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- EMDB-51564: Cryo-EM structure of a contractile injection system in Streptomyc... -

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Basic information

Entry
Database: EMDB / ID: EMD-51564
TitleCryo-EM structure of a contractile injection system in Streptomyces coelicolor, the baseplate complex in extended state applied 6-fold symmetry.
Map data
Sample
  • Complex: The baseplate module applied 6-fold symmetry of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Baseplate protein J-like domain-containing protein
    • Protein or peptide: LysM domain-containing protein
    • Protein or peptide: Secreted protein
    • Protein or peptide: IraD/Gp25-like domain-containing protein
    • Protein or peptide: Phage tail protein
KeywordsContractile injection system / STRUCTURAL PROTEIN
Function / homology
Function and homology information


lytic endotransglycosylase activity / structural molecule activity
Similarity search - Function
Uncharacterised protein family, phage tail-like / Conserved hypothetical protein CHP02243 / Tail protein I / Phage tail protein (Tail_P2_I) / : / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 ...Uncharacterised protein family, phage tail-like / Conserved hypothetical protein CHP02243 / Tail protein I / Phage tail protein (Tail_P2_I) / : / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / 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 / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Phage tail sheath family protein / Phage tail protein / Phage tail protein / LysM domain-containing protein / IraD/Gp25-like domain-containing protein / Baseplate protein J-like domain-containing protein / Secreted protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3(2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCasu B / Sallmen JW / Haas PE / Afanasyev P / Xu J / Schlimpert S / Pilhofer M
Funding support Switzerland, European Union, United Kingdom, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179255 Switzerland
European Research Council (ERC)679209European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T015349/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
CitationJournal: To Be Published
Title: Firing and cellular function of the Streptomyces coelicolor contractile injection system require the membrane protein CisA
Authors: Casu B / Sallmen JW / Haas PE / Afanasyev P / Xu J / Schlimpert S / Pilhofer M
History
DepositionSep 18, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51564.png

Downloads & links

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Map

FileDownload / File: emd_51564.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 420 pix.
= 447.3 Å		1.07 Å/pix.
x 420 pix.
= 447.3 Å		1.07 Å/pix.
x 420 pix.
= 447.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.421
Minimum - Maximum-1.2249856 - 2.964743
Average (Standard dev.)0.01773741 (±0.12206474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 447.30002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51564_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51564_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_51564_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 : The baseplate module applied 6-fold symmetry of a contractile inj...

EntireName: The baseplate module applied 6-fold symmetry of a contractile injection system in Streptomyces coelicolor
Components
  • Complex: The baseplate module applied 6-fold symmetry of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Baseplate protein J-like domain-containing protein
    • Protein or peptide: LysM domain-containing protein
    • Protein or peptide: Secreted protein
    • Protein or peptide: IraD/Gp25-like domain-containing protein
    • Protein or peptide: Phage tail protein

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Supramolecule #1: The baseplate module applied 6-fold symmetry of a contractile inj...

SupramoleculeName: The baseplate module applied 6-fold symmetry of a contractile injection system in Streptomyces coelicolor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)

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Macromolecule #1: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 16.493668 KDa
SequenceString:
MSLPKPEDVL VAPNFGIQID GVMVEYLNSV SNLQIEQDVI RYQQNQGTTG RNNVTLMPGV AKDGSVQVER GMSQSSVFTQ WINDSMAGR MATARKNATI IVMDYEDNPV KRWNLRNAWC SKVVAGTLKA GDTNALTETI TIVFEELVVE

UniProtKB: Phage tail protein

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Macromolecule #2: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 57.009609 KDa
SequenceString: MPSYLSPGVY VEEVASGSRP IEGVGTSVAA FVGLAPTGPL NEPTLVTNWT QYVAAFGDFT GGYYLAHSVY GFFNNGGSAA YVVRVGGSA EDAAADGSVN GAAAPAAVTG STAKALPAAE PKQLGTFAVT ATAAGQSGPL TVEVADPEGE GPAERFKLIV K DGDKPVET ...String:
MPSYLSPGVY VEEVASGSRP IEGVGTSVAA FVGLAPTGPL NEPTLVTNWT QYVAAFGDFT GGYYLAHSVY GFFNNGGSAA YVVRVGGSA EDAAADGSVN GAAAPAAVTG STAKALPAAE PKQLGTFAVT ATAAGQSGPL TVEVADPEGE GPAERFKLIV K DGDKPVET FDVSAKKGNR SYVVTQVKER SKLITVTEAA PSAQLVRPEN QSLTLPAPPS AAPAVPAGQA ESAHPGPAQY LG DSSDRTG FGGLEAIDEI SMVAVPDLMA AYQRGAIDLE AVKAVQLGLI AHCELMGDRV AIIDPPPNQN ARQIRVWRQE TAG YDSKYA ALYYPWIKSF DPATGQSRLV PPSGHVAGIW ARNDSERGVH KAPANEVVRG AVDLELQITR GEQDLLNPIG VNCI RSFPG RGIRVWGART LSSDPAWRYL NIRRYFNYLE ESILIGTQWV VFEPNDHNLW ARIRRNVSAF LVNEWRNGAL FGQSP DQAY YVKCDEETNP PESVDLGRVV CEIGIAPVKP AEFVIFRLAQ FSSGGGELDE

UniProtKB: Phage tail sheath family protein

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Macromolecule #3: Baseplate protein J-like domain-containing protein

MacromoleculeName: Baseplate protein J-like domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 70.889352 KDa
SequenceString: MPLPSPNLDD RRFQQFVDDA KRYIQQRAPE WTDHNVSDPG VTLVETVAHM ADQIVYRLNR VPDKNHLAFL DLVGITLFPP SAARTDVTF WLSAPQEDAI LVPVGTEVAT LRTERDEAVV FATEQDLRIV PCTMGRLVTQ VSGEAVSDRT TDLAESKDVL C FAEAPNPG ...String:
MPLPSPNLDD RRFQQFVDDA KRYIQQRAPE WTDHNVSDPG VTLVETVAHM ADQIVYRLNR VPDKNHLAFL DLVGITLFPP SAARTDVTF WLSAPQEDAI LVPVGTEVAT LRTERDEAVV FATEQDLRIV PCTMGRLVTQ VSGEAVSDRT TDLAESKDVL C FAEAPNPG DCMLIGLSAA VPDCALALEL DSRVDGVGVD PRQPPLVWEA WTEDGWQSCE VDRDGTGGLN RPGDVVLHIP GG HVLSRNG GHEAGWIRCR VTEPLSGQPF YTTSPTIRSA EAYTIGGTTG SIHAETVLDE PLGESTGLPG QRLRLEHAPV VAG EPSVLL QTAADDGWQD WQVVPHFSGS HPDDHHITVD ATTGEIAFGP AVREADGTLR QYGAVPPKGA VIRARRYRTG GGRA GNVAR GAVQVLRTSI PYVSEVVNRE AALGGVDGET IEEAKLRAPI TLRAQERAVT LRDYEELARR AAPETARITC LEGAE NEYG AHAVRVLVVP QAVPDPGGRL RFEQLVPGDA LLNRITRHLD ERRLIGTRLA VGPPYYQGVT VVATVHAFRD VDADRV RRQ THDALYRHLD PLTGGSDGKG WPFGRPVQTG ELFAVLQRVP GVELVDEVVL HPADPLTGKR GDPTNRIDLD APALVFS YD HRVRVIGDSA

UniProtKB: Baseplate protein J-like domain-containing protein

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Macromolecule #4: LysM domain-containing protein

MacromoleculeName: LysM domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 25.716328 KDa
SequenceString: MAKSSKGAGK SLVRANLAIH EPPTGKSTSP GGLIKRFPFE FNPAQLSISQ RSQWKATPTA AVRKAAKPQF MGAEPREMTL EIFLDSSMK PGGNTVMKKV ESLLICCEVT AKSLAAKQPS PPWVIFEWGS FSTARFNAYV ASIETQYTLF GTAGVPIRAT C QMGLVEIP ...String:
MAKSSKGAGK SLVRANLAIH EPPTGKSTSP GGLIKRFPFE FNPAQLSISQ RSQWKATPTA AVRKAAKPQF MGAEPREMTL EIFLDSSMK PGGNTVMKKV ESLLICCEVT AKSLAAKQPS PPWVIFEWGS FSTARFNAYV ASIETQYTLF GTAGVPIRAT C QMGLVEIP GPTPNQNPTS GALTAQRVHR VVAGDSLQSL AWSEYGSANA WRVIAEANGI DDPSHLPTGT ELILPATEEV PH

UniProtKB: LysM domain-containing protein

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Macromolecule #5: Secreted protein

MacromoleculeName: Secreted protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 20.282078 KDa
SequenceString:
MKPASQRGSV DGLGSSLPIA SMLPAVFADD DLALRFVAGL DDVLAPILNV LDCLDTYFDP ALTPADFAQW LGTWVGAETD GTEAEPMLR AAVAAAARLH RVRGTLQGLS ETVRLAFGVA PEITESGGAT WNARPLGPFP GRPRPQLHVA LRLPEPRPVD V HRLDALVA AARPAHMPYT VEVTASERTP ER

UniProtKB: Secreted protein

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Macromolecule #6: IraD/Gp25-like domain-containing protein

MacromoleculeName: IraD/Gp25-like domain-containing protein / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 16.609537 KDa
SequenceString:
MAEQFVGSGW SFPLRIGPTG GIALVSGEQE VEEAMRLILA TAPGERPMRP EFGCAIHDLV FAPVNEQTAG RIQHEVYVTL DRWEPRIEV HDVDVTTGEE QNVLFIDVRY SIRGTNNPRS LVFPFYVIPS HDEPDLPDAP AGLPGSPESD R

UniProtKB: IraD/Gp25-like domain-containing protein

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Macromolecule #7: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 15.194927 KDa
SequenceString:
MTRKDPGSSI WFSLAIDGES LGYFNGCEGL STQVEVEQRQ EGGNNGFVWQ LPTRVTYSNI RLTRPLTPDT AKVAKWISSV QTGIQRPTA QISALRADGS LVARWGLIDV LPVSWQGPSL DPGSASVANE VLEIAHHGFT D

UniProtKB: Phage tail protein

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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: 8
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 1.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22980
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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