[English] 日本語
Yorodumi- EMDB-7472: CryoEM structure of herpes simplex virus 1 capsid with associated... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7472 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of herpes simplex virus 1 capsid with associated tegument protein complexes. | |||||||||||||||||||||
Map data | Icosahedral reconstruction of HSV-1 capsid with associated tegument proteins. | |||||||||||||||||||||
Sample |
| |||||||||||||||||||||
Function / homology | Function and homology information chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / viral process / viral penetration into host nucleus ...chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / 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 / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | |||||||||||||||||||||
Biological species | HHV-1 (Herpes simplex virus type 1) / Human herpesvirus 1 strain KOS | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||||||||
Authors | Dai XH / Zhou ZH | |||||||||||||||||||||
Funding support | United States, 6 items
| |||||||||||||||||||||
Citation | Journal: Science / Year: 2018 Title: Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes. Authors: Xinghong Dai / Z Hong Zhou / Abstract: Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. ...Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. Here we report cryo-electron microscopy structures of the HSV-1 capsid with CATC up to 3.5-angstrom resolution and atomic models of multiple conformers of capsid proteins VP5, VP19c, VP23, and VP26 and tegument proteins pUL17, pUL25, and pUL36. Crowning every capsid vertex are five copies of heteropentameric CATC, each containing a pUL17 monomer supporting the coiled-coil helix bundle of a pUL25 dimer and a pUL36 dimer, thus positioning their flexible domains for potential involvement in nuclear capsid egress and axonal capsid transport. Notwithstanding newly discovered fold conservation between triplex proteins and bacteriophage λ protein gpD and the previously recognized bacteriophage HK97 gp5-like fold in VP5, HSV-1 capsid proteins exhibit extraordinary diversity in forms of domain insertion and conformational polymorphism, not only for interactions with tegument proteins but also for encapsulation of large genomes. | |||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7472.map.gz | 2.8 GB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-7472-v30.xml emd-7472.xml | 25.7 KB 25.7 KB | Display Display | EMDB header |
Images | emd_7472.png | 292.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7472 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7472 | HTTPS FTP |
-Related structure data
Related structure data | 6cgrMC 7473C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_7472.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Icosahedral reconstruction of HSV-1 capsid with associated tegument proteins. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Human herpesvirus 1 strain KOS
Entire | Name: Human herpesvirus 1 strain KOS |
---|---|
Components |
|
-Supramolecule #1: Human herpesvirus 1 strain KOS
Supramolecule | Name: Human herpesvirus 1 strain KOS / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cultured in Vero cells. / NCBI-ID: 10306 / Sci species name: Human herpesvirus 1 strain KOS / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|---|
Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 200 MDa |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 1300.0 Å / T number (triangulation number): 16 |
-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-1 (Herpes simplex virus type 1) |
Molecular weight | Theoretical: 149.229047 KDa |
Sequence | String: MAAPNRDPPG YRYAAAMVPT GSLLSTIEVA SHRRLFDFFS RVRSDANSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPIEQPTHNY MTKIIDRRAL NAAFSLATEA IALLTGEALD GTGIGAHRQL R AIQQLARN ...String: MAAPNRDPPG YRYAAAMVPT GSLLSTIEVA SHRRLFDFFS RVRSDANSLY DVEFDALLGS YCNTLSLVRF LELGLSVACV CTKFPELAY MNEGRVQFEV HQPLIARDGP HPIEQPTHNY MTKIIDRRAL NAAFSLATEA IALLTGEALD GTGIGAHRQL R AIQQLARN VQAVLGAFER GTADQMLHVL LEKAPPLALL LPMQRYLDNG RLATRVARAT LVAELKRSFC ETSFFLGKAG HR REAVEAW LVDLTTATQP SVAVPRLTHA DTRGRPVDGV LVTTAPIKQR LLQSFLKVED TEADVPVTYG EMVLNGANLV TAL VMGKAV RSLDDVGRHL LEMQEEQLDL NRQTLDELES APQTTRVRAD LVSIGEKLVF LEALEKRIYA ATNVPYPLVG AMDL TFVLP LGLFNPVMER FAAHAGDLVP APGHPDPRAF PPRQLFFWGK DRQVLRLSLE HAIGTVCHPS LMNVDAAVGG LNRDP VEAA NPYGAYVAAP AGPAADMQQL FLNAWGQRLA HGRVRWVAEG QMTPEQFMQP DNANLALELH PAFDFFVGVA DVELPG GDV PPAGPGEIQA TWRVVNGNLP LALCPAAFRD ARGLELGVGR HAMAPATIAA VRGAFDDRNY PAVFYLLQAA IHGSEHV FC ALARLVVQCI TSYWNNTRCA AFVNDYSLVS YVVTYLGGDL PEECMAVYRD LVAHVEALAQ LVDDFTLTGP ELGGQAQA E LNHLMRDPAL LPPLVWDCDA LMRRAALDRH RDCRVSAGGH DPVYAAACNV ATADFNRNDG QLLHNTQARA ADAADDRPH RGADWTVHHK IYYYVMVPAF SRGRCCTAGV RFDRVYATLQ NMVVPEIAPG EECPSDPVTD PAHPLHPANL VANTVNAMFH NGRVVVDGP AMLTLQVLAH NMAERTTALL CSAAPDAGAN TASTTNMRIF DGALHAGILL MAPQHLDHTI QNGDYFYPLP V HALFAGAD HVANAPNFPP ALRDLSRQVP LVPPALGANY FSSIRQPVVQ HVRESAAGEN ALTYALMAGY FKISPVALHH QL KTGLHPG FGFTVVRQDR FVTENVLFSE RASEAYFLGQ LQVARHETGG GVNFTLTQPR GNVDLGVGYT AVVATATVRN PVT DMGNLP QNFYLGRGAP PLLDNAAAVY LRNAVVAGNR LGPAQPVPVF GCAQVPRRAG MDHGQDAVCE FIATPVSTDV NYFR RPCNP RGRAAGGVYA GDKEGDVTAL MYDHGQSDPS RAFAATANPW ASQRFSYGDL LYNGAYHLNG ASPVLSPCFK FFTSA DIAA KHRCLERLIV ETGSAVSTAT AASDVQFKRP PGCRELVEDP CGLFQEAYPL TCASDPALLR SARNGEAHAR ETHFAQ YLV YDASPLKGLA L |
-Macromolecule #2: Small capsomere-interacting protein
Macromolecule | Name: Small capsomere-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-1 (Herpes simplex virus type 1) |
Molecular weight | Theoretical: 12.108655 KDa |
Sequence | String: MAVPQFHRPS TVTTDSVRAL GMRGLVLATN NSQFIMDNNH PHPQGTQGAV REFLRGQAAA LTDLGLAHAN NTFTPQPMFA GDAPAAWLR PAFGLRRTYS PFVVREPSTP GTP |
-Macromolecule #3: Triplex capsid protein 1
Macromolecule | Name: Triplex capsid protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-1 (Herpes simplex virus type 1) |
Molecular weight | Theoretical: 50.328281 KDa |
Sequence | String: MKTNPLPATP SVWGGSTVEL PPTTRDTAGQ GLLRRVLRPP ISRRDGPGLP RGSGPRRAAS TLWLLGLDGT DAPPGALTPN DDTEQALDK ILRGTMRGGA ALIGSPRHHL TRQVILTDLC QPNADRAGTL LLALRHPADL PHLAHQRAPP GRQTERLGEA W GQLMEATA ...String: MKTNPLPATP SVWGGSTVEL PPTTRDTAGQ GLLRRVLRPP ISRRDGPGLP RGSGPRRAAS TLWLLGLDGT DAPPGALTPN DDTEQALDK ILRGTMRGGA ALIGSPRHHL TRQVILTDLC QPNADRAGTL LLALRHPADL PHLAHQRAPP GRQTERLGEA W GQLMEATA LGSGRAESGC TRAGLVSFNF LVAACAASYD ARDAADAVRA HVTANYRGTR VGARLDRFSE CLRAMVHTHV FP HEVMRFF GGLVSWVTQD ELASVTAVCA GPQEAAHTGH PGRPRSAVIL PACAFVDLDA ELGLGGPGAA FLYLVFTYRQ RRD QELCCV YVIKSQLPPR GLEPALERLF GRLRITNTIH GTEDMTPPAP NRNPDFPLAG LAANPQTPRC SAGQVTNPQF ADRL YRWQP DLRGRPTART CTYAAFAELG MMPEDSPRCL HRTERFGAVS VPVVILEGVV WRPGEWRACA |
-Macromolecule #4: Triplex capsid protein 2
Macromolecule | Name: Triplex capsid protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-1 (Herpes simplex virus type 1) |
Molecular weight | Theoretical: 34.301617 KDa |
Sequence | String: MLADGFETDI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LTLADVAHES FVSGGVSPDT LGLLLAYRRR FPAVITRVLP TRIVACPLD VGLTHAGTVN LRNTSPVDLC NGDPISLVPP VFEGQATDVR LDSLDLTLRF PVPLPSPLAR EIVARLVARG I RDLNPSPR ...String: MLADGFETDI AIPSGISRPD AAALQRCEGR VVFLPTIRRQ LTLADVAHES FVSGGVSPDT LGLLLAYRRR FPAVITRVLP TRIVACPLD VGLTHAGTVN LRNTSPVDLC NGDPISLVPP VFEGQATDVR LDSLDLTLRF PVPLPSPLAR EIVARLVARG I RDLNPSPR NPGGLPDLNV LYYNGSRLSL LADVQQLGPV NAELRSLVLN MVYSITEGTT IILTLIPRLF ALSAQDGYVN AL LQMQSVT REAAQLIHPE APALMQDGER RLPLYEALVA WLTHAGQLGD TLALAPVVRV CTFDGAAVVR SGDMAPVIRY P |
-Macromolecule #5: Capsid vertex component 1
Macromolecule | Name: Capsid vertex component 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-1 (Herpes simplex virus type 1) |
Molecular weight | Theoretical: 74.699258 KDa |
Sequence | String: MNAHLANEVQ YDLGHGPGRP SSLVHVIISS ECLAAAGIPL AALMRGRPGL GTAANFQVEI QTRAHATGDC TPWCTAFAAY VPADAVGEL LAPVVPAHPG LLPRASSAGG LFVSLPVVCD AQGVYDPYAV AALRLAWGSG ASCARVILFS YDELVPPNTR Y AADSTRIM ...String: MNAHLANEVQ YDLGHGPGRP SSLVHVIISS ECLAAAGIPL AALMRGRPGL GTAANFQVEI QTRAHATGDC TPWCTAFAAY VPADAVGEL LAPVVPAHPG LLPRASSAGG LFVSLPVVCD AQGVYDPYAV AALRLAWGSG ASCARVILFS YDELVPPNTR Y AADSTRIM RVCRHLCRYV ALLGAAAPPA AKEAAAHLSM GLGESASPRP QPLARPHAGA PADPPIVGAS DPPISPEEQL TA PGGDTTA AQDVSIAQEN EEILALVQRA VQDVTRRHPV RARTGRAACG VASGLRQGAL VHQAVSGGAM GAADADAVLA GLE PPGGGR FVAPAPHGPG GEDILNDVLT LTPGTAKPRS LVEWLDRGWE ALAGGDRPDW LWSRRSISVV LRHHYGTKQR FVVV SYENS VAWGGRRARP PLLSSALATA LTEACAAERV VRPHQLSPAG QAELLLRFPA LEVPLRHPRP VLPPFDIAAE VAFTA RIHL ACLRALGQAI RAALQGGPRI SQRLRYDFGP DQRAWLGEVT RRFPILLENL MRAVEGTAPD AFFHTAYALA VLAHLG GRG GRGRRVVPLG DDLPARFADS DGHYVFDYYS TSGDTLRLNN RPIAVAMDGD VSKREQSKCR FMEAVPSTAP RRVCEQY LP GESYAYLCLG FNRRLCGIVV FPGGFAFTIN IAAYLSLSDP VARAAVLRFC RKVSSGNGRS R |
-Macromolecule #6: Capsid vertex component 2
Macromolecule | Name: Capsid vertex component 2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: HHV-1 (Herpes simplex virus type 1) |
Molecular weight | Theoretical: 62.736777 KDa |
Sequence | String: MDPYCPFDAL DVWEHRRFIV ADSRNFITPE FPRDFWMSPV FNLPRETAAE QVVVLQAQRT AAAAALENAA MQAAELPVDI ERRLRPIER NVHEIAGALE ALETAAAAAE EADAARGDEP AGGGDGGAPP GLAVAEMEVQ IVRNDPPLRY DTNLPVDLLH M VYAGRGAT ...String: MDPYCPFDAL DVWEHRRFIV ADSRNFITPE FPRDFWMSPV FNLPRETAAE QVVVLQAQRT AAAAALENAA MQAAELPVDI ERRLRPIER NVHEIAGALE ALETAAAAAE EADAARGDEP AGGGDGGAPP GLAVAEMEVQ IVRNDPPLRY DTNLPVDLLH M VYAGRGAT GSSGVVFGTW YRTIQDRTIT DFPLTTRSAD FRDGRMSKTF MTALVLSLQA CGRLYVGQRH YSAFECAVLC LY LLYRNTH GAADDSDRAP VTFGDLLGRL PRYLACLAAV IGTEGGRPQY RYRDDKLPKT QFAAGGGRYE HGALASHIVI ATL MHHGVL PAAPGDVPRD ASTHVNPDGV AHHDDINRAA AAFLSRGHNL FLWEDQTLLR ATANTITALG VIQRLLANGN VYAD RLNNR LQLGMLIPGA VPSEAIARGA SGSDSGAIKS GDNNLEALCA NYVLPLYRAD PAVELTQLFP GLAALCLDAQ AGRPV GSTR RVVDMSSGAR QAALVRLTAL ELINRTRTNP TPVGEVIHAH DALAIQYEQG LGLLAQQARI GLGSNTKRFS AFNVSS DYD MLYFLCLGFI PQYLSAV |
-Macromolecule #7: Large tegument protein deneddylase
Macromolecule | Name: Large tegument protein deneddylase / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1 |
---|---|
Source (natural) | Organism: HHV-1 (Herpes simplex virus type 1) |
Molecular weight | Theoretical: 333.8095 KDa |
Sequence | String: MIAGTPPHST MERGGDRDIV VTGARNQFAP DLEPGGSVSC MRSSLSFLSL IFDVGPRDVL SAEAIEGCLV EGGEWTRATA GPGPPRMCS IVELPNFLEY PGARGGLRCV FSRVYGEVGF FGEPAAGLLE TQCPAHTFFA GPWALRPLSY TLLTIGPLGM G LFRDGDTA ...String: MIAGTPPHST MERGGDRDIV VTGARNQFAP DLEPGGSVSC MRSSLSFLSL IFDVGPRDVL SAEAIEGCLV EGGEWTRATA GPGPPRMCS IVELPNFLEY PGARGGLRCV FSRVYGEVGF FGEPAAGLLE TQCPAHTFFA GPWALRPLSY TLLTIGPLGM G LFRDGDTA YLFDPHGLPE GTPAFIAKVR AGDMYPYLTY YTRDRPDVRW AGAMVFFVPS GPEPAAPADL TAAALHLYGA SE TYLQDEA FSERRVAITH PLRGEIAGLG EPCVGVGPRE GVGGPGPHPP TAAQSPPPTR ARRDDRASET SRGTAGPSAK PEA KRPNRA PDDVWAVALK GTPPTDPPSA DPPSADPPSA IPPPPPSAPK TPAAEAAEED DDDMRVLEMG VVPVGRHRAR YSAG LPKRR RPTWTPPSSV EDLTSGEKTK RSAPPAKTKK KSTPKGKTPV GAAVPASVPE PVLASAPPDP AGPPVAEAGE DDGPT VPAS SQALEALKTR RSPEPPGADL AQLFEAHPNV AATAVKFTAC SAALAREVAA CSRLTISALR SPYPASPGLL ELCVIF FFE RVLAFLIENG ARTHTQAGVA GPAAALLEFT LNMLPWKTAV GDFLASTRLS LADVAAHLPL VQHVLDENSL IGRLALA KL ILVARDVIRE TDAFYGELAD LELQLRAAPP ANLYTRLGEW LLERSQAHPD TLFAPATPTH PEPLLYRVQA LAKFARGE E IRVEAEDRQM REALDALARG VDAVSQHAGP LGVMPAPAGA APQGAPRPPP LGPEAVQVRL EEVRTQARRA IEGAVKEYF YRGAVYSAKA LQASDNNDRR FHVASAAVVP VVQLLESLPV FDQHTRDIAQ RAAIPAPPPI ATSPTAILLR DLIQRGQTLD APEDLAAWL SVLTDAANQG LIERKPLDEL ARSIRDINDQ QARRSSGLAE LRRFDALDAA LGQQLDSDAA FVPAPGASPY P DDGGLSPE ATRMAEEALR QARAMDAAKL TAELAPDARA RLRERARSLE AMLEGARERA KVARDAREKF LHKLQGVLRP LP DFVGLKA CPAVLATLRA SLPAGWSDLP EAVRGAPPEV TAALRADMWG LLGQYRDALE HPTPDTATAL SGLHPSFVVV LKN LFADAP ETPFLLQFFA DHAPIIAHAV SNAINAGSAA VATADPASTV DAAVRAHRVL VDAVTALGAA ASDPASPLAF LAAM ADSAA GYVKATRLAL DARVAIAQLT TLGSAAADLV VQVRRAANQP EGEHASLIQA ATRATTGARE SLAGHEGRFG GLLHA EGTA GDHSPSGRAL QELGKVIGAT RRRADELEAA TADLREKMAA QRARSSHERW AADVEAVLDR VESGAEFDVV ELRRLQ ALA GTHGYNPRDF RKRAEQALGT NAKAVTLALE TALAFNPYTP ENQRHPMLPP LAAIHRIDWS AAFGAAADTY ADMFRVD TE PLARLLRLAG GLLERAQAND GFIDYHEAVL HLSEDLGGVP ALRQYVPFFQ KGYAEYVDIR DRLDALRADA RRAIGSVA L DLAAAAEEIS AVRNDPAAAA ELVRAGVTLP CPSEDALVAC VAALERVDQS PVKDTAYADY VAFVTRQDLA DTKDAVVRA KQQRAEATER VTAGLREVLA ARERRAQLEA EGLANLKTLL KVVAVPATVA KTLDQARSAE EIADQVEILV DQTEKARELD VQAVAWLEH AQRTFETHPL SAASGDGPGL LTRQGARLQA LFDTRRRVEA LRRSLEEAEA EWDEVWGRFG RVRGGAWKSP E GFRAACEQ LRALQDTTNT VSGLRAQRDY ERLPAKYQGV LGAKSAERAG AVEELGGRVA QHADLSARLR DEVVPRVAWE MN FDTLGGL LAEFDAVAGD LAPWAVEEFR GARELIQRRM GLYSAYAKAT GQTGAGAAAA PAPLLVDLRA LDARARASAP PGQ EADPQM LRRRGEAYLR VSGGPGPLVL REATSTLDRP FAPSFLVPDG TPLQYALCFP AVTDKLGALL MCPEAACIRP PLPT DTLES ASTVTAMYVL TVINRLQLAL SDAQAANFQL FGRFVRHRQA RWGASMDAAA ELYVALVATT LTREFGCRWA QLEWG GDAA APGPPLGPQS STRHRVSFNE NDVLVALVAS SPEHIYTFWR LDLVRQHEYM HLTLPRAFQN AADSMLFVQR LTPHPD ARI RVLPAFSAGG PPTRGLMFGT RLADWRRGKL SETDPLAPWR SVPELGTERG AALGKLSPAQ ALAAVSVLGR MCLPSTA LV ALWTCMFPDD YTEYDSFDAL LTARLESGQT LSPSGGREAS PPAPPNALYR PTGQHVAVPA AATHRTPAAR VTAMDLVL A AVLLGAPVVV ALRNTTAFSR ESELELCLTL FDSRARGPDA ALRDAVSSDI ETWAVRLLHA DLNPIENACL AAQLPRLSA LIAERPLARG PPCLVLVDIS MTPVAVLWEN PDPPGPPDVR FVGSEATEEL PFVAGGEDVL AASATDEDPF LARAILGRPF DASLLSGEL FPGHPVYQRA PDDQSPSVPN PTPGPVDLVG AEGSLGPGSL APTLFTDATP GEPVPPRMWA WIHGLEELAS D DSGGPAPL LAPDPLSPTA DQSVPTSQCA PRPPGPAVTA REARPGVPAE STRPAPVGPR DDFRRLPSPQ SSPAPPDATA PR PPASSRA SAASSSGSRA RRHRRARSLA RATQASATTQ GWRPPALPDT VAPVTDFARP PAPPKPPEPA PHALVSGVPL PLG PQAAGQ ASPALPIDPV PPPVATGTVL PGGENRRPPL TSGPAPTPPR VPVGGPQRRL TRPAVASLSE SRESLPSPWD PADP TAPVL GRNPAEPTSS SPAGPSPPPP AVQPVAPPPT SGPPPTYLTL EGGVAPGGPV SRRPTTRQPV ATPTTSARPR GHLTV SRLS APQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QPQPQPQPQP QNGHVA PGE YPAVRFRAPQ NRPSVPASAS STNPRTGSSL SGVSSWASSL ALHIDATPPP VSLLQTLYVS DDEDSDATSL FLSDSEA EA LDPLPGEPHS PITNEPFSAL SADDSQEVTR LQFGPPPVSA NAVLSRRYVQ RTGRSALAVL IRACYRLQQQ LQRTRRAL L HHSDAVLTSL HHVRMLLG |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Formula: PBS / Component - Name: phosphate buffered saline |
---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER |
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 | Min: 79.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 2.5 µm / Digitization - Frames/image: 1-26 / Number grids imaged: 3 / Number real images: 7356 / 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 | C2 aperture diameter: 70.0 µm / Calibrated magnification: 24271 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / 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 |
---|---|
Output model | PDB-6cgr: |