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- EMDB-68038: Cryo-EM structure of bacteriophage phi92 baseplate -

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Basic information

Entry
Database: EMDB / ID: EMD-68038
TitleCryo-EM structure of bacteriophage phi92 baseplate
Map data
Sample
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp146
    • Protein or peptide: Phi92_gp136
    • Protein or peptide: Phi92_gp139
    • Protein or peptide: Phi92_gp137
    • Protein or peptide: Phi92_gp135
    • Protein or peptide: Phi92_gp134
    • Protein or peptide: Phi92_gp145
    • Protein or peptide: Phi92_gp138
Keywordsbaseplate / VIRAL PROTEIN
Function / homology
Function and homology information


: / : / Gp138, beta helical trimerization domain / Baseplate hub gp41 / : / Dit-like phage tail protein / : / Cyanophage baseplate Pam3 plug gp18 / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain ...: / : / Gp138, beta helical trimerization domain / Baseplate hub gp41 / : / Dit-like phage tail protein / : / Cyanophage baseplate Pam3 plug gp18 / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
Phi92_gp134 / Phi92_gp139 / Phi92_gp137 / Phi92_gp136 / Phi92_gp146 / Phi92_gp138 / Phi92_gp135 / Phi92_gp145
Similarity search - Component
Biological speciesEscherichia phage phi92 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen Y / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: Cryo-EM structure of bacteriophage phi92 baseplate
Authors: Chen Y / Liu HR
History
DepositionDec 31, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68038.png

Downloads & links

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Map

FileDownload / File: emd_68038.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.5073538 - 1.0214587
Average (Standard dev.)0.0021362936 (±0.056908563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68038_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_68038_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 : Escherichia phage phi92

EntireName: Escherichia phage phi92 (virus)
Components
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp146
    • Protein or peptide: Phi92_gp136
    • Protein or peptide: Phi92_gp139
    • Protein or peptide: Phi92_gp137
    • Protein or peptide: Phi92_gp135
    • Protein or peptide: Phi92_gp134
    • Protein or peptide: Phi92_gp145
    • Protein or peptide: Phi92_gp138

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Supramolecule #1: Escherichia phage phi92

SupramoleculeName: Escherichia phage phi92 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage phi92 (virus)

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Macromolecule #1: Phi92_gp146

MacromoleculeName: Phi92_gp146 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 23.294406 KDa
SequenceString: MAVSVDHVTT WDSINEDVKD LLIEDFKSSP NIVKLLYIIS SEKQKIDQAM IYLAKHRLIS TATGKYLDLI GEEMGMERNG ATDEEYRTI LKIRAYRVAS SGTRDDIIDM FARFTGTEKE TINTYVGLNK TFDVFFYNLC LQSDQAVAQL LNVFPILSSY R LGAKAGAA ...String:
MAVSVDHVTT WDSINEDVKD LLIEDFKSSP NIVKLLYIIS SEKQKIDQAM IYLAKHRLIS TATGKYLDLI GEEMGMERNG ATDEEYRTI LKIRAYRVAS SGTRDDIIDM FARFTGTEKE TINTYVGLNK TFDVFFYNLC LQSDQAVAQL LNVFPILSSY R LGAKAGAA FGFTSYYATT PPHGIGGLGS LYTEAEGDDT GRMTMLIAQI E

UniProtKB: Phi92_gp146

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Macromolecule #2: Phi92_gp136

MacromoleculeName: Phi92_gp136 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 16.013732 KDa
SequenceString:
MAISSYSKIS RSTSNSGYNA VFIDRTLGYY SWYLPTEQYP DQTYTVTLDG VDYDIRLRWN TRDQSWQMQL GLSGDNPSVT FKVTNGLDL LEPYKYIESV PDGQLYLVDT VKINGRPNYY DTGVDKRFAL VYIDALPYQA

UniProtKB: Phi92_gp136

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Macromolecule #3: Phi92_gp139

MacromoleculeName: Phi92_gp139 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 23.678242 KDa
SequenceString: MGIPFDLKLD GSNDLVMVDG DLTLTTTKSE IAAQTLGITL RTFRGEWFLN SNFGVPYLQE IIGVAKKKEI VDRIFLSTIA SNVYIDNIN SYTSSYDRDD RYYSMNVTVT VGEQVVSALF STQPSEEYIY PEAGDDNAAI TCEAFEIVES ANRLYRFINI V GLPRDTYS ...String:
MGIPFDLKLD GSNDLVMVDG DLTLTTTKSE IAAQTLGITL RTFRGEWFLN SNFGVPYLQE IIGVAKKKEI VDRIFLSTIA SNVYIDNIN SYTSSYDRDD RYYSMNVTVT VGEQVVSALF STQPSEEYIY PEAGDDNAAI TCEAFEIVES ANRLYRFINI V GLPRDTYS TWWNEWSNEA LIEKYLVNEA NKGLATNYNY AITATMGATN NNG

UniProtKB: Phi92_gp139

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Macromolecule #4: Phi92_gp137

MacromoleculeName: Phi92_gp137 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 37.071875 KDa
SequenceString: MAEKRDYTKA PAPNLNRAYK LLIGTATNTK EKRTKNSSFK STVDLDTKLG DAKKSTPNLY VITEHQISFT IRKDNNKDPN QAEITIYNL SDDTVNYINK GIRNNLAVAL AVGYEGQELI MIFKGTVQWV SDTFNNTDRR TVLHCLDGGI NISEARTSRS Y PKGTKVSK ...String:
MAEKRDYTKA PAPNLNRAYK LLIGTATNTK EKRTKNSSFK STVDLDTKLG DAKKSTPNLY VITEHQISFT IRKDNNKDPN QAEITIYNL SDDTVNYINK GIRNNLAVAL AVGYEGQELI MIFKGTVQWV SDTFNNTDRR TVLHCLDGGI NISEARTSRS Y PKGTKVSK VVKDLVKDLG TTEGNIHVDT EKTLSSATAM CGNTSHYLES ICKGIDHNVS IQDGSVYVTP RSQMSSARCA YI SAETGLI GSPEPFHNDI KPTQKVTKSS KKAKKPTDGV KFRCEMNGAI LPEKTVWLKS HNYDGGFKVV SVVHTGDREG KDW TTEVES VSVSAIIKKG

UniProtKB: Phi92_gp137

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Macromolecule #5: Phi92_gp135

MacromoleculeName: Phi92_gp135 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 26.124039 KDa
SequenceString: MAANTPEQHV QAVYKAEQEI NSTKNTNNSA STVKGENGFC ILASIYNSAS DQYIQNYQAI VFDAVPNIGV KRQADVTSYP VENGANVSD HVQVKNNTFS LSGMITETPV RLMRDMLYSA GVNGTRISQA ITYLDKIFDQ RQPIILITEH KVYENVILKG I SYEYQTEY ...String:
MAANTPEQHV QAVYKAEQEI NSTKNTNNSA STVKGENGFC ILASIYNSAS DQYIQNYQAI VFDAVPNIGV KRQADVTSYP VENGANVSD HVQVKNNTFS LSGMITETPV RLMRDMLYSA GVNGTRISQA ITYLDKIFDQ RQPIILITEH KVYENVILKG I SYEYQTEY AMQFDLEFEQ VRLVSYGETN AIALKTQPNK NTGVKNKKGT SPDADLDART GKATGTEHLS DHSADGKK

UniProtKB: Phi92_gp135

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Macromolecule #6: Phi92_gp134

MacromoleculeName: Phi92_gp134 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 72.914023 KDa
SequenceString: MLEINTSKIK NTVTFTVDKD SLKNTKDAIK NLKTFTESIE PSLNMTKMRR QFKSMEEYAK RIRQQMSGLG GGNPPPIPPT GGSSGGGKG GSGRGGSGSS GGRKTPEERA AEAAAKRAAL ANMKQDDFSF KAMPFTKADN RILEKSKKIV EETVELYRKG V ITSQQMNN ...String:
MLEINTSKIK NTVTFTVDKD SLKNTKDAIK NLKTFTESIE PSLNMTKMRR QFKSMEEYAK RIRQQMSGLG GGNPPPIPPT GGSSGGGKG GSGRGGSGSS GGRKTPEERA AEAAAKRAAL ANMKQDDFSF KAMPFTKADN RILEKSKKIV EETVELYRKG V ITSQQMNN TLARQLEELR RSHKEKNAQL LDEERARRRI ARLQEAEDKR RQRIRERERK DFERQQRREK EARQRDRQRK LS GVGNAAI ALNPAMFGAA LLGAGLYQGI SKIAESITTA AERINMVSKG GQNVQVNPNA ILTMRTWGEM NGVDSASIIK AID NIKDVR ERLGNTVLHS EFDEKSGKWK GGDSGINEIM NQFGWSKEDV AKFQNRPLDF VQALVNEGQK RGMNSAQIGR LMEN LGDDL MHYQRMFLDN GKEYMKVLDM LKNSGATLND ENIKAAQDFV KLRAQISAAG EGFTNNLLIG FMDGLKSAPD FAENM KTFQ EAARGLGEMS GSIVSSLAKI AKYFLDFSNK VGPKNNTKEA VRDYYNGTQY GYDAQVGGNP WAYWPIGRDQ HLPENQ PLG DFDSSFLTSA LNPSASSIGY NRPDLTASML TPRQGVPVPL SVENTVVIPD NAFQINVIPD GYGFSNYLDA TMNTSFS NF SQGLTLQLSS GQSSTGG

UniProtKB: Phi92_gp134

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Macromolecule #7: Phi92_gp145

MacromoleculeName: Phi92_gp145 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 54.028301 KDa
SequenceString: MADYGLTDAG FVIPTFDDIL NNYMTALKNT FGADTATSED TVFGQLFRII AYTDYTLWEG MQGVYNTQTL DGAEGIYLDE IFSKRGFYR KAASAGSGYA YVKSNNKAAW TYELSTDVYF NADNDLTYYV SAPTMLNAKI GAYTISKANA TASGETSITF Y IQSAIDGG ...String:
MADYGLTDAG FVIPTFDDIL NNYMTALKNT FGADTATSED TVFGQLFRII AYTDYTLWEG MQGVYNTQTL DGAEGIYLDE IFSKRGFYR KAASAGSGYA YVKSNNKAAW TYELSTDVYF NADNDLTYYV SAPTMLNAKI GAYTISKANA TASGETSITF Y IQSAIDGG LNSKTLSPSN TNFILDLTNF IKANVSTTDR ALVWNDASNV YMGYNPEDNV NPIGLVTPVK FYASIAIGTK WS EIPVTCS DVGYNPVGTE SITGISSTFT GFLDTGNFYP FSPGTDVETD AEFRSRFNDN MDEANAATRA AIVKALLLTD GVT KVKIYD NPTLHDQEHA PAMTFQTIVY GGTAEEVAQV IYNTKPINTL TYGTTAITIV TEDGGQEVIR FSPGDNAEYS LKLV YQTGN GSVLSTTERE NIVSALSNLQ AYFELGSTVT NDQIKGVIYS ALAFGRLTSL RVYVKLNTED DSKYNEGDIT PAYNV VPSF DLDNISYEYG V

UniProtKB: Phi92_gp145

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Macromolecule #8: Phi92_gp138

MacromoleculeName: Phi92_gp138 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 25.740584 KDa
SequenceString: MDALNFVTAI RGLINEQVAE VHTSLPVRVI GVDYGSKTVT LESIVKNTRS TEDEIDYPTF HDVPFMVNGG GTGRISFPIK AGDIGVVVF SERDPSNAFQ TDGDTASSGT LIQPCGLYPA CFIPKIATAT DSSEEVDSEK VIISNNKQTY ASFDPNGNIS V YNTQGMKI ...String:
MDALNFVTAI RGLINEQVAE VHTSLPVRVI GVDYGSKTVT LESIVKNTRS TEDEIDYPTF HDVPFMVNGG GTGRISFPIK AGDIGVVVF SERDPSNAFQ TDGDTASSGT LIQPCGLYPA CFIPKIATAT DSSEEVDSEK VIISNNKQTY ASFDPNGNIS V YNTQGMKI DMTPNSIVLT DAGGGKLTLQ GGTMTYKGGT VNLNGLTITP DGRMTDSGGI GLHTHTHPVR GVETGGSTVT SD KPNGG

UniProtKB: Phi92_gp138

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 33200
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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