIY DHREADAQTF AATHNPWASQ AGCLSDVLYN TRHRERLGYN SKFYSPCAQY FNTEEIIAAN KTLFK TIDE YLLRAKDCIR GDTDTQYVCV EGTEQLIENP CRLTQEALPI LSTTTLALME TKLKGGAGAF ATSETHFGNY VVGEII PLQ QSMLFNS

UniProtKB: Major capsid 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: 4 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 34.63575 KDa
SequenceString: MAAMEANIFC TFDHKLSIAD VGKLTKLVAA VVPIPQRLHL IKHYQLGLHQ FVDHTRGYVR LRGLLRNMTL TLMRRVEGNQ ILLHVPTHG LLYTVLNTGP VTWEKGDALC VLPPLFHGPL ARENLLTLGQ WELVLPWIVP MPLALEINQR LLIMGLFSLD R SYEEVKAA ...String:
MAAMEANIFC TFDHKLSIAD VGKLTKLVAA VVPIPQRLHL IKHYQLGLHQ FVDHTRGYVR LRGLLRNMTL TLMRRVEGNQ ILLHVPTHG LLYTVLNTGP VTWEKGDALC VLPPLFHGPL ARENLLTLGQ WELVLPWIVP MPLALEINQR LLIMGLFSLD R SYEEVKAA VQQLQTITFR DATFTIPDPV IDQHLLIDMK TACLSMSMVA NLASELTMTY VRKLALEDSS MLLVKCQELL MR LDRERSV GEPRTPARPQ HVSPDDEIAR LSALFVMLRQ LDDLIREQVV FTVCDVSPDN KSATCIFKG

UniProtKB: Capsid triplex subunit 2

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Macromolecule #4: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 33.07127 KDa
SequenceString: MDARAVAKRP RDPADEDNEL VTALKAKREV NTISVRYLYH ADHQALTARF FVPEGLVEFE AQPGALLIRM ETGCDSPRHL YISLYLLGI RASNVSASTR CLLESVYTAS AARAALQWLD LGPHLLHRRL ETLGCVKTVS LGITSLLTCV MRGYLYNTLK T EVFALMIP ...String:
MDARAVAKRP RDPADEDNEL VTALKAKREV NTISVRYLYH ADHQALTARF FVPEGLVEFE AQPGALLIRM ETGCDSPRHL YISLYLLGI RASNVSASTR CLLESVYTAS AARAALQWLD LGPHLLHRRL ETLGCVKTVS LGITSLLTCV MRGYLYNTLK T EVFALMIP KDMYLTWEET RGRLQYVYLI IVYDYDGPET RPGIYVLTSS IAHWQTLVDV ARGKFARERC SFVNRRITRP RQ IPLCTGV IQKLGWCLAD DIHTSFLVHK ELKLSVVRLD NFSVELGDFR EFV

UniProtKB: Capsid triplex subunit 1

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Macromolecule #5: Capsid vertex component 1

MacromoleculeName: Capsid vertex component 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 68.567211 KDa
SequenceString: METHLYSDLA FEARFADDEQ LPLHLVLDQE VLSNEEAETL RYVYYRNVDS AGRSTGRAPG GDEDDAPASD DAEDAVGGDR AFDRERRTW QRACFRVLPR PLELLDYLRQ SGLTVTLEKE QRVRMFYAVF TTLGLRCPDN RLSGAQTLHL RLVWPDGSYR D WEFLARDL ...String:
METHLYSDLA FEARFADDEQ LPLHLVLDQE VLSNEEAETL RYVYYRNVDS AGRSTGRAPG GDEDDAPASD DAEDAVGGDR AFDRERRTW QRACFRVLPR PLELLDYLRQ SGLTVTLEKE QRVRMFYAVF TTLGLRCPDN RLSGAQTLHL RLVWPDGSYR D WEFLARDL LREEMEANKR DRQHQLATTT NHRRRGGLRN NLDNGSDRRL PEAAVASLET AVSTPFFEIP NGAGTSSANG DG RFSNLEQ RVARLLRGDE EFIYHAGPLE PPSKIRGHEL VQLRLDVNPD LMYATDPHDR DEVARTDEWK GAGVSRLREV WDV QHRVRL RVLWYVNSFW RSRELSYDDH EVELYRALDA YRARIAVEYV LIRAVRDEIY AVLRRDGGAL PQRFACHVSR NMSW RVVWE LCRHALALWM DWADVRSCII KALTPRLSRG AAAAAQRARR QRERSAPKPQ ELLFGPRNES GPPAEQTWYA DVVRC VRAQ VDLGVEVRAA RCPRTGLWIV RDRRGRLRRW LSQPEVCVLY VTPDLDFYWV LPGGFAVSSR VTLHGLAQRA LRDRFQ NFE AVLARGMHVE AGRQEPETPR VSGRRLPFDD L

UniProtKB: Capsid vertex component 1

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Macromolecule #6: Capsid vertex component 2

MacromoleculeName: Capsid vertex component 2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 71.26957 KDa
SequenceString: MSLLHTFWRL PVAVFFEPHE ENVLRCPERV LRRLLEDAAV TMRGGGWRED VLMDRVRKRY LRQELRDLGH RVQTYCEDLE GRVSEAEAL LNQQCELDEG PSPRTLLQPP CRPRSSSPGT GVAGASAVPH GLYSRHDAIT GPAAAPSDVV APSDAVAASA A AGASSTWL ...String:
MSLLHTFWRL PVAVFFEPHE ENVLRCPERV LRRLLEDAAV TMRGGGWRED VLMDRVRKRY LRQELRDLGH RVQTYCEDLE GRVSEAEAL LNQQCELDEG PSPRTLLQPP CRPRSSSPGT GVAGASAVPH GLYSRHDAIT GPAAAPSDVV APSDAVAASA A AGASSTWL AQCAERPLPG NVPSYFGITQ NDPFIRFHTD FRGEVVNTMF ENASTWTFSF GIWYYRLKRG LYTQPRWKRV YH LAQMDNF SISQELLLGV VNALENVTVY PTYDCVLSDL EAAACLLAAY GHALWEGRDP PDSVATVLGE LPQLLPRLAD DVS REIAAW EGPVAAGNNY YAYRDSPDLR YYMPLSGGRH YHPGTFDRHV LVRLFHKRGV IQHLPGYGTI TEELVQERLS GQVR DDVLS LWSRRLLVGK LGRDVPVFVH EQQYLRSGLT CLAGLLLLWK VTNADSVFAP RTGKFTLADL LGSDAVAGGG LPGGR AGGE EEGYGGRHGR VRNFEFLVRY YIGPWYARDP AVTLSQLFPG LALLAVTESV RSGWDPSRRE DSAGGGDGGG AVLMQL SKS NPVADYMFAQ SSKQYGDLRR LEVHDALLFH YEHGLGRLLS VTLPRHRVST LGSSLFNVND IYELLYFLVL GFLPSVA VL

UniProtKB: UL77 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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40903
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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