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- EMDB-62362: Baseplate structure of Escherichia phage Mu -

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Basic information

Entry
Database: EMDB / ID: EMD-62362
TitleBaseplate structure of Escherichia phage Mu
Map data
Sample
  • Virus: Escherichia phage Mu (virus)
    • Protein or peptide: x 10 types
  • Ligand: x 2 types
Keywordsphage / sheath / tube / VIRAL PROTEIN
Function / homology
Function and homology information


viral genome circularization / symbiont-mediated evasion of DNA end degradation by host / viral tropism switching / virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail, baseplate / virus tail, fiber / viral tail assembly / adhesion receptor-mediated virion attachment to host cell ...viral genome circularization / symbiont-mediated evasion of DNA end degradation by host / viral tropism switching / virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail, baseplate / virus tail, fiber / viral tail assembly / adhesion receptor-mediated virion attachment to host cell / : / virion component / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / DNA binding / metal ion binding
Similarity search - Function
Bacteriophage Mu, Baseplate protein gp46 / : / Phage protein GP46 / Bacteriophage lambda, Tail fiber protein, repeat-2 / DNA circulation, N-terminal / Phage-associated protein Gp45 / : / : / Phage tail fibre repeat / Bacteriophage Mu Gp45, N-terminal ...Bacteriophage Mu, Baseplate protein gp46 / : / Phage protein GP46 / Bacteriophage lambda, Tail fiber protein, repeat-2 / DNA circulation, N-terminal / Phage-associated protein Gp45 / : / : / Phage tail fibre repeat / Bacteriophage Mu Gp45, N-terminal / DNA circularisation protein N-terminus / Mu phage baseplate assembly protein GpP, fourth domain / Baseplate-like, two-layer sandwich fold / Baseplate protein GpP / : / : / Mu phage baseplate assembly protein GpP-like, N-terminal / Baseplate hub protein gp44-like, second domain / Bacteriophage Mu, GpM, tail tube / Phage tail tube protein / Tail sheath protein / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / Tape measure protein N-terminal / Tape measure protein / Phage baseplate assembly protein V/Gp45 / Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / : / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Baseplate protein J-like / Baseplate J-like protein / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
DNA circularization protein N / Baseplate hub protein gp44 / Tail sheath protein / Tail tube protein / Tail fiber protein S / Baseplate protein gp48 / Baseplate protein gp47 / Baseplate protein gp46 / Baseplate puncturing device gp45 / Probable tape measure protein
Similarity search - Component
Biological speciesEscherichia phage Mu (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhou JQ / 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: J Virol / Year: 2025
Title: structures of the contractile nanomachine myophage Mu in both its extended and contracted states.
Authors: Junquan Zhou / Liwen Wang / Hao Xiao / Wenyuan Chen / Zhonghua Liu / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: Myophage Mu is a representative of contractile nanomachines with a simple tail baseplate. It has the capacity to infect a range of intestinal bacteria and has extensive applications in genetic ...Myophage Mu is a representative of contractile nanomachines with a simple tail baseplate. It has the capacity to infect a range of intestinal bacteria and has extensive applications in genetic engineering research. Nevertheless, a comprehensive understanding of the entire structure and contractile mechanisms of Mu remains elusive. Using cryo-electron microscopy (cryo-EM), we resolved the asymmetric structures of Mu in both its extended and contracted states, the latter of which lacked the tail baseplate, at near-atomic resolutions. We built the atomic models for the extended Mu, encompassing the head, the connector complex, the tail, and the simple baseplate. It is noteworthy that we identified the position and structure of the tail tube initiator protein gp43 (referred to as the DNA circularization protein). The protein gp43 plays a crucial role not only in the baseplate assembly and DNA circularization but also in stabilizing the wedge-hub connection and mediating tail contraction. Except for the baseplate structure, the structural comparison of Mu in its extended and contracted states revealed that only the tail sheath protein gp39 and the C-terminus of the tail terminator protein gp37 undergo notable conformational changes to accommodate the tail contraction, whereas the remaining protein components remained unchanged. Our structures exhibited conserved properties among the majority of myophages, thereby providing valuable insights into the contraction mechanisms across myophages and contractile injection systems (CISs).
IMPORTANCE: Despite extensive study, the asymmetric structures of phage Mu, a highly effective transposable myophage, remain unknown. In this study, we present the high-resolution structures of Mu in ...IMPORTANCE: Despite extensive study, the asymmetric structures of phage Mu, a highly effective transposable myophage, remain unknown. In this study, we present the high-resolution structures of Mu in both its extended and contracted states. The comparison of the two structures allows for the illustration of detailed conformational changes of the head-to-tail complex during the process of tail contraction. The contraction mechanism of Mu is highly conserved and widely adapted to all contractile nanomachines that share common structural features with Mu.
History
DepositionNov 11, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62362.png

Downloads & links

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Map

FileDownload / File: emd_62362.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 300 pix.
= 408. Å		1.36 Å/pix.
x 300 pix.
= 408. Å		1.36 Å/pix.
x 300 pix.
= 408. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.054174423 - 0.11121331
Average (Standard dev.)0.000051217026 (±0.005718484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62362_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_62362_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_62362_half_map_2.map
Projections & Slices
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Sample components

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Entire : Escherichia phage Mu

EntireName: Escherichia phage Mu (virus)
Components
  • Virus: Escherichia phage Mu (virus)
    • Protein or peptide: DNA circularization protein N
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Baseplate protein gp46
    • Protein or peptide: Baseplate hub protein gp44
    • Protein or peptide: Baseplate protein gp47
    • Protein or peptide: Baseplate puncturing device gp45
    • Protein or peptide: Baseplate protein gp48
    • Protein or peptide: Probable tape measure protein
    • Protein or peptide: Tail fiber protein S
  • Ligand: CALCIUM ION
  • Ligand: FE (III) ION

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Supramolecule #1: Escherichia phage Mu

SupramoleculeName: Escherichia phage Mu / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 / NCBI-ID: 2681603 / Sci species name: Escherichia phage Mu / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: DNA circularization protein N

MacromoleculeName: DNA circularization protein N / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 52.085984 KDa
SequenceString: MFEDALNAVN AVRDKTGGGR KTTGKGTFRN VPFLVIEEQK QAGGRRLVKR EYPLRDTGGV NDLGKKLRSR TFSACILNSN AETARDEAG ALMDALDAPG SGELVHPDFG TVDVMVDSWE CRTKADELNY YAFTVTVYPS LQDTAPDAET DTSAAVPAQA V AVTGSLGD ...String:
MFEDALNAVN AVRDKTGGGR KTTGKGTFRN VPFLVIEEQK QAGGRRLVKR EYPLRDTGGV NDLGKKLRSR TFSACILNSN AETARDEAG ALMDALDAPG SGELVHPDFG TVDVMVDSWE CRTKADELNY YAFTVTVYPS LQDTAPDAET DTSAAVPAQA V AVTGSLGD TLSSVWQTVK DGTAAATAVM EAVTGVIDDI SDAVDNLGVT QTVSGLMGSL SAMKGSVTSL INQPAMLASS LM GALSGVS SLCDTRTAFS TWNRLAQRFE RRHAATAGRQ GTITTSYNSP VAEKNIATLN YVMLAAAQTY RAEAASQALT AAL DFSRRM DNAARAPVLD APSTTTGTAS GASSTSATVT QGQLQLTAIT PDGGFSQVSF SDSGTATPPV FESVSDIEKT TAML GAALD SVILTASEQG FSTDSVQLTQ LRLLVVADLE KRGLQLAGSE SHHLPETLPA MVALYRFTGN SRNWQRLARR NGISN PLFV PGGVSIEVIN E

UniProtKB: DNA circularization protein N

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Macromolecule #2: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 53.132508 KDa
SequenceString: MSDISFNAIP SDVRVPLTYI EFDNSNAVSG TPAPRQRVLM FGQSGSKASA APNVPVRIRS GSQASAAFGQ GSMLALMADA FLNANRVAE LWCIPQGNGT GNAAVGEISL SGTAGENGSL VTYIAGQRLA VSVAAGATGA ALADLLVARI KGQPDLPVTA E VRADSGDD ...String:
MSDISFNAIP SDVRVPLTYI EFDNSNAVSG TPAPRQRVLM FGQSGSKASA APNVPVRIRS GSQASAAFGQ GSMLALMADA FLNANRVAE LWCIPQGNGT GNAAVGEISL SGTAGENGSL VTYIAGQRLA VSVAAGATGA ALADLLVARI KGQPDLPVTA E VRADSGDD DTHADVVLSA KFTGALSAVD VRWNYYAGET TPYGIITAFK AASGKNGNPD ISASIAGMGD LQYKYIVMPY TD EPNLNLL RTELQERWGP VNQADGFAVT VLSGTYGDIS TFGVSRNDHL ISCMGIAGAP EPSYLYAATL CAVASQALSI DPA RPLQTL TLPGRMPPAV GDRFTWSERN ALLFDGISTF NVNDGGEMQI ERMITMYRTN KYGDSDPSYL NVNTIATLSY LRYS LRTRI TQKFPNYKLA SDGTRFATGQ AVVTPSVIKT ELLALFEEWE NAGLVEDFDT FKEELYVARN KDDKDRLDVL CGPNL INQF RIFAAQVQFI L

UniProtKB: Tail sheath protein

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Macromolecule #3: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 12.84047 KDa
SequenceString:
MAGNQRQGVA FIRVNGMELE SMEGASFTPS GITREEVTGS RVYGWKGKPR AAKVECKIPG GGPIGLDEII DWENITVEFQ ADTGETWML ANAWQADEPK NDGGEISLVL MAKQSKRIA

UniProtKB: Tail tube protein

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Macromolecule #4: Baseplate protein gp46

MacromoleculeName: Baseplate protein gp46 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 16.340159 KDa
SequenceString:
MTDLAIIWTN GRGDIAQDGI DMLTDDSLTT DVTISLFTDR RALDSDTLPD GSDDRRGWWG DSYRDRPIGS RLWLLSREKA TPDTLERAR GYAEEALEWL KTAGRVSAIN VRAEQLHQGW LYLYIALTLP DGSVIPYEFK AAFNGV

UniProtKB: Baseplate protein gp46

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Macromolecule #5: Baseplate hub protein gp44

MacromoleculeName: Baseplate hub protein gp44 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 41.840078 KDa
SequenceString: MSNTVTLRAD GRLFTGWTSV SVTRSIESVA GYFELGVNVP PGTDLSGLAP GKKFTLEIGG QIVCTGYIDS RRRQMTADSM KITVAGRDK TADLIDCAAV YSGGQWKNRT LEQIARDLCA PYGVTVRWEL SDKESSAAFP GFTLDHSETV YEALVRASRA R GVLMTSNA ...String:
MSNTVTLRAD GRLFTGWTSV SVTRSIESVA GYFELGVNVP PGTDLSGLAP GKKFTLEIGG QIVCTGYIDS RRRQMTADSM KITVAGRDK TADLIDCAAV YSGGQWKNRT LEQIARDLCA PYGVTVRWEL SDKESSAAFP GFTLDHSETV YEALVRASRA R GVLMTSNA AGELVFSRAA STATDELVLG ENLLTLDFEE DFRDRFSEYT VKGYARANGA EGDDIDAKSI VSRKGTATDS DV TRYRPMI IIADSKITAK DAQARALREQ RRRLAKSITF EAEIDGWTRK DGQLWMPNLL VTIDASKYAI KTTELLVSKV TLI LNDQDG LKTRVSLAPR EGFLVPVESD RKNRKGGDSN GGIDALVEDY YRRHPEKTPP WKE

UniProtKB: Baseplate hub protein gp44

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Macromolecule #6: Baseplate protein gp47

MacromoleculeName: Baseplate protein gp47 / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 38.724578 KDa
SequenceString: MAYSPPTLSS LIARTEQNIE QRLPGSWPQA REKTLSAIAY AQAGLAAGCH EHISWVGRQI IPSTADEDEL LEHCRFWGVR RKQATAASG PLTVTTSAAT TIPAGTRWQR ADGVVYSLAD TIVIDRAGTT EITVTALAAG EAGNTGENTL LTLITPVACV V SDAITVKG ...String:
MAYSPPTLSS LIARTEQNIE QRLPGSWPQA REKTLSAIAY AQAGLAAGCH EHISWVGRQI IPSTADEDEL LEHCRFWGVR RKQATAASG PLTVTTSAAT TIPAGTRWQR ADGVVYSLAD TIVIDRAGTT EITVTALAAG EAGNTGENTL LTLITPVACV V SDAITVKG FSGGADIESA AELLSRLEYR VQYPPFGGNQ FDYVRWAREV SGVTRAWCFP TWKGGGTVGV TFVMDNRSNI FP QPADVER VADYIAGHTD PITGLIVGQP DGVNVTVFAP KAKPVNPRIY ISPKTAELKQ AITNAINTMF FNEVMPGGAL APS RIIRAV AGVTGLDDFE VRFPTEIQRS ENTELLTAGT IEWL

UniProtKB: Baseplate protein gp47

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Macromolecule #7: Baseplate puncturing device gp45

MacromoleculeName: Baseplate puncturing device gp45 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 21.720525 KDa
SequenceString: MERVNDSALN RLLTPLMRRV RLMLARAVVN VINDGRKVQN LQVGLLDDEE SDEVERLQNY GHFSVPLPGA EALIACVGAQ RDQGIAVVV EDRRYRPTNL EPGDAGIYHH EGHRIRLTKD GRCIITCKTV EVYADESMTV DTPRTTFTGD VEIQKGLGVK G KSQFDSNI ...String:
MERVNDSALN RLLTPLMRRV RLMLARAVVN VINDGRKVQN LQVGLLDDEE SDEVERLQNY GHFSVPLPGA EALIACVGAQ RDQGIAVVV EDRRYRPTNL EPGDAGIYHH EGHRIRLTKD GRCIITCKTV EVYADESMTV DTPRTTFTGD VEIQKGLGVK G KSQFDSNI TAPDAIINGK STDKHIHRGD SGGTTGPMQ

UniProtKB: Baseplate puncturing device gp45

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Macromolecule #8: Baseplate protein gp48

MacromoleculeName: Baseplate protein gp48 / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 20.489059 KDa
SequenceString:
MAVTPWQTAF LQLLPSGLAW NKSPDSKLSA LAQAISDVIA TAADDARQML RERFPSTSRW YLGEWESFLG LPDCTSENGT LSERQRAAA NKMRMTGNLS RRFYEWLAAQ YGFTVRLTDS TEGQWVTQVN IYGIKNYRNA TVLDNVLTPL RVYESGALEC L LEKYKPAH QIYKFVYHDG DN

UniProtKB: Baseplate protein gp48

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Macromolecule #9: Probable tape measure protein

MacromoleculeName: Probable tape measure protein / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 73.682836 KDa
SequenceString: MTGKRLKASV IIDLNGNLSR RSRQYSNQIN ALSRSGQSSL RALRMEVVRV SGAIDRMGSL STRTFRMLSA GALGIAGVGY TANKLFIGA AAQREQQIIA MNSLYHGDKV RAQAMMAWAK QNAKDTTWGL SGVLDEIRSS KGFGMTDEQT KQFITMLQDQ G AMHGWDLP ...String:
MTGKRLKASV IIDLNGNLSR RSRQYSNQIN ALSRSGQSSL RALRMEVVRV SGAIDRMGSL STRTFRMLSA GALGIAGVGY TANKLFIGA AAQREQQIIA MNSLYHGDKV RAQAMMAWAK QNAKDTTWGL SGVLDEIRSS KGFGMTDEQT KQFITMLQDQ G AMHGWDLP TAQGASLQLK QMFARQQITA ADANLLTGYG INVYQALADA TGTDVKKIRD LGTKGKLGMK SILTVFRTLS EQ SKGAQAS AMNSWDGMFA QMEANLLEFR IKVANSGPFE EIKNEMRRVL NWHDMADKSG ELDALAENIG QKFLTTFRTV KIS AQELWR WLKPGKDALA WVDQNIVSLK KLAAVLVSVW LANKALRAGW AVAKPSWQVA SYPFKTGRRM WRWMRNRKRG QAGL PVPDA MTSETLLQGI GIQRVFVINW PRGFGDYGSG GGRRVRSGGR MAPLLPRQPL LLSGPQPLAL PAPRPVLALP PPGVP VTAR PAPLPLPGKS GLLSRLAGSA AGQLVTGTVG KLADAGRAVG GWFSGIGNKL AGSAIGRVVT KGAGALGWMG KGAGRA LSR LGGPVMGALQ LAPVLMDEQA STHEKAGAIG STAGAWLGGA VGSLAGPLGT VAGATLGSVA GEYLGGFVTD LYQKWTA TD KEPQEQKVNA EASLRVELGE GLRLTSSRVT EDGMGLNIYA GDNYITGW

UniProtKB: Probable tape measure protein

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Macromolecule #10: Tail fiber protein S

MacromoleculeName: Tail fiber protein S / type: protein_or_peptide / ID: 10 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 55.412551 KDa
SequenceString: MFYIDNDSGV TVMPPVSAQR SAIVRWFSEG DGNNVITWPG MDWFNIVQAE LLNTLEEAGI QPDKTKLNQL ALSIKAIMSN NALLIKNNL SEIKTAGASA QRTARENLDI YDASLNKKGL VQLTSATDSP SETLAATAKA VKIAMDNANA RLAKDRNGAD I PNKPLFIQ ...String:
MFYIDNDSGV TVMPPVSAQR SAIVRWFSEG DGNNVITWPG MDWFNIVQAE LLNTLEEAGI QPDKTKLNQL ALSIKAIMSN NALLIKNNL SEIKTAGASA QRTARENLDI YDASLNKKGL VQLTSATDSP SETLAATAKA VKIAMDNANA RLAKDRNGAD I PNKPLFIQ NLGLQETVNR ARNAVQKNGD TLSGGLTFEN DSILAWIRNT DWAKIGFKND ADSDTDSYMW FETGDNGNEY FK WRSKQST TTKDLMNLKW DALSVLVNAI VNGEVISKSA NGLRIAYGNY GFFIRNDGSN TYFMLTNSGD NMGTYNGLRP LWI NNATGA VSMGRGLNVS GDTLSDRFAI NSSNGMWIQM RDNNAIFGKN IVNTDSAQAL LRQNHADRKF MIGGLGNKQF GIYM INNSR TANGTDGQAY MDNNGNWLCG AQVIPGNYAN FDSRYVRDVR LGTQSLTGGL SRDYKAPSGH VITGFHTNGD WEMQG GDDK VYIRPVQKNI NGTWYNVASA

UniProtKB: Tail fiber protein S

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #12: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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