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- PDB-9g8s: C3 reconstruction of extended phiCD508 needle -

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基本情報

登録情報
データベース: PDB / ID: 9g8s
タイトルC3 reconstruction of extended phiCD508 needle
要素
  • 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
キーワードVIRUS / Bacteriophage / needle / baseplate
機能・相同性
機能・相同性情報


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral tail assembly / membrane
類似検索 - 分子機能
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 / Protein of unknown function (DUF2634) / Phage tail tube protein ...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 / Protein of unknown function (DUF2634) / 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 / 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.
類似検索 - ドメイン・相同性
: / 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
類似検索 - 構成要素
生物種Clostridioides phage phiCD508 (ファージ)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.96 Å
データ登録者Wilson, J.S. / Fagan, R.P. / Bullough, P.A.
資金援助 英国, 1件
組織認可番号国
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P02002X/1 英国
引用ジャーナル: Life Sci Alliance / 年: 2025
タイトル: Molecular mechanism of bacteriophage contraction structure of an S-layer-penetrating bacteriophage.
著者: Jason S Wilson / Louis-Charles Fortier / Robert P Fagan / Per A Bullough /
要旨: 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.
履歴
登録2024年7月23日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年4月9日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,841,32552
ポリマ－1,841,26951
非ポリマー561
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_5551
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
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ドメイン領域:
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アンサンブル:
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:
IDCodeMatrixベクター
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

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要素

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タンパク質 , 9種, 51分子 CGAHBIDJEKFLNMOPQRTSUVWXZYabcd...

#1: タンパク質
Baseplate J family protein


分子量: 41502.496 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp23 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QE72
#2: タンパク質
XkdT-related protein


分子量: 18034.832 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp24 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QE20
#3: タンパク質
Peptidoglycan-binding LysM protein


分子量: 25899.830 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp19 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QE19
#4: タンパク質
XkdM-related protein


分子量: 14657.557 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp14 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QE18
#5: タンパク質
Tail sheath


分子量: 51405.023 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp13 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QE70
#6: タンパク質
XkdS-related protein


分子量: 14454.414 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp22 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QEB8
#7: タンパク質 Phage protein


分子量: 12476.309 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp21 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QD14
#8: タンパク質 XkdQ-related protein


分子量: 36291.719 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp20 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QDX2
#9: タンパク質 Tail tape measure


分子量: 150075.156 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Clostridioides phage phiCD508 (ファージ)
遺伝子: phiMMP02_gp17 / 発現宿主: Clostridioides difficile (バクテリア) / 株 (発現宿主): CD117 / 参照: UniProt: J9QEB7

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非ポリマー , 1種, 1分子

#10: 化合物 ChemComp-FE2 / FE (II) ION


分子量: 55.845 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Fe / タイプ: SUBJECT OF INVESTIGATION

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationN

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Extended phiCD508 needle complex / タイプ: COMPLEX / Entity ID: #1-#9 / 由来: NATURAL
由来(天然)生物種: Clostridioides difficile (バクテリア) / 株: CD117
緩衝液pH: 7.4
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R2/2
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: TFS KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 81000 X / 最大 デフォーカス（公称値）: 3000 nm / 最小 デフォーカス（公称値）: 1500 nm
撮影電子線照射量: 42 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

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解析

CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C3 (3回回転対称)
3次元再構成解像度: 3.96 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 17759 / 対称性のタイプ: POINT
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 107.1 Å2
拘束条件
Refine-IDタイプDev ideal数
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-IDタイプRms 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

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る