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- PDB-7rk9: Cryo-EM Structure of Adeno-Associated Virus Serotype 1 with Engin... -

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基本情報

登録情報
データベース: PDB / ID: 7rk9
タイトルCryo-EM Structure of Adeno-Associated Virus Serotype 1 with Engineered Peptide Domain PHP.B (AAV1-PHP.B)
要素Capsid protein
キーワードVIRUS / Gene Therapy / Adeno-associated virus / 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
機能・相同性情報
生物種Adeno-associated virus - 1 (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: 2.32 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
改定 1.32024年6月5日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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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
  • ダウンロード
  • 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-24495
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-24495
  • UCSF Chimeraによる作画
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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
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
N: Capsid protein
O: Capsid protein
P: Capsid protein
Q: Capsid protein
R: Capsid protein
S: Capsid protein
T: Capsid protein
V: Capsid protein
W: Capsid protein
X: Capsid protein
Y: Capsid protein
Z: Capsid protein
AA: Capsid protein
BA: Capsid protein
CA: Capsid protein
DA: Capsid protein
EA: Capsid protein
FA: Capsid protein
GA: Capsid protein
HA: Capsid protein
IA: Capsid protein
JA: Capsid protein
KA: Capsid protein
LA: Capsid protein
MA: Capsid protein
NA: Capsid protein
OA: Capsid protein
PA: Capsid protein
QA: Capsid protein
RA: Capsid protein
SA: Capsid protein
TA: Capsid protein
UA: Capsid protein
VA: Capsid protein
WA: Capsid protein
XA: Capsid protein
YA: Capsid protein
ZA: Capsid protein
AB: Capsid protein
BB: Capsid protein
CB: Capsid protein
DB: Capsid protein
EB: Capsid protein
FB: Capsid protein
GB: Capsid protein
HB: Capsid protein
IB: Capsid protein


分子量 (理論値)分子数
合計 (水以外)4,932,77260
ポリマ－4,932,77260
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
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 "Y"
d_2ens_1chain "J"
d_3ens_1chain "JA"
d_4ens_1chain "K"
d_5ens_1chain "KA"
d_6ens_1chain "L"
d_7ens_1chain "S"
d_8ens_1chain "M"
d_9ens_1chain "MA"
d_10ens_1chain "N"
d_11ens_1chain "A"
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 "LA"
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 "FB"
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_1ASPLEUY1 - 523
d_21ens_1ASPLEUJ1 - 523
d_31ens_1ASPLEUJA1 - 523
d_41ens_1ASPLEUK1 - 523
d_51ens_1ASPLEUKA1 - 523
d_61ens_1ASPLEUL1 - 523
d_71ens_1ASPLEUS1 - 523
d_81ens_1ASPLEUM1 - 523
d_91ens_1ASPLEUMA1 - 523
d_101ens_1ASPLEUN1 - 523
d_111ens_1ASPLEUA1 - 523
d_121ens_1ASPLEUAA1 - 523
d_131ens_1ASPLEUAB1 - 523
d_141ens_1ASPLEUB1 - 523
d_151ens_1ASPLEUBA1 - 523
d_161ens_1ASPLEUBB1 - 523
d_171ens_1ASPLEUC1 - 523
d_181ens_1ASPLEUCA1 - 523
d_191ens_1ASPLEUCB1 - 523
d_201ens_1ASPLEUD1 - 523
d_211ens_1ASPLEUDA1 - 523
d_221ens_1ASPLEUDB1 - 523
d_231ens_1ASPLEUE1 - 523
d_241ens_1ASPLEUEA1 - 523
d_251ens_1ASPLEUEB1 - 523
d_261ens_1ASPLEUF1 - 523
d_271ens_1ASPLEUFA1 - 523
d_281ens_1ASPLEULA1 - 523
d_291ens_1ASPLEUG1 - 523
d_301ens_1ASPLEUGA1 - 523
d_311ens_1ASPLEUGB1 - 523
d_321ens_1ASPLEUH1 - 523
d_331ens_1ASPLEUHA1 - 523
d_341ens_1ASPLEUHB1 - 523
d_351ens_1ASPLEUI1 - 523
d_361ens_1ASPLEUIA1 - 523
d_371ens_1ASPLEUNA1 - 523
d_381ens_1ASPLEUO1 - 523
d_391ens_1ASPLEUOA1 - 523
d_401ens_1ASPLEUP1 - 523
d_411ens_1ASPLEUPA1 - 523
d_421ens_1ASPLEUQ1 - 523
d_431ens_1ASPLEUQA1 - 523
d_441ens_1ASPLEUR1 - 523
d_451ens_1ASPLEURA1 - 523
d_461ens_1ASPLEUS1 - 523
d_471ens_1ASPLEUSA1 - 523
d_481ens_1ASPLEUT1 - 523
d_491ens_1ASPLEUTA1 - 523
d_501ens_1ASPLEUUA1 - 523
d_511ens_1ASPLEUV1 - 523
d_521ens_1ASPLEUVA1 - 523
d_531ens_1ASPLEUW1 - 523
d_541ens_1ASPLEUWA1 - 523
d_551ens_1ASPLEUX1 - 523
d_561ens_1ASPLEUXA1 - 523
d_571ens_1ASPLEUFB1 - 523
d_581ens_1ASPLEUYA1 - 523
d_591ens_1ASPLEUZ1 - 523
d_601ens_1ASPLEUZA1 - 523

NCS oper:
IDCodeMatrixベクター
1given(-0.808966168683, 0.308964399306, 0.500114724726), (0.309121150294, -0.500049602522, 0.808946543017), (0.500017852049, 0.80900642456, 0.30901578059)147.007648411, 56.1654217451, -90.8724246406
2given(-0.309101427881, 0.500062028288, -0.808946398191), (-0.49998138375, -0.809012727323, -0.309058284039), (-0.808996244235, 0.308927782652, 0.500088694053)237.888859154, 384.93629882, 147.025995298
3given(0.500085315524, -0.809026723105, 0.308853425591), (-0.80895586765, -0.309157238649, 0.500012205837), (-0.309038964197, -0.499897552597, -0.809071909978)147.051728538, 237.915984019, 384.923980845
4given(-0.808974513838, -0.309175672716, 0.499970638499), (-0.309024841694, -0.499841754483, -0.809111777007), (0.500063879096, -0.809054153859, 0.308816277012)237.932607033, 384.916937361, 147.069589808
5given(-0.499867514054, -0.809160241824, 0.308856231028), (-0.809038511, 0.308936840551, -0.500014716053), (0.309174960359, -0.499817698368, -0.809069287691)294.102323154, 294.085069328, 294.001268808
6given(3.91542743339E-6, -4.96441658587E-5, 0.99999999876), (-0.999999998565, -5.34285784315E-5, 3.91277501588E-6), (5.34283841184E-5, -0.99999999734, -4.96443749836E-5)0.00972041730657, 294.071256343, 294.060180274
7given(-0.808994828175, -0.309064521047, -0.500006489773), (0.308902425775, 0.500166464627, -0.808957847488), (0.500106647962, -0.808895932424, -0.309161302838)384.937165281, 147.001044231, 237.880724054
8given(0.308939577988, 0.50010808989, -0.808979749795), (0.500045767111, -0.808946920441, -0.309126366886), (-0.809018274174, -0.309025530232, -0.499992653663)147.010737015, 237.895718004, 384.929178097
9given(4.11889962404E-6, 3.91448803498E-5, -0.999999999225), (0.999999998204, 5.97853399471E-5, 4.12123991006E-6), (5.97855012264E-5, -0.999999997447, -3.914463403E-5)294.050348869, -0.0140021071107, 294.057340373
10given(0.500631796494, -0.808755506886, 0.308678367272), (0.808694247196, 0.309726832912, -0.500082896655), (0.308838823485, 0.499983818794, 0.80909502659)146.922944934, 56.0875125299, -90.8601897028
11given(0.808978965117, 0.309169662313, -0.499967152824), (0.309023194926, 0.49984249077, 0.809111951104), (0.500057695667, -0.809055995791, 0.308821464083)56.1269817327, -90.8567056805, 147.070290264
12given(-0.309068608536, 0.499901559395, 0.809058110479), (0.499948396361, 0.809081828468, -0.308930729806), (-0.809029168939, 0.309006514102, -0.499986777874)0.0232532423593, -0.024108806091, 294.062031352
13given(-0.499869657409, -0.809154942825, 0.308866644529), (0.809039657534, -0.308935725134, 0.500013550089), (-0.309168494737, 0.499826966297, 0.80906603292)294.100024338, -0.0250843867036, 0.0566778276526
14given(0.809051045192, -0.308944701539, 0.499989577556), (-0.309130395827, 0.499844284858, 0.809069891462), (-0.499874788971, -0.809140817341, 0.308895343222)-0.0201861477329, 0.0449370707707, 294.091949441
15given(-0.500030536033, 0.808955206228, 0.309129321404), (0.809027783755, 0.309014447097, 0.499984116345), (0.308939327613, 0.500101535493, -0.808983897276)56.1592700464, -90.8671341638, 147.013543449
16given(-0.80899889711, -0.309061679368, -0.500001662818), (-0.308899685279, -0.500164846869, 0.808959894179), (-0.500101758554, 0.808898018481, 0.309163754002)384.936800404, 147.057866752, 56.1781257025
17given(-0.308942409849, -0.500108300682, 0.808978538025), (-0.500036435253, 0.808950817701, 0.309131263317), (-0.809022960623, -0.309014986902, -0.499991586984)147.0493685, 56.1609710637, 384.927751705
18given(1.18674369984E-5, 0.999999999919, 4.70645221617E-6), (6.69459162983E-6, -4.70653166418E-6, 0.999999999967), (0.999999999907, -1.18674054905E-5, -6.69464748393E-6)-0.00304731974524, -0.000326025289553, 0.0034856435658
19given(1.85219404503E-6, 5.29895532891E-5, -0.999999998594), (-0.999999998147, -6.0852282215E-5, -1.85541857939E-6), (-6.08523804473E-5, 0.999999996745, 5.29894404806E-5)294.048158368, 294.073914485, 0.000406340195639
20given(-0.999999999992, -5.27706559653E-7, -4.08110940046E-6), (-5.27727063425E-7, 0.999999999987, 5.02406864036E-6), (4.08110674918E-6, 5.02407079403E-6, -0.999999999979)294.061183032, -0.000597045145554, 294.058474574
21given(0.4999980164, 0.808975264224, 0.309129431582), (-0.808998528329, 0.30891440653, 0.500093261902), (0.309068543786, -0.500130894179, 0.808916388714)-90.8857148098, 147.028888585, 56.1984565005
22given(0.808999463592, -0.308924226055, -0.500085683123), (-0.30909347686, 0.500072220452, -0.808943135761), (0.499981090113, 0.809007785432, 0.309071694985)147.032281758, 237.884411419, -90.8781872111
23given(-0.309112990199, 0.500048789047, -0.808950164017), (0.500008051587, 0.809009287784, 0.309024142468), (0.808975344271, -0.308958218619, -0.500103700756)237.893738223, -90.8729635221, 147.047530145
24given(0.309073275358, 0.499861887098, 0.809080839154), (0.500070079254, -0.809051165012, 0.308814067404), (0.808952178002, 0.30915094407, -0.500022067)-90.8629039048, 147.068871502, 56.1468574776
25given(-0.500060271509, 0.80905620236, -0.308816751944), (-0.808977327121, -0.309174092539, 0.499967063623), (0.309023314757, 0.499839416138, 0.809113804734)146.989679016, 237.933576872, -90.8565811719
26given(0.808954850106, 0.309161965029, -0.500010929751), (-0.309034169549, -0.499900325079, -0.809072028337), (-0.500089924456, 0.809023203849, -0.308855181423)56.143006935, 384.923586604, 147.009615941
27given(-0.809050017165, 0.308937234705, -0.499995854721), (0.309142097759, -0.499840118199, -0.809067994443), (-0.499869216015, -0.809146242191, 0.308890151396)294.082417479, 294.011577994, 294.09328485
28given(0.499866434168, 0.809160159424, -0.308858194635), (-0.809039102717, 0.308934837482, -0.50001499624), (-0.309175157907, 0.499819069855, 0.809068364937)-0.0417718424735, 294.085205566, 0.0585612822244
29given(0.809053744389, -0.30893886425, 0.49998881672), (0.309132343792, -0.499843507333, -0.809069627535), (0.499869215606, 0.809143526411, -0.308897266022)-0.0215161997579, 294.014324409, -0.0313573056367
30given(-0.500037541544, 0.808948358275, 0.30913590974), (-0.809025345922, -0.309017766898, -0.499986009202), (-0.308934372808, -0.500110561163, 0.808980209839)56.1604059496, 384.927616166, 147.047783667
31given(0.808998189885, 0.309065813992, 0.500000251384), (0.308897299221, 0.500163867495, -0.808961410814), (-0.500104376403, 0.808897044298, 0.309162068225)-90.8767762069, 147.002979631, 56.1784099726
32given(-0.308936437238, -0.500110191284, 0.808979650128), (0.500039482436, -0.808948059588, -0.309133551873), (0.809023357977, 0.309019147405, 0.49998837265)147.04904211, 237.898360909, -90.8679842534
33given(5.15860995942E-6, 0.999999999986, 1.49445747644E-6), (-8.62261392687E-6, 1.49450195708E-6, -0.999999999962), (-0.99999999995, 5.15859707323E-6, 8.62262163626E-6)-0.00159899966627, 294.061191571, 294.057049113
34given(4.9068838619E-6, -3.94290622929E-5, 0.999999999211), (0.999999998504, 5.44795761321E-5, -4.90473577935E-6), (-5.44793826995E-5, 0.999999997739, 3.94293295591E-5)0.00796525553324, -0.0114118028757, 0.00169294637993
35given(-0.999999999979, -1.54322542019E-6, 6.27957723446E-6), (1.5432077839E-6, -0.999999999995, -2.80852006825E-6), (6.27958156861E-6, -2.8085103775E-6, 0.999999999976)294.059561123, 294.060049349, -0.000493450615579
36given(0.999999403189, 0.0005613639937, 0.000937279301669), (0.000560913325576, -0.999999726998, 0.000481019510233), (0.000937549072823, -0.000480493490705, -0.999999445064)-0.323440685046, 293.850919499, 293.987069497
37given(0.808997585941, -0.308934976935, -0.500082079231), (0.309092927939, -0.500060632411, 0.808950508876), (-0.499984467599, -0.809010842905, -0.309058227881)147.03343399, 56.1717209024, 384.93665829
38given(0.309122291348, -0.500051386905, 0.808945003969), (-0.500012172331, -0.809008078593, -0.30902064056), (0.808969243243, -0.308957180247, -0.500114211217)56.1659955862, 384.93280366, 147.050209058
39given(-0.50006158608, 0.809053096639, -0.30882275976), (0.808976572323, 0.309171286026, -0.499970020431), (-0.309023163467, -0.499846179056, -0.809109684607)146.991147033, 56.1278649184, 384.917074307
40given(-0.309071388187, -0.499914904105, -0.809048803014), (-0.500098716012, 0.809019708394, -0.308850102271), (0.808935195951, 0.309147537727, -0.500051646002)384.928103638, 147.010526976, 56.1584932781
41given(0.499871621786, 0.809155223961, -0.308862728847), (0.809037006963, -0.308937036318, 0.500017028666), (0.309172254735, -0.499825700748, -0.809065377935)-0.0411964796166, -0.02488331932, 294.002342732
42given(0.500025631982, 0.808976431371, 0.30908170578), (0.808971634761, -0.308945074171, -0.500117821416), (-0.309094259917, 0.500110062518, -0.808919442129)-90.880987199, 147.047412621, 237.869786712
43given(0.809000739772, 0.309058332283, 0.500000750294), (-0.308901143766, -0.500163080969, 0.808960429079), (0.500097876848, -0.808900389221, -0.309163830178)-90.8761774016, 147.057576665, 237.883233498
44given(0.50068220291, -0.808542069946, -0.309155386201), (0.808623311268, 0.309398517259, 0.500400737401), (-0.308942829927, -0.500531995626, 0.808716297098)237.694783348, -90.9631883315, 147.198084835
45given(0.309068313438, -0.499897261091, -0.809060879033), (0.499943703653, 0.809085219047, -0.308929444206), (0.809032181564, -0.309004590052, 0.499983092235)294.03657608, -0.0241591796829, -0.00184168552144
46given(-7.04152141839E-6, -0.999999999973, -2.15386478197E-6), (1.03934253157E-5, -2.15393796754E-6, 0.999999999944), (-0.999999999921, 7.04149903175E-6, 1.03934404823E-5)294.061695752, -0.00120922174924, 294.056962092
47given(-0.808970468089, 0.308958343548, 0.500111511277), (-0.309120720355, 0.500048841492, -0.808947177738), (-0.500011161882, -0.809009207658, -0.309019319652)147.009660557, 237.894800617, 384.932543279
48given(-0.499994949497, -0.808975909047, -0.309132704608), (-0.809000745373, 0.308911008726, 0.500091774252), (-0.309067702072, 0.500131949858, -0.808916057615)384.945915421, 147.030728998, 237.861100772
49given(-0.309064660841, -0.499863333159, -0.809083236498), (0.500075083544, -0.80904744402, 0.308815712266), (-0.808952375754, -0.309158343712, 0.500017171981)384.921939861, 147.067188822, 237.915792869
50given(-0.808958757209, -0.3091540606, 0.500009495859), (0.309035824279, 0.499900210596, 0.809071467028), (-0.500082581627, 0.80902629516, -0.308858973145)237.916409786, -90.8638341874, 147.008931892
51given(0.309060673069, -0.499898101634, -0.809063278332), (-0.499945699514, -0.809083021502, 0.308931969621), (-0.809033866967, 0.309008984174, -0.499977649301)294.038236724, 294.083729685, 294.060702275
52given(-0.808968054541, 0.308994050979, -0.500093354477), (-0.309155200231, 0.499941607195, 0.809000279089), (0.499993748864, 0.809061843035, -0.308909671656)294.075863361, 0.0454244708245, -0.0302874274356
53given(0.500043498639, -0.808945777472, -0.309133027319), (-0.809019906074, -0.309020383794, -0.49999319393), (0.308938976249, 0.500113118714, -0.808976870772)237.896971613, 384.928547646, 147.0095886
54given(0.308942550511, 0.500111723032, -0.80897636861), (-0.500046070411, 0.808945850159, 0.309128677054), (0.809016951584, 0.309022452254, 0.499996696042)147.009550303, 56.1641233573, -90.8690795439
55given(1.71929500725E-6, -0.99999999999, -4.09530940415E-6), (-7.69393718708E-6, 4.09529617551E-6, -0.999999999962), (0.999999999969, 1.71932651649E-6, -7.69393014632E-6)294.06062989, 294.06048457, 0.00114498116952
56given(-0.309056129527, 0.499900346906, 0.809063626648), (-0.499949709973, -0.80907996972, 0.308933471958), (0.809033124353, -0.309013342368, 0.49997615737)0.0201749262977, 294.083222847, 0.000357788836993
57given(-0.500015150329, -0.808979714201, -0.30909007013), (0.808978710733, -0.308934393986, -0.50011297303), (0.309092696488, -0.500111349826, 0.808919243654)384.941267736, 147.042834611, 56.1909657778
58given(0.309093153758, -0.500059734903, 0.808950977395), (0.499986337971, 0.809010504492, 0.309056087892), (-0.808996343714, 0.308937315892, 0.500082643878)56.1713644683, -90.8764279548, 147.025413206
59given(0.309072830483, 0.49991542456, 0.809047930437), (-0.50009633574, 0.809020629782, -0.308851542923), (-0.808936116412, -0.309144284879, 0.500052167969)-90.8683380398, 147.010058353, 237.900949829

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要素

#1: タンパク質 ...
Capsid protein


分子量: 82212.859 Da / 分子数: 60 / 由来タイプ: 組換発現
由来: (組換発現) Adeno-associated virus - 1 (アデノ随伴ウイルス)
細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9WBP8

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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 - 1 / タイプ: VIRUS
詳細: AAV1-PHP.B trans plasmids with cis plasmids 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 - 1 (アデノ随伴ウイルス)
由来(組換発現)生物種: Homo sapiens (ヒト)
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 chlorideNaCl1
22.7 mMpotassium chlorideKCl1
310 mMsodium phosphate dibasicNa2HPO41
41.8 mMpotassium phosphate monobasicKH2P041
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: Talos Arctica / 画像提供: FEI Company
顕微鏡モデル: FEI TECNAI ARCTICA
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 / Cs: 2.7 mm
試料ホルダ凍結剤: NITROGEN
撮影電子線照射量: 37.5 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 1950

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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: 151543
対称性点対称性: I (正20面体型対称)
3次元再構成解像度: 2.32 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 59346 / 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: 35.24 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.0076255060
ELECTRON MICROSCOPYf_angle_d0.6666347940
ELECTRON MICROSCOPYf_chiral_restr0.047736300
ELECTRON MICROSCOPYf_plane_restr0.005546140
ELECTRON MICROSCOPYf_dihedral_angle_d14.660434020
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2XELECTRON MICROSCOPYNCS constraints0.000707074065692
ens_1d_3XELECTRON MICROSCOPYNCS constraints0.00070251728213
ens_1d_4XELECTRON MICROSCOPYNCS constraints0.000704605071227
ens_1d_5XELECTRON MICROSCOPYNCS constraints0.000702985023729
ens_1d_6XELECTRON MICROSCOPYNCS constraints0.000707878886305
ens_1d_7XELECTRON MICROSCOPYNCS constraints0.000706620197044
ens_1d_8XELECTRON MICROSCOPYNCS constraints0.000699075146481
ens_1d_9XELECTRON MICROSCOPYNCS constraints0.000702912969163
ens_1d_10XELECTRON MICROSCOPYNCS constraints0.000719633455803
ens_1d_11XELECTRON MICROSCOPYNCS constraints0.000703021709324
ens_1d_12XELECTRON MICROSCOPYNCS constraints0.000705421912732
ens_1d_13XELECTRON MICROSCOPYNCS constraints0.049230892279
ens_1d_14XELECTRON MICROSCOPYNCS constraints0.000703666531842
ens_1d_15XELECTRON MICROSCOPYNCS constraints0.000708483296773
ens_1d_16XELECTRON MICROSCOPYNCS constraints0.000708939765707
ens_1d_17XELECTRON MICROSCOPYNCS constraints0.000704344808941
ens_1d_18XELECTRON MICROSCOPYNCS constraints0.000703752956502
ens_1d_19XELECTRON MICROSCOPYNCS constraints0.00070261566365
ens_1d_20XELECTRON MICROSCOPYNCS constraints0.000714347207893
ens_1d_21XELECTRON MICROSCOPYNCS constraints0.000773135889623
ens_1d_22XELECTRON MICROSCOPYNCS constraints0.000703121588923
ens_1d_23XELECTRON MICROSCOPYNCS constraints0.000703962328818
ens_1d_24XELECTRON MICROSCOPYNCS constraints0.000705193857344
ens_1d_25XELECTRON MICROSCOPYNCS constraints0.00070661927764
ens_1d_26XELECTRON MICROSCOPYNCS constraints0.000703484860797
ens_1d_27XELECTRON MICROSCOPYNCS constraints0.000705468341775
ens_1d_28XELECTRON MICROSCOPYNCS constraints0.000702280344431
ens_1d_29XELECTRON MICROSCOPYNCS constraints0.000706649313644
ens_1d_30XELECTRON MICROSCOPYNCS constraints0.000710752789883
ens_1d_31XELECTRON MICROSCOPYNCS constraints0.0007002793638
ens_1d_32XELECTRON MICROSCOPYNCS constraints0.000701970961075
ens_1d_33XELECTRON MICROSCOPYNCS constraints0.000704663926197
ens_1d_34XELECTRON MICROSCOPYNCS constraints0.000626318997457
ens_1d_35XELECTRON MICROSCOPYNCS constraints0.000700598241281
ens_1d_36XELECTRON MICROSCOPYNCS constraints0.000727371876408
ens_1d_37XELECTRON MICROSCOPYNCS constraints0.000704160565451
ens_1d_38XELECTRON MICROSCOPYNCS constraints0.000710651949667
ens_1d_39XELECTRON MICROSCOPYNCS constraints0.000705655043483
ens_1d_40XELECTRON MICROSCOPYNCS constraints0.000705919403761
ens_1d_41XELECTRON MICROSCOPYNCS constraints0.0492345234344
ens_1d_42XELECTRON MICROSCOPYNCS constraints0.000702878641071
ens_1d_43XELECTRON MICROSCOPYNCS constraints0.000709162299193
ens_1d_44XELECTRON MICROSCOPYNCS constraints0.000702860699378
ens_1d_45XELECTRON MICROSCOPYNCS constraints0.000703249183582
ens_1d_46XELECTRON MICROSCOPYNCS constraints0.000707085110406
ens_1d_47XELECTRON MICROSCOPYNCS constraints0.000676605106886
ens_1d_48XELECTRON MICROSCOPYNCS constraints0.000706289612995
ens_1d_49XELECTRON MICROSCOPYNCS constraints0.000705897288268
ens_1d_50XELECTRON MICROSCOPYNCS constraints0.0492321255831
ens_1d_51XELECTRON MICROSCOPYNCS constraints0.000708440888454
ens_1d_52XELECTRON MICROSCOPYNCS constraints0.000701651236083
ens_1d_53XELECTRON MICROSCOPYNCS constraints0.00070649083896
ens_1d_54XELECTRON MICROSCOPYNCS constraints0.0492400856424
ens_1d_55XELECTRON MICROSCOPYNCS constraints0.000698493274882
ens_1d_56XELECTRON MICROSCOPYNCS constraints0.000548473379306
ens_1d_57XELECTRON MICROSCOPYNCS constraints0.000709389766008
ens_1d_58XELECTRON MICROSCOPYNCS constraints0.000705565404634
ens_1d_59XELECTRON MICROSCOPYNCS constraints0.000706593013721
ens_1d_60XELECTRON MICROSCOPYNCS constraints0.000700322643884

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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

他の情報も見る