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- PDB-9gb1: Extended phiCD508 tail -

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Basic information

Entry
Database: PDB / ID: 9gb1
TitleExtended phiCD508 tail
Components
  • gp55 - Tail sheath protein
  • gp56 - Tail tube protein
KeywordsVIRUS / Bacteriophage / needle / baseplate
Function / homology
Function and homology information


Phage tail tube protein / XkdM-like superfamily / Phage tail tube protein / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / 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
Protein of uncharacterized function (DUF2001) / Phage tail sheath protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsWilson, J.S. / Fagan, R.P. / Bullough, P.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P02002X/1 United Kingdom
CitationJournal: Life Sci Alliance / Year: 2025
Title: Molecular mechanism of bacteriophage contraction structure of an S-layer-penetrating bacteriophage.
Authors: Jason S Wilson / Louis-Charles Fortier / Robert P Fagan / Per A Bullough /
Abstract: The molecular details of phage tail contraction and bacterial cell envelope penetration remain poorly understood and are completely unknown for phages infecting bacteria enveloped by proteinaceous S- ...The molecular details of phage tail contraction and bacterial cell envelope penetration remain poorly understood and are completely unknown for phages infecting bacteria enveloped by proteinaceous S-layers. Here, we reveal the extended and contracted atomic structures of an intact contractile-tailed phage (φCD508) that binds to and penetrates the protective S-layer of the Gram-positive human pathogen The tail is unusually long (225 nm), and it is also notable that the tail contracts less than those studied in related contractile injection systems such as the model phage T4 (∼20% compared with ∼50%). Surprisingly, we find no evidence of auxiliary enzymatic domains that other phages exploit in cell wall penetration, suggesting that sufficient energy is released upon tail contraction to penetrate the S-layer and the thick cell wall without enzymatic activity. Instead, the unusually long tail length, which becomes more flexible upon contraction, likely contributes toward the required free energy release for envelope penetration.
History
DepositionJul 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: gp56 - Tail tube protein
Y: gp55 - Tail sheath protein
T: gp56 - Tail tube protein
Z: gp55 - Tail sheath protein
U: gp56 - Tail tube protein
a: gp55 - Tail sheath protein
V: gp56 - Tail tube protein
b: gp55 - Tail sheath protein
W: gp56 - Tail tube protein
c: gp55 - Tail sheath protein
X: gp56 - Tail tube protein
d: gp55 - Tail sheath protein
e: gp56 - Tail tube protein
k: gp55 - Tail sheath protein
f: gp56 - Tail tube protein
l: gp55 - Tail sheath protein
g: gp56 - Tail tube protein
m: gp55 - Tail sheath protein
h: gp56 - Tail tube protein
n: gp55 - Tail sheath protein
i: gp56 - Tail tube protein
o: gp55 - Tail sheath protein
j: gp56 - Tail tube protein
p: gp55 - Tail sheath protein
q: gp56 - Tail tube protein
w: gp55 - Tail sheath protein
r: gp56 - Tail tube protein
x: gp55 - Tail sheath protein
s: gp56 - Tail tube protein
y: gp55 - Tail sheath protein
t: gp56 - Tail tube protein
z: gp55 - Tail sheath protein
u: gp56 - Tail tube protein
1: gp55 - Tail sheath protein
v: gp56 - Tail tube protein
2: gp55 - Tail sheath protein


Theoretical massNumber of molelcules
Total (without water)1,234,60736
Polymers1,234,60736
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "n"
d_2ens_1chain "2"
d_3ens_1chain "Y"
d_4ens_1chain "Z"
d_5ens_1chain "a"
d_6ens_1chain "b"
d_7ens_1chain "c"
d_8ens_1chain "d"
d_9ens_1chain "k"
d_10ens_1chain "l"
d_11ens_1chain "m"
d_12ens_1chain "1"
d_13ens_1chain "o"
d_14ens_1chain "p"
d_15ens_1chain "w"
d_16ens_1chain "x"
d_17ens_1chain "y"
d_18ens_1chain "z"
d_1ens_2chain "V"
d_2ens_2chain "T"
d_3ens_2chain "U"
d_4ens_2chain "S"
d_5ens_2chain "W"
d_6ens_2chain "X"
d_7ens_2chain "e"
d_8ens_2chain "f"
d_9ens_2chain "g"
d_10ens_2chain "h"
d_11ens_2chain "i"
d_12ens_2chain "j"
d_13ens_2chain "q"
d_14ens_2chain "r"
d_15ens_2chain "s"
d_16ens_2chain "t"
d_17ens_2chain "u"
d_18ens_2chain "v"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLUGLULEULEUnT13 - 47213 - 472
d_2ens_1GLUGLULEULEU2JA13 - 47213 - 472
d_3ens_1GLUGLULEULEUYB13 - 47213 - 472
d_4ens_1GLUGLULEULEUZD13 - 47213 - 472
d_5ens_1GLUGLULEULEUaF13 - 47213 - 472
d_6ens_1GLUGLULEULEUbH13 - 47213 - 472
d_7ens_1GLUGLULEULEUcJ13 - 47213 - 472
d_8ens_1GLUGLULEULEUdL13 - 47213 - 472
d_9ens_1GLUGLULEULEUkN13 - 47213 - 472
d_10ens_1GLUGLULEULEUlP13 - 47213 - 472
d_11ens_1GLUGLULEULEUmR13 - 47213 - 472
d_12ens_1GLUGLULEULEU1HA13 - 47213 - 472
d_13ens_1GLUGLULEULEUoV13 - 47213 - 472
d_14ens_1GLUGLULEULEUpX13 - 47213 - 472
d_15ens_1GLUGLULEULEUwZ13 - 47213 - 472
d_16ens_1GLUGLULEULEUxBA13 - 47213 - 472
d_17ens_1GLUGLULEULEUyDA13 - 47213 - 472
d_18ens_1GLUGLULEULEUzFA13 - 47213 - 472
d_1ens_2ILEILEGLUGLUVG7 - 1367 - 136
d_2ens_2ILEILEGLUGLUTC7 - 1367 - 136
d_3ens_2ILEILEGLUGLUUE7 - 1367 - 136
d_4ens_2ILEILEGLUGLUSA7 - 1367 - 136
d_5ens_2ILEILEGLUGLUWI7 - 1367 - 136
d_6ens_2ILEILEGLUGLUXK7 - 1367 - 136
d_7ens_2ILEILEGLUGLUeM7 - 1367 - 136
d_8ens_2ILEILEGLUGLUfO7 - 1367 - 136
d_9ens_2ILEILEGLUGLUgQ7 - 1367 - 136
d_10ens_2ILEILEGLUGLUhS7 - 1367 - 136
d_11ens_2ILEILEGLUGLUiU7 - 1367 - 136
d_12ens_2ILEILEGLUGLUjW7 - 1367 - 136
d_13ens_2ILEILEGLUGLUqY7 - 1367 - 136
d_14ens_2ILEILEGLUGLUrAA7 - 1367 - 136
d_15ens_2ILEILEGLUGLUsCA7 - 1367 - 136
d_16ens_2ILEILEGLUGLUtEA7 - 1367 - 136
d_17ens_2ILEILEGLUGLUuGA7 - 1367 - 136
d_18ens_2ILEILEGLUGLUvIA7 - 1367 - 136

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.187644698531, -0.982236970567, 2.76546991839E-5), (0.982236970852, -0.187644698027, 1.98443424699E-5), (-1.43025891531E-5, 3.08871536165E-5, 0.999999999421)575.007086505, 54.4244112284, -38.9057752409
2given(-0.944917061769, 0.32730986294, -4.59948934076E-8), (-0.32730986294, -0.944917061767, -1.91669694672E-6), (-6.70815174465E-7, -1.79606506494E-6, 0.999999999998)428.665023448, 602.139547079, 38.9085293092
3given(-0.188999929396, 0.981977100897, 1.66388714971E-6), (-0.981977100898, -0.188999929394, -9.80125163742E-7), (-6.47985912993E-7, -1.81914266624E-6, 0.999999999998)54.8602310534, 575.308328277, 38.9085292302
4given(0.755917198852, 0.65466723492, 1.60453681243E-6), (-0.654667234921, 0.755917198852, 7.88822499836E-7), (-6.96480727897E-7, -1.64672217279E-6, 0.999999999998)-108.805630849, 238.168282633, 38.9085031147
5given(0.944917061768, -0.327309862943, 4.59998215164E-8), (0.327309862942, 0.944917061766, 1.91669616659E-6), (-6.70819575778E-7, -1.79606271476E-6, 0.999999999998)101.332976551, -72.1405470796, 38.9085293096
6given(0.18899987195, -0.981977111953, -1.56624451993E-6), (0.981977111954, 0.188999871949, 1.0030808148E-6), (-6.88982387869E-7, -1.72759841585E-6, 0.999999999998)475.138048576, -45.309363526, 38.9085187005
7given(-0.755917223506, -0.654667206451, -1.87365998324E-6), (0.654667206454, -0.755917223506, -9.57144110296E-7), (-7.89720991468E-7, -1.95014546542E-6, 0.999999999998)638.804000212, 291.830739892, 38.9085881409
8given(-0.999999999999, -6.60225018308E-7, -1.28940390985E-6), (6.60229436287E-7, -0.999999999994, -3.42637521145E-6), (-1.28940164766E-6, -3.42637606275E-6, 0.999999999993)530.000059846, 529.999650889, 0.00101188823533
9given(-0.500000101177, 0.866025345369, 1.1299993783E-6), (-0.866025345368, -0.500000101173, -2.54969475094E-6), (-1.64310047379E-6, -2.2534557353E-6, 0.999999999996)168.003139915, 626.996381633, 0.0008394403377
10given(0.499999887521, 0.866025468724, 7.37447605034E-7), (-0.866025468724, 0.499999887521, -7.84855094083E-7), (-1.0484282203E-6, -2.46220949048E-7, 0.999999999999)-96.9965408566, 361.996494641, 0.000281810529714
11given(0.756819409076, -0.653624036647, 2.76048425007E-5), (0.653624036253, 0.756819409579, 2.27278157197E-5), (-3.57473272578E-5, 8.42336512828E-7, 0.999999999361)237.642088389, -108.776554045, -38.8923297207
12given(0.500000120963, -0.866025333945, -1.25597347105E-6), (0.866025333946, 0.500000120963, 4.25122530941E-7), (2.59820005625E-7, -1.30026616159E-6, 0.999999999999)361.996421802, -96.9969808205, 0.000220109406428
13given(-0.499999631146, -0.866025616737, -3.0225640732E-6), (0.866025616742, -0.499999631144, -1.30083885967E-6), (-3.84721145988E-7, -3.26803686565E-6, 0.999999999995)626.996715464, 168.002818052, 0.000780243827307
14given(-0.94446450557, -0.328613446254, 2.56741507901E-5), (0.32861344677, -0.944464505542, 1.93187634939E-5), (1.78999186821E-5, 2.66827575955E-5, 0.999999999484)602.354857555, 428.191447616, -38.9133163473
15given(-0.756819694023, 0.65362370668, 2.83715583879E-5), (-0.653623706445, -0.75681969454, 1.81553324259E-5), (3.3338909829E-5, -4.80401001968E-6, 0.999999999433)292.33596799, 638.75860576, -38.9090189006
16given(0.18764514735, 0.982236884754, 3.009221338E-5), (-0.982236885128, 0.187645146838, 1.90496785442E-5), (1.30646391104E-5, -3.31322616744E-5, 0.999999999366)-45.0297763048, 475.55812553, -38.8961577812
17given(0.944464745413, 0.328612756485, 3.07769412023E-5), (-0.328612757199, 0.944464745412, 2.19223535477E-5), (-2.18637709092E-5, -3.0818585569E-5, 0.999999999286)-72.3769898428, 101.790316278, -38.8876446696
18given(-0.499999438047, 0.866025728228, -9.11544923197E-8), (-0.866025728228, -0.499999438047, -3.58128668687E-7), (-3.55725836034E-7, -1.00121997499E-7, 1)168.00203819, 626.995047787, 0.000125577804113
19given(0.499999239126, 0.866025843075, 3.046765969E-7), (-0.866025843075, 0.499999239126, 4.45422065744E-7), (2.33408953381E-7, -4.86568500657E-7, 1)-96.9965954058, 361.995633095, 5.43296813476E-5
20given(-1), (-1), (1)529.998, 529.999
21given(0.499999849653, -0.866025490587, 3.92698342505E-7), (0.866025490587, 0.499999849653, 1.59763345378E-7), (-3.3470824177E-7, 2.60205126051E-7, 1)361.995968619, -96.9960562079, 3.04143290464E-5
22given(-0.49999969295, -0.86602558106, -2.63122504943E-8), (0.86602558106, -0.49999969295, 1.12235689207E-7), (-1.10355095129E-7, 3.3330728118E-8, 1)626.994856387, 168.003341607, 2.30156825296E-5
23given(-0.944916959758, -0.327310157435, -7.91140345446E-7), (0.327310157436, -0.944916959758, -1.24027278693E-6), (-3.41608048809E-7, -1.43090306211E-6, 0.999999999999)602.138993446, 428.665567057, -38.9075489522
24given(-0.755917278866, 0.654667142532, -1.1934465079E-6), (-0.65466714253, -0.755917278866, -1.80937755975E-6), (-2.08668687353E-6, -5.86429546317E-7, 0.999999999998)291.830911604, 638.803787923, -38.9072635796
25given(0.188998757536, 0.981977326443, -9.02902647405E-7), (-0.981977326443, 0.188998757534, -1.83082994559E-6), (-1.62718601661E-6, 1.23265451271E-6, 0.999999999998)-45.3078741101, 475.138304087, -38.9078441349
26given(0.944917147278, 0.327309616082, -3.72435439095E-7), (-0.327309616082, 0.944917147276, -1.89842046836E-6), (-2.69450642007E-7, 1.91575175388E-6, 0.999999999998)-72.1389542832, 101.334130879, -38.908397949
27given(0.755917661587, -0.65466670062, -7.7257152413E-7), (0.654666700619, 0.755917661587, -1.10698323198E-6), (1.30870552005E-6, 3.3101132544E-7, 0.999999999999)238.169088114, -108.803928866, -38.9084527537
28given(-0.188999007952, -0.981977278246, -1.03132799437E-6), (0.981977278245, -0.188999007949, -2.28903706858E-6), (2.0528624226E-6, -1.44536639201E-6, 0.999999999997)575.308135452, 54.8619695877, -38.9082238106
29given(-0.784883076213, -0.619643894571, 2.4402741903E-5), (0.619643895009, -0.784883076013, 1.91626476332E-5), (7.27928151827E-6, 3.01614478644E-5, 0.999999999519)637.187458138, 308.7793672, -77.8193012565
30given(-0.929069266419, 0.369905795305, 2.82191748806E-5), (-0.369905794862, -0.929069266813, 1.97677541681E-5), (3.35297749433E-5, 7.92717654914E-6, 0.999999999406)413.165207762, 609.217987896, -77.8203160467
31given(-0.144188425544, 0.989550249824, 3.18090752654E-5), (-0.989550249919, -0.144188426341, 2.43929849517E-5), (2.87245848588E-5, -2.79594922841E-5, 0.999999999197)40.9661253279, 565.428536109, -77.8096637739
32given(0.784881785842, 0.61964552897, 2.61087728521E-5), (-0.619645529478, 0.784881785582, 2.14330384475E-5), (-7.21141380934E-6, -3.30005858707E-5, 0.999999999429)-107.210056236, 221.202015588, -77.7987951711
33given(0.929069149605, -0.369906088706, 2.80941645089E-5), (0.369906088337, 0.929069150011, 1.7566398507E-5), (-3.25993393049E-5, -5.92819642392E-6, 0.999999999451)116.810502901, -79.2364310013, -77.7990706536
34given(0.144186323431, -0.989550556308, 2.54250202616E-5), (0.98955055632, 0.144186323985, 2.15080267589E-5), (-2.49492200531E-5, 2.20581796417E-5, 0.999999999445)489.009877384, -35.4491711628, -77.8085627816

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Components

#1: Protein
gp56 - Tail tube protein


Mass: 15572.538 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: A0A9X8RMX9
#2: Protein
gp55 - Tail sheath protein


Mass: 53016.762 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: A0A9X8RMY4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Extended phiCD508 tail / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 19.2 ° / Axial rise/subunit: 38.9 Å / Axial symmetry: C6
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157557 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 133.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005184744
ELECTRON MICROSCOPYf_angle_d0.7237114120
ELECTRON MICROSCOPYf_chiral_restr0.048313068
ELECTRON MICROSCOPYf_plane_restr0.003914616
ELECTRON MICROSCOPYf_dihedral_angle_d5.266111232
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2TnELECTRON MICROSCOPYNCS constraints4.85761569306E-12
ens_1d_3TnELECTRON MICROSCOPYNCS constraints1.69856689614E-10
ens_1d_4TnELECTRON MICROSCOPYNCS constraints1.15742214554E-12
ens_1d_5TnELECTRON MICROSCOPYNCS constraints1.48700364657E-12
ens_1d_6TnELECTRON MICROSCOPYNCS constraints1.18624961502E-11
ens_1d_7TnELECTRON MICROSCOPYNCS constraints8.80295521883E-13
ens_1d_8TnELECTRON MICROSCOPYNCS constraints2.25713149714E-12
ens_1d_9TnELECTRON MICROSCOPYNCS constraints1.30587518509E-12
ens_1d_10TnELECTRON MICROSCOPYNCS constraints9.69336454869E-13
ens_1d_11TnELECTRON MICROSCOPYNCS constraints1.24744192355E-12
ens_1d_12TnELECTRON MICROSCOPYNCS constraints7.80894824236E-11
ens_1d_13TnELECTRON MICROSCOPYNCS constraints7.69368479997E-13
ens_1d_14TnELECTRON MICROSCOPYNCS constraints1.76327719434E-12
ens_1d_15TnELECTRON MICROSCOPYNCS constraints1.09207774123E-10
ens_1d_16TnELECTRON MICROSCOPYNCS constraints2.23804303055E-11
ens_1d_17TnELECTRON MICROSCOPYNCS constraints2.095531641E-10
ens_1d_18TnELECTRON MICROSCOPYNCS constraints1.51849534381E-12
ens_2d_2GVELECTRON MICROSCOPYNCS constraints7.95324896345E-13
ens_2d_3GVELECTRON MICROSCOPYNCS constraints6.83074841371E-13
ens_2d_4GVELECTRON MICROSCOPYNCS constraints8.37508240978E-13
ens_2d_5GVELECTRON MICROSCOPYNCS constraints7.12231364301E-13
ens_2d_6GVELECTRON MICROSCOPYNCS constraints4.2911624493E-13
ens_2d_7GVELECTRON MICROSCOPYNCS constraints1.43322191137E-12
ens_2d_8GVELECTRON MICROSCOPYNCS constraints7.48613862307E-13
ens_2d_9GVELECTRON MICROSCOPYNCS constraints1.08342865617E-12
ens_2d_10GVELECTRON MICROSCOPYNCS constraints4.47652740613E-13
ens_2d_11GVELECTRON MICROSCOPYNCS constraints1.56496374449E-11
ens_2d_12GVELECTRON MICROSCOPYNCS constraints1.1102553881E-12
ens_2d_13GVELECTRON MICROSCOPYNCS constraints3.89998584867E-12
ens_2d_14GVELECTRON MICROSCOPYNCS constraints7.83574868731E-13
ens_2d_15GVELECTRON MICROSCOPYNCS constraints1.10130957053E-12
ens_2d_16GVELECTRON MICROSCOPYNCS constraints1.2760645575E-12
ens_2d_17GVELECTRON MICROSCOPYNCS constraints2.33031801018E-12
ens_2d_18GVELECTRON MICROSCOPYNCS constraints4.159014408E-13

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