+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35175 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Portal-tail complex structure of the Cyanophage P-SCSP1u | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Whole virus / Capsid / cyanophage / T7-like virus / VIRUS | |||||||||
Biological species | Prochlorococcus phage P-SCSP1u (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.81 Å | |||||||||
Authors | Liu H / Dang S | |||||||||
Funding support | Hong Kong, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses. Authors: Cai L / Liu H / Zhang W / Xiao S / Zeng Q / Dang S | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_35175.map.gz | 32.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-35175-v30.xml emd-35175.xml | 20 KB 20 KB | Display Display | EMDB header |
Images | emd_35175.png | 43.8 KB | ||
Masks | emd_35175_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-35175.cif.gz | 7.3 KB | ||
Others | emd_35175_half_map_1.map.gz emd_35175_half_map_2.map.gz | 48 MB 48 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35175 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35175 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_35175.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.7 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_35175_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_35175_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_35175_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Prochlorococcus phage P-SCSP1u
Entire | Name: Prochlorococcus phage P-SCSP1u (virus) |
---|---|
Components |
|
-Supramolecule #1: Prochlorococcus phage P-SCSP1u
Supramolecule | Name: Prochlorococcus phage P-SCSP1u / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1, #4 / NCBI-ID: 2914505 / Sci species name: Prochlorococcus phage P-SCSP1u / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|---|
Host (natural) | Organism: Prochlorococcus (bacteria) |
-Supramolecule #2: The portal-tail complex of cyanophage P-SCSP1u
Supramolecule | Name: The portal-tail complex of cyanophage P-SCSP1u / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#4, #1 |
---|---|
Source (natural) | Organism: Prochlorococcus phage P-SCSP1u (virus) |
-Macromolecule #1: Portal protein(gp 16) of the cyanophage P-SCSP1u
Macromolecule | Name: Portal protein(gp 16) of the cyanophage P-SCSP1u / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Prochlorococcus phage P-SCSP1u (virus) |
Molecular weight | Theoretical: 62.460434 KDa |
Sequence | String: MKTRLTNNVD RQSALYGSSG GTAAQRYEQL RVDRNSPLKR ARDCSKVTIP GLIEDENYGD AGRLDTPYQS SGARGVGHMT SKLAVTLFP TNEHFFKLEI DSLAILASDQ NPEMITEFDS ALVKVEQAVM RMFETIGGRA AMHEALKHLL VGGNVLLYVS D EGIKVIHL ...String: MKTRLTNNVD RQSALYGSSG GTAAQRYEQL RVDRNSPLKR ARDCSKVTIP GLIEDENYGD AGRLDTPYQS SGARGVGHMT SKLAVTLFP TNEHFFKLEI DSLAILASDQ NPEMITEFDS ALVKVEQAVM RMFETIGGRA AMHEALKHLL VGGNVLLYVS D EGIKVIHL DSYVLCRDPM GNVTEIVVEE EIFKDALPEE YLDEEDDDDD DMGKKMVKIY TCIKFMDDQC HWYQEIKGKE VP GTHGKCA ADVAPWIALR QDRVDSEMYG RSYVEQYYGD LLALENLYKA ILEASASLSK VLFLCNPNGT TRPRTLSQAS NGS IVQGNA ADVTVLQAAG KSQDLQIANQ TIERIENRLA FAFMLNTAIQ RPGERVTAEE IRYMAQELDA GISGLYSILS RELQ LPLVR RLIHILRRKR KLPDFPRSEV TGEPLIKEKA VTGIEAIGRG DDRNKLIDFI TTANQALGPQ AMTQFLNVEE ALRRL AASG SIDTTNLVKT KAQLQQEAAA QAEAEQQAQQ QQLLETGIKS PAMAQAVKNF QGADPERAAQ ALSAITSETG GIDADQ LTE AV |
-Macromolecule #2: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
Macromolecule | Name: Nozzle protein(gp 23) of the cyanophage P-SCSP1u / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Prochlorococcus phage P-SCSP1u (virus) |
Molecular weight | Theoretical: 87.444898 KDa |
Sequence | String: MPLISSSIPN LINGVSQQPA ALRLASQAEE VINCMPSPVE GLKKRPPMQH IKKLFAGSAG TGRPFTHIVD RDGVIRYLIF IQDNAIKVF DLDGNAQTVS TPNGTSYLNI TGEPSSTFRV ASIADFTFIV NREKTVAMDT TNKSYNWGTK SMVFIKSADF S TTYRVKLN ...String: MPLISSSIPN LINGVSQQPA ALRLASQAEE VINCMPSPVE GLKKRPPMQH IKKLFAGSAG TGRPFTHIVD RDGVIRYLIF IQDNAIKVF DLDGNAQTVS TPNGTSYLNI TGEPSSTFRV ASIADFTFIV NREKTVAMDT TNKSYNWGTK SMVFIKSADF S TTYRVKLN GTEKSVTTGN SSGSAPDTVT IASDLATQLN TISGFTVTST DYIIRITKDD GGDYTLESSD TKTADATSAI KG TVDSITD LPTIAEHNFT VRIQGSATTA FDDYFVKFEA TAGSGFGPGV WRETVAPNID HLLDKSTMPH TLVRNANGTF TFA QFNYTG RVAGDTTTAP NPTFVGSKIK NINLFRNRLV FLADENVILS AADSFERFFP ETVQTLLDSD PIDISSGGTS VNFL NSSLA FANTLLLFSL HGQFRLDTGS TSVGTALTPK TATITAITTF DIVDAIDPIG VGRTVYFGIP KGDFSGLREY FLPDA SGPI PLSEEVTSSV PRFVPGNLIS MSPSVSEEVI TMISKDQPRR VYIYKFFFDD DQKLQSSWSY WEVAANKTLL GGNVLD SDL YTCVEYSDGV YLEKTQLRPE TVDSGTEFEI LLDRKTTEAA CSTSLINSGA LGVQTVITLP YPMSGTGTMA VVGRFAS NN TIAHGQVIKA TAETLTGGAS GNGTMTVPGD LSSAKFFVGE IYNMTYEFST PYLKETPPGG GLAVLANPRL QLRTWSIV F DETSNFSMKI TPGQRDELTY PFNGYKIGSG QFPIGTPSLA TGRFRVPVMA QNIETKIVLF SDSPLPCRVQ SAEWEGWYQ ERARRL |
-Macromolecule #3: Adaptor protein(gp22) of the cyanophage P-SCSP1u
Macromolecule | Name: Adaptor protein(gp22) of the cyanophage P-SCSP1u / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Prochlorococcus phage P-SCSP1u (virus) |
Molecular weight | Theoretical: 22.81148 KDa |
Sequence | String: MAARTSFLDA VNRVLQMLGE APVNSLQGQF GLAKQAEVAL NDVSRTIQTE GWSFNTDLEK KLERNSSNEI ELSSNVSRVV VDNLEYPDI DVVQRGDKLY DRKNNRYTFD EDLIVDMTTI LEWDLLPEHA RQYITIKAGR QLQEAIIGSA ELTKLNLTQE V EARSAFLE ...String: MAARTSFLDA VNRVLQMLGE APVNSLQGQF GLAKQAEVAL NDVSRTIQTE GWSFNTDLEK KLERNSSNEI ELSSNVSRVV VDNLEYPDI DVVQRGDKLY DRKNNRYTFD EDLIVDMTTI LEWDLLPEHA RQYITIKAGR QLQEAIIGSA ELTKLNLTQE V EARSAFLE EETTKSEHSM LRGHLNRTSP VNTYIPSRTL ER |
-Macromolecule #4: Fiber protein(gp 28) of the cyanophage P-SCSP1u
Macromolecule | Name: Fiber protein(gp 28) of the cyanophage P-SCSP1u / type: protein_or_peptide / ID: 4 / Number of copies: 18 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Prochlorococcus phage P-SCSP1u (virus) |
Molecular weight | Theoretical: 113.856602 KDa |
Sequence | String: MAFAQRIITS NSAGDQEFTF TFDYIKEEHI KVFVNFVEKA QGTGSNEFQV ITNTTPKKIS LNTGLSADNT RVEIRRVSSL STPLVDFAD GSTLTAADLD TAEKQSLFID QELDDALKQG ISIDTSTGVP TLNSQRLSNV SDPVNAQDAV TKAYLERSGS I TSTQILNG ...String: MAFAQRIITS NSAGDQEFTF TFDYIKEEHI KVFVNFVEKA QGTGSNEFQV ITNTTPKKIS LNTGLSADNT RVEIRRVSSL STPLVDFAD GSTLTAADLD TAEKQSLFID QELDDALKQG ISIDTSTGVP TLNSQRLSNV SDPVNAQDAV TKAYLERSGS I TSTQILNG TIVDADINAS AAIAKSKLAA LNIVNADVNA SAAIAGSKLA DASIAYTKIQ NVSATNRILG RDSSGAGVIE EI TPANLRT MINVEDGATA DQSAAEIRTL VESASDSNVF TDADHTKLNA IEASADVTDA TNVDAAGAVM NSDTSTAAMQ FVI DEDTFG SNLDTKVPTQ QSVKAYITAT SQPLDSELSQ LAGMQSGTAS KLADSTALTA DIADLNQLDG MAKETSITNS NTKF PTSAA VVNFVANQIA PVGGLEVIAD EDSFPATQPV SGVVISISNA DGLVINNAGE ASNARTVGSG SDNVTIKNFP ASLRN QTLA PNLGLLVSST GASQEYNYHK LLAKETDVLQ LSDDINDFNN RYRVENTLPA ANDSSNHDGD LVYAKEEKKI YVYSGD YNG TPVGSFGEVQ SIGNFFISTL SPAFNGSLQD FTITNAPSNA QQIILSINGV IQKPNSGTST PSEGFALSGS TIKLAAA PP SGADYFAIVL GSTVNIGTPS NNTVTSSILQ NGSVIEAKLG SGAVTRTKLN LVSTSSAPGL EVKGDGSSDG YLQLNCSQ N SHGIKLKSPP HSAGQSYTLT FPSNIVSGQF LTTDANGNLS WAAVVTDLVN DTSPQLGGNL DCNDKNILLN DSSGSANNR IRLGASQDFA LFHNGTINII EAVSGDLHLR LNGSEEGIIV KQNGAVELYY DNSKKFHTSS VGATVTGNLF LSGGYINLND NYSYGMGSG NRAQLYHSGN HQYLLNTVGN MYFQPKSGEN GIVIIPDDAV ELYHNNVKRL ETTSGGVTVS GSVTATGHLF V GANTHYLY FTSTAGYSPR IGNADGGTGV NMTFHTNNTM RMMLQNDGHL RPASNNTYDL GTSSDRWRNV YTNDLNLSNE GG ANDVDGT WGSYTIQEGA EDLFLINKRT SKKYKFNLTE VS |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 4.5 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 86469 |
-Atomic model buiding 1
Initial model | Details: the initial model of our models was predicted by the alpha fold according to the protein sequence. |
---|---|
Output model | PDB-8i4m: |