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- PDB-8pkh: Borrelia bacteriophage BB1 procapsid, fivefold-symmetrized outer shell -

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基本情報

登録情報
データベース: PDB / ID: 8pkh
タイトルBorrelia bacteriophage BB1 procapsid, fivefold-symmetrized outer shell
要素
  • Decorator protein P03
  • Decorator protein P04
  • Decorator protein P05
  • Major capsid protein
  • Scaffold protein
キーワードVIRAL PROTEIN / Bacteriophage / capsid / procapsid
機能・相同性Protein of unknown function DUF1357 / Protein of unknown function (DUF1357) / Uncharacterized protein
機能・相同性情報
生物種Borreliella burgdorferi B31 (バクテリア)
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: 3.35 Å
データ登録者Rumnieks, J. / Fuzik, T. / Tars, K.
資金援助European Union, 3件
組織認可番号国
European Regional Development Fund1.1.1.2/VIAA/4/20/704European Union
iNEXT-Discovery18826European Union
iNEXT-Discovery24421European Union
引用ジャーナル: J Mol Biol / 年: 2023
タイトル: Structure of the Borrelia Bacteriophage φBB1 Procapsid.
著者: Jānis Rūmnieks / Tibor Füzik / Kaspars Tārs /
要旨: Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all ...Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all B. burgdorferi isolates carry a prophage φBB1 as resident circular plasmids. Like its host, the φBB1 phage is quite distinctive and shares little sequence similarity with other known bacteriophages. We expressed φBB1 head morphogenesis proteins in Escherichia coli which resulted in assembly of homogeneous prolate procapsid structures and used cryo-electron microscopy to determine the three-dimensional structure of these particles. The φBB1 procapsids consist of 415 copies of the major capsid protein and an equal combined number of three homologous capsid decoration proteins that form trimeric knobs on the outside of the particle. One of the end vertices of the particle is occupied by a portal assembled from twelve copies of the portal protein. The φBB1 scaffolding protein is entirely α-helical and has an elongated shape with a small globular domain in the middle. Within the tubular section of the procapsid, the internal scaffold is built of stacked rings, each composed of 32 scaffolding protein molecules, which run in opposite directions from both caps with a heterogeneous part in the middle. Inside the portal-containing cap, the scaffold is organized asymmetrically with ten scaffolding protein molecules bound to the portal. The φBB1 procapsid structure provides better insight into the vast structural diversity of bacteriophages and presents clues of how elongated bacteriophage particles might be assembled.
履歴
登録2023年6月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年7月12日Provider: repository / タイプ: Initial release
改定 1.12023年7月19日Group: Database references
カテゴリ: struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
改定 1.22023年11月1日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32023年11月15日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.title

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
AA: Major capsid protein
AB: Major capsid protein
AC: Major capsid protein
AD: Major capsid protein
AE: Major capsid protein
AF: Major capsid protein
AG: Major capsid protein
AH: Major capsid protein
AI: Major capsid protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Major capsid protein
AN: Major capsid protein
AO: Major capsid protein
AP: Major capsid protein
AQ: Major capsid protein
AR: Major capsid protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Major capsid protein
AW: Major capsid protein
AX: Major capsid protein
AY: Major capsid protein
AZ: Major capsid protein
BA: Major capsid protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Major capsid protein
BF: Major capsid protein
BG: Major capsid protein
BH: Major capsid protein
BI: Major capsid protein
BJ: Major capsid protein
BK: Major capsid protein
BL: Major capsid protein
BM: Major capsid protein
BN: Major capsid protein
BO: Major capsid protein
BP: Major capsid protein
BQ: Major capsid protein
BR: Major capsid protein
BS: Major capsid protein
BT: Major capsid protein
BU: Major capsid protein
BV: Major capsid protein
BW: Major capsid protein
BX: Major capsid protein
BY: Major capsid protein
BZ: Major capsid protein
CA: Major capsid protein
CB: Major capsid protein
CC: Major capsid protein
CD: Major capsid protein
CE: Major capsid protein
CF: Major capsid protein
CG: Major capsid protein
CH: Major capsid protein
CI: Major capsid protein
CJ: Major capsid protein
CK: Major capsid protein
CL: Major capsid protein
CM: Major capsid protein
CN: Major capsid protein
CO: Major capsid protein
CP: Major capsid protein
CQ: Major capsid protein
CR: Major capsid protein
CS: Major capsid protein
CT: Major capsid protein
CU: Major capsid protein
CV: Major capsid protein
CW: Major capsid protein
CX: Major capsid protein
CY: Major capsid protein
CZ: Major capsid protein
DA: Major capsid protein
DB: Major capsid protein
DC: Major capsid protein
DD: Major capsid protein
DE: Major capsid protein
DF: Decorator protein P03
DG: Decorator protein P03
DH: Decorator protein P03
DI: Decorator protein P03
DJ: Decorator protein P03
DK: Decorator protein P03
DL: Decorator protein P03
DM: Decorator protein P03
DN: Decorator protein P03
DO: Decorator protein P03
DP: Decorator protein P03
DQ: Decorator protein P03
DR: Decorator protein P03
DS: Decorator protein P03
DT: Decorator protein P03
DU: Decorator protein P03
DV: Decorator protein P03
DW: Decorator protein P03
DX: Decorator protein P03
DY: Decorator protein P03
DZ: Decorator protein P03
EA: Decorator protein P03
EB: Decorator protein P03
EC: Decorator protein P03
ED: Decorator protein P03
EE: Decorator protein P03
EF: Decorator protein P03
EG: Decorator protein P03
EH: Decorator protein P03
EI: Decorator protein P03
EJ: Decorator protein P03
EK: Decorator protein P03
EL: Decorator protein P03
EM: Decorator protein P03
EN: Decorator protein P03
EO: Decorator protein P03
EP: Decorator protein P03
EQ: Decorator protein P03
ER: Decorator protein P03
ES: Decorator protein P03
ET: Decorator protein P03
EU: Decorator protein P03
EV: Decorator protein P03
EW: Decorator protein P03
EX: Decorator protein P03
EY: Decorator protein P03
EZ: Decorator protein P03
FA: Decorator protein P03
FB: Decorator protein P03
FC: Decorator protein P03
FD: Decorator protein P03
FE: Decorator protein P03
FF: Decorator protein P03
FG: Decorator protein P03
FH: Decorator protein P03
FI: Decorator protein P03
FJ: Decorator protein P04
FK: Decorator protein P05
FL: Decorator protein P05
FM: Decorator protein P05
FN: Decorator protein P05
FO: Decorator protein P05
FP: Decorator protein P05
FQ: Decorator protein P05
FR: Decorator protein P05
FS: Decorator protein P05
FT: Decorator protein P05
FU: Decorator protein P05
FV: Decorator protein P05
FW: Decorator protein P05
FX: Decorator protein P05
FY: Decorator protein P05
FZ: Decorator protein P05
GA: Decorator protein P05
GB: Decorator protein P05
GC: Decorator protein P05
GD: Decorator protein P05
GE: Decorator protein P05
GF: Decorator protein P05
GG: Decorator protein P05
GH: Decorator protein P05
GI: Decorator protein P05
GJ: Decorator protein P05
GK: Scaffold protein
GL: Scaffold protein
GM: Scaffold protein
GN: Scaffold protein
GO: Scaffold protein
GP: Scaffold protein
GQ: Scaffold protein
GR: Scaffold protein
GS: Scaffold protein
GT: Scaffold protein
GU: Scaffold protein
GV: Scaffold protein
GW: Scaffold protein
GX: Scaffold protein
GY: Scaffold protein
GZ: Scaffold protein
HA: Scaffold protein
HB: Scaffold protein
HC: Scaffold protein
HD: Scaffold protein
HE: Scaffold protein
HF: Scaffold protein
HG: Scaffold protein
HH: Scaffold protein
HI: Scaffold protein
HJ: Scaffold protein
HK: Scaffold protein
HL: Scaffold protein
HM: Scaffold protein
HN: Scaffold protein
HO: Scaffold protein
HP: Scaffold protein
HQ: Scaffold protein
HR: Scaffold protein
HS: Scaffold protein
HT: Scaffold protein
HU: Scaffold protein
HV: Scaffold protein
HW: Scaffold protein
HX: Scaffold protein
HY: Scaffold protein
HZ: Scaffold protein
IA: Scaffold protein
IB: Scaffold protein
IC: Scaffold protein
ID: Scaffold protein
IE: Scaffold protein
IF: Scaffold protein
IG: Scaffold protein
IH: Scaffold protein
II: Scaffold protein
IJ: Scaffold protein
IK: Scaffold protein
IL: Scaffold protein
IM: Scaffold protein
IN: Scaffold protein
IO: Scaffold protein
IP: Scaffold protein
IQ: Scaffold protein
IR: Scaffold protein
IS: Scaffold protein
IT: Scaffold protein
IU: Scaffold protein
IV: Scaffold protein
IW: Scaffold protein
IX: Scaffold protein
IY: Scaffold protein
IZ: Scaffold protein
JA: Scaffold protein
JB: Scaffold protein
JC: Scaffold protein
JD: Scaffold protein
JE: Scaffold protein
JF: Scaffold protein
JG: Scaffold protein
JH: Scaffold protein
JI: Scaffold protein
JJ: Scaffold protein
JK: Scaffold protein
JL: Scaffold protein
JM: Scaffold protein
JN: Scaffold protein
JO: Scaffold protein


分子量 (理論値)分子数
合計 (水以外)6,928,869249
ポリマ－6,928,869249
非ポリマー00
水00
1
AA: Major capsid protein
AB: Major capsid protein
AC: Major capsid protein
AD: Major capsid protein
AE: Major capsid protein
AF: Major capsid protein
AG: Major capsid protein
AH: Major capsid protein
AI: Major capsid protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Major capsid protein
AN: Major capsid protein
AO: Major capsid protein
AP: Major capsid protein
AQ: Major capsid protein
AR: Major capsid protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Major capsid protein
AW: Major capsid protein
AX: Major capsid protein
AY: Major capsid protein
AZ: Major capsid protein
BA: Major capsid protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Major capsid protein
BF: Major capsid protein
BG: Major capsid protein
BH: Major capsid protein
BI: Major capsid protein
BJ: Major capsid protein
BK: Major capsid protein
BL: Major capsid protein
BM: Major capsid protein
BN: Major capsid protein
BO: Major capsid protein
BP: Major capsid protein
BQ: Major capsid protein
BR: Major capsid protein
BS: Major capsid protein
BT: Major capsid protein
BU: Major capsid protein
BV: Major capsid protein
BW: Major capsid protein
BX: Major capsid protein
BY: Major capsid protein
BZ: Major capsid protein
CA: Major capsid protein
CB: Major capsid protein
CC: Major capsid protein
CD: Major capsid protein
CE: Major capsid protein
CF: Major capsid protein
CG: Major capsid protein
CH: Major capsid protein
CI: Major capsid protein
CJ: Major capsid protein
CK: Major capsid protein
CL: Major capsid protein
CM: Major capsid protein
CN: Major capsid protein
CO: Major capsid protein
CP: Major capsid protein
CQ: Major capsid protein
CR: Major capsid protein
CS: Major capsid protein
CT: Major capsid protein
CU: Major capsid protein
CV: Major capsid protein
CW: Major capsid protein
CX: Major capsid protein
CY: Major capsid protein
CZ: Major capsid protein
DA: Major capsid protein
DB: Major capsid protein
DC: Major capsid protein
DD: Major capsid protein
DE: Major capsid protein
DF: Decorator protein P03
DG: Decorator protein P03
DH: Decorator protein P03
DI: Decorator protein P03
DJ: Decorator protein P03
DK: Decorator protein P03
DL: Decorator protein P03
DM: Decorator protein P03
DN: Decorator protein P03
DO: Decorator protein P03
DP: Decorator protein P03
DQ: Decorator protein P03
DR: Decorator protein P03
DS: Decorator protein P03
DT: Decorator protein P03
DU: Decorator protein P03
DV: Decorator protein P03
DW: Decorator protein P03
DX: Decorator protein P03
DY: Decorator protein P03
DZ: Decorator protein P03
EA: Decorator protein P03
EB: Decorator protein P03
EC: Decorator protein P03
ED: Decorator protein P03
EE: Decorator protein P03
EF: Decorator protein P03
EG: Decorator protein P03
EH: Decorator protein P03
EI: Decorator protein P03
EJ: Decorator protein P03
EK: Decorator protein P03
EL: Decorator protein P03
EM: Decorator protein P03
EN: Decorator protein P03
EO: Decorator protein P03
EP: Decorator protein P03
EQ: Decorator protein P03
ER: Decorator protein P03
ES: Decorator protein P03
ET: Decorator protein P03
EU: Decorator protein P03
EV: Decorator protein P03
EW: Decorator protein P03
EX: Decorator protein P03
EY: Decorator protein P03
EZ: Decorator protein P03
FA: Decorator protein P03
FB: Decorator protein P03
FC: Decorator protein P03
FD: Decorator protein P03
FE: Decorator protein P03
FF: Decorator protein P03
FG: Decorator protein P03
FH: Decorator protein P03
FI: Decorator protein P03
FJ: Decorator protein P04
FK: Decorator protein P05
FL: Decorator protein P05
FM: Decorator protein P05
FN: Decorator protein P05
FO: Decorator protein P05
FP: Decorator protein P05
FQ: Decorator protein P05
FR: Decorator protein P05
FS: Decorator protein P05
FT: Decorator protein P05
FU: Decorator protein P05
FV: Decorator protein P05
FW: Decorator protein P05
FX: Decorator protein P05
FY: Decorator protein P05
FZ: Decorator protein P05
GA: Decorator protein P05
GB: Decorator protein P05
GC: Decorator protein P05
GD: Decorator protein P05
GE: Decorator protein P05
GF: Decorator protein P05
GG: Decorator protein P05
GH: Decorator protein P05
GI: Decorator protein P05
GJ: Decorator protein P05
GK: Scaffold protein
GL: Scaffold protein
GM: Scaffold protein
GN: Scaffold protein
GO: Scaffold protein
GP: Scaffold protein
GQ: Scaffold protein
GR: Scaffold protein
GS: Scaffold protein
GT: Scaffold protein
GU: Scaffold protein
GV: Scaffold protein
GW: Scaffold protein
GX: Scaffold protein
GY: Scaffold protein
GZ: Scaffold protein
HA: Scaffold protein
HB: Scaffold protein
HC: Scaffold protein
HD: Scaffold protein
HE: Scaffold protein
HF: Scaffold protein
HG: Scaffold protein
HH: Scaffold protein
HI: Scaffold protein
HJ: Scaffold protein
HK: Scaffold protein
HL: Scaffold protein
HM: Scaffold protein
HN: Scaffold protein
HO: Scaffold protein
HP: Scaffold protein
HQ: Scaffold protein
HR: Scaffold protein
HS: Scaffold protein
HT: Scaffold protein
HU: Scaffold protein
HV: Scaffold protein
HW: Scaffold protein
HX: Scaffold protein
HY: Scaffold protein
HZ: Scaffold protein
IA: Scaffold protein
IB: Scaffold protein
IC: Scaffold protein
ID: Scaffold protein
IE: Scaffold protein
IF: Scaffold protein
IG: Scaffold protein
IH: Scaffold protein
II: Scaffold protein
IJ: Scaffold protein
IK: Scaffold protein
IL: Scaffold protein
IM: Scaffold protein
IN: Scaffold protein
IO: Scaffold protein
IP: Scaffold protein
IQ: Scaffold protein
IR: Scaffold protein
IS: Scaffold protein
IT: Scaffold protein
IU: Scaffold protein
IV: Scaffold protein
IW: Scaffold protein
IX: Scaffold protein
IY: Scaffold protein
IZ: Scaffold protein
JA: Scaffold protein
JB: Scaffold protein
JC: Scaffold protein
JD: Scaffold protein
JE: Scaffold protein
JF: Scaffold protein
JG: Scaffold protein
JH: Scaffold protein
JI: Scaffold protein
JJ: Scaffold protein
JK: Scaffold protein
JL: Scaffold protein
JM: Scaffold protein
JN: Scaffold protein
JO: Scaffold protein
x 5


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
  • 34.6 MDa, 1245 ポリマー
分子量 (理論値)分子数
合計 (水以外)34,644,3471245
ポリマ－34,644,3471245
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation4

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要素

#1: タンパク質 ...
Major capsid protein


分子量: 36255.551 Da / 分子数: 83 / 由来タイプ: 組換発現
由来: (組換発現) Borreliella burgdorferi B31 (バクテリア)
遺伝子: BB_L06 / 発現宿主: Escherichia coli BL21 (大腸菌) / Variant (発現宿主): AI
#2: タンパク質 ...
Decorator protein P03


分子量: 20026.479 Da / 分子数: 56 / 由来タイプ: 組換発現
由来: (組換発現) Borreliella burgdorferi B31 (バクテリア)
遺伝子: BB_L03 / 発現宿主: Escherichia coli BL21 (大腸菌) / Variant (発現宿主): AI
#3: タンパク質 Decorator protein P04


分子量: 28067.344 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Borreliella burgdorferi B31 (バクテリア)
遺伝子: BB_L04 / 発現宿主: Escherichia coli BL21 (大腸菌) / Variant (発現宿主): AI
#4: タンパク質 ...
Decorator protein P05


分子量: 21274.934 Da / 分子数: 26 / 由来タイプ: 組換発現
由来: (組換発現) Borreliella burgdorferi B31 (バクテリア)
遺伝子: BbuZS7_P05 / 発現宿主: Escherichia coli BL21 (大腸菌) / Variant (発現宿主): AI
#5: タンパク質 ...
Scaffold protein


分子量: 26710.363 Da / 分子数: 83 / 由来タイプ: 組換発現
由来: (組換発現) Borreliella burgdorferi B31 (バクテリア)
遺伝子: BB_L02 / 発現宿主: Escherichia coli BL21 (大腸菌) / Variant (発現宿主): AI / 参照: UniProt: Q9R2Q2

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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: Procapsid of Borrelia bacteriophage BB1 / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
由来(天然)生物種: Borreliella burgdorferi B31 (バクテリア)
由来(組換発現)生物種: Escherichia coli (大腸菌) / 株: BL21-AI
緩衝液pH: 7.5
緩衝液成分
ID濃度名称式Buffer-ID
120 mMTris-HCl1
2100 mMsodium chlorideNaCl1
310 mMmagnesium sulfateMgSO41
試料濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドの材料: GOLD / 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: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 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 FIELD / 倍率（公称値）: 16500 X / 最大 デフォーカス（公称値）: 1800 nm / 最小 デフォーカス（公称値）: 500 nm / Cs: 2.7 mm
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 44 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)
電子光学装置エネルギーフィルター名称: GIF Bioquantum

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解析

EMソフトウェア
ID名称バージョンカテゴリ
1RELION3.1.3粒子像選択
4Gctf1.18CTF補正
7Coot0.9.8.4モデルフィッティング
9PHENIX1.20.1-4487モデル精密化
10RELION3.1.3初期オイラー角割当
11RELION3.1.3最終オイラー角割当
13RELION3.1.3３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C5 (5回回転対称)
3次元再構成解像度: 3.35 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 25958 / 対称性のタイプ: POINT
原子モデル構築詳細: previous reconstruction / Source name: Other / タイプ: experimental 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://pdbjlvh1.pdbj.org/emnavi/covid19.php

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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