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- PDB-9h28: Alternative conformation LGTV with TBEV prME -

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基本情報

登録情報
データベース: PDB / ID: 9h28
タイトルAlternative conformation LGTV with TBEV prME
要素
  • Envelope protein E
  • Small envelope protein M
キーワードVIRUS / Chimeric virus / Flavivirus / Tick-borne Encephalitis virus / Langat virus / recombinant virus
機能・相同性
機能・相同性情報


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
類似検索 - 分子機能
Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. ...Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Chem-CPL / Genome polyprotein / Genome polyprotein
類似検索 - 構成要素
生物種tick-borne encephalitis virus-European subtype (ウイルス)
Langat virus (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: 3.22 Å
データ登録者Bisikalo, K. / Rosendal, E.
資金援助 スウェーデン, 1件
組織認可番号国
Swedish Research Council2018-05851 スウェーデン
引用
ジャーナル: J Virol / 年: 2025
タイトル: Influence of the pre-membrane and envelope proteins on structure, pathogenicity, and tropism of tick-borne encephalitis virus.
著者: Ebba Rosendal / Kyrylo Bisikalo / Stefanie M A Willekens / Marie Lindgren / Jiří Holoubek / Pavel Svoboda / Amanda Lappalainen / Ebba Könighofer / Ekaterina Mirgorodskaya / Rickard Nordén ...著者: Ebba Rosendal / Kyrylo Bisikalo / Stefanie M A Willekens / Marie Lindgren / Jiří Holoubek / Pavel Svoboda / Amanda Lappalainen / Ebba Könighofer / Ekaterina Mirgorodskaya / Rickard Nordén / Federico Morini / William Rosenbaum / Daniel Růžek / Ulf Ahlgren / Maria Anastasina / Andres Merits / Sarah J Butcher / Emma Nilsson / Anna K Överby /
要旨: Tick-borne encephalitis virus (TBEV) is a neurotropic flavivirus that causes thousands of human infections annually. Viral tropism in the brain is determined by the presence of necessary receptors, ...Tick-borne encephalitis virus (TBEV) is a neurotropic flavivirus that causes thousands of human infections annually. Viral tropism in the brain is determined by the presence of necessary receptors, entry factors, and the ability of the virus to overcome host defenses. The viral structural proteins, pre-membrane (prM), and envelope (E) play an important role in receptor binding, membrane fusion, particle maturation, and antibody neutralization. To understand how these proteins influence virus distribution and tropism in the brain, we generated a chimeric virus harboring the prM and ectodomain of E from TBEV in the background of the low-pathogenic Langat virus (LGTV). We solved the atomic structures of both the chimeric virus and LGTV to compare them to the known TBEV structure. We show that this chimeric virus remains low-pathogenic, while being structurally and antigenically similar to TBEV. Using 3D optical whole brain imaging combined with immunohistochemistry, we found that both LGTV and the chimeric virus primarily infect the cerebral cortex, with no significant differences in their localization or tropism. In contrast, TBEV shows high infection of the cerebellum and a strong preference toward Purkinje cells, indicating that factors other than the prM and E proteins are important for determining TBEV tropism in the brain. Together, this provides new insights into the roles of the structural and non-structural proteins of tick-borne flaviviruses.
IMPORTANCE: Although an effective vaccine exists, there is no treatment for those infected by the tick-borne encephalitis virus (TBEV). This study aimed to better understand how the virus's surface ...IMPORTANCE: Although an effective vaccine exists, there is no treatment for those infected by the tick-borne encephalitis virus (TBEV). This study aimed to better understand how the virus's surface proteins influence viral tropism and pathogenicity. We created a chimeric virus with prM and E proteins of TBEV in the genetic background of the low-pathogenic Langat virus (LGTV). The chimeric virus remained low pathogenic, similar to LGTV. Both viruses infected similar brain regions, while TBEV showed a strong preference for the cerebellum and Purkinje cells. This means that other parts of the virus, such as non-structural proteins or NCR, likely decide how the virus behaves in the brain. This study also presents the first cryogenic electron microscopy structure of LGTV, the first whole-brain imaging of TBEV infection in mouse brain, and a new model system to study surface proteins in tick-borne flaviviruses-laying groundwork for future studies on viral tropism, antibody cross-reactivity, and virus-receptor interaction.
#1: ジャーナル: Biorxiv / 年: 2024
タイトル: The influence of the pre-membrane and envelope proteins on structure, pathogenicity and tropism of tick-borne encephalitis virus
著者: Rosendal, E. / Bisikalo, K. / Willekens, S.M. / Lindgren, M. / Holoubek, J. / Svoboda, P. / Lappalainen, A. / Konighofer, E. / Mirgorodskaya, E. / Norden, R. / Morini, F. / Rosenbaum, W. / ...著者: Rosendal, E. / Bisikalo, K. / Willekens, S.M. / Lindgren, M. / Holoubek, J. / Svoboda, P. / Lappalainen, A. / Konighofer, E. / Mirgorodskaya, E. / Norden, R. / Morini, F. / Rosenbaum, W. / Ruzek, D. / Ahlgren, U. / Anastasina, M. / Merits, A. / Butcher, S.J. / Nilsson, E. / Overby, A.K.
履歴
登録2024年10月11日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年11月6日Provider: repository / タイプ: Initial release
改定 1.12024年11月13日Group: Database references / Structure summary
カテゴリ: entity / entity_name_com ...entity / entity_name_com / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref.db_code ..._entity.pdbx_description / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
改定 1.22025年9月3日Group: Database references / Structure summary / カテゴリ: citation / citation_author / entity / Item: _entity.pdbx_description
改定 1.32025年10月1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 1.42025年10月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)191,69615
ポリマ－185,8756
非ポリマー5,8229
水00
1
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)11,501,783900
ポリマ－11,152,490360
非ポリマー349,294540
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation59

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要素

#1: タンパク質 Envelope protein E


分子量: 53646.422 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) tick-borne encephalitis virus-European subtype (ウイルス), (組換発現) Langat virus (strain TP21) (ウイルス)
株: 93/783 / 細胞株 (発現宿主): A549 MAVS -/- / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A0A7M3UFX3, UniProt: P29837
#2: タンパク質 Small envelope protein M


分子量: 8311.854 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) tick-borne encephalitis virus-European subtype (ウイルス)
株: 93/783 / 細胞株 (発現宿主): A549 MAVS -/- / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A0A7M3UFX3
#3: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 化合物
ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


分子量: 758.060 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C42H80NO8P / コメント: リン脂質*YM
研究の焦点であるリガンドがあるかN
Has protein modificationY

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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
ID名称タイプ詳細Entity IDParent-ID由来
1LGTV with TBEV prMEVIRUSChimeric virus based on the Langat virus (LGTV) and Tick-borne Encephalitis virus (TBEV). prM and ectodomains of E are taken from TBEV (European subtype, strain 93/873), while the rest of the virus genome is from LGTV TP21.#1-#20MULTIPLE SOURCES
2Envelope protein ECOMPLEX#11RECOMBINANT
3Small envelope protein MCOMPLEX#21RECOMBINANT
分子量実験値: NO
由来(天然)
IDEntity assembly-ID生物種Ncbi tax-ID株
22tick-borne encephalitis virus-European subtype (ウイルス)2848310Chimeric virus (prME from TBEV)
32Langat virus (strain TP21) (ウイルス)31638Chimeric virus (prME from TBEV)
43tick-borne encephalitis virus-European subtype (ウイルス)2848310Chimeric virus (prME from TBEV)
由来(組換発現)
IDEntity assembly-ID生物種Ncbi tax-ID細胞
22Homo sapiens (ヒト)9606A549 MAVS -/-
33Homo sapiens (ヒト)9606A549 MAVS -/-
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: YES / 単離: OTHER / タイプ: VIRION
ウイルス殻直径: 500 nm / 三角数 (T数): 3
緩衝液pH: 8
詳細: VP-SFM growth medium, supplemented with rapamycin and glutamate.
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: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3
急速凍結装置: LEICA EM GP / 凍結剤: ETHANE / 湿度: 90 % / 凍結前の試料温度: 298 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: TFS 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 FIELD / 倍率（公称値）: 130000 X / 最大 デフォーカス（公称値）: 1500 nm / 最小 デフォーカス（公称値）: 500 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm
試料ホルダ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影平均露光時間: 4.27 sec. / 電子線照射量: 40 e/Å2 / 検出モード: COUNTING
フィルム・検出器のモデル: TFS FALCON 4i (4k x 4k)
撮影したグリッド数: 1 / 実像数: 32122

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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
2EPU画像取得
4cryoSPARCCTF補正
7UCSF ChimeraX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
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: 97855
対称性点対称性: I (正20面体型対称)
3次元再構成解像度: 3.22 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 18724 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 2 / 対称性のタイプ: POINT
原子モデル構築Source name: AlphaFold / タイプ: in silico model

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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