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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: Nat Commun / Year: 2026
Title: SNX-mediated biogenesis of a plant-unique vesicle derived from the multivesicular body.
Authors: Yanbin Li / Ran Tao / Hai Zhang / Xiaokang Wen / Stephen King Pong Leung / Qing Qi / Xiaohui Zheng / Haoxuan Guo / Congxian Wu / Zhifei Fu / Xiaorong Huang / Wilson Chun Yu Lau / Liwen Jiang / Yong Cui /
Abstract: Retrograde transport is central to endomembrane homeostasis, yet the identity and origin of plant retrograde carriers remain unresolved. Prevailing models propose that plant vacuolar sorting ...Retrograde transport is central to endomembrane homeostasis, yet the identity and origin of plant retrograde carriers remain unresolved. Prevailing models propose that plant vacuolar sorting receptors (VSRs) recycle either from multivesicular bodies (MVBs) to the trans-Golgi network (TGN) or from the TGN to the Golgi apparatus and/or endoplasmic reticulum (ER). However, the ultrastructural features of plant retrograde transport carriers remain largely unresolved. Here, we show that plant retrograde transport is likely mediated by a previously unrecognized class of MVB-derived spherical vesicles. Using correlative light and electron microscopy and three-dimensional electron tomography, we identify a distinct population of ~30-50 nm spherical vesicles adjacent to MVBs, including nascent vesicles budding from the MVB limiting membrane in Arabidopsis root cells. Immunogold labeling shows that these vesicles are enriched in retromer components and VSRs, suggesting that they possibly function as retrograde transport carriers. To investigate their biogenesis, we perform cryo-electron microscopy and liposome tubulation assays, showing that Arabidopsis SNX1 generates shorter membrane tubules than its mammalian counterpart, consistent with reduced membrane affinity linked to differences in the amphipathic helix. Notably, the SNX1-SNX2 heterodimer produces heterogeneous structures, including spherical vesicles, recapitulating in vivo observations. Lastly, knockdown of SNX1 or SNX2 results in vacuolar mislocalization and increased degradation of GFP-VSR2, and defects in SNX1 and VPS29 inhibit formation of spherical vesicles adjacent to MVBs, resulting in embryonic lethality before the globular stage. Together, these findings establish MVB-derived spherical vesicles as plant retrograde carriers and reveal a distinct SNX-mediated mechanism underlying their formation.
History
DepositionJan 30, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 (eV)
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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