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- PDB-8ari: Cryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament -

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基本情報

登録情報
データベース: PDB / ID: 8ari
タイトルCryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament
要素
  • C-terminal-binding protein 1
  • Retinoic acid-induced protein 2
キーワードANTITUMOR PROTEIN / Complex / Tumor suppressor / oncogenic / filament assembly
機能・相同性
機能・相同性情報


Signaling by TCF7L2 mutants / Repression of WNT target genes / animal organ development / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / 酸化還元酵素; CH-OHの結合に対し酸化酵素として働く; NAD又はNADPを用いる / embryo development ending in birth or egg hatching / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / lncRNA binding / white fat cell differentiation ...Signaling by TCF7L2 mutants / Repression of WNT target genes / animal organ development / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / 酸化還元酵素; CH-OHの結合に対し酸化酵素として働く; NAD又はNADPを用いる / embryo development ending in birth or egg hatching / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / lncRNA binding / white fat cell differentiation / synaptic vesicle endocytosis / Notch signaling pathway / transcription repressor complex / SUMOylation of transcription cofactors / viral genome replication / transcription corepressor binding / transcription coregulator binding / Deactivation of the beta-catenin transactivating complex / Negative Regulation of CDH1 Gene Transcription / GABA-ergic synapse / NAD binding / transcription corepressor activity / DNA-binding transcription factor binding / protein phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / negative regulation of cell population proliferation / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
類似検索 - 分子機能
Retinoic acid-induced protein 2/sine oculis-binding protein homologue / Sine oculis-binding protein / C-terminal binding protein / : / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain ...Retinoic acid-induced protein 2/sine oculis-binding protein homologue / Sine oculis-binding protein / C-terminal binding protein / : / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / C-terminal-binding protein 1 / Retinoic acid-induced protein 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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 Å
データ登録者Mullapudi, E. / Goradia, N. / Wilmanns, M.
資金援助 ドイツ, 1件
組織認可番号国
German Research Foundation (DFG)218826742 ドイツ
引用ジャーナル: To Be Published
タイトル: Cryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament
著者: Goradia, N. / Mullapudi, E. / Wilmanns, M.
履歴
登録2022年8月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年8月23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
A: C-terminal-binding protein 1
B: C-terminal-binding protein 1
C: C-terminal-binding protein 1
D: C-terminal-binding protein 1
E: C-terminal-binding protein 1
F: C-terminal-binding protein 1
G: C-terminal-binding protein 1
H: C-terminal-binding protein 1
I: C-terminal-binding protein 1
J: C-terminal-binding protein 1
K: C-terminal-binding protein 1
L: C-terminal-binding protein 1
M: C-terminal-binding protein 1
N: C-terminal-binding protein 1
O: C-terminal-binding protein 1
P: C-terminal-binding protein 1
Q: C-terminal-binding protein 1
R: C-terminal-binding protein 1
S: C-terminal-binding protein 1
T: C-terminal-binding protein 1
U: C-terminal-binding protein 1
V: C-terminal-binding protein 1
W: C-terminal-binding protein 1
X: C-terminal-binding protein 1
a: Retinoic acid-induced protein 2
b: Retinoic acid-induced protein 2
c: Retinoic acid-induced protein 2
d: Retinoic acid-induced protein 2
e: Retinoic acid-induced protein 2
f: Retinoic acid-induced protein 2
g: Retinoic acid-induced protein 2
h: Retinoic acid-induced protein 2
i: Retinoic acid-induced protein 2
j: Retinoic acid-induced protein 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,347,05858
ポリマ－1,331,13634
非ポリマー15,92224
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法
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_1(chain "A" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_2ens_1(chain "B" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_3ens_1(chain "C" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_4ens_1(chain "D" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_5ens_1(chain "E" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_6ens_1(chain "F" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_7ens_1(chain "G" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_8ens_1(chain "H" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_9ens_1(chain "I" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_10ens_1(chain "J" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_11ens_1(chain "K" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_12ens_1(chain "L" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_13ens_1(chain "M" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_14ens_1(chain "N" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_15ens_1(chain "O" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_16ens_1(chain "P" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_17ens_1(chain "Q" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_18ens_1(chain "R" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_19ens_1(chain "S" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_20ens_1(chain "T" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_21ens_1(chain "U" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_22ens_1(chain "V" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_23ens_1(chain "W" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_24ens_1(chain "X" and (resid 28 through 32 or resid 34 through 53 or resid 55 through 357 or resid 401))
d_1ens_2(chain "a" and (resid 315 through 346 or (resid 347...
d_2ens_2(chain "b" and (resid 315 through 346 or (resid 347...
d_3ens_2chain "c"
d_4ens_2chain "d"
d_5ens_2chain "e"
d_6ens_2chain "f"
d_7ens_2(chain "h" and (resid 315 through 346 or (resid 347...
d_8ens_2(chain "a" and (resid 315 through 346 or (resid 347...
d_9ens_2chain "i"
d_10ens_2chain "j"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROLEUA45 - 49
d_12ens_1ASPPHEA51 - 71
d_13ens_1ASPTHRA73 - 375
d_14ens_1NADNADA
d_21ens_1PROLEUB45 - 49
d_22ens_1ASPPHEB51 - 71
d_23ens_1ASPTHRB73 - 375
d_24ens_1NADNADB
d_31ens_1PROLEUC45 - 49
d_32ens_1ASPPHEC51 - 71
d_33ens_1ASPTHRC73 - 375
d_34ens_1NADNADC
d_41ens_1PROLEUD - G45 - 49
d_42ens_1ASPPHED - G51 - 71
d_43ens_1ASPTHRD - G73 - 375
d_44ens_1NADNADD - H
d_51ens_1PROLEUE45 - 49
d_52ens_1ASPPHEE51 - 71
d_53ens_1ASPTHRE73 - 375
d_54ens_1NADNADE
d_61ens_1PROLEUF45 - 49
d_62ens_1ASPPHEF51 - 71
d_63ens_1ASPTHRF73 - 375
d_64ens_1NADNADF
d_71ens_1PROLEUG45 - 49
d_72ens_1ASPPHEG51 - 71
d_73ens_1ASPTHRG73 - 375
d_74ens_1NADNADG
d_81ens_1PROLEUH45 - 49
d_82ens_1ASPPHEH51 - 71
d_83ens_1ASPTHRH73 - 375
d_84ens_1NADNADH
d_91ens_1PROLEUI45 - 49
d_92ens_1ASPPHEI51 - 71
d_93ens_1ASPTHRI73 - 375
d_94ens_1NADNADI
d_101ens_1PROLEUJ45 - 49
d_102ens_1ASPPHEJ51 - 71
d_103ens_1ASPTHRJ73 - 375
d_104ens_1NADNADJ
d_111ens_1PROLEUK45 - 49
d_112ens_1ASPPHEK51 - 71
d_113ens_1ASPTHRK73 - 375
d_114ens_1NADNADK
d_121ens_1PROLEUL45 - 49
d_122ens_1ASPPHEL51 - 71
d_123ens_1ASPTHRL73 - 375
d_124ens_1NADNADL
d_131ens_1PROLEUM45 - 49
d_132ens_1ASPPHEM51 - 71
d_133ens_1ASPTHRM73 - 375
d_134ens_1NADNADM
d_141ens_1PROLEUN45 - 49
d_142ens_1ASPPHEN51 - 71
d_143ens_1ASPTHRN73 - 375
d_144ens_1NADNADN
d_151ens_1PROLEUO45 - 49
d_152ens_1ASPPHEO51 - 71
d_153ens_1ASPTHRO73 - 375
d_154ens_1NADNADO
d_161ens_1PROLEUP45 - 49
d_162ens_1ASPPHEP51 - 71
d_163ens_1ASPTHRP73 - 375
d_164ens_1NADNADP
d_171ens_1PROLEUQ45 - 49
d_172ens_1ASPPHEQ51 - 71
d_173ens_1ASPTHRQ73 - 375
d_174ens_1NADNADQ
d_181ens_1PROLEUR45 - 49
d_182ens_1ASPPHER51 - 71
d_183ens_1ASPTHRR73 - 375
d_184ens_1NADNADR
d_191ens_1PROLEUS45 - 49
d_192ens_1ASPPHES51 - 71
d_193ens_1ASPTHRS73 - 375
d_194ens_1NADNADS
d_201ens_1PROLEUT45 - 49
d_202ens_1ASPPHET51 - 71
d_203ens_1ASPTHRT73 - 375
d_204ens_1NADNADT
d_211ens_1PROLEUU45 - 49
d_212ens_1ASPPHEU51 - 71
d_213ens_1ASPTHRU73 - 375
d_214ens_1NADNADU
d_221ens_1PROLEUV45 - 49
d_222ens_1ASPPHEV51 - 71
d_223ens_1ASPTHRV73 - 375
d_224ens_1NADNADV
d_231ens_1PROLEUW45 - 49
d_232ens_1ASPPHEW51 - 71
d_233ens_1ASPTHRW73 - 375
d_234ens_1NADNADW
d_241ens_1PROLEUX45 - 49
d_242ens_1ASPPHEX51 - 71
d_243ens_1ASPTHRX73 - 375
d_244ens_1NADNADX
d_11ens_2GLUVALY1 - 22
d_21ens_2GLUVALZ1 - 22
d_31ens_2GLUVALAA1 - 22
d_41ens_2GLUVALBA1 - 22
d_51ens_2GLUVALCA1 - 22
d_61ens_2GLUVALDA1 - 22
d_71ens_2GLUVALEA1 - 22
d_81ens_2GLUVALFA1 - 22
d_91ens_2GLUVALGA1 - 22
d_101ens_2GLUVALHA1 - 22

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.998908904896, 0.0011544248914, 0.0466869041968), (-0.00123749642118, 0.999997702229, 0.00175046852007), (-0.0466847761365, -0.0018063334693, 0.998908038228)-10.6017243198, -151.558597986, 11.2832307255
2given(-0.998915854346, -0.000432624045598, -0.0465502821958), (-0.000504597990056, 0.999998695475, 0.00153441499686), (0.046549557645, 0.00155624064635, -0.998914769536)462.792630491, -151.663183063, 441.207543279
3given(0.526590511973, -0.000879830683371, 0.850118614428), (-0.00143575901561, -0.999998958699, -0.000145594614681), (0.850117857297, -0.00114389672232, -0.526591226859)-84.983925161, 351.76931043, 153.285112467
4given(-0.486295493297, 1.85059155485E-5, 0.873794422537), (-0.000243777872887, -0.999999963732, -0.000114491651003), (0.873794388727, -0.000268688519569, 0.486295480171)138.567218071, 401.991101291, -81.38396926
5given(-0.526440534523, -0.0018778686159, 0.850209878337), (-0.00124786694858, 0.999998190303, 0.00143604244695), (-0.850211036414, -0.000304957853162, -0.526441925155)153.463210209, -100.996781129, 537.666882369
6given(0.52640114161, 0.00207591283499, -0.850233808254), (-0.00116867733796, 0.999997841305, 0.00171801597946), (0.850235539309, 8.92834107815E-5, 0.526402431343)298.895677037, -101.066596042, -85.2086173272
7given(0.486232847534, 0.00027851112904, -0.873829239846), (-5.92559844223E-5, -0.999999936399, -0.000351697223384), (-0.873829282221, 0.00022278635422, -0.486232800106)313.776234827, 401.997780589, 533.790388621
8given(-0.999999967948, -0.000234120056744, 9.63921096621E-5), (0.000234096199233, -0.999999941986, -0.000247441751549), (9.64500351469E-5, -0.000247419178591, 0.999999964741)452.442241887, 452.398103091, 0.0434829442076
9given(0.48712935175, -9.25649269021E-5, 0.873329826638), (-0.000476065609857, 0.999999817663, 0.000371532532209), (-0.873329701788, -0.000596746698093, 0.487129218861)-81.4979402405, -50.4570175121, 313.731064323
10given(-0.486941875805, -8.88740027696E-7, -0.873434376233), (-0.000422403423206, 0.999999883299, 0.000234473454321), (0.873434274094, 0.00048311661414, -0.486941819354)533.901452476, -50.4428336151, 138.63791527
11given(0.999999990343, 0.00013829803771, -1.37036166738E-5), (0.000138295212389, -0.999999969227, -0.000205960335229), (-1.37321001623E-5, 0.000205958438096, -0.999999978696)-0.0351463996915, 452.411260188, 452.347819164
12given(-0.999999993367, 2.72016325222E-5, 0.000111919166958), (2.72251974396E-5, 0.999999977462, 0.000210556873965), (-0.000111913436945, 0.00021055991959, -0.99999997157)452.371790798, -0.0473640592345, 452.368480485
13given(0.486965062822, 9.80137145198E-6, 0.873421448955), (0.000311331080681, -0.999999938357, -0.000162356888057), (0.873421393523, 0.000350985375785, -0.486965035855)-81.5058722301, 502.852174509, 138.681260253
14given(-0.486036853183, -0.000282847346685, -0.873938268613), (-1.87129394894E-5, -0.999999944029, 0.000334053925274), (-0.873938314184, 0.000178716472572, 0.486036820686)533.87567503, 502.803875104, 313.889893532
15given(-0.526294381902, 0.000624146226704, -0.850302201585), (-0.00125314712892, -0.999999213945, 4.16070398156E-5), (-0.850301507232, 0.00108745131393, 0.526294750353)537.412183452, 351.691480956, 299.227068785
16given(0.486244536442, 1.73524751754E-5, -0.873822779789), (0.000233671537069, 0.999999961466, 0.000149886207773), (0.873822748718, -0.000277068861697, 0.486244513651)313.842639697, 50.4031177137, -81.3773625989
17given(0.526430561516, 0.00177174717862, -0.850216281198), (0.00110700272365, -0.999998409441, -0.00139844921984), (-0.850217406577, -0.000205005330928, -0.526431685526)298.963309859, 553.414566902, 537.638302059
18given(-0.526448419669, -0.00172465927605, 0.850205320484), (0.00106197234305, -0.999998496364, -0.00137094298633), (0.850206406494, 0.000181163767661, 0.526449459622)153.43150097, 553.416570479, -85.2341614596
19given(-0.486197145152, -0.000368176440837, 0.873849071918), (0.000121451692235, 0.999999873113, 0.000488901200319), (-0.87384914104, 0.000343832816399, -0.486197038744)138.635586388, 50.3603308888, 533.756215649
20given(-0.526778863846, 0.00114227505685, -0.850001602241), (0.00148301019834, 0.999998810125, 0.000424770105582), (0.85000107605, -0.00103680113111, -0.526779931051)537.330919067, 100.565203092, 153.31980027
21given(0.998914112325, 0.00120073562871, 0.0465741820236), (0.00131898678773, -0.999995984253, -0.00250833625621), (0.0465709831448, 0.00256704321553, -0.998911684694)-10.5927615453, 604.084250094, 440.940391735
22given(-0.998910926026, -0.00106989125907, -0.0466456557253), (0.00117925300347, -0.999996620278, -0.00231706607841), (-0.0466430190672, -0.00236954965166, 0.998908811657)462.974167995, 604.074415385, 11.4235143037
23given(0.5263823354, -0.000830859936336, 0.850247579621), (0.00146023022525, 0.999998931186, 7.31782760746E-5), (-0.850246731665, 0.00120303746285, 0.526382986042)-84.9759605688, 100.640044834, 299.169260158
24given(0.998764717138, -0.0282394701061, -0.040884864291), (-0.0290981006742, -0.999365080255, -0.0205605667218), (-0.0402782861741, 0.0217248405033, -0.998952296643)14.647040214, 310.455887531, 457.852193584
25given(-0.998366456242, 0.0376016337531, 0.0430178589694), (-0.0384845475257, -0.999061354057, -0.0198834210169), (0.0422298313158, -0.0215064634166, 0.998876425479)435.609769733, 312.0812934, -5.86113558142
26given(-0.999921237992, 0.0115080473456, -0.00500825896372), (0.011461292056, 0.999891381362, 0.0092662971137), (0.00511435195935, 0.00920816616286, -0.999944525001)451.487679187, -3.98563188659, 449.789974882
27given(-0.483881027626, -0.0119272669993, 0.875052507799), (-0.053525530718, -0.997631745367, -0.0431962752693), (0.873495374152, -0.067739507953, 0.482096660844)139.901392329, 420.407343643, -68.6984420999
28given(0.50596877728, 0.0491125424477, -0.86115245723), (0.0482307972204, -0.998426576638, -0.0286035183693), (-0.861202291345, -0.0270615823253, -0.507541411261)299.466286183, 398.705483254, 540.568964879
29given(0.999979541185, 0.00621748065275, -0.00150337778738), (0.00620930385507, -0.999966229132, -0.0053837851143), (-0.0015368005968, 0.00537434003895, -0.999984377235)-0.787240246369, 452.389600293, 451.760812559
30given(-0.999941402127, 0.0106493603407, -0.00194510599235), (-0.010647107489, -0.999942639385, -0.00116492143522), (-0.001957400088, -0.00114414342073, 0.999997429757)450.955491431, 454.543308908, 0.564576934596
31given(-0.999382210819, 0.0163919536403, 0.0310885920179), (0.0167841015022, 0.999782303587, 0.0123951350004), (-0.0308786436646, 0.0129092715041, -0.99943977311)441.971723384, 145.794728958, 457.673961538
32given(0.998008058705, -0.0415083604815, -0.0475075864433), (0.0424370416133, 0.998923958717, 0.018708880248), (0.0466798913735, -0.0206876946797, 0.998695652854)18.4875461408, 139.888406711, -6.66233461319

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要素

#1: タンパク質 ...
C-terminal-binding protein 1 / CtBP1


分子量: 49525.348 Da / 分子数: 24 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CTBP1, CTBP / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q13363, 酸化還元酵素; CH-OHの結合に対し酸化酵素として働く; NAD又はNADPを用いる
#2: タンパク質
Retinoic acid-induced protein 2


分子量: 14252.756 Da / 分子数: 10 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAI2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9Y5P3
#3: 化合物...
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


分子量: 663.425 Da / 分子数: 24 / 由来タイプ: 合成 / 式: C21H27N7O14P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: NAD*YM
研究の焦点であるリガンドがあるかY

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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: FILAMENT / 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: Complex of hCtBP1 with hRAI2 / タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT
分子量値: 1.0 MDa / 実験値: YES
由来(天然)生物種: Homo sapiens (ヒト)
由来(組換発現)生物種: Escherichia coli (大腸菌)
緩衝液pH: 7.2
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 / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/2
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE-PROPANE / 湿度: 100 % / 凍結前の試料温度: 277 K

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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）: 105000 X / 最大 デフォーカス（公称値）: 2750 nm / 最小 デフォーカス（公称値）: 750 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
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

ソフトウェア
名称バージョン分類
phenix.real_space_refine1.19.2_4158精密化
PHENIX1.19.2_4158精密化
EMソフトウェア
ID名称カテゴリ
2EPU画像取得
7UCSF ChimeraXモデルフィッティング
9PHENIXモデル精密化
10cryoSPARC初期オイラー角割当
11cryoSPARC最終オイラー角割当
12cryoSPARC分類
13cryoSPARC３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: D2 (2回x2回 2面回転対称)
3次元再構成解像度: 3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 189823 / 対称性のタイプ: POINT
原子モデル構築PDB-ID: 6CDF

6cdf

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: 71.34 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.001864830
ELECTRON MICROSCOPYf_angle_d0.414587939
ELECTRON MICROSCOPYf_chiral_restr0.041210263
ELECTRON MICROSCOPYf_plane_restr0.00311440
ELECTRON MICROSCOPYf_dihedral_angle_d8.340824325
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BELECTRON MICROSCOPYNCS constraints0.000704571069865
ens_1d_3CELECTRON MICROSCOPYNCS constraints0.000708126084204
ens_1d_4DELECTRON MICROSCOPYNCS constraints0.00071237821505
ens_1d_5EELECTRON MICROSCOPYNCS constraints0.000699921829112
ens_1d_6FELECTRON MICROSCOPYNCS constraints0.000709327636205
ens_1d_7GELECTRON MICROSCOPYNCS constraints0.000706125711891
ens_1d_8HELECTRON MICROSCOPYNCS constraints0.000703814191878
ens_1d_9IELECTRON MICROSCOPYNCS constraints0.000707079692691
ens_1d_10JELECTRON MICROSCOPYNCS constraints0.0626387438912
ens_1d_11KELECTRON MICROSCOPYNCS constraints0.0626421917958
ens_1d_12LELECTRON MICROSCOPYNCS constraints0.000704790669422
ens_1d_13MELECTRON MICROSCOPYNCS constraints0.000698587570219
ens_1d_14NELECTRON MICROSCOPYNCS constraints0.0626435484658
ens_1d_15OELECTRON MICROSCOPYNCS constraints0.0626394713354
ens_1d_16PELECTRON MICROSCOPYNCS constraints0.000704856444564
ens_1d_17QELECTRON MICROSCOPYNCS constraints0.000706302323644
ens_1d_18RELECTRON MICROSCOPYNCS constraints0.000699246686121
ens_1d_19SELECTRON MICROSCOPYNCS constraints0.000708053554798
ens_1d_20TELECTRON MICROSCOPYNCS constraints0.000710598316497
ens_1d_21UELECTRON MICROSCOPYNCS constraints0.000694591743356
ens_1d_22VELECTRON MICROSCOPYNCS constraints0.000698042953225
ens_1d_23WELECTRON MICROSCOPYNCS constraints0.000708501580065
ens_1d_24XELECTRON MICROSCOPYNCS constraints0.000703957302887
ens_2d_2aELECTRON MICROSCOPYNCS constraints0.000711199220255
ens_2d_3bELECTRON MICROSCOPYNCS constraints0.000686466577863
ens_2d_4cELECTRON MICROSCOPYNCS constraints0.000692236678082
ens_2d_5dELECTRON MICROSCOPYNCS constraints0.000685764416639
ens_2d_6eELECTRON MICROSCOPYNCS constraints0.000715128094572
ens_2d_7fELECTRON MICROSCOPYNCS constraints0.000687821667424
ens_2d_8gELECTRON MICROSCOPYNCS constraints0.000721232175836
ens_2d_9hELECTRON MICROSCOPYNCS constraints0.000710589916905
ens_2d_10iELECTRON MICROSCOPYNCS constraints0.000733879432772

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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

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