[English] 日本語
Yorodumi
- PDB-9g8s: C3 reconstruction of extended phiCD508 needle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g8s
TitleC3 reconstruction of extended phiCD508 needle
Components
  • Baseplate J family protein
  • Peptidoglycan-binding LysM protein
  • Phage protein
  • Tail sheath
  • Tail tape measure
  • XkdM-related protein
  • XkdQ-related protein
  • XkdS-related protein
  • XkdT-related protein
KeywordsVIRUS / Bacteriophage / needle / baseplate
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral tail assembly / membrane
Similarity search - Function
Phage tail tape measure protein / Phage-related minor tail protein / : / YQBQ-like / Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / : / Protein of unknown function DUF2634 / Contractile injection system sheath initiator ...Phage tail tape measure protein / Phage-related minor tail protein / : / YQBQ-like / Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / : / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / 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 / Baseplate protein J-like / Baseplate J-like protein barrel 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 / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / Phage protein / XkdQ-related protein / XkdM-related protein / Peptidoglycan-binding LysM protein / XkdT-related protein / Tail sheath / Baseplate J family protein / Tail tape measure / XkdS-related protein
Similarity search - Component
Biological speciesClostridioides phage phiCD508 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 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 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Baseplate J family protein
N: XkdT-related protein
T: Peptidoglycan-binding LysM protein
Z: XkdM-related protein
g: Tail sheath
m: XkdS-related protein
G: Baseplate J family protein
A: Baseplate J family protein
M: XkdT-related protein
S: Peptidoglycan-binding LysM protein
Y: XkdM-related protein
e: Tail sheath
k: XkdS-related protein
H: Baseplate J family protein
B: Baseplate J family protein
O: XkdT-related protein
U: Peptidoglycan-binding LysM protein
a: XkdM-related protein
f: Tail sheath
l: XkdS-related protein
I: Baseplate J family protein
D: Baseplate J family protein
P: XkdT-related protein
V: Peptidoglycan-binding LysM protein
b: XkdM-related protein
h: Tail sheath
n: XkdS-related protein
J: Baseplate J family protein
E: Baseplate J family protein
Q: XkdT-related protein
W: Peptidoglycan-binding LysM protein
c: XkdM-related protein
i: Tail sheath
o: XkdS-related protein
K: Baseplate J family protein
F: Baseplate J family protein
R: XkdT-related protein
X: Peptidoglycan-binding LysM protein
d: XkdM-related protein
j: Tail sheath
p: XkdS-related protein
L: Baseplate J family protein
r: Phage protein
v: Phage protein
q: XkdQ-related protein
s: Phage protein
t: XkdQ-related protein
u: XkdQ-related protein
w: Tail tape measure
x: Tail tape measure
y: Tail tape measure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,841,32552
Polymers1,841,26951
Non-polymers561
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "D"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "A"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_1ens_2(chain "K" and (resid 2 through 134 or resid 136 through 375))
d_2ens_2(chain "I" and (resid 2 through 134 or resid 136 through 375))
d_3ens_2(chain "G" and (resid 2 through 134 or resid 136 through 375))
d_1ens_3(chain "H" and (resid 2 through 116 or resid 118 through 162 or resid 164 through 375))
d_2ens_3(chain "J" and (resid 2 through 116 or resid 118 through 162 or resid 164 through 375))
d_3ens_3(chain "L" and (resid 2 through 116 or resid 118 through 162 or resid 164 through 375))
d_1ens_4chain "M"
d_2ens_4chain "N"
d_3ens_4chain "O"
d_4ens_4chain "P"
d_5ens_4chain "Q"
d_6ens_4chain "R"
d_1ens_5(chain "V" and (resid 2 through 140 or resid 154 through 221))
d_2ens_5(chain "T" and (resid 2 through 140 or resid 154 through 221))
d_3ens_5(chain "U" and (resid 2 through 140 or resid 154 through 221))
d_4ens_5(chain "S" and (resid 2 through 140 or resid 154 through 221))
d_5ens_5(chain "W" and (resid 2 through 140 or resid 154 through 221))
d_6ens_5(chain "X" and (resid 2 through 140 or resid 154 through 221))
d_1ens_6chain "b"
d_2ens_6chain "Z"
d_3ens_6chain "a"
d_4ens_6chain "Y"
d_5ens_6chain "c"
d_6ens_6chain "d"
d_1ens_7(chain "e" and (resid 13 through 371 or resid 373 through 472))
d_2ens_7(chain "f" and (resid 13 through 371 or resid 373 through 472))
d_3ens_7(chain "g" and (resid 13 through 371 or resid 373 through 472))
d_4ens_7(chain "h" and (resid 13 through 371 or resid 373 through 472))
d_5ens_7(chain "i" and (resid 13 through 371 or resid 373 through 472))
d_6ens_7(chain "j" and (resid 13 through 371 or resid 373 through 472))
d_1ens_8chain "n"
d_2ens_8chain "l"
d_3ens_8chain "m"
d_4ens_8chain "k"
d_5ens_8chain "o"
d_6ens_8chain "p"
d_1ens_9chain "q"
d_2ens_9chain "t"
d_3ens_9chain "u"
d_1ens_10chain "s"
d_2ens_10chain "r"
d_3ens_10chain "v"
d_1ens_11chain "x"
d_2ens_11chain "w"
d_3ens_11chain "y"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUGLYGLYDV2 - 3782 - 378
d_21ens_1GLUGLUGLYGLYBO2 - 3782 - 378
d_31ens_1GLUGLUGLYGLYCA2 - 3782 - 378
d_41ens_1GLUGLUGLYGLYAH2 - 3782 - 378
d_51ens_1GLUGLUGLYGLYECA2 - 3782 - 378
d_61ens_1GLUGLUGLYGLYFJA2 - 3782 - 378
d_11ens_2GLUGLUASNASNKIA2 - 1342 - 134
d_12ens_2THRTHRGLUGLUKIA136 - 375136 - 375
d_21ens_2GLUGLUASNASNIU2 - 1342 - 134
d_22ens_2THRTHRGLUGLUIU136 - 375136 - 375
d_31ens_2GLUGLUASNASNGG2 - 1342 - 134
d_32ens_2THRTHRGLUGLUGG136 - 375136 - 375
d_11ens_3GLUGLUASPASPHN2 - 1162 - 116
d_12ens_3LYSLYSGLYGLYHN118 - 162118 - 162
d_13ens_3ILEILEGLUGLUHN164 - 375164 - 375
d_21ens_3GLUGLUASPASPJBA2 - 1162 - 116
d_22ens_3LYSLYSGLYGLYJBA118 - 162118 - 162
d_23ens_3ILEILEGLUGLUJBA164 - 375164 - 375
d_31ens_3GLUGLUASPASPLPA2 - 1162 - 116
d_32ens_3LYSLYSGLYGLYLPA118 - 162118 - 162
d_33ens_3ILEILEGLUGLULPA164 - 375164 - 375
d_11ens_4METMETSERSERMI1 - 1571 - 157
d_21ens_4METMETSERSERNB1 - 1571 - 157
d_31ens_4METMETSERSEROP1 - 1571 - 157
d_41ens_4METMETSERSERPW1 - 1571 - 157
d_51ens_4METMETSERSERQDA1 - 1571 - 157
d_61ens_4METMETSERSERRKA1 - 1571 - 157
d_11ens_5VALVALLYSLYSVX2 - 1402 - 140
d_12ens_5THRTHRSERSERVX154 - 221154 - 222
d_21ens_5VALVALLYSLYSTC2 - 1402 - 140
d_22ens_5THRTHRSERSERTC154 - 221154 - 222
d_31ens_5VALVALLYSLYSUQ2 - 1402 - 140
d_32ens_5THRTHRSERSERUQ154 - 221154 - 222
d_41ens_5VALVALLYSLYSSJ2 - 1402 - 140
d_42ens_5THRTHRSERSERSJ154 - 221154 - 222
d_51ens_5VALVALLYSLYSWEA2 - 1402 - 140
d_52ens_5THRTHRSERSERWEA154 - 221154 - 222
d_61ens_5VALVALLYSLYSXLA2 - 1402 - 140
d_62ens_5THRTHRSERSERXLA154 - 221154 - 222
d_11ens_6GLUGLULEULEUbY8 - 1371 - 130
d_21ens_6GLUGLULEULEUZD8 - 1371 - 130
d_31ens_6GLUGLULEULEUaR8 - 1371 - 130
d_41ens_6GLUGLULEULEUYK8 - 1371 - 130
d_51ens_6GLUGLULEULEUcFA8 - 1371 - 130
d_61ens_6GLUGLULEULEUdMA8 - 1371 - 130
d_11ens_7GLUGLUASPASPeL13 - 3711 - 359
d_12ens_7LYSLYSLEULEUeL373 - 472361 - 460
d_21ens_7GLUGLUASPASPfS13 - 3711 - 359
d_22ens_7LYSLYSLEULEUfS373 - 472361 - 460
d_31ens_7GLUGLUASPASPgE13 - 3711 - 359
d_32ens_7LYSLYSLEULEUgE373 - 472361 - 460
d_41ens_7GLUGLUASPASPhZ13 - 3711 - 359
d_42ens_7LYSLYSLEULEUhZ373 - 472361 - 460
d_51ens_7GLUGLUASPASPiGA13 - 3711 - 359
d_52ens_7LYSLYSLEULEUiGA373 - 472361 - 460
d_61ens_7GLUGLUASPASPjNA13 - 3711 - 359
d_62ens_7LYSLYSLEULEUjNA373 - 472361 - 460
d_11ens_8LEULEUGLYGLYnAA24 - 1481 - 125
d_21ens_8LEULEUGLYGLYlT24 - 1481 - 125
d_31ens_8LEULEUGLYGLYmF24 - 1481 - 125
d_41ens_8LEULEUGLYGLYkM24 - 1481 - 125
d_51ens_8LEULEUGLYGLYoHA24 - 1481 - 125
d_61ens_8LEULEUGLYGLYpOA24 - 1481 - 125
d_11ens_9LYSLYSTYRTYRqSA2 - 3171 - 316
d_21ens_9LYSLYSTYRTYRtUA2 - 3171 - 316
d_31ens_9LYSLYSTYRTYRuVA2 - 3171 - 316
d_11ens_10PHEPHEPROPROsTA6 - 1171 - 112
d_21ens_10PHEPHEPROPROrQA6 - 1171 - 112
d_31ens_10PHEPHEPROPROvRA6 - 1171 - 112
d_11ens_11LYSLYSGLYGLYxXA1401 - 14241401 - 1424
d_21ens_11LYSLYSGLYGLYwWA1401 - 14241401 - 1424
d_31ens_11LYSLYSGLYGLYyYA1401 - 14241401 - 1424

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8
ens_9
ens_10
ens_11

NCS oper:
IDCodeMatrixVector
1given(0.497385293858, 0.867529068277, -0.0010886454948), (-0.867529747679, 0.497385015366, -0.000532335209732), (7.96596876497E-5, 0.00120920805614, 0.999999265735)-96.2396123369, 362.989962886, -0.223016538866
2given(-0.999994790026, -0.00322330409336, 0.00017387047596), (0.00322353683004, -0.999993885945, 0.00135531690856), (0.000169500814367, 0.00135587032528, 0.999999066442)530.458878027, 528.747059064, -0.291814335694
3given(-0.500201573323, 0.865908816631, 0.000554368911046), (-0.865908856842, -0.500201751991, 0.000242792235374), (0.000487532237775, -0.000358587891907, 0.999999816864)167.852264675, 626.92400362, -0.0392391787274
4given(0.502703884206, -0.864458001282, 0.00108112165286), (0.864458677038, 0.502703523208, -0.000602866631756), (-2.23307803837E-5, 0.00123764839119, 0.999999233864)360.680376936, -96.8461978503, -0.23935880195
5given(-0.500004788966, -0.866022623237, 0.000164477965317), (0.866022618381, -0.500004809426, -0.000122490125446), (0.000188318993463, 8.11959888658E-5, 0.999999978972)626.924673584, 168.070569694, -0.0903690592303
6given(-0.500631761076, 0.865660348916, 1.07734515996E-5), (-0.865660238871, -0.500631703634, 0.00049815106612), (0.000436623157138, 0.000240064096828, 0.999999875865)168.254198137, 626.879767348, -0.124742821823
7given(-0.499766430553, -0.866158707002, 0.0016152948332), (0.866159245705, -0.499767790613, -0.0005626231903), (0.00129459330502, 0.00111792237075, 0.999998537138)626.357488705, 168.147324716, -0.649958958434
8given(-0.499832704229, -0.866117905607, 0.00265355783487), (0.866121325043, -0.49983372624, 0.000310512976838), (0.00105739685123, 0.00245350756892, 0.9999964311)625.982286168, 167.858756511, -0.958823058023
9given(-0.499598135804, 0.866257271963, 0.000203645463426), (-0.866256906752, -0.499598120396, 0.000830422255824), (0.000821100208663, 0.000238468121719, 0.999999634464)167.728170353, 626.636321735, -0.309119075164
10given(0.497357335019, 0.86754215005, -0.00250981872542), (-0.867532250767, 0.497363654273, 0.00414599655595), (0.00484511937908, 0.000115306889822, 0.999988255692)-96.1127095988, 361.691713575, -1.06134747549
11given(0.502561839122, -0.864539601118, -0.00169586465251), (0.864527254125, 0.502563895348, -0.00470722502553), (0.00492186279169, 0.000899550454591, 0.999987482959)361.599148744, -95.8707800776, -1.27616723663
12given(-0.500384436329, -0.865803042647, 0.000712195407896), (0.86580323487, -0.50038460557, -7.06874912826E-5), (0.000417573063298, 0.000581250167535, 0.99999974389)626.742041691, 168.218024664, -0.271376822721
13given(-0.999988342458, -0.00211355316471, 0.0043414101441), (0.00211721308874, -0.999997407073, 0.000838603747732), (0.00433962645354, 0.000847785662054, 0.999990224403)529.164753969, 529.300779139, -1.20322266925
14given(-0.499890645551, 0.866088497766, 0.000237756859262), (-0.866088306042, -0.499890694815, 0.000582559496393), (0.000623400520663, 8.52976072356E-5, 0.999999802048)167.836109226, 626.771233203, -0.189434904155
15given(-0.999995068543, 0.00312354115851, 0.000326160941612), (-0.00312427054419, -0.999992565099, -0.00226023903401), (0.000319098566986, -0.00226124690276, 0.999997392466)529.05593057, 531.584879911, 0.411781589472
16given(0.502953845667, 0.864309109762, 0.00268177383187), (-0.864313201345, 0.502952623488, 0.00116125269687), (-0.000345123899695, -0.00290194903559, 0.999995729782)-98.2626601873, 360.441007672, 0.751067195693
17given(-0.500212677147, 0.865901911835, 0.00107550099919), (-0.865902374134, -0.500213028484, 6.78519509447E-5), (0.000596732745989, -0.000897338462554, 0.999999419347)167.674261082, 626.978640938, 0.0556602056139
18given(0.497079461077, -0.867704796675, -0.000628651695613), (0.867703934024, 0.497077557411, 0.00194545552468), (-0.00137559244116, -0.00151252953317, 0.999997909998)363.363269374, -97.322669149, 0.681230565107
19given(-0.499461884689, -0.86633505437, 0.0011829252846), (0.866335107499, -0.49946278616, -0.000637775178757), (0.00114335415263, 0.00070626531081, 0.999999096965)626.491315604, 168.0533975, -0.496252301813
20given(-0.999999716335, -0.000716575990409, -0.000232054655845), (0.00071699952176, -0.999998068091, -0.0018302253888), (-0.000230742711966, -0.00183039125271, 0.999998298211)530.144152363, 530.335282435, 0.528596739565
21given(0.50034913507, 0.865823126033, 0.00102832926502), (-0.865823525394, 0.500349489835, -0.000104386449733), (-0.000604904225357, -0.000838121999666, 0.999999465821)-97.3584664062, 361.85299281, 0.402660103229
22given(-0.499142555424, 0.866519835878, -0.000288783107238), (-0.866519848511, -0.499142411883, 0.000452543691383), (0.000247994188527, 0.000476120108894, 0.999999855904)167.645013581, 626.763909446, -0.172972157161
23given(0.499842048078, -0.866116499197, 0.000369854823772), (0.86611587939, 0.499842141675, 0.00105682292784), (-0.00110020080175, -0.000207907400767, 0.999999373166)361.928466965, -97.2352711177, 0.361045103676
24given(-0.500790320941, -0.86556768054, 0.00128251934854), (0.865568521028, -0.500790453646, 0.00023862639779), (0.000435726148714, 0.00122961016604, 0.9999991491)626.669462691, 168.305378982, -0.413944713174
25given(0.501137750109, -0.865367431025, 0.000405877252042), (0.865367390135, 0.501137353165, -0.000795835472091), (0.000485289846204, 0.000750056136256, 0.999999600955)361.463912994, -96.9207585663, -0.328379186706
26given(0.498929773163, 0.866642023047, -0.000827852804209), (-0.86664221934, 0.49893007842, 0.00020125840806), (0.000587459658441, 0.000617038379646, 0.999999637077)-96.7353431711, 362.33241598, -0.330259290132
27given(-0.500287016865, -0.865859609423, 0.000193719319984), (0.86585924518, -0.500286570133, 0.00105606839663), (-0.000817491795263, 0.000696070971931, 0.999999423596)626.916810785, 167.842381751, -0.0574432964494
28given(-0.999999475, -0.000834498469363, -0.000594652415628), (0.000833978468821, -0.99999927015, 0.000874173396482), (-0.000595381477982, 0.00087367701023, 0.999999441105)530.361145892, 529.583358109, -0.183219737976
29given(-0.500012920805, 0.866017589732, -0.000783136680696), (-0.866017791874, -0.500013164321, -0.000140225408205), (-0.000513016319844, 0.000608095783024, 0.999999683517)168.197601717, 627.027419246, -0.113652678966
30given(0.503198244744, 0.864168112628, -0.00223597912779), (-0.864170495263, 0.503199074609, -0.000215473774765), (0.000938937062691, 0.00204069321551, 0.999997476981)-96.8409788693, 360.704867851, -0.746905053817
31given(-0.999991266029, 0.00401347128471, 0.00116615330188), (-0.00400842403751, -0.999982726753, 0.00429868952073), (0.00118338582558, 0.00429397753918, 0.999990080628)528.582984789, 529.863696347, -1.31342922253
32given(-0.500000031154, 0.866023787323, 0.00166392203735), (-0.866024119148, -0.50000166307, 0.000749653945795), (0.00148118193522, -0.00106616962048, 0.99999833469)167.394895892, 626.742776233, -0.159604569375
33given(0.49706249334, -0.867711375717, 0.0024178846112), (0.867714660064, 0.497059286447, -0.00182605197456), (0.000382654071422, 0.00300569587092, 0.999995409674)362.529533259, -96.1683039547, -0.851595036091
34given(-0.500290366291, -0.865857191719, 0.000934315458558), (0.865857059995, -0.500291015344, -0.000672029249362), (0.00104931098802, 0.000472773876733, 0.999999337715)626.705411407, 168.387464921, -0.417630409692
35given(-0.499872865455, 0.86609877405, -0.000178802695859), (-0.866098173449, -0.499872744344, -0.00109243309239), (-0.00103553355632, -0.000391216971917, 0.99999938731)167.896328979, 627.276789523, 0.416806689293
36given(-0.500854585063, -0.865531416344, -0.000227908212079), (0.865531397374, -0.50085462794, 0.000204526006962), (-0.00029117256725, -9.48239249224E-5, 0.999999953113)627.0413314, 168.342226331, 0.119661432555
37given(-0.492279099953, -0.870423608849, 0.00490192889012), (0.870433108771, -0.492286567733, -0.000372000240343), (0.00273695154028, 0.00408367325931, 0.999987916281)624.33684604, 164.932250984, -1.78550672782
38given(-0.503602663734, 0.863923120074, -0.00460431114083), (-0.863933990412, -0.503604287298, 0.000884322717852), (-0.00155476398902, 0.00442316817331, 0.999989009086)171.211811484, 627.093193096, -0.767098696433
39given(-0.477039498166, -0.878785741744, -0.0129975881453), (0.878875968799, -0.477038264643, -0.00339492765316), (-0.00321693287755, -0.0130427824573, 0.999909764513)628.733541668, 159.938150709, 4.11584077424
40given(-0.514775631452, 0.857293580097, 0.00733258398239), (-0.857307524504, -0.51469183511, -0.0107760521946), (-0.00546421925924, -0.0118335284952, 0.999915051347)171.499782853, 632.244210322, 4.44401388902

-
Components

-
Protein , 9 types, 51 molecules CGAHBIDJEKFLNMOPQRTSUVWXZYabcd...

#1: Protein
Baseplate J family protein


Mass: 41502.496 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp23 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QE72
#2: Protein
XkdT-related protein


Mass: 18034.832 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp24 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QE20
#3: Protein
Peptidoglycan-binding LysM protein


Mass: 25899.830 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp19 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QE19
#4: Protein
XkdM-related protein


Mass: 14657.557 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp14 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QE18
#5: Protein
Tail sheath


Mass: 51405.023 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp13 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QE70
#6: Protein
XkdS-related protein


Mass: 14454.414 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp22 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QEB8
#7: Protein Phage protein


Mass: 12476.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp21 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QD14
#8: Protein XkdQ-related protein


Mass: 36291.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp20 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QDX2
#9: Protein Tail tape measure


Mass: 150075.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides phage phiCD508 (virus) / Gene: phiMMP02_gp17 / Production host: Clostridioides difficile (bacteria) / Strain (production host): CD117 / References: UniProt: J9QEB7

-
Non-polymers , 1 types, 1 molecules

#10: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Extended phiCD508 needle complex / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

-
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 magnification: 81000 X / 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)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17759 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 107.1 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00397884
ELECTRON MICROSCOPYf_angle_d0.5748132015
ELECTRON MICROSCOPYf_chiral_restr0.044515267
ELECTRON MICROSCOPYf_plane_restr0.003916860
ELECTRON MICROSCOPYf_dihedral_angle_d5.112412969
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2VDELECTRON MICROSCOPYNCS constraints1.22833740356E-12
ens_1d_3VDELECTRON MICROSCOPYNCS constraints1.93819846667E-10
ens_1d_4VDELECTRON MICROSCOPYNCS constraints5.9223960548E-12
ens_1d_5VDELECTRON MICROSCOPYNCS constraints5.84860519792E-11
ens_1d_6VDELECTRON MICROSCOPYNCS constraints8.70563892269E-12
ens_2d_2IAKELECTRON MICROSCOPYNCS constraints1.40837893854E-11
ens_2d_3IAKELECTRON MICROSCOPYNCS constraints3.96282615705E-10
ens_3d_2NHELECTRON MICROSCOPYNCS constraints1.74584692012E-12
ens_3d_3NHELECTRON MICROSCOPYNCS constraints1.91491778345E-12
ens_4d_2IMELECTRON MICROSCOPYNCS constraints5.05605765203E-10
ens_4d_3IMELECTRON MICROSCOPYNCS constraints1.9086300289E-10
ens_4d_4IMELECTRON MICROSCOPYNCS constraints1.1826621108E-12
ens_4d_5IMELECTRON MICROSCOPYNCS constraints1.64941173873E-12
ens_4d_6IMELECTRON MICROSCOPYNCS constraints1.57476352607E-12
ens_5d_2XVELECTRON MICROSCOPYNCS constraints2.39570664513E-12
ens_5d_3XVELECTRON MICROSCOPYNCS constraints8.9335231731E-12
ens_5d_4XVELECTRON MICROSCOPYNCS constraints1.51171203466E-12
ens_5d_5XVELECTRON MICROSCOPYNCS constraints1.4632353194E-12
ens_5d_6XVELECTRON MICROSCOPYNCS constraints8.43396680329E-11
ens_6d_2YbELECTRON MICROSCOPYNCS constraints2.87786503606E-13
ens_6d_3YbELECTRON MICROSCOPYNCS constraints2.3861889313E-11
ens_6d_4YbELECTRON MICROSCOPYNCS constraints6.50676937562E-12
ens_6d_5YbELECTRON MICROSCOPYNCS constraints9.36534007748E-12
ens_6d_6YbELECTRON MICROSCOPYNCS constraints7.79289649139E-13
ens_7d_2LeELECTRON MICROSCOPYNCS constraints5.38877168204E-10
ens_7d_3LeELECTRON MICROSCOPYNCS constraints3.81797682291E-10
ens_7d_4LeELECTRON MICROSCOPYNCS constraints1.20832112722E-12
ens_7d_5LeELECTRON MICROSCOPYNCS constraints2.67391048561E-12
ens_7d_6LeELECTRON MICROSCOPYNCS constraints1.30924118293E-12
ens_8d_2AAnELECTRON MICROSCOPYNCS constraints4.72715251083E-13
ens_8d_3AAnELECTRON MICROSCOPYNCS constraints7.63801903205E-13
ens_8d_4AAnELECTRON MICROSCOPYNCS constraints3.59165188956E-12
ens_8d_5AAnELECTRON MICROSCOPYNCS constraints2.68392676568E-12
ens_8d_6AAnELECTRON MICROSCOPYNCS constraints2.87096153038E-12
ens_9d_2SAqELECTRON MICROSCOPYNCS constraints4.99193303814E-12
ens_9d_3SAqELECTRON MICROSCOPYNCS constraints1.91229202653E-10
ens_10d_2TAsELECTRON MICROSCOPYNCS constraints7.37081527435E-12
ens_10d_3TAsELECTRON MICROSCOPYNCS constraints6.73736795315E-13
ens_11d_2XAxELECTRON MICROSCOPYNCS constraints3.95505792281E-13
ens_11d_3XAxELECTRON MICROSCOPYNCS constraints6.50377029695E-13

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more