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- PDB-23as: Structure of Arabidopsis SNX1 (Class l, 7-fold) -

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Basic information

Entry
Database: PDB / ID: 23as
TitleStructure of Arabidopsis SNX1 (Class l, 7-fold)
ComponentsSorting nexin 1
KeywordsMEMBRANE PROTEIN / SNX protein / Arabidopsis thaliana / tube
Function / homology
Function and homology information


positive gravitropism / root development / Golgi to vacuole transport / retromer complex / protein targeting to vacuole / endosome to lysosome transport / multivesicular body / phosphatidylinositol binding / protein localization to plasma membrane / endosome ...positive gravitropism / root development / Golgi to vacuole transport / retromer complex / protein targeting to vacuole / endosome to lysosome transport / multivesicular body / phosphatidylinositol binding / protein localization to plasma membrane / endosome / endosome membrane / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsLi, Y.B. / Tao, R. / Zhang, H. / Wen, X.K. / Leung, S.K.P. / Lau, W.C.Y. / Jiang, L.W. / Cui, Y.
Funding support China, Hong Kong, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270727, 32000141 China
Other government2021J01029
Other government20720210094
The University Grants Committee, Research Grants Council (RGC)CUHK14106823, C4033-19E, C4002-20W, C4002-21EF, C4014-23G, R4005-18, Senior Research Fellow Scheme SRFS2122-4S01 and CRS_CUHK405/23 Hong Kong
CitationJournal: To Be Published
Title: Plant unique recycling endosomes are derived from multivesicular bodies
Authors: Li, Y.B. / Tao, R. / Zhang, H. / Wen, X.K. / Leung, S.K.P. / Qi, Q. / Zheng, X.H. / Guo, H.X. / Wu, C.X. / Fu, Z.F. / Huang, X.R. / Sun, M.X. / Lau, W.C.Y. / Jiang, L.W. / Cui, Y.
History
DepositionJan 30, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Sorting nexin 1
1: Sorting nexin 1
2: Sorting nexin 1
3: Sorting nexin 1
4: Sorting nexin 1
5: Sorting nexin 1
6: Sorting nexin 1
7: Sorting nexin 1
8: Sorting nexin 1
9: Sorting nexin 1
A: Sorting nexin 1
AA: Sorting nexin 1
AB: Sorting nexin 1
AC: Sorting nexin 1
AD: Sorting nexin 1
AE: Sorting nexin 1
AF: Sorting nexin 1
AG: Sorting nexin 1
AH: Sorting nexin 1
AI: Sorting nexin 1
AJ: Sorting nexin 1
AK: Sorting nexin 1
AL: Sorting nexin 1
AM: Sorting nexin 1
AN: Sorting nexin 1
AO: Sorting nexin 1
AP: Sorting nexin 1
AQ: Sorting nexin 1
AR: Sorting nexin 1
AS: Sorting nexin 1
B: Sorting nexin 1
C: Sorting nexin 1
D: Sorting nexin 1
E: Sorting nexin 1
F: Sorting nexin 1
G: Sorting nexin 1
H: Sorting nexin 1
I: Sorting nexin 1
J: Sorting nexin 1
K: Sorting nexin 1
L: Sorting nexin 1
M: Sorting nexin 1
N: Sorting nexin 1
O: Sorting nexin 1
P: Sorting nexin 1
Q: Sorting nexin 1
R: Sorting nexin 1
S: Sorting nexin 1
T: Sorting nexin 1
U: Sorting nexin 1
V: Sorting nexin 1
W: Sorting nexin 1
X: Sorting nexin 1
Y: Sorting nexin 1
Z: Sorting nexin 1
a: Sorting nexin 1
b: Sorting nexin 1
c: Sorting nexin 1
d: Sorting nexin 1
e: Sorting nexin 1
f: Sorting nexin 1
g: Sorting nexin 1
h: Sorting nexin 1
i: Sorting nexin 1
j: Sorting nexin 1
k: Sorting nexin 1
l: Sorting nexin 1
m: Sorting nexin 1
n: Sorting nexin 1
o: Sorting nexin 1
p: Sorting nexin 1
q: Sorting nexin 1
r: Sorting nexin 1
s: Sorting nexin 1
t: Sorting nexin 1
u: Sorting nexin 1
v: Sorting nexin 1
w: Sorting nexin 1
x: Sorting nexin 1
y: Sorting nexin 1
z: Sorting nexin 1


Theoretical massNumber of molelcules
Total (without water)3,774,12481
Polymers3,774,12481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "0"
d_2ens_1chain "1"
d_3ens_1chain "2"
d_4ens_1chain "3"
d_5ens_1chain "4"
d_6ens_1chain "5"
d_7ens_1chain "6"
d_8ens_1chain "7"
d_9ens_1chain "8"
d_10ens_1chain "9"
d_11ens_1chain "A"
d_12ens_1chain "AA"
d_13ens_1chain "AB"
d_14ens_1chain "AC"
d_15ens_1chain "AD"
d_16ens_1chain "AE"
d_17ens_1chain "AF"
d_18ens_1chain "AG"
d_19ens_1chain "AH"
d_20ens_1chain "AI"
d_21ens_1chain "AJ"
d_22ens_1chain "AK"
d_23ens_1chain "AL"
d_24ens_1chain "AM"
d_25ens_1chain "AN"
d_26ens_1chain "AO"
d_27ens_1chain "AP"
d_28ens_1chain "AQ"
d_29ens_1chain "AR"
d_30ens_1chain "AS"
d_31ens_1chain "B"
d_32ens_1chain "C"
d_33ens_1chain "D"
d_34ens_1chain "E"
d_35ens_1chain "F"
d_36ens_1chain "G"
d_37ens_1chain "H"
d_38ens_1chain "I"
d_39ens_1chain "J"
d_40ens_1chain "K"
d_41ens_1chain "L"
d_42ens_1chain "M"
d_43ens_1chain "N"
d_44ens_1chain "O"
d_45ens_1chain "P"
d_46ens_1chain "Q"
d_47ens_1chain "R"
d_48ens_1chain "S"
d_49ens_1chain "T"
d_50ens_1chain "U"
d_51ens_1chain "V"
d_52ens_1chain "W"
d_53ens_1chain "X"
d_54ens_1chain "Y"
d_55ens_1chain "Z"
d_56ens_1chain "a"
d_57ens_1chain "b"
d_58ens_1chain "c"
d_59ens_1chain "d"
d_60ens_1chain "e"
d_61ens_1chain "f"
d_62ens_1chain "g"
d_63ens_1chain "h"
d_64ens_1chain "i"
d_65ens_1chain "j"
d_66ens_1chain "k"
d_67ens_1chain "l"
d_68ens_1chain "m"
d_69ens_1chain "n"
d_70ens_1chain "o"
d_71ens_1chain "p"
d_72ens_1chain "q"
d_73ens_1chain "r"
d_74ens_1chain "s"
d_75ens_1chain "t"
d_76ens_1chain "u"
d_77ens_1chain "v"
d_78ens_1chain "w"
d_79ens_1chain "x"
d_80ens_1chain "y"
d_81ens_1chain "z"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 24 - 402 / Label seq-ID: 24 - 402

Dom-IDAuth asym-IDLabel asym-ID
d_10A
d_21B
d_32C
d_43D
d_54E
d_65F
d_76G
d_87H
d_98I
d_109J
d_11AK
d_12AAL
d_13ABM
d_14ACN
d_15ADO
d_16AEP
d_17AFQ
d_18AGR
d_19AHS
d_20AIT
d_21AJU
d_22AKV
d_23ALW
d_24AMX
d_25ANY
d_26AOZ
d_27APAA
d_28AQBA
d_29ARCA
d_30ASDA
d_31BEA
d_32CFA
d_33DGA
d_34EHA
d_35FIA
d_36GJA
d_37HKA
d_38ILA
d_39JMA
d_40KNA
d_41LOA
d_42MPA
d_43NQA
d_44ORA
d_45PSA
d_46QTA
d_47RUA
d_48SVA
d_49TWA
d_50UXA
d_51VYA
d_52WZA
d_53XAB
d_54YBB
d_55ZCB
d_56aDB
d_57bEB
d_58cFB
d_59dGB
d_60eHB
d_61fIB
d_62gJB
d_63hKB
d_64iLB
d_65jMB
d_66kNB
d_67lOB
d_68mPB
d_69nQB
d_70oRB
d_71pSB
d_72qTB
d_73rUB
d_74sVB
d_75tWB
d_76uXB
d_77vYB
d_78wZB
d_79xAC
d_80yBC
d_81zCC

NCS oper:
IDCodeMatrixVector
1given(-0.53970797675681, -0.84180595546009, 0.0088336389438567), (-0.84180946183767, 0.53954494159127, -0.015750744866397), (0.0084929256234635, -0.015937043489652, -0.9998369271332)876.30561068229, 484.37586709031, 615.20168028404
2given(-0.83756363324268, -0.54606927255693, 0.017190399601682), (0.54633253790178, -0.83729988208461, 0.02120531751471), (0.002813947249879, 0.027152477423618, 0.99962734289866)874.04120130278, 469.50974829102, 246.23621539598
3given(0.93479843930121, -0.35456354075487, 0.020894340080176), (-0.35492967366478, -0.93472767195425, 0.017581411638605), (0.013296790298111, -0.023851097466578, -0.99962709072804)147.51385121643, 839.9586743658, 658.11242435321
4given(-0.81398890765373, -0.58074082041926, 0.012734116202324), (0.58079707739408, -0.81330520429008, 0.034776422546926), (-0.009839365181764, 0.035703559674583, 0.99931398605212)881.35935455059, 444.2491823318, 303.28561935175
5given(0.91895518348039, -0.39434693701194, 0.0034444192274261), (-0.39434542300686, -0.91896158512542, -0.0011368453338706), (0.0036136004283401, -0.00031358104487644, -0.9999934217578)173.78329831442, 851.26589967085, 706.644884279
6given(0.64491120919188, -0.76413328350126, 0.013778871660839), (0.76425631718398, 0.64483715755837, -0.0098651850674858), (-0.0013468121781713, 0.016892758141237, 0.9998564000992)408.4426326631, -148.95575716567, 40.566543096744
7given(-0.46813226966342, -0.88346405840548, 0.018532015688798), (-0.883556738396, 0.46765734410776, -0.024981964236164), (0.013404034273036, -0.028068950956423, -0.99951611585677)863.40020693197, 528.68910986353, 448.18247389873
8given(0.6651969306906, -0.74652008531765, 0.014859529505889), (0.7466618625322, 0.66514019002413, -0.0091973177938608), (-0.0030176878150496, 0.017213071544281, 0.99984729020399)394.18825262935, -150.07685073539, 98.218305163631
9given(-0.49661759216417, -0.86796912940724, -0.00074669209979306), (-0.86791438686339, 0.49659559318187, -0.010836692664305), (0.0097767187037114, -0.0047336274020025, -0.99994100253115)871.79516697612, 508.51600150421, 494.51249726952
10given(-0.23470422699121, 0.97192405079178, -0.016660291862884), (-0.97206584617776, -0.23469392356051, 0.0025986416639294), (-0.0013843869324009, 0.016804812890223, 0.99985783076223)101.01297881677, 811.83710586221, 7.9520377601039
11given(0.9994197329276, 0.034042183111378, 0.001152043371651), (-0.034025129850483, 0.99934261393155, -0.012515211509043), (-0.0015773311562567, 0.012468750918586, 0.9999210180194)-13.522847079317, 15.556074321891, 51.241149564602
12given(-0.98374596779282, -0.17950455940194, -0.0046887104082346), (-0.17939940272962, 0.98362313356517, -0.017360455515165), (0.007728204942394, -0.016237126265281, -0.99983830221642)799.91496941982, 75.724084373285, 452.4259424827
13given(-0.1716635814825, -0.98480114465689, 0.026425750227534), (0.98515240426065, -0.17166989118014, 0.0020466659864162), (0.0025209466597613, 0.026384729384373, 0.99964868373007)787.79637984256, 67.184025676559, 83.451889682858
14given(0.37794848428382, -0.92540561767849, 0.027917485500394), (-0.92572455516212, -0.37818271902324, -0.0034465928241916), (0.013747406936188, -0.02454126731225, -0.9996042892071)562.89619563321, 851.2413988732, 495.02503264641
15given(-0.13036768602985, -0.99090585132961, 0.033314564982239), (0.99141425950948, -0.12994497489055, 0.014562607663547), (-0.01010111283432, 0.034927028236404, 0.99933881652725)774.26591714374, 44.611569012157, 140.49293373102
16given(0.33832054254839, -0.94102806597765, 0.0023215365891275), (-0.94102228417854, -0.33832697972367, -0.0034518792653079), (0.0040337537315386, -0.0010167759980544, -0.99999134746127)589.04584816774, 839.74715076765, 543.57774048181
17given(-0.19752482212972, -0.98028914170651, 0.0041404462241759), (0.98029786858265, -0.19752384536018, 0.00064758508628983), (0.00018301623128529, 0.004186784737524, 0.99999121863075)800.81222075417, 78.485782043996, 38.535957262678
18given(0.39332755458956, -0.91920058996232, 0.019071188046868), (-0.91938130761921, -0.39336212915998, 0.0020607142266624), (0.0056076734028345, -0.018344229491862, -0.99981600469454)556.90350888387, 851.73698852302, 437.65731540874
19given(0.99623144879937, 0.086734473498386, 0.00017756707836698), (-0.086732533540647, 0.99621931070144, -0.004955059148341), (-0.00060667019879874, 0.0049209849116582, 0.99998770785384)-31.285028726786, 34.386179535423, 169.02293320611
20given(-0.9929574294622, -0.11840000095317, -0.0041210496368187), (-0.11830766480897, 0.99281236614667, -0.018080433448661), (0.0062321523784931, -0.017465548961651, -0.99982804265344)779.65168863928, 50.186212102825, 567.57096515777
21given(0.99821812877151, 0.059670387006175, -0.00011093435940027), (-0.059670344449804, 0.99820985864823, -0.0040654754611872), (-0.00013185272291697, 0.0040648507988695, 0.99999172976722)-21.985721083826, 23.495408247621, 112.15765913569
22given(-0.98938449812291, -0.14528607132992, -0.0032050509493166), (-0.14519993732632, 0.98921857699059, -0.019067908567648), (0.005940797463537, -0.018400119951488, -0.99981305378119)788.05468784316, 61.644290914151, 511.01501556569
23given(0.61507827868347, 0.78845730964158, -0.0037124068398748), (-0.78846597162739, 0.61507349170672, -0.0024518126730214), (0.00035025341372212, 0.0044351631846544, 0.99999010327606)-148.01302279412, 433.01543130755, 5.7130719757121
24given(-0.95618112165648, 0.29276767186002, -0.0021801149994135), (-0.29277533429875, -0.95616624993558, 0.0053578083566953), (-0.00051595930455563, 0.0057613191018884, 0.99998327035416)613.69920394258, 826.27957022031, 307.95226881221
25given(0.87633661151307, 0.48169113161379, -0.0027923191819654), (0.48166220194968, -0.87618266490252, 0.017477440811149), (0.0059721465799226, -0.016661075864095, -0.9998433587399)-132.33353911553, 508.18205875052, 706.64534640097
26given(0.50498136140164, 0.86311944102647, -0.0043191618521862), (-0.86312999148224, 0.50497103254084, -0.0032975898032654), (-0.00066516224751957, 0.005393219520885, 0.99998523526219)-134.57528735037, 501.0488039469, 291.86012350099
27given(-0.6704205270779, 0.74179204588625, -0.016759401316321), (0.74195549372107, 0.6704146813291, -0.0067970872817644), (0.0061937234119402, -0.016991636716155, -0.99983644766132)346.84091591054, -151.72374479236, 690.40151639766
28given(-0.064990807632258, -0.99786782415497, 0.0060000366280594), (0.99788583866095, -0.064988312184677, 0.00061014696527582), (-0.00021891377115072, 0.0060270055266351, 0.99998181347519)758.11006346687, 23.778360367517, 323.0426042935
29given(0.26718080007053, -0.96348991415676, 0.017366789912692), (-0.96362998414002, -0.26723810457204, -0.0010242709871569), (0.0056279427842576, -0.016461493946292, -0.99984866128683)620.25230686955, 822.86399624022, 721.99764000018
30given(0.023228915997841, 0.99934266901276, -0.027832487348836), (0.99963954777455, -0.022842958805741, 0.014105805829538), (0.013460757284295, -0.028150117645527, -0.99951307089496)-2.5502159181417, 2.211338407472, 415.53088337989
31given(-0.26071944907269, 0.96525914019798, -0.017325159147339), (-0.96540978319139, -0.26073290679576, 0.0015171790243126), (-0.0030527681846504, 0.017121436215552, 0.99984875707695)113.26257905442, 819.21577572313, 65.60457706899
32given(0.055700899830697, 0.99843840384811, -0.004261863358499), (0.9983991027372, -0.055655665246463, 0.010083579698254), (0.0098306363785928, -0.0048167050158212, -0.99994007717522)-19.081326725262, 16.491241476286, 461.86312007483
33given(0.55479172838916, 0.83198919679907, 0.00033840893337533), (-0.83198866104235, 0.55479176969755, -0.00097988408287259), (-0.0010029994620941, 0.0002620791885942, 0.99999946265314)-142.07828012943, 470.32429768219, 179.74281976548
34given(-0.71280169651497, 0.70105754997128, -0.020785886405073), (0.70132478089502, 0.71276694278939, -0.010336197038651), (0.0075692237341746, -0.02194531601341, -0.99973051866847)378.61325499669, -152.02957056178, 577.56657731353
35given(-0.90898092738432, 0.41678623645762, -0.0065503244991108), (-0.416834903978, -0.90892020252249, 0.010617357115551), (-0.0015285539570029, 0.012381379000876, 0.9999221794604)551.98803392718, 853.5577918006, 18.595484899485
36given(0.79945424958138, 0.60071585962243, -0.0036549725513146), (0.60067765834815, -0.79929585481435, 0.017677308561255), (0.0076976351984593, -0.016327659803907, -0.99983706369472)-148.48806853384, 435.6984558742, 419.809962405
37given(0.59438964016329, 0.8038585089372, -0.022637430856961), (-0.80417352658512, 0.59423637313056, -0.013713934092191), (0.0024279221984229, 0.02635584295535, 0.9996496760045)-141.50210003698, 448.77969023366, 50.836371683983
38given(-0.7522674733422, 0.65832131872423, -0.026583639038569), (0.65871239721118, 0.75233669924348, -0.009352471957774), (0.013842915575584, -0.024546533046871, -0.99960284183457)410.5321514872, -151.75914333124, 462.33055219741
39given(0.56026545558274, 0.82798830507817, -0.023194523803151), (-0.82825040276434, 0.55965877859802, -0.027987887717245), (-0.010192624851886, 0.034891520344588, 0.99933912772725)-139.49977015288, 475.01391035081, 107.88006775663
40given(-0.7236789776992, 0.6901268302661, -0.0037007273754126), (0.6901243951103, 0.72368770471196, 0.002103645020614), (0.0041299527701585, -0.0010315985634648, -0.99999093960621)382.01085505569, -153.18501469622, 510.88776872566
41given(0.99364428764973, 0.11256544541719, -0.0002238729229085), (-0.11255136905098, 0.99348440308132, -0.017914523685956), (-0.0017941420809646, 0.017825861330483, 0.9998394969804)-39.392349923298, 47.823752925478, 219.8621157448
42given(-0.99482081242728, -0.10106433887266, -0.010842074052864), (-0.10072447778009, 0.99451170468209, -0.028302805978501), (0.013642973923061, -0.027064158190476, -0.99954059477541)776.94539559996, 44.859936749731, 627.19931279494
43given(0.99025939177128, 0.13923171022344, 0.000931599181886), (-0.13919107692683, 0.99009379351947, -0.018442454776068), (-0.0034901450872235, 0.018133143755927, 0.99982948945548)-48.215054409568, 59.005672875993, 277.52820162974
44given(-0.99761114563621, -0.068385161331998, -0.0097709678136049), (-0.068344720646107, 0.99765199740152, -0.004414888511251), (0.010049938418894, -0.0037365479199023, -0.99994251682155)764.83592512553, 26.638702201075, 673.51494877588
45given(0.52616170897457, 0.85033221897717, -0.0094325700806635), (-0.85038059868977, 0.52609315890433, -0.0088783740676795), (-0.0025871569315564, 0.012692735064744, 0.99991609702794)-136.62137045101, 490.15396808114, 231.00304965464
46given(-0.69503017654902, 0.7187704036381, -0.017382765607162), (0.71892833589274, 0.695067953397, -0.0047526846086364), (0.008666114280436, -0.015800221973793, -0.99983761253959)364.862805408, -153.62773973494, 631.38719224773
47given(0.72439957033273, -0.68917795501476, 0.016703557208622), (0.68937403755156, 0.72407660709696, -0.021828957941473), (0.0029493815641386, 0.027327886427995, 0.99962217250908)350.90886424246, -147.92228567654, 262.4228132231
48given(-0.56050479483667, -0.82806012404116, 0.01228030691958), (-0.82804712807759, 0.56013769775355, -0.024160158066693), (0.013127400639919, -0.023710557317062, -0.99963267294749)878.6035970634, 473.77816444809, 674.42486088156
49given(-0.59522060187027, -0.80356004170331, -0.0019221048271743), (-0.80355493111679, 0.59522368269841, -0.0028705805741993), (0.0034507661596794, -0.00016411188509271, -0.9999940326223)883.56403843392, 445.59854732667, 722.95000440777
50given(-0.91885263787148, 0.39451837702946, -0.0080672214954689), (-0.39459822606145, -0.91872902949387, 0.015139694660252), (-0.0014387028091602, 0.017094459666498, 0.99985284396402)563.68118758128, 847.68161535959, 73.155395680214
51given(0.81420036907167, 0.58056049992127, -0.0052215835461819), (0.58042811652168, -0.8137404830886, 0.030489797208682), (0.013452157992613, -0.0278555580432, -0.99952143915548)-146.60970201851, 445.53372138409, 480.716062027
52given(-0.92854665699932, 0.37120966382457, 0.0021192589811741), (-0.37121506548106, -0.92854057014604, -0.0034328927679882), (0.00069349497231583, -0.0039743019650204, 0.99999186196119)573.29768034118, 846.8704864305, 140.20557865599
53given(0.83691177561315, 0.5473356495784, -0.001538356469882), (0.54726260395851, -0.83674688250165, 0.018928732982388), (0.0090731553822612, -0.016683564497921, -0.99981965200083)-141.56642847587, 469.79282966612, 533.13121718068
54given(-0.89415240654767, -0.44776271338449, -0.0001623809166878), (0.44776269191735, -0.89415241902017, 0.00015260179185278), (-0.00021352268184645, 6.3741143056512E-5, 0.99999997517256)862.20297024967, 531.59957345325, 32.683084501767
55given(0.96665980757235, -0.25576765787381, 0.012317532623215), (-0.25597278858866, -0.96648093283308, 0.019812571066206), (0.0068372455218243, -0.022304969308469, -0.99972783317152)101.79012724806, 813.95689038678, 431.1282678747
56given(-0.93631691752686, 0.35114935613421, 0.0021816598087581), (-0.35115489018288, -0.93631206374903, -0.003156323602693), (0.00093437339709973, -0.0037214196969517, 0.9999926389638)582.76752531476, 841.80880256616, 197.16115073018
57given(0.84878832186347, 0.52872299538902, -0.0032216168383112), (0.5286533052458, -0.84853927547758, 0.022511793013321), (0.0091688342157334, -0.020810865403723, -0.99974138673973)-139.50986963928, 479.86467904865, 592.38101147993
58given(-0.28758714362599, 0.95743547266824, -0.024717412841658), (-0.95775093538967, -0.28742012720807, 0.010139834116799), (0.0026039549271914, 0.026589211200002, 0.99964305292764)127.68261293507, 824.27440102425, 115.97447530439
59given(0.07655890712408, 0.99679386909182, -0.023253306881337), (0.99697214999752, -0.076212579435078, 0.015432914992551), (0.013611240548968, -0.024364426461607, -0.99961047856348)-22.347633908738, 22.578886046292, 527.6399061329
60given(-0.88116654596592, -0.47280211888297, -0.0019169377321113), (0.47279543387403, -0.88116671416572, 0.0031144107395438), (-0.003161641719393, 0.0018379951473198, 0.99999331287538)866.79313561626, 517.142969199, 89.583617806907
61given(0.95735737584534, -0.28869010484332, 0.011174895080993), (-0.28882656382174, -0.95728562982763, 0.013543963837627), (0.0067875581355876, -0.016194020225447, -0.99984582949748)118.24428345186, 823.84478599437, 484.66791230793
62given(-0.86828926058781, -0.49603833472077, -0.0044418954644743), (0.49604689976461, -0.86829513163181, -0.0010186355631469), (-0.0033515939185897, -0.0030878587941642, 0.99998961591922)871.34266545681, 504.61161155915, 149.47708633485
63given(0.95007041286971, -0.31193724013131, 0.0078338246617057), (-0.312003199676, -0.95003409720418, 0.0094455037648657), (0.0044959961640773, -0.011418072021801, -0.99992470399015)130.04198312991, 830.68407067339, 540.19771907991
64given(-0.94775573091097, 0.31887628389642, -0.0087743999128306), (-0.31898020306599, -0.94762941558496, 0.015815206924926), (-0.003271785048231, 0.017787812864618, 0.99983643119067)602.35529894703, 830.24637859796, 244.92725120423
65given(0.8613978767193, 0.50788994109667, 0.0064424930191254), (0.5078341785516, -0.86141212446696, 0.0085789810668655), (0.0099068197871881, -0.0041181979252211, -0.99994244602755)-138.98955234938, 495.00302616889, 641.06222382297
66given(-0.3113353275661, 0.95029912058812, 0.0013766694408316), (-0.95029910364425, -0.31133255224039, -0.0019119436256213), (-0.0013883163354366, -0.0019035033306074, 0.99999722462256)133.02946474726, 833.05022806895, 188.86330826949
67given(0.11156005607099, 0.9935469123846, -0.020466723735454), (0.99372784512028, -0.11137341823803, 0.010046469159671), (0.0077021894314076, -0.021459137937073, -0.99974005705331)-34.364759953797, 39.293733181183, 585.07203804272
68given(-0.85125932354599, -0.52472350208098, 0.0047760276272739), (0.52474071229203, -0.85117892566779, 0.01190047739712), (-0.0021792061115099, 0.012636568478009, 0.99991778071891)874.45488370242, 484.34324568172, 198.22736631786
69given(0.94338808126235, -0.33143237510745, 0.013096139231572), (-0.33158764164114, -0.94334434483346, 0.012291581736751), (0.008280340754416, -0.015938249632714, -0.99983869106753)137.90381949149, 835.30256749397, 598.9352559356
70given(-0.33778986481997, 0.94121512102563, -0.0034789621453486), (-0.94121854215686, -0.33779582302001, -0.0012797852717993), (-0.0023797321306269, 0.0028421651847042, 0.99999312946242)147.22169286478, 839.62552828307, 243.8114542451
71given(0.14377988820954, 0.98958102631339, -0.0075323374192703), (0.98960106364862, -0.14374268423245, 0.0052702519072542), (0.0041326228921202, -0.0082117653519313, -0.9999577432761)-47.343361476218, 54.565641726011, 636.52906087047
72given(-0.37797612468067, 0.92509250678894, -0.036577357126299), (-0.92576312033784, -0.37807934089584, 0.0043193761263597), (-0.0098333205855243, 0.035494589316233, 0.99932148977971)175.73026819927, 849.47429024269, 287.0124111046
73given(0.17237874591581, 0.98503073779327, 0.00011644289237842), (0.98502398444064, -0.17237799964046, 0.0036844696560498), (0.0036493880565362, -0.00052042521686433, -0.99999320553912)-57.523910466905, 67.216932081187, 690.36162500532
74given(-0.11910713735097, -0.99273104339959, 0.017279042300419), (0.99287986723011, -0.11905825836015, 0.0038341055495448), (-0.0017490229202843, 0.017612682561412, 0.99984335489706)773.36526242426, 44.640348665989, 203.62259346728
75given(0.32693117028861, -0.94456397268589, 0.030247502336131), (-0.94494967560514, -0.32719166205213, -0.0039657101895441), (0.013642597533441, -0.0272858532471, -0.99953457256121)588.32300254595, 839.72709318109, 610.97997061055
76given(-0.092407342627094, -0.99556708793144, 0.017523026459677), (0.99571536028576, -0.092331759066891, 0.0050761755897806), (-0.0034357414925488, 0.017917022501555, 0.99983357414375)764.50354530159, 33.480432453394, 261.28704586967
77given(0.29606254234795, -0.95514470001321, 0.0067507818164137), (-0.95511579243299, -0.29611308044673, -0.0084182322048154), (0.010039624672992, -0.0039554550954931, -0.99994177846083)608.83309074502, 832.13133937717, 657.29882289854
78given(0.68200354204538, -0.73134856636114, 0.0006656718888443), (0.73134842486727, 0.68200384853444, 0.00048169323420135), (-0.00080627644631201, 0.00015832159548008, 0.99999966242622)385.84044203408, -152.50399249093, 163.40866726882
79given(-0.51848892697791, -0.85495187894802, 0.015050491172723), (-0.85505234059983, 0.51823692749603, -0.017775877312338), (0.007397799405475, -0.022085553258179, -0.99972871365248)871.59758546486, 497.39184281469, 561.38115519556
80given(0.70648917079384, -0.70764445073227, 0.01060108007974), (0.70771982748319, 0.70645640921912, -0.0072102469022634), (-0.002386909758181, 0.012596555920368, 0.99991781134289)365.27723878511, -151.75980461922, 214.66411579019

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Components

#1: Protein ...
Sorting nexin 1 / AtSNX1 / Vacuolar protein sorting-associated protein 5 homolog


Mass: 46594.121 Da / Num. of mol.: 81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SNX1, VPS5, At5g06140, K16F4.11, MBL20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FG38
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Arabidopsis thaliana SNX1 complex with liposome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -51.6 ° / Axial rise/subunit: 8.18 Å / Axial symmetry: C1
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49380 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 297.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028255879
ELECTRON MICROSCOPYf_angle_d0.588343764
ELECTRON MICROSCOPYf_chiral_restr0.040437422
ELECTRON MICROSCOPYf_plane_restr0.00544469
ELECTRON MICROSCOPYf_dihedral_angle_d14.916199549
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2A0ELECTRON MICROSCOPYNCS constraints0.00070511703926909
ens_1d_3A0ELECTRON MICROSCOPYNCS constraints0.00070156989548573
ens_1d_4A0ELECTRON MICROSCOPYNCS constraints0.00070542338723078
ens_1d_5A0ELECTRON MICROSCOPYNCS constraints0.00070645801044226
ens_1d_6A0ELECTRON MICROSCOPYNCS constraints0.00070875896247095
ens_1d_7A0ELECTRON MICROSCOPYNCS constraints0.00070598539204958
ens_1d_8A0ELECTRON MICROSCOPYNCS constraints0.00071097756126116
ens_1d_9A0ELECTRON MICROSCOPYNCS constraints0.00070371465308703
ens_1d_10A0ELECTRON MICROSCOPYNCS constraints0.00070818933398667
ens_1d_11A0ELECTRON MICROSCOPYNCS constraints0.00070807413141661
ens_1d_12A0ELECTRON MICROSCOPYNCS constraints0.00070948931667275
ens_1d_13A0ELECTRON MICROSCOPYNCS constraints0.00070911072491866
ens_1d_14A0ELECTRON MICROSCOPYNCS constraints0.00070600362510427
ens_1d_15A0ELECTRON MICROSCOPYNCS constraints0.00070567125967525
ens_1d_16A0ELECTRON MICROSCOPYNCS constraints0.00070009188232149
ens_1d_17A0ELECTRON MICROSCOPYNCS constraints0.00070193738239512
ens_1d_18A0ELECTRON MICROSCOPYNCS constraints0.0007082693184429
ens_1d_19A0ELECTRON MICROSCOPYNCS constraints0.00070644410390617
ens_1d_20A0ELECTRON MICROSCOPYNCS constraints0.00071130931709112
ens_1d_21A0ELECTRON MICROSCOPYNCS constraints0.00070694100669292
ens_1d_22A0ELECTRON MICROSCOPYNCS constraints0.00070678197147926
ens_1d_23A0ELECTRON MICROSCOPYNCS constraints0.00071379417589062
ens_1d_24A0ELECTRON MICROSCOPYNCS constraints0.00070227957845971
ens_1d_25A0ELECTRON MICROSCOPYNCS constraints0.00070545324391049
ens_1d_26A0ELECTRON MICROSCOPYNCS constraints0.00070725971917738
ens_1d_27A0ELECTRON MICROSCOPYNCS constraints0.00070133211554681
ens_1d_28A0ELECTRON MICROSCOPYNCS constraints0.00070805694330913
ens_1d_29A0ELECTRON MICROSCOPYNCS constraints0.00070457336878072
ens_1d_30A0ELECTRON MICROSCOPYNCS constraints0.00071262773887476
ens_1d_31A0ELECTRON MICROSCOPYNCS constraints0.00070600912428199
ens_1d_32A0ELECTRON MICROSCOPYNCS constraints0.00071346737505612
ens_1d_33A0ELECTRON MICROSCOPYNCS constraints0.0007028033434839
ens_1d_34A0ELECTRON MICROSCOPYNCS constraints0.00070022997248185
ens_1d_35A0ELECTRON MICROSCOPYNCS constraints0.00071144526273523
ens_1d_36A0ELECTRON MICROSCOPYNCS constraints0.00070297399293052
ens_1d_37A0ELECTRON MICROSCOPYNCS constraints0.00070526562908513
ens_1d_38A0ELECTRON MICROSCOPYNCS constraints0.00070712157346541
ens_1d_39A0ELECTRON MICROSCOPYNCS constraints0.00071630478629355
ens_1d_40A0ELECTRON MICROSCOPYNCS constraints0.00071857414710859
ens_1d_41A0ELECTRON MICROSCOPYNCS constraints0.00070752073960086
ens_1d_42A0ELECTRON MICROSCOPYNCS constraints0.00070785704292703
ens_1d_43A0ELECTRON MICROSCOPYNCS constraints0.00070129523284597
ens_1d_44A0ELECTRON MICROSCOPYNCS constraints0.00070037104709747
ens_1d_45A0ELECTRON MICROSCOPYNCS constraints0.00070658825653969
ens_1d_46A0ELECTRON MICROSCOPYNCS constraints0.00069973126000954
ens_1d_47A0ELECTRON MICROSCOPYNCS constraints0.00070382811678376
ens_1d_48A0ELECTRON MICROSCOPYNCS constraints0.00070294167939588
ens_1d_49A0ELECTRON MICROSCOPYNCS constraints0.00070277724552555
ens_1d_50A0ELECTRON MICROSCOPYNCS constraints0.00070716609611101
ens_1d_51A0ELECTRON MICROSCOPYNCS constraints0.00070645611435996
ens_1d_52A0ELECTRON MICROSCOPYNCS constraints0.00070619028970529
ens_1d_53A0ELECTRON MICROSCOPYNCS constraints0.00071032468869834
ens_1d_54A0ELECTRON MICROSCOPYNCS constraints0.00070645603867588
ens_1d_55A0ELECTRON MICROSCOPYNCS constraints0.00070021726344193
ens_1d_56A0ELECTRON MICROSCOPYNCS constraints0.0007095371003083
ens_1d_57A0ELECTRON MICROSCOPYNCS constraints0.00070754932951901
ens_1d_58A0ELECTRON MICROSCOPYNCS constraints0.00070564613215737
ens_1d_59A0ELECTRON MICROSCOPYNCS constraints0.037825494009146
ens_1d_60A0ELECTRON MICROSCOPYNCS constraints0.00071245339747721
ens_1d_61A0ELECTRON MICROSCOPYNCS constraints0.00070880464718586
ens_1d_62A0ELECTRON MICROSCOPYNCS constraints0.00070644332250046
ens_1d_63A0ELECTRON MICROSCOPYNCS constraints0.0007107439404872
ens_1d_64A0ELECTRON MICROSCOPYNCS constraints0.00070639071170178
ens_1d_65A0ELECTRON MICROSCOPYNCS constraints0.00070706248891939
ens_1d_66A0ELECTRON MICROSCOPYNCS constraints0.00070614970842357
ens_1d_67A0ELECTRON MICROSCOPYNCS constraints0.00069900746064436
ens_1d_68A0ELECTRON MICROSCOPYNCS constraints0.00070126454388923
ens_1d_69A0ELECTRON MICROSCOPYNCS constraints0.00071312164591519
ens_1d_70A0ELECTRON MICROSCOPYNCS constraints0.00070360188804958
ens_1d_71A0ELECTRON MICROSCOPYNCS constraints0.00070867372120045
ens_1d_72A0ELECTRON MICROSCOPYNCS constraints0.00071078402648322
ens_1d_73A0ELECTRON MICROSCOPYNCS constraints0.00070955061794778
ens_1d_74A0ELECTRON MICROSCOPYNCS constraints0.00070729326552761
ens_1d_75A0ELECTRON MICROSCOPYNCS constraints0.00071539953656877
ens_1d_76A0ELECTRON MICROSCOPYNCS constraints0.00069868183300051
ens_1d_77A0ELECTRON MICROSCOPYNCS constraints0.00070876292797868
ens_1d_78A0ELECTRON MICROSCOPYNCS constraints0.00070790675951223
ens_1d_79A0ELECTRON MICROSCOPYNCS constraints0.00071024956390593
ens_1d_80A0ELECTRON MICROSCOPYNCS constraints0.00071077890257213
ens_1d_81A0ELECTRON MICROSCOPYNCS constraints0.0007052764454407

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