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- PDB-7rk8: Cryo-EM Structure of Adeno-Associated Virus Serotype 9 with Engin... -

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基本情報

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データベース: PDB / ID: 7rk8
タイトルCryo-EM Structure of Adeno-Associated Virus Serotype 9 with Engineered Peptide Domain PHP.B (AAV9-PHP.B)
要素Capsid protein VP1カプシド
キーワードVIRUS (ウイルス) / Gene Therapy (遺伝子治療) / Adeno-associated virus (アデノ随伴ウイルス) / AAV
機能・相同性Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein VP1
機能・相同性情報
生物種Adeno-associated virus 9 (アデノ随伴ウイルス)
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: 2.27 Å
データ登録者Fluck, E.C. / Pumroy, R.A. / Moiseenkova-Bell, V.Y.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM103899 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129357 米国
引用ジャーナル: J Virol / 年: 2021
タイトル: Context-Specific Function of the Engineered Peptide Domain of PHP.B.
著者: R Alexander Martino / Edwin C Fluck / Jacqueline Murphy / Qiang Wang / Henry Hoff / Ruth A Pumroy / Claudia Y Lee / Joshua J Sims / Soumitra Roy / Vera Y Moiseenkova-Bell / James M Wilson /
要旨: One approach to improve the utility of adeno-associated virus (AAV)-based gene therapy is to engineer the AAV capsid to (i) overcome poor transport through tissue barriers and (ii) redirect the ...One approach to improve the utility of adeno-associated virus (AAV)-based gene therapy is to engineer the AAV capsid to (i) overcome poor transport through tissue barriers and (ii) redirect the broadly tropic AAV to disease-relevant cell types. Peptide- or protein-domain insertions into AAV surface loops can achieve both engineering goals by introducing a new interaction surface on the AAV capsid. However, we understand little about the impact of insertions on capsid structure and the extent to which engineered inserts depend on a specific capsid context to function. Here, we examine insert-capsid interactions for the engineered variant AAV9-PHP.B. The 7-amino-acid peptide insert in AAV9-PHP.B facilitates transport across the murine blood-brain barrier via binding to the receptor Ly6a. When transferred to AAV1, the engineered peptide does not bind Ly6a. Comparative structural analysis of AAV1-PHP.B and AAV9-PHP.B revealed that the inserted 7-amino-acid loop is highly flexible and has remarkably little impact on the surrounding capsid conformation. Our work demonstrates that Ly6a binding requires interactions with both the PHP.B peptide and specific residues from the AAV9 HVR VIII region. An AAV1-based vector that incorporates a larger region of AAV9-PHP.B-including the 7-amino-acid loop and adjacent HVR VIII amino acids-can bind to Ly6a and localize to brain tissue. However, unlike AAV9-PHP.B, this AAV1-based vector does not penetrate the blood-brain barrier. Here we discuss the implications for AAV capsid engineering and the transfer of engineered activities between serotypes. Targeting AAV vectors to specific cellular receptors is a promising strategy for enhancing expression in target cells or tissues while reducing off-target transgene expression. The AAV9-PHP.B/Ly6a interaction provides a model system with a robust biological readout that can be interrogated to better understand the biology of AAV vectors' interactions with target receptors. In this work, we analyzed the sequence and structural features required to successfully transfer the Ly6a receptor-binding epitope from AAV9-PHP.B to another capsid of clinical interest, AAV1. We found that AAV1- and AAV9-based vectors targeted to the same receptor exhibited different brain-transduction profiles. Our work suggests that, in addition to attachment-receptor binding, the capsid context in which this binding occurs is important for a vector's performance.
履歴
登録2021年7月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年8月4日Provider: repository / タイプ: Initial release
改定 1.12021年8月25日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22021年10月6日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
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  • 単純化した表面モデル + あてはめた原子モデル
  • マップデータ: EMDB-24494
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  • EMマップとの重ね合わせ
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ムービービューア
構造ビューア分子:
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集合体

登録構造単位
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
AA: Capsid protein VP1
BA: Capsid protein VP1
CA: Capsid protein VP1
DA: Capsid protein VP1
EA: Capsid protein VP1
FA: Capsid protein VP1
GA: Capsid protein VP1
HA: Capsid protein VP1
IA: Capsid protein VP1
JA: Capsid protein VP1
KA: Capsid protein VP1
LA: Capsid protein VP1
MA: Capsid protein VP1
NA: Capsid protein VP1
OA: Capsid protein VP1
PA: Capsid protein VP1
QA: Capsid protein VP1
RA: Capsid protein VP1
SA: Capsid protein VP1
TA: Capsid protein VP1
UA: Capsid protein VP1
VA: Capsid protein VP1
WA: Capsid protein VP1
XA: Capsid protein VP1
YA: Capsid protein VP1
ZA: Capsid protein VP1
AB: Capsid protein VP1
BB: Capsid protein VP1
CB: Capsid protein VP1
DB: Capsid protein VP1
EB: Capsid protein VP1
FB: Capsid protein VP1
GB: Capsid protein VP1
HB: Capsid protein VP1
IB: Capsid protein VP1


分子量 (理論値)分子数
合計 (水以外)4,932,94060
ポリマ－4,932,94060
非ポリマー00
水0
1


  • 登録構造と同一
  • 登録者が定義した集合体
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 "J"
d_3ens_1chain "JA"
d_4ens_1chain "K"
d_5ens_1chain "KA"
d_6ens_1chain "L"
d_7ens_1chain "LA"
d_8ens_1chain "M"
d_9ens_1chain "MA"
d_10ens_1chain "N"
d_11ens_1chain "NA"
d_12ens_1chain "AA"
d_13ens_1chain "AB"
d_14ens_1chain "B"
d_15ens_1chain "BA"
d_16ens_1chain "BB"
d_17ens_1chain "C"
d_18ens_1chain "CA"
d_19ens_1chain "CB"
d_20ens_1chain "D"
d_21ens_1chain "DA"
d_22ens_1chain "DB"
d_23ens_1chain "E"
d_24ens_1chain "EA"
d_25ens_1chain "EB"
d_26ens_1chain "F"
d_27ens_1chain "FA"
d_28ens_1chain "FB"
d_29ens_1chain "G"
d_30ens_1chain "GA"
d_31ens_1chain "GB"
d_32ens_1chain "H"
d_33ens_1chain "HA"
d_34ens_1chain "HB"
d_35ens_1chain "I"
d_36ens_1chain "IA"
d_37ens_1chain "NA"
d_38ens_1chain "O"
d_39ens_1chain "OA"
d_40ens_1chain "P"
d_41ens_1chain "PA"
d_42ens_1chain "Q"
d_43ens_1chain "QA"
d_44ens_1chain "R"
d_45ens_1chain "RA"
d_46ens_1chain "S"
d_47ens_1chain "SA"
d_48ens_1chain "T"
d_49ens_1chain "TA"
d_50ens_1chain "UA"
d_51ens_1chain "V"
d_52ens_1chain "VA"
d_53ens_1chain "W"
d_54ens_1chain "WA"
d_55ens_1chain "X"
d_56ens_1chain "XA"
d_57ens_1chain "Y"
d_58ens_1chain "YA"
d_59ens_1chain "Z"
d_60ens_1chain "ZA"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYLEUA1 - 517
d_21ens_1GLYLEUJ1 - 517
d_31ens_1GLYLEUJA1 - 517
d_41ens_1GLYLEUK1 - 517
d_51ens_1GLYLEUKA1 - 517
d_61ens_1GLYLEUL1 - 517
d_71ens_1GLYLEULA1 - 517
d_81ens_1GLYLEUM1 - 517
d_91ens_1GLYLEUMA1 - 517
d_101ens_1GLYLEUN1 - 517
d_111ens_1GLYLEUNA1 - 517
d_121ens_1GLYLEUAA1 - 517
d_131ens_1GLYLEUAB1 - 517
d_141ens_1GLYLEUB1 - 517
d_151ens_1GLYLEUBA1 - 517
d_161ens_1GLYLEUBB1 - 517
d_171ens_1GLYLEUC1 - 517
d_181ens_1GLYLEUCA1 - 517
d_191ens_1GLYLEUCB1 - 517
d_201ens_1GLYLEUD1 - 517
d_211ens_1GLYLEUDA1 - 517
d_221ens_1GLYLEUDB1 - 517
d_231ens_1GLYLEUE1 - 517
d_241ens_1GLYLEUEA1 - 517
d_251ens_1GLYLEUEB1 - 517
d_261ens_1GLYLEUF1 - 517
d_271ens_1GLYLEUFA1 - 517
d_281ens_1GLYLEUFB1 - 517
d_291ens_1GLYLEUG1 - 517
d_301ens_1GLYLEUGA1 - 517
d_311ens_1GLYLEUGB1 - 517
d_321ens_1GLYLEUH1 - 517
d_331ens_1GLYLEUHA1 - 517
d_341ens_1GLYLEUHB1 - 517
d_351ens_1GLYLEUI1 - 517
d_361ens_1GLYLEUIA1 - 517
d_371ens_1GLYLEUNA1 - 517
d_381ens_1GLYLEUO1 - 517
d_391ens_1GLYLEUOA1 - 517
d_401ens_1GLYLEUP1 - 517
d_411ens_1GLYLEUPA1 - 517
d_421ens_1GLYLEUQ1 - 517
d_431ens_1GLYLEUQA1 - 517
d_441ens_1GLYLEUR1 - 517
d_451ens_1GLYLEURA1 - 517
d_461ens_1GLYLEUS1 - 517
d_471ens_1GLYLEUSA1 - 517
d_481ens_1GLYLEUT1 - 517
d_491ens_1GLYLEUTA1 - 517
d_501ens_1GLYLEUUA1 - 517
d_511ens_1GLYLEUV1 - 517
d_521ens_1GLYLEUVA1 - 517
d_531ens_1GLYLEUW1 - 517
d_541ens_1GLYLEUWA1 - 517
d_551ens_1GLYLEUX1 - 517
d_561ens_1GLYLEUXA1 - 517
d_571ens_1GLYLEUY1 - 517
d_581ens_1GLYLEUYA1 - 517
d_591ens_1GLYLEUZ1 - 517
d_601ens_1GLYLEUZA1 - 517

NCS oper:
IDCodeMatrixベクター
1given(0.309038098342, 0.499873860069, 0.809086879014), (0.499988562104, -0.809072611407, 0.30888986263), (0.809016002028, 0.309075449511, -0.499965473779)-141.480223411, 229.007474356, 87.4365760198
2given(0.500014625038, 0.809007396763, -0.309018456943), (0.809008602848, -0.309026176621, 0.500007902617), (0.309015299403, -0.500009854049, -0.809011551579)0.0162758541392, 0.0089181359254, 457.921900244
3given(-0.499995278592, 0.808988722965, 0.30909863717), (0.809024108257, 0.308970406563, 0.500017279829), (0.309006009075, 0.500074528429, -0.808975124693)87.4284213909, -141.493315091, 228.916481082
4given(-0.808879906588, -0.309194229752, -0.500112212414), (0.308943115741, 0.500191470773, -0.808926847003), (0.500267376464, -0.808830897564, -0.309071401446)599.450710261, 228.924347389, 370.371961513
5given(-0.999999954958, -0.000283468145067, -9.86388161843E-5), (-0.000283500462104, 0.999999906097, 0.000327770420203), (9.85458944488E-5, 0.00032779836959, -0.999999941418)457.979008626, 0.0121020090581, 457.807814388
6given(1.82300781311E-5, -0.000202651997793, 0.9999999793), (0.999999999531, -2.462361124E-5, -1.82350685234E-5), (2.46273061041E-5, 0.999999979163, 0.000202651548808)0.0464457573636, 0.00273884932193, -0.045485795436
7given(-0.499792311064, -0.80917322694, 0.308943902035), (-0.809063819485, 0.308801978519, -0.500057070806), (0.309230305438, -0.499880012469, -0.809009636118)457.894954874, 457.977017207, 457.813408717
8given(-0.308918109169, -0.499522128847, 0.809349890109), (-0.500101919008, 0.809145958424, 0.308514000607), (-0.808991762895, -0.309451871473, -0.499771814741)228.753827449, 87.5397756823, 599.497221429
9given(-0.809043877117, 0.308913283642, -0.500020587666), (-0.309103495509, 0.499957434405, 0.809010255094), (0.49990302456, 0.809082904883, -0.309001325341)457.92802756, 0.029869024429, -0.00497119432566
10given(0.809080483659, -0.309240292483, -0.49975915446), (0.30929566921, -0.499020916165, 0.809514863506), (-0.499724884281, -0.809536019418, -0.308101400997)228.955366186, 87.0546008252, 599.337367934
11given(-0.499632357281, -0.809184104534, -0.309174048922), (-0.809213926411, 0.308643870714, 0.499911774589), (-0.309095986483, 0.499960044443, -0.809011511105)599.374993401, 229.114463508, 370.49249026
12given(-0.49961086811, -0.808918463334, 0.309903049586), (0.809196737669, -0.308130696812, 0.500256047867), (-0.309175710901, 0.500705895071, 0.808519626496)457.640285606, -0.322822911557, -0.0296076876438
13given(0.809013666604, 0.309292311327, -0.499835126219), (-0.308695552134, -0.50008309424, -0.809088348049), (-0.500203901765, 0.808860411325, -0.309096896861)87.3545055662, 599.355075477, 229.071810361
14given(-0.000695763936322, 0.000176632982021, 0.999999742357), (-0.999999742537, -0.00017573426262, -0.000695732895972), (0.000175611327967, -0.999999968959, 0.000176755206107)0.188496908875, 458.078172058, 457.849663677
15given(-0.309002789734, 0.500017660101, 0.809011505186), (0.499934864836, 0.809033051623, -0.309080333091), (-0.809062671774, 0.308946372319, -0.499969731256)0.00552879496666, 0.0463753926123, 457.91928196
16given(0.809063619179, -0.309193768724, -0.499815239367), (-0.309239373604, 0.499231693057, -0.809406403767), (0.499787024575, 0.809423825958, 0.308295313031)228.943447701, 370.776934596, -141.440202374
17given(-0.80891653496, -0.308975780016, -0.500187971499), (-0.308970407232, -0.500404848911, 0.808784442631), (-0.500191290331, 0.808782390109, 0.309321383882)599.39188107, 229.098206138, 87.5025490769
18given(0.808913153776, 0.309796487587, 0.499685547046), (0.308820187989, 0.499328312145, -0.809506842578), (-0.500289517318, 0.809133717607, 0.308241830212)-141.613022877, 229.27484321, 87.6126443053
19given(0.808991297351, 0.309378575581, -0.499817944637), (0.308762144238, 0.499894317851, 0.809179590243), (0.500198979503, -0.808944106816, 0.308885760359)87.3369002839, -141.462814551, 228.920941107
20given(-0.500005994365, 0.809023902583, -0.30898920798), (-0.80901143522, -0.30903487159, 0.499997945821), (0.309021849201, 0.499977772696, 0.809028876819)228.954254233, 370.457216453, -141.501630437
21given(0.308983814451, 0.500069203825, -0.808986893462), (0.500013894704, -0.808980408677, -0.309090283704), (-0.809021079769, -0.309000792496, -0.500003402715)228.940720817, 370.473229917, 599.401957365
22given(0.000197309697175, 0.000204611208871, -0.999999959602), (0.999999933183, 0.000307696544235, 0.000197372650126), (0.000307736916461, -0.999999931729, -0.000204550483688)457.816630328, -0.120566430936, 457.869216677
23given(0.500404173203, -0.808450934753, 0.309843104712), (-0.808844307068, -0.308880709206, 0.5003634623), (-0.308814750887, -0.500998795984, -0.808476132027)228.575697479, 370.335839528, 599.514705903
24given(0.500266908308, -0.808821926064, -0.309095636284), (0.808890742473, 0.309196031984, 0.500093571792), (-0.308915501706, -0.500204863754, 0.808929111284)370.345294297, -141.506939466, 229.020542537
25given(0.500261384496, -0.808601832183, 0.309679873697), (0.808894817988, 0.308832329112, -0.500311668791), (0.308913775373, 0.500785053177, 0.808570720407)228.6507878, 87.5819739153, -141.599716699
26given(0.808995019569, 0.309583652523, 0.499684921129), (-0.308830271748, -0.499442264725, 0.809432694829), (0.500150898794, -0.809144848774, -0.308437501188)-141.616793981, 228.723646935, 370.365194104
27given(-0.308836288344, -0.499798638375, -0.809210397907), (0.500125806093, -0.809019427313, 0.308806969334), (-0.809008235485, -0.309336204328, 0.499816754031)599.332800477, 228.985771371, 370.580488002
28given(0.500032012651, 0.808921258816, 0.309215755354), (0.809001347865, -0.308920614998, -0.50008486558), (-0.309006157669, 0.500214404694, -0.808888585566)-141.543932077, 228.971427274, 370.370580805
29given(0.000182156629005, 2.34580794685E-5, -0.999999983134), (-0.999999936683, -0.000305696449675, -0.000182163791596), (-0.000305700717732, 0.999999953, 2.34023933485E-5)457.862078555, 458.018163293, 0.06728829216
30given(0.30914792231, -0.4992924113, 0.809403885677), (0.499815767162, 0.809376397338, 0.3083732257), (-0.809080812421, 0.309219882043, 0.499771251196)87.1719311994, -141.447446145, 228.987510336
31given(0.309301082425, -0.499826916982, -0.809015385188), (0.499787430817, 0.809205678049, -0.308866791045), (0.809039779249, -0.308802888059, 0.500095402817)457.788281934, -0.0104044851051, -0.054015737365
32given(0.30864686357, 0.500251325709, -0.809002920103), (-0.500389633605, 0.808717994383, 0.30916891846), (0.808917380323, 0.30939265778, 0.499928850061)228.991965966, 87.6183075946, -141.538238277
33given(-1.4381653286E-6, 0.999999953095, 0.000306280942869), (3.98513964411E-6, 0.000306280948598, -0.999999953088), (-0.999999999991, -1.43694468863E-6, -3.98557993997E-6)-0.0802511906566, 457.841626193, 457.918865166
34given(0.308998409382, -0.500062315422, 0.808985576939), (-0.500122040543, -0.808943855575, -0.30901097568), (0.808948655703, -0.309107617542, -0.500054550239)87.4471095096, 599.422584608, 229.014438327
35given(0.99999982628, 0.000584203398036, 7.84008079268E-5), (0.00058420322573, -0.999999829351, 2.22064422253E-6), (7.84020918556E-5, -2.17484183187E-6, -0.999999996924)-0.142535359404, 457.749176049, 457.86874801
36given(0.499983976529, 0.809072342991, 0.30889798805), (-0.808991444808, 0.309023291499, 0.500037446136), (0.309109795124, -0.499906540384, 0.809039297834)-141.493697296, 228.942528742, 87.425615541
37given(-0.000382564738988, 0.999999926576, 2.2166099791E-5), (-0.000205893391355, -2.22448685006E-5, 0.999999978557), (0.999999905626, 0.000382560166931, 0.00020590188634)0.085420445595, 0.0711069989133, -0.108073834257
38given(0.309290982106, -0.499510468791, -0.809214668649), (-0.499721550648, -0.809350103231, 0.30859485125), (-0.809084334421, 0.308936404408, -0.499940834325)457.75302704, 458.023962967, 457.920398337
39given(0.500256166756, -0.808771614523, -0.309244633202), (-0.808886296974, -0.309079306733, -0.50017291082), (0.308944535783, 0.500358329292, -0.808823105579)370.372182885, 599.439358418, 228.858616286
40given(0.500122894838, 0.809065896278, -0.308689918103), (-0.808914436106, 0.309252087354, -0.500020581103), (-0.309086598089, 0.499775471534, 0.809129132423)-0.123785473069, 457.818318985, 0.0304013472089
41given(-0.308897303442, -0.500949209687, -0.808475321355), (-0.500339676996, 0.808506643777, -0.309801895719), (0.808852683466, 0.308815310958, -0.500390287844)599.517427346, 229.322629553, 87.587839935
42given(0.809135639448, -0.308494034982, 0.500130930213), (-0.30899445948, 0.500571804398, 0.808671931411), (-0.49982190927, -0.808862966776, 0.309707539449)-0.164159379987, -0.082917875106, 457.71322179
43given(-0.309049413107, 0.50003643752, -0.808982089673), (0.499711169625, 0.809118054421, 0.30921953522), (0.809183049261, -0.308693270355, -0.499931252901)370.451248844, -141.465105984, 228.825545429
44given(0.000182221616777, -0.999999936049, -0.00030772856041), (-7.5274754104E-5, -0.000307742281335, 0.999999949814), (-0.999999980564, -0.000182198443441, -7.53308265865E-5)457.914723284, 0.111835579039, 457.9652192
45given(0.809210252059, -0.308214227856, 0.500182724322), (0.309055384162, -0.50073031864, -0.808550503998), (0.4996634242, 0.808871521159, -0.309940840766)-0.272543229021, 457.993130978, 0.269204119324
46given(0.308884893926, 0.500713075705, 0.808626327869), (-0.500174239088, 0.808658444084, -0.309672813408), (-0.808959735004, -0.308800804127, 0.500226159365)-141.574478001, 229.212829588, 370.386218974
47given(0.00030043436419, -0.999999567164, 0.000880573967928), (-0.000126174577232, -0.000880611907825, -0.999999604301), (0.99999994691, 0.000300323139261, -0.000126439088698)457.687865301, 458.137218623, -0.0374643067197
48given(-0.309024947212, 0.500224693892, -0.808875044504), (-0.500014327751, -0.80892682081, -0.309229802281), (-0.809005101371, 0.308889388286, 0.50009808214)370.370883257, 599.459874544, 228.967776322
49given(-0.499984615861, 0.808907895156, 0.30932733642), (-0.809013674269, -0.30879488597, -0.500142572918), (-0.30905057636, -0.500313637185, 0.808810240846)87.3940892721, 599.396104186, 229.079272488
50given(-0.30881357592, -0.499332007482, 0.809507085597), (0.500279539132, -0.809135167596, -0.308254218599), (0.808921849163, 0.309786744168, 0.499677511086)228.653998511, 370.302300609, -141.62862489
51given(-0.809130081285, 0.308714837049, 0.500003660933), (-0.309003080838, 0.500215287364, -0.808889215109), (-0.499825577169, -0.80899926803, -0.309345400376)229.067652073, 370.373919184, 599.430170714
52given(-0.80891882631, -0.308817801503, 0.500281818495), (-0.308904765177, -0.500760375809, -0.80858944593), (0.500228126451, -0.808622663233, 0.309679205006)370.342370152, 599.503989489, 228.68884374
53given(-0.9999999557, -0.000296868286952, 2.16460758115E-5), (0.00029688491671, -0.999999657671, 0.000772344744918), (2.14167837401E-5, 0.000772351137097, 0.999999701507)458.003989949, 457.714337616, -0.203931921075
54given(-0.809009795074, -0.309208778582, 0.499893071289), (0.309035105161, 0.49967916435, 0.809208277573), (-0.500000455253, 0.809141930666, -0.308688970948)370.50528764, -141.471546174, 228.866875434
55given(-0.500222430686, 0.808931091949, -0.3088818679), (0.808955572686, 0.309361116824, -0.499886567951), (-0.308817747643, -0.499926182427, -0.809138684568)228.999982625, 87.3580132286, 599.367612175
56given(-0.808993022567, 0.30891204546, 0.500103626869), (0.309011401703, -0.50024156592, 0.80886978516), (0.500042241271, 0.808907735095, 0.309234592257)228.951289747, 87.5404652641, -141.532135534
57given(-0.499817510138, -0.809404908443, -0.308295557457), (0.809079064581, -0.309267833367, -0.499744409175), (0.309149678662, -0.499216487541, 0.809450044629)599.34438739, 228.952125858, 87.1360380032
58given(-0.309281058227, 0.500556988236, 0.808571535828), (-0.499955898522, -0.808859389773, 0.309500544603), (0.808943339521, -0.308527452758, 0.50042130684)0.00724746493944, 457.803544633, -0.160908223381
59given(-0.80902560514, 0.308692117317, -0.500186712073), (0.309342013696, -0.49997693364, -0.808907030746), (-0.499785042583, -0.809155264788, 0.309002700111)458.033136367, 457.780900281, 457.854466742

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要素

#1: タンパク質 ...
Capsid protein VP1 / カプシド


分子量: 82215.672 Da / 分子数: 60 / 由来タイプ: 組換発現
由来: (組換発現) Adeno-associated virus 9 (アデノ随伴ウイルス)
遺伝子: cap / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q6JC40

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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: Adeno-associated virus 9アデノ随伴ウイルス / タイプ: VIRUS
詳細: AAV9-PHP.B trans plasmid with cis plasmid encoding the CB7-EGFP reporter gene to produce vectors in HEK293 cells via triple transfection.
Entity ID: all / 由来: RECOMBINANT
分子量実験値: NO
由来(天然)生物種: Adeno-associated virus 9 (アデノ随伴ウイルス)
由来(組換発現)生物種: Homo sapiens (ヒト) / 株: HEK293
ウイルスについての詳細中空か: NO / エンベロープを持つか: NO / 単離: SEROTYPE / タイプ: SATELLITE
緩衝液pH: 7.4 / 詳細: Supplemented with 0.001% Pluronic F68
緩衝液成分
ID濃度名称式Buffer-ID
1137 mMsodium chloride塩化ナトリウムNaCl塩化ナトリウム1
22.7 mMpotassium chlorideKCl1
310 mMsodium phosphate dibasicNa2HPO41
41.8 mMpotassium phosphate monobasicKH2PO41
試料包埋: 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: GOLD / グリッドのサイズ: 300 divisions/in.
グリッドのタイプ: PELCO Ultrathin Carbon with Lacey Carbon
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: 277.15 K

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
試料ホルダ凍結剤: NITROGEN
撮影電子線照射量: 38.1 e/Å2 / 検出モード: SUPER-RESOLUTION
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
実像数: 1380

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解析

ソフトウェア
名称バージョン分類NB
phenix.real_space_refine1.18.2_3874精密化
PHENIX1.18.2_3874精密化
EMソフトウェア
ID名称バージョンカテゴリ
1RELION3粒子像選択
4Gctf1.06CTF補正
7Coot0.8.9.1モデルフィッティング
9RELION3初期オイラー角割当
10RELION3最終オイラー角割当
11RELION3分類
12RELION3３次元再構成
13PHENIX1.18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: 89358
対称性点対称性: I (正20面体型対称)
3次元再構成解像度: 2.27 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 42570 / 対称性のタイプ: POINT
原子モデル構築空間: REAL
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: 8.17 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.0041254160
ELECTRON MICROSCOPYf_angle_d0.5946346260
ELECTRON MICROSCOPYf_chiral_restr0.045235520
ELECTRON MICROSCOPYf_plane_restr0.003846020
ELECTRON MICROSCOPYf_dihedral_angle_d12.017433720
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000709813145996
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000709714679171
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000710354218742
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000705926489565
ens_1d_6AELECTRON MICROSCOPYNCS constraints0.000711134246535
ens_1d_7AELECTRON MICROSCOPYNCS constraints0.000719089728095
ens_1d_8AELECTRON MICROSCOPYNCS constraints0.000709505103607
ens_1d_9AELECTRON MICROSCOPYNCS constraints0.000714112529974
ens_1d_10AELECTRON MICROSCOPYNCS constraints0.000705354871048
ens_1d_11AELECTRON MICROSCOPYNCS constraints0.000705975022356
ens_1d_12AELECTRON MICROSCOPYNCS constraints0.000698778352852
ens_1d_13AELECTRON MICROSCOPYNCS constraints0.00071149048483
ens_1d_14AELECTRON MICROSCOPYNCS constraints0.000720421808603
ens_1d_15AELECTRON MICROSCOPYNCS constraints0.000713625593644
ens_1d_16AELECTRON MICROSCOPYNCS constraints0.000700350507542
ens_1d_17AELECTRON MICROSCOPYNCS constraints0.000704946516574
ens_1d_18AELECTRON MICROSCOPYNCS constraints0.000713719376044
ens_1d_19AELECTRON MICROSCOPYNCS constraints0.000712956028614
ens_1d_20AELECTRON MICROSCOPYNCS constraints0.00070747697773
ens_1d_21AELECTRON MICROSCOPYNCS constraints0.000706444295408
ens_1d_22AELECTRON MICROSCOPYNCS constraints0.000711345801075
ens_1d_23AELECTRON MICROSCOPYNCS constraints0.000708132732193
ens_1d_24AELECTRON MICROSCOPYNCS constraints0.000711710783177
ens_1d_25AELECTRON MICROSCOPYNCS constraints0.000715965002812
ens_1d_26AELECTRON MICROSCOPYNCS constraints0.000712027250906
ens_1d_27AELECTRON MICROSCOPYNCS constraints0.000714191184306
ens_1d_28AELECTRON MICROSCOPYNCS constraints0.00071169508132
ens_1d_29AELECTRON MICROSCOPYNCS constraints0.000713143422997
ens_1d_30AELECTRON MICROSCOPYNCS constraints0.000711372881441
ens_1d_31AELECTRON MICROSCOPYNCS constraints0.00070688329414
ens_1d_32AELECTRON MICROSCOPYNCS constraints0.000710703016201
ens_1d_33AELECTRON MICROSCOPYNCS constraints0.000713736157782
ens_1d_34AELECTRON MICROSCOPYNCS constraints0.000683612318491
ens_1d_35AELECTRON MICROSCOPYNCS constraints0.000711986143175
ens_1d_36AELECTRON MICROSCOPYNCS constraints0.000714582080441
ens_1d_37AELECTRON MICROSCOPYNCS constraints0.000708898136025
ens_1d_38AELECTRON MICROSCOPYNCS constraints0.00071503922839
ens_1d_39AELECTRON MICROSCOPYNCS constraints0.000708948426257
ens_1d_40AELECTRON MICROSCOPYNCS constraints0.000705997934318
ens_1d_41AELECTRON MICROSCOPYNCS constraints0.000708334579904
ens_1d_42AELECTRON MICROSCOPYNCS constraints0.000708454954533
ens_1d_43AELECTRON MICROSCOPYNCS constraints0.000711325258553
ens_1d_44AELECTRON MICROSCOPYNCS constraints0.000704023351319
ens_1d_45AELECTRON MICROSCOPYNCS constraints0.000709998797772
ens_1d_46AELECTRON MICROSCOPYNCS constraints0.000707666879236
ens_1d_47AELECTRON MICROSCOPYNCS constraints0.000709790658626
ens_1d_48AELECTRON MICROSCOPYNCS constraints0.000706694886528
ens_1d_49AELECTRON MICROSCOPYNCS constraints0.000712187430085
ens_1d_50AELECTRON MICROSCOPYNCS constraints0.000706693133829
ens_1d_51AELECTRON MICROSCOPYNCS constraints0.000712524793568
ens_1d_52AELECTRON MICROSCOPYNCS constraints0.000709238719841
ens_1d_53AELECTRON MICROSCOPYNCS constraints0.000707884060791
ens_1d_54AELECTRON MICROSCOPYNCS constraints0.000713438262898
ens_1d_55AELECTRON MICROSCOPYNCS constraints0.000707993691647
ens_1d_56AELECTRON MICROSCOPYNCS constraints0.000711624907605
ens_1d_57AELECTRON MICROSCOPYNCS constraints0.000712552273371
ens_1d_58AELECTRON MICROSCOPYNCS constraints0.000709774421872
ens_1d_59AELECTRON MICROSCOPYNCS constraints0.000713984449073
ens_1d_60AELECTRON MICROSCOPYNCS constraints0.000706537394019

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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://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

他の情報も見る