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基本情報
登録情報 | データベース: EMDB / ID: EMD-11225 | |||||||||
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タイトル | negative staining 3D reconstruction of p2 virion baseplate in activated conformation (3D class with closed Tal trimer) | |||||||||
![]() | negative staining 3D reconstruction of p2 virion baseplate bound to VHH5 (3D class with closed Tal trimer) | |||||||||
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![]() | lactococcal siphophage p2 / baseplate / receptor-binding protein / Distal Tail protein / Tail-associated lysin / VIRAL PROTEIN | |||||||||
機能・相同性 | ![]() symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / ネガティブ染色法 / 解像度: 42.2 Å | |||||||||
![]() | Spinelli S / Cambillau C | |||||||||
![]() | ![]() タイトル: Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism. 著者: Silvia Spinelli / Denise Tremblay / Sylvain Moineau / Christian Cambillau / Adeline Goulet / ![]() ![]() 要旨: Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated ...Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the model siphophage for this viral genus. The baseplate of phage p2, which is used to recognize its host, was previously shown to display two conformations by X-ray crystallography, a rested state and an activated state ready to bind to the host. The baseplate became only activated and opened in the presence of Ca. However, such an activated state was not previously observed in the virion. Here, using nanobodies binding to the baseplate, we report on the negative staining electron microscopy structure of the activated form of the baseplate directly observed in the p2 virion, that is compatible with the activated baseplate crystal structure. Analyses of this new structure also established the presence of a second distal tail (Dit) hexamer as a component of the baseplate, the topology of which differs largely from the first one. We also observed an uncoupling between the baseplate activation and the tail tip protein (Tal) opening, suggesting an infection mechanism more complex than previously expected. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 2.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 13.2 KB 13.2 KB | 表示 表示 | ![]() |
画像 | ![]() | 122.5 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | negative staining 3D reconstruction of p2 virion baseplate bound to VHH5 (3D class with closed Tal trimer) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 3.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : Lactococcus virus P2
全体 | 名称: ![]() |
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要素 |
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-超分子 #1: Lactococcus virus P2
超分子 | 名称: Lactococcus virus P2 / タイプ: virus / ID: 1 / 親要素: 0 / 含まれる分子: all / NCBI-ID: 254252 / 生物種: Lactococcus virus P2 / ウイルスタイプ: VIRION / ウイルス・単離状態: STRAIN / ウイルス・エンベロープ: No / ウイルス・中空状態: No |
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宿主 | 生物種: ![]() |
-分子 #1: Receptor binding protein
分子 | 名称: Receptor binding protein / タイプ: protein_or_peptide / ID: 1 / コピー数: 18 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 28.668057 KDa |
配列 | 文字列: MTIKNFTFFS PNSTEFPVGS NNDGKLYMML TGMDYRTIRR KDWSSPLNTA LNVQYTNTSI IAGGRYFELL NETVALKGDS VNYIHANID LTQTANPVSL SAETANNSNG VDINNGSGVL KVCFDIVTTS GTGVTSTKPI VQTSTLDSIS VNDMTVSGSI D VPVQTLTV ...文字列: MTIKNFTFFS PNSTEFPVGS NNDGKLYMML TGMDYRTIRR KDWSSPLNTA LNVQYTNTSI IAGGRYFELL NETVALKGDS VNYIHANID LTQTANPVSL SAETANNSNG VDINNGSGVL KVCFDIVTTS GTGVTSTKPI VQTSTLDSIS VNDMTVSGSI D VPVQTLTV EAGNGLQLQL TKKNNDLVIV RFFGSVSNIQ KGWNMSGTWV DRPFRPAAVQ SLVGHFAGRD TSFHIDINPN GS ITWWGAN IDKTPIATRG NGSYFIK UniProtKB: Receptor binding protein |
-分子 #2: Distal tail protein
分子 | 名称: Distal tail protein / タイプ: protein_or_peptide / ID: 2 / コピー数: 12 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 34.511992 KDa |
配列 | 文字列: MVRQYKIHTN LDGTDDKVWD VTNGKVRFYQ PSNLGLQSTN NIWQSNGIGV MGTRSITQPQ IEFKLETFGE SLEENYQLMK DFVNDILSK KFVTLEYQTE IFQVYADLAL ADVTKTEGYG KNGTFSEKIT FDIITKWYTY ENLTFDKIQN GKVIAGMSKI Y GGTAPGNY ...文字列: MVRQYKIHTN LDGTDDKVWD VTNGKVRFYQ PSNLGLQSTN NIWQSNGIGV MGTRSITQPQ IEFKLETFGE SLEENYQLMK DFVNDILSK KFVTLEYQTE IFQVYADLAL ADVTKTEGYG KNGTFSEKIT FDIITKWYTY ENLTFDKIQN GKVIAGMSKI Y GGTAPGNY KYIKGTSYTY YGESDIDRLS RWDIKEEIFS FMGILYPKLP KTPAGVRFLD DIGNEYTAIV FKTEQVQDYI LI NTDVNDE TYQGWKGTTA LNLFPVMDFE RYRTRIIEKG QMELINLSKA EFKIKRKADF V UniProtKB: Distal tail protein |
-分子 #3: Baseplate protein gp16
分子 | 名称: Baseplate protein gp16 / タイプ: protein_or_peptide / ID: 3 / コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 42.883266 KDa |
配列 | 文字列: MLEANVYDNF NPNYYNISDF SMPNGKKEKR GLPIPKARCQ VINYELWETG YLYTSSATLT VSVEVGDIVQ ILFPEVVPIE EALGKKKKL NLDMVYLVTD VDESNKATLK NYFWAMIESL DVPNAITKTT NFAIIDYLID PNKNNLMSYG YFFNSSIFAG K ATINRKAE ...文字列: MLEANVYDNF NPNYYNISDF SMPNGKKEKR GLPIPKARCQ VINYELWETG YLYTSSATLT VSVEVGDIVQ ILFPEVVPIE EALGKKKKL NLDMVYLVTD VDESNKATLK NYFWAMIESL DVPNAITKTT NFAIIDYLID PNKNNLMSYG YFFNSSIFAG K ATINRKAE TSSAHDVAKR IFSKVQFQPT TTIQHAPSET DPRNLLFINF ASRNWNRKRI TTRVDIKQSV TMDTETIVER SA YNFAVVF VKNKATDDYT DPPKMYIAKN NGDVIDYSTY HGDGTDLPDV RTAKTLFYDR DDHGNPPELS TIKVEISPST IVT RLIFNQ NELLPLYVND LVDIWYEGKL YSGYIADRVK TEFNDRLIFV ESGDKPNVI UniProtKB: Baseplate protein gp16 |
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 |
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染色 | タイプ: NEGATIVE / 材質: uranyl acetate |
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電子顕微鏡法
顕微鏡 | FEI TECNAI SPIRIT |
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撮影 | フィルム・検出器のモデル: OTHER / 平均電子線量: 25.0 e/Å2 |
電子線 | 加速電圧: 120 kV / 電子線源: LAB6 |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Tecnai Spirit / 画像提供: FEI Company |