[English] 日本語
Yorodumi- EMDB-20436: Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20436 | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, CATC-binding structure | |||||||||||||||||||||||||||||||||||||||||||||
Map data | None | |||||||||||||||||||||||||||||||||||||||||||||
Sample |
| |||||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information icosahedral viral capsid / T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral penetration into host nucleus / viral capsid ...icosahedral viral capsid / T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral penetration into host nucleus / viral capsid / 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 / viral envelope / host cell nucleus / structural molecule activity / proteolysis / DNA binding Similarity search - Function | |||||||||||||||||||||||||||||||||||||||||||||
Biological species | HHV-8 (virus) / Human gammaherpesvirus 8 | |||||||||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||||||||||||||||||||||||||||||||
Authors | Gong D / Dai X / Jih J / Liu YT / Bi GQ / Sun R / Zhou ZH | |||||||||||||||||||||||||||||||||||||||||||||
Funding support | United States, China, 14 items
| |||||||||||||||||||||||||||||||||||||||||||||
Citation | Journal: Cell / Year: 2019 Title: DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV. Authors: Danyang Gong / Xinghong Dai / Jonathan Jih / Yun-Tao Liu / Guo-Qiang Bi / Ren Sun / Z Hong Zhou / Abstract: Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes ...Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes (CATCs) and facilitates translocation of an ∼150-kb dsDNA genome, followed by acquisition of a pleomorphic tegument and envelope. Because of deviation from icosahedral symmetry, KSHV portal and tegument structures have largely been obscured in previous studies. Using symmetry-relaxed cryo-EM, we determined the in situ structure of the KSHV portal and its interactions with surrounding capsid proteins, CATCs, and the terminal end of KSHV's dsDNA genome. Our atomic models of the portal and capsid/CATC, together with visualization of CATCs' variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Structure-based mutageneses confirm that a triplex deep binding groove for CATCs is a hotspot that holds promise for antiviral development. | |||||||||||||||||||||||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20436.map.gz | 193.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-20436-v30.xml emd-20436.xml | 31.7 KB 31.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20436_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_20436.png | 237.8 KB | ||
Masks | emd_20436_msk_1.map | 216 MB | Mask map | |
Others | emd_20436_half_map_1.map.gz emd_20436_half_map_2.map.gz | 167.5 MB 167.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20436 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20436 | HTTPS FTP |
-Validation report
Summary document | emd_20436_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_20436_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_20436_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | emd_20436_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20436 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20436 | HTTPS FTP |
-Related structure data
Related structure data | 6pphMC 6ppbC 6ppdC 6ppiC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_20436.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_20436_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: None
File | emd_20436_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: None
File | emd_20436_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human gammaherpesvirus 8
Entire | Name: Human gammaherpesvirus 8 |
---|---|
Components |
|
-Supramolecule #1: Human gammaherpesvirus 8
Supramolecule | Name: Human gammaherpesvirus 8 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 37296 / Sci species name: Human gammaherpesvirus 8 / Sci species strain: BAC16 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|---|
Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 1250.0 Å / T number (triangulation number): 16 |
-Macromolecule #1: Capsid vertex component 1
Macromolecule | Name: Capsid vertex component 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-8 (virus) / Strain: GK18 |
Molecular weight | Theoretical: 49.586555 KDa |
Sequence | String: MDAHAINERY VGPRCHRLAH VVLPRTFLLH HAIPLEPEII FSTYTRFSRS PGSSRRLVVC GKRVLPGEEN QLASSPSGLA LSLPLFSHD GNFHPFDISV LRISCPGSNL SLTVRFLYLS LVVAMGAGRN NARSPTVDGV SPPEGAVAHP LEELQRLARA T PDPAPTRG ...String: MDAHAINERY VGPRCHRLAH VVLPRTFLLH HAIPLEPEII FSTYTRFSRS PGSSRRLVVC GKRVLPGEEN QLASSPSGLA LSLPLFSHD GNFHPFDISV LRISCPGSNL SLTVRFLYLS LVVAMGAGRN NARSPTVDGV SPPEGAVAHP LEELQRLARA T PDPAPTRG PLQVLTGLLR AGSDGDRATH HMALEAPGTV RGESLDPPVS QKGPARTRHR PPPVRLSFNP VNADVPATWR DA TNVYSGA PYYVCVYERG GRQEDDWLPI PLSFPEEPVP PPPSLVFMDD LFINTKQCDF VDTLEAACRT QGYTLRQRVP VAI PRDAEI ADAVKSHFLE ACLVLRGLAS EASAWIRAAT SPPLGRHACW MDVLGLWESR PHTLGLELRG VNCGGTDGDW LEIL KQPDV QKTVSGSLVA CVIVTPALEA WLVLPGGFAI KGRYRASKED LVFIRGRYG |
-Macromolecule #2: Capsid vertex component 2
Macromolecule | Name: Capsid vertex component 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-8 (virus) / Strain: GK18 |
Molecular weight | Theoretical: 61.494383 KDa |
Sequence | String: MLTSERSYLR YPKNRRWTEA GRFWAPHPEN VLFIHKPTME ETRRVALGLR SQLVRNRERK TKAHLLSLEL DRLVQVHDSR VRVINADID AVKQMIGNMT WSDNIDMPQS RSHEPPLVTS PPQASHRNFT VAIVPGDPHF SVDRDLRGEL MPTLYMNQNQ W LPSFGPWF ...String: MLTSERSYLR YPKNRRWTEA GRFWAPHPEN VLFIHKPTME ETRRVALGLR SQLVRNRERK TKAHLLSLEL DRLVQVHDSR VRVINADID AVKQMIGNMT WSDNIDMPQS RSHEPPLVTS PPQASHRNFT VAIVPGDPHF SVDRDLRGEL MPTLYMNQNQ W LPSFGPWF ISLTDNAMQR RVFPKELKGT VNFQNSTSLK LISHTLTTVA STTADFFADA RHLTDTQAAL CLVNAYFCQK TS RQLPATP DDLLADLPQK LDLLITQLKQ ESGPGDFSFT YSNPQERASL APLNKESRYP TAFFQRHKLH AMMAKAGLFP HNK GTGAPG TAPAMDLVFA ITSAMFGSDI PPFSAYQWNL RAGIVALEVF ILAYGLLEFG QVARGHPNRR LNLVSLLGPK FQPG ALPDP NAPMLKRGQL FSFISEHYII PTLQANPNAP VSFIFPGIIL AALEARSTVS HKQPGPFVNL TGSRFNEIFE ILNQQ LTFR DPLALLQART ALRLATEEGL DVLLSHPSPP TLLQEIIKSQ FGGGDDYDRA YFMVLGCLPV VLAVV |
-Macromolecule #3: Large tegument protein deneddylase
Macromolecule | Name: Large tegument protein deneddylase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1 |
---|---|
Source (natural) | Organism: HHV-8 (virus) / Strain: GK18 |
Molecular weight | Theoretical: 290.024844 KDa |
Sequence | String: MAAQPLYMEG MASTHQANCI FGEHAGSQCL SNCVMYLASS YYNSETPLVD RASLDDVLEQ GMRLDLLLRK SGMLGFRQYA QLHHIPGFL RTDDWATKIF QSPEFYGLIG QDAAIREPFI ESLRSVLSRN YAGTVQYLII ICQSKAGAIV VKDKTYYMFD P HCIPNIPN ...String: MAAQPLYMEG MASTHQANCI FGEHAGSQCL SNCVMYLASS YYNSETPLVD RASLDDVLEQ GMRLDLLLRK SGMLGFRQYA QLHHIPGFL RTDDWATKIF QSPEFYGLIG QDAAIREPFI ESLRSVLSRN YAGTVQYLII ICQSKAGAIV VKDKTYYMFD P HCIPNIPN SPAHVIKTND VGVLLPYIAT HDTEYTGCFL YFIPHDYISP EHYIANHYRT IVFEELHGPR MDISRGVESC SI TEITSPS VSPAPSEAPL RRDSTQSQDE TRPRRPRVVI PPYDPTDRPR PPHQDRPPEQ AAGYGGNKGR GGNKGRGGKT GRG GNEGRG GHQPPDEHQP PHITAEHMDQ SDGQGADGDM DSTPANGETS VTETPGPEPN PPARPDREPP PTPPATPGAT ALLS DLTAT RGQKRKFSSL KESYPIDSPP SDDDDVSQPS QQTAPDTEDI WIDDPLTPLY PLTDTPSFDI TADVTPDNTH PEKAA DGDF TNKTTSTDAD RYASASQESL GTLVSPYDFT NLDTLLAELG RLGTAQPIPV IVDRLTSRPF REASALQAMD RILTHV VLE YGLVSGYSTA APSKCTHVLQ FFILWGEKLG IPTEDAKTLL ESALEIPAMC EIVQQGRLKE PTFSRHIISK LNPCLES LH ATSRQDFKSL IQAFNAEGIR IASRERETSM AELIETITAR LKPNFNIVCA RQDAQTIQDG VGLLRAEVNK RNAQIAQE A AYFENIITAL STFQPPPQSQ QTFEVLPDLK LRTLVEHLTL VEAQVTTQTV ESLQAYLQSA ATAEHHLTNV PNVHSILSN ISNTLKVIDY VIPKFIINTD TLAPYKQQFS YLGGELASMF SLDWPHAPAE AVEPLPVLTS LRGKIAEALT RQENKNAVDQ ILTDAEGLL KNITDPNGAH FHAQAVSIPV LENYVHNAGV LLKGEKSERF SRLKTAIQNL VSSESFITVT LHSTNLGNLV T NVPKLGEA FTGGPHLLTS PSVRQSLSTL CTTLLRDALD ALEKKDPALL GEGTTLALET LLGYGSVQDY KETVQIISSL VG IQKLVRD QGADKWATAV TRLTDLKSTL ATTAIETATK RKLYRLIQRD LKEAQKHETN RAMEEWKQKV LALDNASPER VAT LLQQAP TAKAREFAEK HFKILLPVPA DAPVQASPTP MEYSASPLPD PKDIDRATSI HGEQAWKKIQ QAFKDFNFAV LRPA DWDAL AAEYQRRGSP LPAAVGPALS GFLETILGTL NDIYMDKLRS FLPDAQPFQA PPFDWLTPYQ DQVSFFLRTI GLPLV RALA DKISVQALRL SHALQSGDLQ QATVGTPLEL PATEYARIAS NMKSVFNDHG LQVRSEVADY VEAQRADAHT PHVPRP KIQ APKTLIPHPD AIVADGLPAF LKTSLLQQEA KLLALQRADF ESLESDMRAA EAQRKASREE TQRKMAHAIT QLLQQAP SA ISGRPLSLQD PVGFLEGIIY DKVLERESYE TGLEGLSWLE QTIKSITVYA PVEEKQRMHV LLDEVKKQRA NTETALEL E AAATHGDDAR LLQRAVDELS PLRVKGGKAA VESWRQKIQT LKSLVQEAEQ AGLLLATIDT VAGQAQETIS PSTLQGLYQ QGQEAMAAIK RFRDSPQLAG LQEKLAELQQ YVKYKKQYLE HFEATQSVVF TAFPLTQEVT IPALHYAGPF DNLERLSRYL HIGQTQPAP GQWLLTLPTF DPTRPACVPA GGHEPPLHRQ VVFSSFLEAQ IRLALSVAGP VPGRGLPGTP QIRRGVEAAA C FLHQWDEI SRLLPEVLDT FFHNAPLPAE SSSNAFLAMC VLTHLVYLAG RAVLGPREPE HAAPDAYPRE VALAPRDLTY LL LAMWPSW ISAILKQPSH AEAAHACLVT LPTMLKAVPY LTLEASAGPL PADMRHFATP EARLFFPARW HHVNVQEKLW LRN DFMSLC HRSPGRARIA VLVWAVTCLD PEVIRQLWST LRPLTADESD TASGLLRVLV EMEFGPPPKT PRREAVAPGA TLPP YPYGL ATGERLVGQA QERSGGAGKM PVSGFEIVLG ALLFRAPLRI FSTASTHRIS DFEGGFQILT PLLDCCPDRE PFASL AAAP RRTVPLGDPC ANIHTPEEIQ IFARQAAWLQ YTFANYQIPS TDNPIPIVVL NANNNLENSY IPRDRKADPL RPFYVV PLK PQGRWPEIMT TATTPCRLPT SPEEAGSQFA RLLQSQVSAT WSDIFSRVPE RLAPNATQKS SQTMSEIHEV AATPPLT IT PNKPTGTPHV SPEADPITER KRGQQPKIVA DNMPSRILPS LPTPKPREPR ITLPHALPVI SPPAHRPSPI PHLPAPQV T EPKGVLQSKR GTLVLRPAAV IDPRKPVSAP ITRYERTALQ PPRTEGEGRR PPDTQPVTLT FRLPPTAPTP ATAALETKT TPPSTPPHAI DISPPQTPPM STSPHARDTS PPAEKRAAPV IRVMAPTQPS GEARVKRVEI EQGLSTRNEA PPLERSNHAV PAVTPRRTV AREIRIPPEI KAGWDTAPDI PLPHSSPESS PPTSPQPIRV DDKSPLPNLV ERYARGFLDT PSVEVMSLEN Q DIAVDPGL LTRRIPSVVP MPHPIMWSPI VPISLQNTDI DTAKITLISF IRRIKQKVAA LSASLAETVD RIKKWYL |
-Macromolecule #4: Triplex capsid protein 1
Macromolecule | Name: Triplex capsid protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-8 (virus) / Strain: GK18 |
Molecular weight | Theoretical: 36.37484 KDa |
Sequence | String: MKVQAENAAR LGRQVLGLLP PPTHRVSLTR GPEFARGVRD LLSKYAASTR PTVGSLHEAL RQAPFRQPTY GDFLVYSQTF SPQEPLGTF LFSFKQEDNG SSMDMLLTPT SLFMLSGMEA AKAPQTHKVA GVWYGSGSGL ADFIPNLSEL MDTGEFHTLL T PVGPMVQS ...String: MKVQAENAAR LGRQVLGLLP PPTHRVSLTR GPEFARGVRD LLSKYAASTR PTVGSLHEAL RQAPFRQPTY GDFLVYSQTF SPQEPLGTF LFSFKQEDNG SSMDMLLTPT SLFMLSGMEA AKAPQTHKVA GVWYGSGSGL ADFIPNLSEL MDTGEFHTLL T PVGPMVQS VHSTFVTKVT SAMKGVGLAR DEPRAHVGLT LPCDMLVDLD ESCPMVQRRE PAGLNVTIYA SLVYLRVNQR PS MALTFFQ SGKGFAEVVA MIKDHFTDVI RTKYIQLRHE LYINRLVFGA VCTLGTVPFD SHPVHQSLNV KGTSLPVLVF ANF EAACGP WTVFL |
-Macromolecule #5: Triplex capsid protein 2
Macromolecule | Name: Triplex capsid protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-8 (virus) / Strain: GK18 |
Molecular weight | Theoretical: 34.278473 KDa |
Sequence | String: MALDKSIVVN LTSRLFADEL AALQSKIGSV LPLGDCHRLQ NIQALGLGCV CSRETSPDYI QIMQYLSKCT LAVLEEVRPD SLRLTRMDP SDNLQIKNVY APFFQWDSNT QLAVLPPLFS RKDSTIVLES NGFDIVFPMV VPQQLGHAIL QQLLVYHIYS K ISAGAPGD ...String: MALDKSIVVN LTSRLFADEL AALQSKIGSV LPLGDCHRLQ NIQALGLGCV CSRETSPDYI QIMQYLSKCT LAVLEEVRPD SLRLTRMDP SDNLQIKNVY APFFQWDSNT QLAVLPPLFS RKDSTIVLES NGFDIVFPMV VPQQLGHAIL QQLLVYHIYS K ISAGAPGD VNMAELDLYT TNVSFMGRTY RLDVDNTDPR TALRVLDDLS MYLCILSALV PRGCLRLLTA LVRHDRHPLT EV FEGVVPD EVTRIDLDQL SVPDDITRMR VMFSYLQSLS SIFNLGPRLH VYAYSAETLA ASCWYSPR |
-Macromolecule #6: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 6 / Number of copies: 5 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-8 (virus) / Strain: GK18 |
Molecular weight | Theoretical: 153.574188 KDa |
Sequence | String: MEATLEQRPF PYLATEANLL TQIKESAADG LFKSFQLLLG KDAREGSVRF EALLGVYTNV VEFVKFLETA LAAACVNTEF KDLRRMIDG KIQFKISMPT IAHGDGRRPN KQRQYIVMKA CNKHHIGAEI ELAAADIELL FAEKETPLDF TEYAGAIKTI T SALQFGMD ...String: MEATLEQRPF PYLATEANLL TQIKESAADG LFKSFQLLLG KDAREGSVRF EALLGVYTNV VEFVKFLETA LAAACVNTEF KDLRRMIDG KIQFKISMPT IAHGDGRRPN KQRQYIVMKA CNKHHIGAEI ELAAADIELL FAEKETPLDF TEYAGAIKTI T SALQFGMD ALERGLVDTV LAVKLRHAPP VFILKTLGDP VYSERGLKKA VKSDMVSMFK AHLIEHSFFL DKAELMTRGK QY VLTMLSD MLAAVCEDTV FKGVSTYTTA SGQQVAGVLE TTDSVMRRLM NLLGQVESAM SGPAAYASYV VRGANLVTAV SYG RAMRNF EQFMARIVDH PNALPSVEGD KAALADGHDE IQRTRIAASL VKIGDKFVAI ESLQRMYNET QFPCPLNRRI QYTY FFPVG LHLPVPRYST SVSVRGVESP AIQSTETWVV NKNNVPLCFG YQNALKSICH PRMHNPTQSA QALNQAFPDP DGGHG YGLR YEQTPNMNLF RTFHQYYMGK NVAFVPDVAQ KALVTTEDLL HPTSHRLLRL EVHPFFDFFV HPCPGARGSY RATHRT MVG NIPQPLAPRE FQESRGAQFD AVTNMTHVID QLTIDVIQET AFDPAYPLFC YVIEAMIHGQ EEKFVMNMPL IALVIQT YW VNSGKLAFVN SYHMVRFICT HMGNGSIPKE AHGHYRKILG ELIALEQALL KLAGHETVGR TPITHLVSAL LDPHLLPP F AYHDVFTDLM QKSSRQPIIK IGDQNYDNPQ NRATFINLRG RMEDLVNNLV NIYQTRVNED HDERHVLDVA PLDENDYNP VLEKLFYYVL MPVCSNGHMC GMGVDYQNVA LTLTYNGPVF ADVVNAQDDI LLHLENGTLK DILQAGDIRP TVDMIRVLCT SFLTCPFVT QAARVITKRD PAQSFATHEY GKDVAQTVLV NGFGAFAVAD RSREAAETMF YPVPFNKLYA DPLVAATLHP L LANYVTRL PNQRNAVVFN VPSNLMAEYE EWHKSPVAAY AASCQATPGA ISAMVSMHQK LSAPSFICQA KHRMHPGFAM TV VRTDEVL AEHILYCSRA STSMFVGLPS VVRREVRSDA VTFEITHEIA SLHTALGYSS VIAPAHVAAI TTDMGVHCQD LFM IFPGDA YQDRQLHDYI KMKAGVQTGP PGNRMDHVGY AAGVPRCENL PGLSHGQLAT CEIIPTPVTS DVAYFQTPSN PRGR AACVV SCDAYSNESA ERLLYDHSIP DPAYECRSTN NPWASQRGSL GDVLYNITFR QTALPGMYSP CRQFFHKEDI MRYNR GLYT LVNEYSARLA GAPATSTTDL QYVVVNGTDV FLDQPCHMLQ EAYPTLAASH RVMLDEYMSN KQTHAPVHMG QYLIEE VAP MKRLLKLGNK VVY |
-Macromolecule #7: Small capsomere-interacting protein
Macromolecule | Name: Small capsomere-interacting protein / type: protein_or_peptide / ID: 7 / Number of copies: 5 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-8 (virus) / Strain: GK18 |
Molecular weight | Theoretical: 18.597824 KDa |
Sequence | String: MSNFKVRDPV IQERLDHDYA HHPLVARMNT LDQGNMSQAE YLVQKRHYLV FLIAHHYYEA YLRRMGGIQR RDHLQTLRDQ KPRERADRV SAASAYDAGT FTVPSRPGPA SGTTPGGQDS LGVSGSSITT LSSGPHSLSP ASDILTTLSS TTETAAPAVA D ARKPPSGK KK |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER Details: The sample was manually blotted and frozen with a homemade plunger.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Max: 79.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 1440 pixel / Digitization - Dimensions - Height: 1440 pixel / Digitization - Sampling interval: 2.5 µm / Number real images: 8007 / Average exposure time: 13.0 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 24271 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 14000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 180.4 / Target criteria: Correlation coefficient |
---|---|
Output model | PDB-6pph: |