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- PDB-8v2d: Computational Designed Nanocage O43_129 -

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基本情報

登録情報
データベース: PDB / ID: 8v2d
タイトルComputational Designed Nanocage O43_129
要素
  • O43_129 component A
  • O43_129 component B
キーワードDE NOVO PROTEIN / De Novo / Nanocage / O43_129 / extendable nanomaterials
生物種synthetic construct (人工物)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.77 Å
データ登録者Weidle, C. / Kibler, R.D.
資金援助 米国, 1件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
引用ジャーナル: Nature / 年: 2024
タイトル: Blueprinting extendable nanomaterials with standardized protein blocks.
著者: 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 / ...著者: 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 /
要旨: 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.
履歴
登録2023年11月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年3月13日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年4月10日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
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


分子量 (理論値)分子数
合計 (水以外)1,642,94148
ポリマ－1,642,94148
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_5551
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_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ドメイン領域:

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アンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
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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要素

#1: タンパク質 ...
O43_129 component B


分子量: 34478.918 Da / 分子数: 24 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)
#2: タンパク質 ...
O43_129 component A


分子量: 33976.965 Da / 分子数: 24 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Nanocage O43_129 / タイプ: COMPLEX
詳細: 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 / 由来: RECOMBINANT
分子量値: 1.60 MDa / 実験値: NO
由来(天然)生物種: unidentified (未定義)
由来(組換発現)生物種: Escherichia coli (大腸菌)
緩衝液pH: 8 / 詳細: 25mM Tris HCl, 300mM NaCl, pH 8
緩衝液成分
ID濃度名称式Buffer-ID
125 mMTrisTrisHCl1
2300 mMSodium ChlorideNaCl1
試料濃度: 0.8 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 295.15 K

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電子顕微鏡撮影

顕微鏡モデル: TFS GLACIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 2000 nm / 最小 デフォーカス（公称値）: 900 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1

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解析

EMソフトウェア
ID名称カテゴリ
1cryoSPARC粒子像選択
2SerialEM画像取得
4cryoSPARCCTF補正
7UCSF Chimeraモデルフィッティング
9cryoSPARC初期オイラー角割当
10cryoSPARC最終オイラー角割当
11cryoSPARC分類
12cryoSPARC３次元再構成
13ISOLDEモデル精密化
14Cootモデル精密化
15PHENIXモデル精密化
16UCSF ChimeraXモデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 40928
対称性点対称性: O (正8面体型対称)
3次元再構成解像度: 6.77 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 13400 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT
原子モデル構築B value: 955.4 / プロトコル: FLEXIBLE FIT / 空間: REAL
詳細: Model was initially fit in Chimera. Model was further refined with Namdinator, Isolde, and Coot
原子モデル構築詳細: De Novo Design / Source name: Other / タイプ: in silico model
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 0 Å2
拘束条件
Refine-IDタイプDev ideal数
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-IDタイプRms 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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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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