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- EMDB-39996: Cryo-EM structure of Mycobacteriophage Douge baseplate (gp13, gp1... -

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Basic information

Entry
Database: EMDB / ID: EMD-39996
TitleCryo-EM structure of Mycobacteriophage Douge baseplate (gp13, gp17, gp23, gp16, gp18 and gp20)
Map data
Sample
  • Virus: Mycolicibacterium smegmatis MC2 155 (bacteria)
    • Protein or peptide: Tail tube protein (gp13)
    • Protein or peptide: Tape measure protein (gp16)
    • Protein or peptide: Baseplate upper protein (gp23)
    • Protein or peptide: Distal tail protein (gp17)
    • Protein or peptide: Baseplate hub protein (gp18)
    • Protein or peptide: Central fiber protein (gp20)
KeywordsMycobacteriophage / phage structure / Icosahedral / cryo-EM / protein assembly / VIRUS / VIRAL PROTEIN
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsMaharana J / Wang CH / Tsai LA / Lowary TL / Ho MC
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Mycobacteriophage cryo-EM studies reveal the siphophage architecture at the amino acid level and its host interaction for viral genome ejection
Authors: Maharana J / Wang CH / Tsai LA / Lowary TL / Ho MC
History
DepositionMay 2, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39996.png

Downloads & links

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Map

FileDownload / File: emd_39996.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 543.232 Å		1.06 Å/pix.
x 512 pix.
= 543.232 Å		1.06 Å/pix.
x 512 pix.
= 543.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.9509176 - 3.5557456
Average (Standard dev.)0.0008186864 (±0.09240069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 543.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39996_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_39996_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 : Mycolicibacterium smegmatis MC2 155

EntireName: Mycolicibacterium smegmatis MC2 155 (bacteria)
Components
  • Virus: Mycolicibacterium smegmatis MC2 155 (bacteria)
    • Protein or peptide: Tail tube protein (gp13)
    • Protein or peptide: Tape measure protein (gp16)
    • Protein or peptide: Baseplate upper protein (gp23)
    • Protein or peptide: Distal tail protein (gp17)
    • Protein or peptide: Baseplate hub protein (gp18)
    • Protein or peptide: Central fiber protein (gp20)

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Supramolecule #1: Mycolicibacterium smegmatis MC2 155

SupramoleculeName: Mycolicibacterium smegmatis MC2 155 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 246196 / Sci species name: Mycolicibacterium smegmatis MC2 155 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Tail tube protein (gp13)

MacromoleculeName: Tail tube protein (gp13) / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 32.112025 KDa
SequenceString: MTDFYTIKDA QADLAIAPLN LTVLLAPYST TPATTLESPT DGSLAIPPGY KSVGHFEKQA GLTLGNEFDS KDIEAYGEPE PIRTIINKR TTTFDFAMYQ NQRNVLELIW TQDFSNIQPS EFGGIVLEAP KVPKNIYYRA ILVGMDDRND RPIWLYWLMP K VKLDKLDN ...String:
MTDFYTIKDA QADLAIAPLN LTVLLAPYST TPATTLESPT DGSLAIPPGY KSVGHFEKQA GLTLGNEFDS KDIEAYGEPE PIRTIINKR TTTFDFAMYQ NQRNVLELIW TQDFSNIQPS EFGGIVLEAP KVPKNIYYRA ILVGMDDRND RPIWLYWLMP K VKLDKLDN QTLNDDNVIE YKPTLKAFRD DVVGYSVAQG FAGPGWRDLV ATAGFGEALT ALTITPGSPT VTVATGASHT AQ LLVEGDN GINYTPDVVF TSSAPDKASV SAAGLVTGVA AGSATITATK GALTATATVT VTA

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Macromolecule #2: Tape measure protein (gp16)

MacromoleculeName: Tape measure protein (gp16) / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 176.109203 KDa
SequenceString: MAEFVAAQAS VLIVPTLGKG ANSFHQKLKE QLQTVRESVD VKIKADTAAM VAEVQATKEM LERDPINIRV ETDNNGIKEL VKSVTEVRH KYEDLKGDFR RGLTLNLKVV GLSALSQLGP MLASLNTSIV QLSQSSLLLP GIMSGVASSV GAAVVGSRGL T DAFKAQSD ...String:
MAEFVAAQAS VLIVPTLGKG ANSFHQKLKE QLQTVRESVD VKIKADTAAM VAEVQATKEM LERDPINIRV ETDNNGIKEL VKSVTEVRH KYEDLKGDFR RGLTLNLKVV GLSALSQLGP MLASLNTSIV QLSQSSLLLP GIMSGVASSV GAAVVGSRGL T DAFKAQSD ASKNVAEAGK QQRDANRAIR DSTRDLNNAI RDAKRNIEDL NAQLRDAPLD EAEAMLNLQE AQYEASQKWG KT AFQQQRD ALGLAKAESQ LAETRRRNVR LGQDVAEANA KGVNGNDAVV AAQERLTKAL EDLAMQTGPI RALNDAMAKL SPN ARDFVD QVSSLKGAWD GLRSTVQDRL FDGLGASVQT LAGQDLPILE RGLAGIAGAI NGNLKTAMSQ LATDENKGFL GRIF GNTEE AQNRFSTALK PLLDSFMQLS AVGSDYLPRL SNAFGDVLNR FDGFIERADA DGSLDKWINN GLDAMTQLGN SLINV GSIM NTISEAFTGT GGKGLLELLE TGTKRLADFL KGAEGQQKLK QFFLDARTEL NNWKPLLSQL PGLIKNVATA GQQWAN LVL PFLTSAASLL KEHPGLVTAI FTAYMTWRTI SPIIGTINLL LSSETGMVGA AKKAGRAVGK GEGLTGKLGV LAGMVGQ GG VVMTGLSLVA GFLINEWVTA QNEAAEAVSY HASMISRLKG EMDGLTGSLT TQGLQGKLDA ARQWTDIHQT DGKPKDLV A AANSFGVDLP TFMGALTPTN QAARNAVTGK ARQTVLDDLN KQGLETVLGK DALNALNLYN QNAAPDKKIT NDVLADIAT GVNPESKKLF EDAKKSNLIH FNESDLLYGY NKPWGFIPGT DPSGKGLSPV ARDAANVSGF VLNDTGNALQ VGSDIRSTNE ALYGKAVLT PAGQQMFGQF GSPQASFENG SKDAAVRVDT TLQNLPPQFV KDVESNGGHF EELPDGVIIH MRKDRAAQYV T AGSYAGGG FLSGPGTGRS DSMLARVSNG EFITRAASVA KYGRGLFDAL NSGTLDPSML PRFDSGGLVD IFLPGGGTAA PP PTGSANP VDLARGLPRG PAVQSAPANR FDPSPLPTDL LPKPVIPMPD LANPGLYDPA TGKYGAAPAS AVQQPLKPGV DGD KGETSG PNVPPTDPRS PGYKQPNHGL GGSPGPGNGT PHLTGPGGTP VSPGAASALP SNGGIPGLTP SATDPLGLSG LPKE IQPVT ILEQIGEILL SAVLGFFGLD PTYFNIGKRI FTGIKGDKPN EANPGVQSIL DGYKNPLADG QNPYVGTSIY DASFD PASQ RASNMAELMR GKPYTWGGSS LDGTDCSGLV MYVVDAYEGK EFSGRTGGTG GFASSLPAKG GVIISDPSQA PPGTLR VGW NASHTAGTLP DGRNFESSTF GKPIAVGAGA SGYNDPQFTN WAYFPAPGYA NGGFLSGAGT GRSDSMLARV SNGEFIT RA SSVAKYGRSL FDALNAGTVD PGMLPGFADG TPPIPGLPVP QPQTPQQAGP LPDPNGQDAQ AAQQVTDTAA SALDGVAG A MNGVNMGSSG AIPGADAPDG AQQGKDPRSI LGAAPTNTDH NNPALSKGIQ GAFSTVGSLA SMAASAAMSA GTMGAGAAG ASGAAGSGIQ AGAQIAGQVA TGALNILSSL LVGSAPGSTG TTQSAYGAPV LPQGPPQSSG GGPAVVNNYG DIHTANYDEF YKGQQRREA QQQAPILPVR

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Macromolecule #3: Baseplate upper protein (gp23)

MacromoleculeName: Baseplate upper protein (gp23) / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 33.673859 KDa
SequenceString: MLSTGPIMET LTLTVGSAFE IPGWKLRGEY PAGTTSHLVF TDAAGGTLGE FEGTVSAKEI HYLQAPDDVK NIPHGANFQL FVTYPSMQP QCLYFGTAIR KEPRYPLSTV VSPEDSAVQY KANFVGQYIG PMWKPMGNGW GSLGIHTHAL ISEAPSMGPN Y SLFSSAAA ...String:
MLSTGPIMET LTLTVGSAFE IPGWKLRGEY PAGTTSHLVF TDAAGGTLGE FEGTVSAKEI HYLQAPDDVK NIPHGANFQL FVTYPSMQP QCLYFGTAIR KEPRYPLSTV VSPEDSAVQY KANFVGQYIG PMWKPMGNGW GSLGIHTHAL ISEAPSMGPN Y SLFSSAAA RWLWSMNMDS VTIVVRVLNV GAGKFNVIVC ADYQMQTYLG IQFETGISNN KVHVITGDGP LNWGYQGDAV NN TTANGDV YTIKYNDLLD TISCYKGTSL TPLIEASGLD VPHGEGFRYT GLAWNTALLS PGVEPTAWEA KDGV

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Macromolecule #4: Distal tail protein (gp17)

MacromoleculeName: Distal tail protein (gp17) / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 33.771953 KDa
SequenceString: MTDFLKIELI GRDGSHWVLS GPGMGQQGVT LNPNLQQFYD APVKTLYVPG PFGEEYAGKR VQRREIVFSV QAYDEDPDTW STVDSLWRW AWDYDEESEL RVSTSDGTRF LKVRLMEEPK PYYEKDPHIT ADNPIVMTVT ATFPYWQDEP EELIWTTLST E DMTRFPVR ...String:
MTDFLKIELI GRDGSHWVLS GPGMGQQGVT LNPNLQQFYD APVKTLYVPG PFGEEYAGKR VQRREIVFSV QAYDEDPDTW STVDSLWRW AWDYDEESEL RVSTSDGTRF LKVRLMEEPK PYYEKDPHIT ADNPIVMTVT ATFPYWQDEP EELIWTTLST E DMTRFPVR NDGDVPVWLK WTLTAPGLWI LPDFSWGNDM YSRGREDLGR TVAMPELVAG EHVSVDSDPR VQTLIAVNGM PT QNRWKGN DLLYPLMPGK GAEIPVQLKN APEGGACKLT RPRWYSRPWS RPGVRLNG

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Macromolecule #5: Baseplate hub protein (gp18)

MacromoleculeName: Baseplate hub protein (gp18) / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 65.02632 KDa
SequenceString: MANNWTDILA ASDGDEWAAF KTIEAQADEV RAGHQALRRA KPLIRLWMNN PDGSEGLVYV GRVDYDDTIR GSFPFKNNTP SQGVLELRD DNYLAVWLKQ LPNNPELKKN VVITVDFYGG KKRWSGLLDK WTIKSKEHVK YLEVTFNDDL TMLQYLLCPP N PALPIPVL ...String:
MANNWTDILA ASDGDEWAAF KTIEAQADEV RAGHQALRRA KPLIRLWMNN PDGSEGLVYV GRVDYDDTIR GSFPFKNNTP SQGVLELRD DNYLAVWLKQ LPNNPELKKN VVITVDFYGG KKRWSGLLDK WTIKSKEHVK YLEVTFNDDL TMLQYLLCPP N PALPIPVL QFPRIFGIAG PAKWAISTLI FINLFRVQGN LWTLPDDPFN LESWDDILDW SDWQCFVKSN SFLLDDSSVW TF LSSRMNP VDSIIADALD DAQLTITYRR VLTDDGETAE GFPGAHGIKN GALVFEIVDN SNATALEGTF FSGTIVDGFA RSV LLYGGG FVEDTLSVVS DDQTLQPDEY YQSGWLATMA KMPWLVVRDN EWTPIESSDL SWGPAKNVSV IVGGDNPAAD AIAK LIIET TGNLLGYFLL GGFSSAGTIA ADIIMPFLVG TIAAWLQWKN TGRATELGWV HYWELYQQGA ETNSWSLAAL AALRG GFLV GRSETVHLMA LHDSWIIPGL HIDIGQRMGS TVNSKGVENI VWVNQLEEMT AAWDNSAGQT MPLSWVLKAG KSDRAM SIG ERVARLAKKM SEALNNVGVH IVQS

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Macromolecule #6: Central fiber protein (gp20)

MacromoleculeName: Central fiber protein (gp20) / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 92.774414 KDa
SequenceString: MTMPNGSGGL DPGAWLSHWV NQADLSSLAG RTEDEVRAYF ENLVQADSGW GDASNTFFNL ILGGFQNLSE FVTLIVQAVT GAPGGLTDL QAFLTERWGD LADAFQAVAN LIDAIAGEVG SSLADAIAKL ATFLTELSPL NAGMLFGLIG TNHLPLLSVS H IANINPEL ...String:
MTMPNGSGGL DPGAWLSHWV NQADLSSLAG RTEDEVRAYF ENLVQADSGW GDASNTFFNL ILGGFQNLSE FVTLIVQAVT GAPGGLTDL QAFLTERWGD LADAFQAVAN LIDAIAGEVG SSLADAIAKL ATFLTELSPL NAGMLFGLIG TNHLPLLSVS H IANINPEL LVNAGFDSDV SVVDNPYWDW DGTVGRTAPL GAVKVVADGT IKDLLSGPDA IPVVEGQKLN VSAWLKYSGL VA GAGAGSI RLSGTAYSAD GEVVAYPDFG GIPDGASGTS DWTQVTGQYV VPAGVTQFRL RLSVRENATG GTVWFDDCSV KKA GLLPQG LVDGLVQALS DLLTWLESLV DNVLSALGLD PIGTIVDKIL DLADEFGDWL GATEDTAANL SNLLTKLLSD PASV IGPLA QSMITGLTGA LGNLNTAINQ IGDVLVGTVV TPINSAISNV IDWFNSLLNF QDTTTSNQIN QQNFQIATLA SGIKK QQWE CRYSTAFVTF PEMFCDWGFA LGGTTGAQST GTAHTHTLNT DGLAALQIQI LPAGYAIGGY IGISDTTIVD TIAMKM YKE TSSAINNVYL EVFREDSTGA LTSVGSVDVS GQLTTASDYV EATLPAGVIV NAGERYVVRM RNATTVGNRV GVSVMKE LV GGRELSIRTE TATDSNKTFY TPSEVLTAQG VSVIMPWAMM AAKNLATTDQ SFSDDFNRSA MGGLWFLKSD TGTNQVGV S GGRAAFSGLT DGNQNALYIR PTAGDKQWVE ATLYETGIAA SGAREGLLMH ANRDLSQVVY LGVNLNTAKI YTGPWNSLT ERASVSTTGN DVLWQMYFDP ATAAYTVLKN GQASGLTWTD SGSVVAHGPN YRFGGLRISR ATFFNAGRID NWTLKDWA

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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: 7.5
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.43 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78927
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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