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- PDB-8v2d: Computational Designed Nanocage O43_129 -

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Basic information

Entry
Database: PDB / ID: 8v2d
TitleComputational Designed Nanocage O43_129
Components
  • O43_129 component A
  • O43_129 component B
KeywordsDE NOVO PROTEIN / De Novo / Nanocage / O43_129 / extendable nanomaterials
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.77 Å
AuthorsWeidle, C. / Kibler, R.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2024
Title: Blueprinting extendable nanomaterials with standardized protein blocks.
Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / ...Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / Nicolas Coudray / S John Calise / Fatima A Davila-Hernandez / Hannah L Han / Kenneth D Carr / Zhe Li / Ryan McHugh / Gabriella Reggiano / Alex Kang / Banumathi Sankaran / Miles S Dickinson / Brian Coventry / T J Brunette / Yulai Liu / Justas Dauparas / Andrew J Borst / Damian Ekiert / Justin M Kollman / Gira Bhabha / David Baker /
Abstract: A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The ...A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints.
History
DepositionNov 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
y: O43_129 component B
A: O43_129 component B
C: O43_129 component B
D: O43_129 component B
E: O43_129 component B
F: O43_129 component B
G: O43_129 component B
H: O43_129 component B
I: O43_129 component B
J: O43_129 component A
K: O43_129 component A
L: O43_129 component B
M: O43_129 component B
N: O43_129 component B
O: O43_129 component B
P: O43_129 component B
Q: O43_129 component B
R: O43_129 component B
S: O43_129 component B
T: O43_129 component B
U: O43_129 component B
V: O43_129 component B
W: O43_129 component B
X: O43_129 component A
Y: O43_129 component A
Z: O43_129 component A
a: O43_129 component A
b: O43_129 component A
c: O43_129 component A
d: O43_129 component A
e: O43_129 component A
f: O43_129 component A
g: O43_129 component A
h: O43_129 component A
i: O43_129 component A
j: O43_129 component A
k: O43_129 component A
l: O43_129 component A
m: O43_129 component A
n: O43_129 component A
o: O43_129 component A
p: O43_129 component A
q: O43_129 component A
r: O43_129 component A
s: O43_129 component A
t: O43_129 component B
u: O43_129 component B
z: O43_129 component B


Theoretical massNumber of molelcules
Total (without water)1,642,94148
Polymers1,642,94148
Non-polymers00
Water0
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 "A"
d_2ens_1chain "C"
d_3ens_1chain "D"
d_4ens_1chain "E"
d_5ens_1chain "F"
d_6ens_1chain "G"
d_7ens_1chain "H"
d_8ens_1chain "I"
d_9ens_1chain "L"
d_10ens_1chain "M"
d_11ens_1chain "N"
d_12ens_1chain "O"
d_13ens_1chain "P"
d_14ens_1chain "Q"
d_15ens_1chain "R"
d_16ens_1chain "S"
d_17ens_1chain "T"
d_18ens_1chain "U"
d_19ens_1chain "V"
d_20ens_1chain "W"
d_21ens_1chain "t"
d_22ens_1chain "u"
d_23ens_1chain "y"
d_24ens_1chain "z"
d_1ens_2chain "J"
d_2ens_2chain "K"
d_3ens_2chain "X"
d_4ens_2chain "Y"
d_5ens_2chain "Z"
d_6ens_2chain "a"
d_7ens_2chain "b"
d_8ens_2chain "c"
d_9ens_2chain "d"
d_10ens_2chain "e"
d_11ens_2chain "f"
d_12ens_2chain "g"
d_13ens_2chain "h"
d_14ens_2chain "i"
d_15ens_2chain "j"
d_16ens_2chain "k"
d_17ens_2chain "l"
d_18ens_2chain "m"
d_19ens_2chain "n"
d_20ens_2chain "o"
d_21ens_2chain "p"
d_22ens_2chain "q"
d_23ens_2chain "r"
d_24ens_2chain "s"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ASPASPTYRTYRAB1 - 3073 - 309
d_2ens_1ASPASPTYRTYRCC1 - 3073 - 309
d_3ens_1ASPASPTYRTYRDD1 - 3073 - 309
d_4ens_1ASPASPTYRTYREE1 - 3073 - 309
d_5ens_1ASPASPTYRTYRFF1 - 3073 - 309
d_6ens_1ASPASPTYRTYRGG1 - 3073 - 309
d_7ens_1ASPASPTYRTYRHH1 - 3073 - 309
d_8ens_1ASPASPTYRTYRII1 - 3073 - 309
d_9ens_1ASPASPTYRTYRLL1 - 3073 - 309
d_10ens_1ASPASPTYRTYRMM1 - 3073 - 309
d_11ens_1ASPASPTYRTYRNN1 - 3073 - 309
d_12ens_1ASPASPTYRTYROO1 - 3073 - 309
d_13ens_1ASPASPTYRTYRPP1 - 3073 - 309
d_14ens_1ASPASPTYRTYRQQ1 - 3073 - 309
d_15ens_1ASPASPTYRTYRRR1 - 3073 - 309
d_16ens_1ASPASPTYRTYRSS1 - 3073 - 309
d_17ens_1ASPASPTYRTYRTT1 - 3073 - 309
d_18ens_1ASPASPTYRTYRUU1 - 3073 - 309
d_19ens_1ASPASPTYRTYRVV1 - 3073 - 309
d_20ens_1ASPASPTYRTYRWW1 - 3073 - 309
d_21ens_1ASPASPTYRTYRtTA1 - 3073 - 309
d_22ens_1ASPASPTYRTYRuUA1 - 3073 - 309
d_23ens_1ASPASPTYRTYRyA1 - 3073 - 309
d_24ens_1ASPASPTYRTYRzVA1 - 3073 - 309
d_1ens_2CYSCYSGLUGLUJJ1 - 3123 - 314
d_2ens_2CYSCYSGLUGLUKK1 - 3123 - 314
d_3ens_2CYSCYSGLUGLUXX1 - 3123 - 314
d_4ens_2CYSCYSGLUGLUYY1 - 3123 - 314
d_5ens_2CYSCYSGLUGLUZZ1 - 3123 - 314
d_6ens_2CYSCYSGLUGLUaAA1 - 3123 - 314
d_7ens_2CYSCYSGLUGLUbBA1 - 3123 - 314
d_8ens_2CYSCYSGLUGLUcCA1 - 3123 - 314
d_9ens_2CYSCYSGLUGLUdDA1 - 3123 - 314
d_10ens_2CYSCYSGLUGLUeEA1 - 3123 - 314
d_11ens_2CYSCYSGLUGLUfFA1 - 3123 - 314
d_12ens_2CYSCYSGLUGLUgGA1 - 3123 - 314
d_13ens_2CYSCYSGLUGLUhHA1 - 3123 - 314
d_14ens_2CYSCYSGLUGLUiIA1 - 3123 - 314
d_15ens_2CYSCYSGLUGLUjJA1 - 3123 - 314
d_16ens_2CYSCYSGLUGLUkKA1 - 3123 - 314
d_17ens_2CYSCYSGLUGLUlLA1 - 3123 - 314
d_18ens_2CYSCYSGLUGLUmMA1 - 3123 - 314
d_19ens_2CYSCYSGLUGLUnNA1 - 3123 - 314
d_20ens_2CYSCYSGLUGLUoOA1 - 3123 - 314
d_21ens_2CYSCYSGLUGLUpPA1 - 3123 - 314
d_22ens_2CYSCYSGLUGLUqQA1 - 3123 - 314
d_23ens_2CYSCYSGLUGLUrRA1 - 3123 - 314
d_24ens_2CYSCYSGLUGLUsSA1 - 3123 - 314

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.00581583775649, -0.999909911872, -0.0120972795205), (0.00969861238644, -0.0120405127364, 0.999880474342), (-0.99993605443, -0.00593246943966, 0.00962771298802)484.384622599, 1.80021083813, 483.075691648
2given(-0.0123423200996, 0.0123846859192, -0.99984713166), (0.00987610735798, -0.999873011675, -0.012506919199), (-0.999875057014, -0.0100289620141, 0.0122184402813)481.830370406, 483.737071543, 483.690493764
3given(-0.999959062379, -0.00622989416294, 0.00656216316347), (0.00658066317922, -0.00295371542833, 0.99997398488), (-0.00621034932892, 0.999976231709, 0.00299459134538)483.766043661, -0.290826637911, 0.522157879384
4given(-0.99998599516, -0.00354962446064, 0.00392551276702), (0.00353435265894, -0.999986186028, -0.00389051475274), (0.00393926840643, -0.00387658612022, 0.999984727006)483.466582647, 483.316527124, 0.446359646487
5given(0.00013842227561, -0.999969878197, -0.00776038258716), (0.999966412256, 0.000202008458027, -0.00819350671636), (0.00819482757609, -0.00775898776957, 0.999936319427)484.563831086, 1.39889104353, 0.734271460763
6given(0.00536228323525, -0.99994236727, -0.00930097074263), (-0.999901975991, -0.00548190352446, 0.0128835997836), (-0.0129338442909, 0.00923097351306, -0.99987374443)483.982524097, 482.372692324, 482.839265462
7given(0.00664832963235, 0.000370033619043, 0.999977831148), (0.00764217748492, -0.999970747182, 0.000319222156277), (0.999948697102, 0.0076398857725, -0.00665096301257)-1.31171133505, 481.770569442, -0.97339206437
8given(-0.999917578459, -0.00660782885559, 0.0110078556459), (-0.0110429736067, 0.00530184966021, -0.999924968747), (0.0065489710662, -0.99996411285, -0.00537438275324)483.047724971, 483.652196002, 482.986401055
9given(-0.999910290258, -0.0105763430906, 0.00821902689519), (-0.0105511409105, 0.999939518538, 0.00310365786452), (-0.00825135514683, 0.00301665932525, -0.999961406708)484.673660185, 1.34784448818, 483.721555916
10given(0.999985325164, 0.0039270844609, -0.00373195169524), (-0.00374786335575, 0.00405224609866, -0.999984766295), (-0.00391190185016, 0.999984078528, 0.00406690480856)-0.361902130529, 482.642626771, -0.104457746595
11given(-0.000343980818518, 0.00606483628194, -0.999981549549), (-0.999952415221, -0.00975121355765, 0.000284830191735), (-0.00974930619488, 0.999934063624, 0.00606790191846)481.236730329, 485.737150508, 0.4759301681
12given(-0.00527346216755, 0.999986063698, 0.000251010275632), (-0.000407429174656, -0.000253162337239, 0.999999884955), (0.999986012201, 0.00527335929195, 0.000408758538608)0.909865786662, 0.226977547172, -1.5214375262
13given(-0.00905950519279, 0.999958683199, -0.000746498635239), (-0.999923471197, -0.00905289151588, 0.00843189798836), (0.00842479163815, 0.000822830330203, 0.999964172276)1.77711953473, 484.193163804, -1.74664956975
14given(-0.0100778718756, 0.00343469271387, -0.999943318086), (0.999936885313, 0.00500091252696, -0.0100606294718), (0.00496607389493, -0.999981596711, -0.00348487449002)484.164571344, 0.368063021345, 482.828999806
15given(0.999959344127, -0.00250593948735, -0.00866200667267), (0.00862911340138, -0.0128519376421, 0.999880175871), (-0.00261696278495, -0.999914270308, -0.0128297910993)2.27025841052, 2.12190565534, 485.930904036
16given(0.00658650325305, -0.00409977903026, 0.999969904441), (-0.999970017584, -0.00409914663601, 0.00656969789708), (0.00407208896023, -0.999983194263, -0.00412665515163)-0.0355319743167, 483.179965201, 483.121461923
17given(0.00507669140435, -0.00551219756206, 0.999971921047), (0.999959438103, 0.00746768077894, -0.00503546354288), (-0.00743971462441, 0.999956923783, 0.00554988508769)0.723276850231, -1.13222988134, 0.271154201107
18given(-0.0063624758834, 0.999829902988, 0.0173113832685), (-0.010095355867, 0.0172466283072, -0.999800298861), (-0.99992879881, -0.00653596986436, 0.00998390742046)-2.07134303789, 479.883054128, 483.111448695
19given(0.00660105145319, -0.999972955562, 0.00324257064946), (-0.00545522027851, -0.00327860383043, -0.999979745459), (0.999963332673, 0.00658322881476, -0.00547671497773)481.39239353, 485.186308065, -0.935868905102
20given(0.00898663915353, -0.00250568055387, 0.999956479994), (-0.0125706791832, 0.999917557196, 0.00261855609585), (-0.999880602043, -0.0125936641259, 0.00895440016342)-0.773111372194, 1.71577219226, 485.014599249
21given(-0.00697955763908, 0.999961141578, 0.00538526775941), (0.999957272893, 0.00701197099574, -0.00602367427027), (-0.00606120154113, 0.00534299508073, -0.999967356587)0.268418328813, -0.866004687981, 482.58213727
22given(-0.00290772428554, -0.001151802852, -0.999995109233), (-0.00213991457297, 0.999997054199, -0.00114558278022), (0.999993482931, 0.00213657306828, -0.00291018047967)484.041841475, 0.590823679252, -0.0980975710924
23given(0.99998076798, 0.00278895869033, -0.00553943859521), (0.00278525837606, -0.999995892944, -0.000675596623827), (-0.0055413000555, 0.000660154862993, -0.999984428973)0.196214238527, 482.808791255, 483.986479318
24given(0.999918535206, -0.0111319295935, -0.00624524578706), (-0.00623041125615, 0.00136679280639, -0.99997965672), (0.0111402390906, 0.999937104033, 0.00129732496146)3.60597423173, 484.936667758, -3.94246475241
25given(0.999892950398, -0.014425681656, -0.00244692723679), (0.00250019101451, 0.00367541096537, 0.999990120151), (-0.0144165456693, -0.999889189392, 0.00371108447375)3.51515885413, -1.70919389543, 487.151309603
26given(-0.00486089746578, -0.000641112765338, -0.999987980253), (-0.999925258738, 0.0112214732672, 0.00485339826303), (0.0112182268123, 0.999936831761, -0.000695611278728)485.050455924, 479.662424692, -3.59163299855
27given(-0.000135151569951, -0.999999988626, -6.69513754926E-5), (-0.00360941389121, -6.64631220287E-5, 0.999993483836), (-0.999993476911, 0.000135392344506, -0.00360940486756)483.347375555, 1.13241980424, 483.907945922
28given(0.999956205806, 0.00935757282401, 0.000149336018371), (0.00935660348247, -0.999940919077, 0.00553284075762), (0.000201101155774, -0.0055312011734, -0.999984682569)-1.93587634238, 478.98156294, 484.336409091
29given(0.000836486664268, -0.99999911982, -0.00102987866934), (-0.99999815139, -0.000838268028886, 0.00173046901436), (-0.0017313308056, 0.00102842925125, -0.999997972411)483.217048783, 482.838989051, 483.455370268
30given(0.00366327662914, -0.00372065139916, -0.999986368486), (-0.00383184160391, -0.999985788908, 0.00370661195558), (-0.999985948598, 0.00381821102516, -0.00367748151681)482.906489392, 483.736853942, 483.111422383
31given(-0.0120615593993, 0.00513298753132, 0.999914081921), (-0.00462149929963, 0.999975857451, -0.0051890519296), (-0.999916576785, -0.00468369028736, -0.0120375461042)2.72074192949, 2.54354633731, 486.706971053
32given(-0.0031049828209, -0.00238782652571, -0.999992328654), (-0.00571833420177, 0.99998084159, -0.00237004363072), (0.999978829644, 0.00571093138969, -0.00311857772446)484.758532941, 2.35796491385, -0.657647687364
33given(0.0112104644439, 0.999933068712, 0.00286069643121), (-0.999927057632, 0.0111974448921, 0.00452732183702), (0.0044949863269, -0.00291124114572, 0.999985659784)-4.35938440393, 479.851204448, -0.85978284658
34given(-0.00582863584683, -0.999982299138, 0.00119516294352), (0.999958666953, -0.00582014973851, 0.00698500129725), (-0.00697792162941, 0.00123582657274, 0.999974890356)484.881561112, -0.388307866566, 1.81204091243
35given(-0.000658221040753, 0.0002337966287, 0.999999756042), (-0.999890185208, 0.0148047220815, -0.000661610213864), (-0.014804873152, -0.999890376763, 0.000224026174796)0.118415938795, 480.022473822, 488.029660906
36given(-0.00926718859334, -0.999955574404, 0.00172291430954), (0.00071404127389, -0.00172960528713, -0.999998249304), (0.999956803747, -0.00926594213738, 0.000730038130568)485.953772922, 483.371847194, 1.83657259334
37given(0.00332321803223, -0.00255868658791, -0.999991204634), (0.999978757939, -0.00559863827243, 0.00333750195544), (-0.00560712865184, -0.999981054007, 0.00254002674048)482.808849786, 0.388383506325, 484.570640146
38given(0.0037858177598, 0.999992459301, 0.000865404682698), (-0.00417810657918, 0.000881220988258, -0.999990883396), (-0.999984105378, 0.003782167493, 0.0041814112154)-1.46959811605, 484.453844328, 481.495172982
39given(0.00875626948431, 0.999960230228, -0.00169284005055), (-0.00132418137108, 0.00170449878372, 0.999997670611), (0.999960786375, -0.00875400746029, 0.00133905375937)-2.55824713629, 0.013450979888, 1.34283060016
40given(-0.00419943355398, 0.00110869208062, 0.999990567735), (0.999982705964, 0.00412203471458, 0.00419483042834), (-0.00411734505918, 0.999990889774, -0.00112598311775)1.14184302694, -1.72540597722, 1.49496870852
41given(-0.00358553918486, 0.00228861667561, 0.99999095303), (-0.00938491161695, -0.999953418389, 0.00225488049965), (0.999949532398, -0.00937674174955, 0.00360685062989)0.511240357853, 485.747978459, 1.01072026052
42given(-0.99999248795, 0.000119139886608, -0.00387425461919), (-0.00387390736192, 0.00278852365013, 0.999988608424), (0.000129941980049, 0.999996104963, -0.00278804116572)484.030646941, 0.612957238428, 0.531231937078
43given(0.011585853424, 0.99992760277, 0.00324918739862), (0.999908847752, -0.0115629846856, -0.00697090904288), (-0.00693283406424, 0.00332965515829, -0.999970424167)-4.47280905085, 4.04855917377, 484.662144289
44given(-0.999995250279, 0.00246082993729, -0.0018557305063), (0.00246049129102, 0.999996955921, 0.000184747706716), (0.00185617949, 0.000180180820466, -0.999998261065)482.98576494, -0.921374062134, 482.522528604
45given(-0.99996466924, 0.00839566103671, -0.000416109500814), (-0.00839431386923, -0.999959837372, -0.003139926278), (-0.000442454545473, -0.00313632238826, 0.999994983845)481.412692647, 486.675093227, 0.838476954024
46given(-0.999924808931, 0.0122126137759, 0.00110839927947), (-0.00111350537529, -0.000411308435933, -0.999999295465), (-0.0122121492777, -0.999925338658, 0.000424876320298)480.187620271, 483.696858889, 487.175993025

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Components

#1: Protein ...
O43_129 component B


Mass: 34478.918 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein ...
O43_129 component A


Mass: 33976.965 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Nanocage O43_129 / Type: COMPLEX
Details: Chain A and Chain B are expressed separately in E coli. Complex is formed by mixing the cell lysis of both expressions, forming the nanocage. Nanocage was purified through a His tag on chain A.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.60 MDa / Experimental value: NO
Source (natural)Organism: unidentified (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 25mM Tris HCl, 300mM NaCl, pH 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisTrisHCl1
2300 mMSodium ChlorideNaClSodium chloride1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 900 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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13ISOLDEmodel refinement
14Cootmodel refinement
15PHENIXmodel refinement
16UCSF ChimeraXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 40928
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 6.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13400 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 955.4 / Protocol: FLEXIBLE FIT / Space: REAL
Details: Model was initially fit in Chimera. Model was further refined with Namdinator, Isolde, and Coot
Atomic model buildingDetails: De Novo Design / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 0 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00973752
ELECTRON MICROSCOPYf_angle_d1.3915102744
ELECTRON MICROSCOPYf_chiral_restr0.057714184
ELECTRON MICROSCOPYf_plane_restr0.0114856
ELECTRON MICROSCOPYf_dihedral_angle_d5.89714856
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAELECTRON MICROSCOPYNCS constraints0.774367206399
ens_1d_3BAELECTRON MICROSCOPYNCS constraints0.778508302979
ens_1d_4BAELECTRON MICROSCOPYNCS constraints0.70050247213
ens_1d_5BAELECTRON MICROSCOPYNCS constraints0.609476439896
ens_1d_6BAELECTRON MICROSCOPYNCS constraints0.594107714359
ens_1d_7BAELECTRON MICROSCOPYNCS constraints0.730343658648
ens_1d_8BAELECTRON MICROSCOPYNCS constraints0.637088541278
ens_1d_9BAELECTRON MICROSCOPYNCS constraints0.791949494264
ens_1d_10BAELECTRON MICROSCOPYNCS constraints0.745267296931
ens_1d_11BAELECTRON MICROSCOPYNCS constraints0.558942141011
ens_1d_12BAELECTRON MICROSCOPYNCS constraints0.674378232013
ens_1d_13BAELECTRON MICROSCOPYNCS constraints0.522156945354
ens_1d_14BAELECTRON MICROSCOPYNCS constraints0.702850595746
ens_1d_15BAELECTRON MICROSCOPYNCS constraints0.670785606682
ens_1d_16BAELECTRON MICROSCOPYNCS constraints0.763018658134
ens_1d_17BAELECTRON MICROSCOPYNCS constraints0.639167199513
ens_1d_18BAELECTRON MICROSCOPYNCS constraints0.72321940113
ens_1d_19BAELECTRON MICROSCOPYNCS constraints0.923377737148
ens_1d_20BAELECTRON MICROSCOPYNCS constraints0.630990383034
ens_1d_21BAELECTRON MICROSCOPYNCS constraints0.723876426751
ens_1d_22BAELECTRON MICROSCOPYNCS constraints0.650504627601
ens_1d_23BAELECTRON MICROSCOPYNCS constraints0.213897920368
ens_1d_24BAELECTRON MICROSCOPYNCS constraints0.216927682287
ens_2d_2JJELECTRON MICROSCOPYNCS constraints0.564145825543
ens_2d_3JJELECTRON MICROSCOPYNCS constraints0.63550022157
ens_2d_4JJELECTRON MICROSCOPYNCS constraints0.628713844019
ens_2d_5JJELECTRON MICROSCOPYNCS constraints0.603029278572
ens_2d_6JJELECTRON MICROSCOPYNCS constraints0.668386181432
ens_2d_7JJELECTRON MICROSCOPYNCS constraints0.731686749829
ens_2d_8JJELECTRON MICROSCOPYNCS constraints0.448125969564
ens_2d_9JJELECTRON MICROSCOPYNCS constraints0.780569280581
ens_2d_10JJELECTRON MICROSCOPYNCS constraints0.737923242528
ens_2d_11JJELECTRON MICROSCOPYNCS constraints0.645911682942
ens_2d_12JJELECTRON MICROSCOPYNCS constraints0.7153367191
ens_2d_13JJELECTRON MICROSCOPYNCS constraints0.626532799656
ens_2d_14JJELECTRON MICROSCOPYNCS constraints0.553038414369
ens_2d_15JJELECTRON MICROSCOPYNCS constraints0.76629476235
ens_2d_16JJELECTRON MICROSCOPYNCS constraints0.61931617891
ens_2d_17JJELECTRON MICROSCOPYNCS constraints0.727492006646
ens_2d_18JJELECTRON MICROSCOPYNCS constraints0.832582357166
ens_2d_19JJELECTRON MICROSCOPYNCS constraints0.70856444012
ens_2d_20JJELECTRON MICROSCOPYNCS constraints0.564239981147
ens_2d_21JJELECTRON MICROSCOPYNCS constraints0.570297357842
ens_2d_22JJELECTRON MICROSCOPYNCS constraints0.704058409682
ens_2d_23JJELECTRON MICROSCOPYNCS constraints0.661760180048
ens_2d_24JJELECTRON MICROSCOPYNCS constraints0.510232043555

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