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

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Basic information

Entry
Database: PDB / ID: 8ari
TitleCryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament
Components
  • C-terminal-binding protein 1
  • Retinoic acid-induced protein 2
KeywordsANTITUMOR PROTEIN / Complex / Tumor suppressor / oncogenic / filament assembly
Function / homology
Function and homology information


Signaling by TCF7L2 mutants / Repression of WNT target genes / animal organ development / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / embryo development ending in birth or egg hatching / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / synaptic vesicle endocytosis / white fat cell differentiation ...Signaling by TCF7L2 mutants / Repression of WNT target genes / animal organ development / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / embryo development ending in birth or egg hatching / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex / viral genome replication / transcription corepressor binding / SUMOylation of transcription cofactors / Deactivation of the beta-catenin transactivating complex / transcription coregulator binding / transcription corepressor activity / NAD binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / 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 ...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 dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / 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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / C-terminal-binding protein 1 / Retinoic acid-induced protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMullapudi, E. / Goradia, N. / Wilmanns, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)218826742 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament
Authors: Goradia, N. / Mullapudi, E. / Wilmanns, M.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,347,05858
Polymers1,331,13634
Non-polymers15,92224
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
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 domain segments:
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 ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
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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Components

#1: Protein ...
C-terminal-binding protein 1 / CtBP1


Mass: 49525.348 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP1, CTBP / Production host: Escherichia coli (E. coli)
References: UniProt: Q13363, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Protein
Retinoic acid-induced protein 2


Mass: 14252.756 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAI2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5P3
#3: Chemical...
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of hCtBP1 with hRAI2 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 1.0 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2750 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameCategory
2EPUimage acquisition
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189823 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6CDF

6cdf

RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 71.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
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-IDTypeRms 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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