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基本情報

登録情報
データベース: PDB / ID: 6pwb
タイトルRigid body fitting of flagellin FlaB, and flagellar coiling proteins, FcpA and FcpB, into a 10 Angstrom structure of the asymmetric flagellar filament purified from Leptospira biflexa Patoc WT cells resolved via subtomogram averaging
要素
  • Flagellar coiling protein A (FcpA)
  • Flagellar coiling protein B (FcpB)
  • Flagellin B1 (FlaB1)
キーワードSTRUCTURAL PROTEIN (タンパク質) / bacterial flagella (鞭毛) / FcpA / FcpB / FlaA / FlaB / Leptospira (レプトスピラ属)
機能・相同性
機能・相同性情報


periplasmic flagellum / bacterial-type flagellum filament / bacterial-type flagellum-dependent cell motility / structural molecule activity
類似検索 - 分子機能
Flagellin, C-terminal domain, subdomain 2 / Bacterial flagellin C-terminal helical region / フラジェリン / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
類似検索 - ドメイン・相同性
Uncharacterized protein / フラジェリン / Uncharacterized protein
類似検索 - 構成要素
生物種Leptospira biflexa serovar Patoc (バクテリア)
手法電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 9.83 Å
データ登録者Gibson, K.H. / Sindelar, C.V. / Trajtenberg, F. / Buschiazzo, A. / San Martin, F. / Mechaly, A.
資金援助 米国, ウルグアイ, 10件
組織認可番号国
National Institutes of Health/National Library of Medicine (NIH/NLM)R01 GM 110530 米国
National Institutes of Health/National Library of Medicine (NIH/NLM)U01 AI088752 米国
National Institutes of Health/National Library of Medicine (NIH/NLM)R01 TW009504 米国
National Institutes of Health/National Library of Medicine (NIH/NLM)R01 AI052473 米国
National Institutes of Health/National Library of Medicine (NIH/NLM)R01 298 AI121207 米国
Agencia Nacional de Investigacion e Innovacion (ANII)FCE_3_2016_1_126797ウルグアイ
Agencia Nacional de Investigacion e Innovacion (ANII)ALI_1_2014_1_4982ウルグアイ
Agencia Nacional de Investigacion e Innovacion (ANII)FCE_3_2016_1_126797ウルグアイ
French National Research AgencyANR-18-CE15-0027-1ウルグアイ
French National Research AgencyANR-08-300 MIE-018ウルグアイ
引用
ジャーナル: Elife / 年: 2020
タイトル: An asymmetric sheath controls flagellar supercoiling and motility in the leptospira spirochete.
著者: Kimberley H Gibson / Felipe Trajtenberg / Elsio A Wunder / Megan R Brady / Fabiana San Martin / Ariel Mechaly / Zhiguo Shang / Jun Liu / Mathieu Picardeau / Albert Ko / Alejandro Buschiazzo / ...著者: Kimberley H Gibson / Felipe Trajtenberg / Elsio A Wunder / Megan R Brady / Fabiana San Martin / Ariel Mechaly / Zhiguo Shang / Jun Liu / Mathieu Picardeau / Albert Ko / Alejandro Buschiazzo / Charles Vaughn Sindelar /
要旨: Spirochete bacteria, including important pathogens, exhibit a distinctive means of swimming via undulations of the entire cell. Motility is powered by the rotation of supercoiled 'endoflagella' that ...Spirochete bacteria, including important pathogens, exhibit a distinctive means of swimming via undulations of the entire cell. Motility is powered by the rotation of supercoiled 'endoflagella' that wrap around the cell body, confined within the periplasmic space. To investigate the structural basis of flagellar supercoiling, which is critical for motility, we determined the structure of native flagellar filaments from the spirochete by integrating high-resolution cryo-electron tomography and X-ray crystallography. We show that these filaments are coated by a highly asymmetric, multi-component sheath layer, contrasting with flagellin-only homopolymers previously observed in exoflagellated bacteria. Distinct sheath proteins localize to the filament inner and outer curvatures to define the supercoiling geometry, explaining a key functional attribute of this spirochete flagellum.
#1: ジャーナル: Acta Crystallogr F Struct Biol Commun / 年: 2017
タイトル: Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis.
著者: Fabiana San Martin / Ariel E Mechaly / Nicole Larrieux / Elsio A Wunder / Albert I Ko / Mathieu Picardeau / Felipe Trajtenberg / Alejandro Buschiazzo /
要旨: The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and ...The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be obtained. This challenge was solved by expressing a close orthologue from the related saprophytic species L. biflexa. Three different crystal forms were obtained: a primitive and a centred monoclinic form, as well as a hexagonal variant. All forms diffracted X-rays to suitable resolutions for crystallographic analyses, with the hexagonal type typically reaching the highest limits of 2.0 Å and better. A variation of the quick-soaking procedure resulted in an iodide derivative that was instrumental for single-wavelength anomalous diffraction methods.
#2: ジャーナル: Mol Microbiol / 年: 2016
タイトル: A novel flagellar sheath protein, FcpA, determines filament coiling, translational motility and virulence for the Leptospira spirochete.
著者: Elsio A Wunder / Cláudio P Figueira / Nadia Benaroudj / Bo Hu / Brian A Tong / Felipe Trajtenberg / Jun Liu / Mitermayer G Reis / Nyles W Charon / Alejandro Buschiazzo / Mathieu Picardeau / Albert I Ko /
要旨: Leptospira are unique among bacteria based on their helical cell morphology with hook-shaped ends and the presence of periplasmic flagella (PF) with pronounced spontaneous supercoiling. The factors ...Leptospira are unique among bacteria based on their helical cell morphology with hook-shaped ends and the presence of periplasmic flagella (PF) with pronounced spontaneous supercoiling. The factors that provoke such supercoiling, as well as the role that PF coiling plays in generating the characteristic hook-end cell morphology and motility, have not been elucidated. We have now identified an abundant protein from the pathogen L. interrogans, exposed on the PF surface, and named it Flagellar-coiling protein A (FcpA). The gene encoding FcpA is highly conserved among Leptospira and was not found in other bacteria. fcpA(-) mutants, obtained from clinical isolates or by allelic exchange, had relatively straight, smaller-diameter PF, and were not able to produce translational motility. These mutants lost their ability to cause disease in the standard hamster model of leptospirosis. Complementation of fcpA restored the wild-type morphology, motility and virulence phenotypes. In summary, we identified a novel Leptospira 36-kDa protein, the main component of the spirochete's PF sheath, and a key determinant of the flagella's coiled structure. FcpA is essential for bacterial translational motility and to enable the spirochete to penetrate the host, traverse tissue barriers, disseminate to cause systemic infection and reach target organs.
#3: ジャーナル: Front Cell Infect Microbiol / 年: 2018
タイトル: FcpB Is a Surface Filament Protein of the Endoflagellum Required for the Motility of the Spirochete .
著者: Elsio A Wunder / Leyla Slamti / David N Suwondo / Kimberley H Gibson / Zhiguo Shang / Charles V Sindelar / Felipe Trajtenberg / Alejandro Buschiazzo / Albert I Ko / Mathieu Picardeau /
要旨: The spirochete endoflagellum is a unique motility apparatus among bacteria. Despite its critical importance for pathogenesis, the full composition of the flagellum remains to be determined. We have ...The spirochete endoflagellum is a unique motility apparatus among bacteria. Despite its critical importance for pathogenesis, the full composition of the flagellum remains to be determined. We have recently reported that FcpA is a novel flagellar protein and a major component of the sheath of the filament of the spirochete . By screening a library of random transposon mutants in the spirochete , we found a motility-deficient mutant harboring a disruption in a hypothetical gene of unknown function. Here, we show that this gene encodes a surface component of the endoflagellar filament and is required for typical hook- and spiral-shaped ends of the cell body, coiled structure of the endoflagella, and high velocity phenotype. We therefore named the gene for flagellar-coiling protein B. is conserved in all members of the genus, but not present in other organisms including other spirochetes. Complementation of the mutant restored the wild-type morphology and motility phenotypes. Immunoblotting with anti-FcpA and anti-FcpB antisera and cryo-electron microscopy of the filament indicated that FcpB assembled onto the surface of the sheath of the filament and mostly located on the outer (convex) side of the coiled filament. We provide evidence that FcpB, together with FcpA, are -specific novel components of the sheath of the filament, key determinants of the coiled and asymmetric structure of the endoflagella and are essential for high velocity. Defining the components of the endoflagella and their functions in these atypical bacteria should greatly enhance our understanding of the mechanisms by which these bacteria produce motility.
履歴
登録2019年7月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年3月25日Provider: repository / タイプ: Initial release
改定 1.12024年3月20日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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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
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-20504
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
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
AG: Flagellin B1 (FlaB1)
AH: Flagellin B1 (FlaB1)
AI: Flagellin B1 (FlaB1)
AL: Flagellar coiling protein A (FcpA)
AM: Flagellar coiling protein A (FcpA)
AO: Flagellar coiling protein B (FcpB)
AR: Flagellin B1 (FlaB1)
AU: Flagellar coiling protein A (FcpA)
BA: Flagellin B1 (FlaB1)
BB: Flagellin B1 (FlaB1)
BC: Flagellin B1 (FlaB1)
BD: Flagellin B1 (FlaB1)
BE: Flagellar coiling protein A (FcpA)
BF: Flagellar coiling protein A (FcpA)
BG: Flagellar coiling protein A (FcpA)
BH: Flagellar coiling protein A (FcpA)
BI: Flagellar coiling protein B (FcpB)
BJ: Flagellar coiling protein B (FcpB)
BK: Flagellar coiling protein B (FcpB)
BL: Flagellin B1 (FlaB1)
BM: Flagellin B1 (FlaB1)
BN: Flagellar coiling protein A (FcpA)
BO: Flagellar coiling protein B (FcpB)
BP: Flagellar coiling protein A (FcpA)
CA: Flagellar coiling protein A (FcpA)
CB: Flagellar coiling protein A (FcpA)
CC: Flagellar coiling protein A (FcpA)
CD: Flagellar coiling protein B (FcpB)
CE: Flagellar coiling protein B (FcpB)
CF: Flagellar coiling protein B (FcpB)
CG: Flagellin B1 (FlaB1)
CH: Flagellin B1 (FlaB1)
CI: Flagellar coiling protein A (FcpA)
CJ: Flagellar coiling protein B (FcpB)
CK: Flagellar coiling protein A (FcpA)
BS: Flagellin B1 (FlaB1)
BT: Flagellin B1 (FlaB1)
BU: Flagellin B1 (FlaB1)
BV: Flagellin B1 (FlaB1)
BW: Flagellin B1 (FlaB1)
BX: Flagellin B1 (FlaB1)
BY: Flagellin B1 (FlaB1)
BZ: Flagellar coiling protein A (FcpA)
DA: Flagellar coiling protein B (FcpB)
DB: Flagellin B1 (FlaB1)
DC: Flagellin B1 (FlaB1)
DD: Flagellar coiling protein A (FcpA)
DE: Flagellar coiling protein B (FcpB)
DF: Flagellar coiling protein A (FcpA)
CL: Flagellin B1 (FlaB1)
CM: Flagellin B1 (FlaB1)
CN: Flagellin B1 (FlaB1)
CO: Flagellin B1 (FlaB1)
CP: Flagellin B1 (FlaB1)
CQ: Flagellin B1 (FlaB1)
CR: Flagellin B1 (FlaB1)
CS: Flagellin B1 (FlaB1)
CT: Flagellin B1 (FlaB1)
CU: Flagellar coiling protein A (FcpA)
CV: Flagellar coiling protein A (FcpA)
CW: Flagellar coiling protein A (FcpA)
CX: Flagellar coiling protein A (FcpA)
CY: Flagellar coiling protein B (FcpB)
CZ: Flagellar coiling protein B (FcpB)
EA: Flagellar coiling protein A (FcpA)
DG: Flagellin B1 (FlaB1)
DH: Flagellin B1 (FlaB1)
DI: Flagellin B1 (FlaB1)
DJ: Flagellin B1 (FlaB1)
DK: Flagellin B1 (FlaB1)
DL: Flagellin B1 (FlaB1)
DM: Flagellin B1 (FlaB1)
DN: Flagellin B1 (FlaB1)
DO: Flagellin B1 (FlaB1)
DP: Flagellar coiling protein A (FcpA)
DQ: Flagellar coiling protein A (FcpA)
DR: Flagellar coiling protein A (FcpA)
DS: Flagellar coiling protein A (FcpA)
DT: Flagellar coiling protein B (FcpB)
DU: Flagellar coiling protein B (FcpB)
DV: Flagellar coiling protein B (FcpB)
DW: Flagellin B1 (FlaB1)
DX: Flagellin B1 (FlaB1)
DY: Flagellar coiling protein A (FcpA)
DZ: Flagellar coiling protein B (FcpB)
EB: Flagellin B1 (FlaB1)
EC: Flagellin B1 (FlaB1)
ED: Flagellin B1 (FlaB1)
EE: Flagellin B1 (FlaB1)
EF: Flagellin B1 (FlaB1)
EG: Flagellin B1 (FlaB1)
EH: Flagellin B1 (FlaB1)
EI: Flagellin B1 (FlaB1)
EJ: Flagellin B1 (FlaB1)
EK: Flagellar coiling protein A (FcpA)
EL: Flagellar coiling protein A (FcpA)
EM: Flagellar coiling protein A (FcpA)
EN: Flagellar coiling protein A (FcpA)
EO: Flagellar coiling protein B (FcpB)
EP: Flagellar coiling protein B (FcpB)
EQ: Flagellar coiling protein B (FcpB)
ER: Flagellin B1 (FlaB1)
ES: Flagellin B1 (FlaB1)
ET: Flagellar coiling protein A (FcpA)
EU: Flagellar coiling protein B (FcpB)
EV: Flagellar coiling protein A (FcpA)
FA: Flagellin B1 (FlaB1)
FB: Flagellin B1 (FlaB1)
FC: Flagellin B1 (FlaB1)
FD: Flagellin B1 (FlaB1)
FE: Flagellin B1 (FlaB1)
FF: Flagellar coiling protein A (FcpA)
FG: Flagellar coiling protein A (FcpA)
FH: Flagellar coiling protein A (FcpA)
FI: Flagellar coiling protein A (FcpA)
FJ: Flagellar coiling protein B (FcpB)
FK: Flagellar coiling protein B (FcpB)
FL: Flagellar coiling protein B (FcpB)
FM: Flagellin B1 (FlaB1)
FN: Flagellin B1 (FlaB1)
FO: Flagellar coiling protein A (FcpA)
FP: Flagellar coiling protein B (FcpB)
FQ: Flagellar coiling protein A (FcpA)
EW: Flagellin B1 (FlaB1)
EX: Flagellin B1 (FlaB1)
EY: Flagellin B1 (FlaB1)
EZ: Flagellin B1 (FlaB1)
GA: Flagellar coiling protein A (FcpA)
GB: Flagellar coiling protein A (FcpA)
GC: Flagellar coiling protein A (FcpA)
GE: Flagellar coiling protein B (FcpB)
GF: Flagellar coiling protein B (FcpB)
GG: Flagellar coiling protein B (FcpB)
GH: Flagellin B1 (FlaB1)
GI: Flagellin B1 (FlaB1)
GJ: Flagellar coiling protein A (FcpA)
GK: Flagellar coiling protein B (FcpB)
GL: Flagellar coiling protein A (FcpA)
FR: Flagellin B1 (FlaB1)
FS: Flagellin B1 (FlaB1)
FT: Flagellin B1 (FlaB1)
FU: Flagellin B1 (FlaB1)
FV: Flagellin B1 (FlaB1)
FW: Flagellin B1 (FlaB1)
FX: Flagellin B1 (FlaB1)
HB: Flagellar coiling protein B (FcpB)
HC: Flagellin B1 (FlaB1)
HE: Flagellar coiling protein A (FcpA)
HF: Flagellar coiling protein B (FcpB)
GM: Flagellin B1 (FlaB1)
GN: Flagellin B1 (FlaB1)
GO: Flagellin B1 (FlaB1)
GP: Flagellin B1 (FlaB1)
GQ: Flagellin B1 (FlaB1)
GR: Flagellin B1 (FlaB1)
GV: Flagellar coiling protein A (FcpA)
GW: Flagellar coiling protein A (FcpA)
GZ: Flagellar coiling protein B (FcpB)
HH: Flagellin B1 (FlaB1)
HI: Flagellin B1 (FlaB1)
HJ: Flagellin B1 (FlaB1)
HK: Flagellin B1 (FlaB1)
HL: Flagellin B1 (FlaB1)


分子量 (理論値)分子数
合計 (水以外)4,652,257163
ポリマ－4,652,257163
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

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要素

#1: タンパク質 ...
Flagellin B1 (FlaB1)


分子量: 29467.033 Da / 分子数: 84 / 由来タイプ: 天然
由来: (天然) Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris) (バクテリア)
Cell: bacteria / 株: Patoc 1 / ATCC 23582 / Paris / 参照: UniProt: B0SSZ5
#2: タンパク質 ...
Flagellar coiling protein A (FcpA)


分子量: 28931.002 Da / 分子数: 47 / 由来タイプ: 天然
由来: (天然) Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris) (バクテリア)
Cell: bacteria / 株: Patoc 1 / ATCC 23582 / Paris / 参照: UniProt: B0STJ8
#3: タンパク質 ...
Flagellar coiling protein B (FcpB)


分子量: 25539.666 Da / 分子数: 32 / 由来タイプ: 天然
由来: (天然) Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris) (バクテリア)
Cell: bacteria / 株: Patoc 1 / ATCC 23582 / Paris / 参照: UniProt: B0SR03

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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: FILAMENT / ３次元再構成法: サブトモグラム平均法

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試料調製

構成要素名称: Flagellar filament purified from the periplasm of the Spirochete bacterium, Leptospira biflexa
タイプ: ORGANELLE OR CELLULAR COMPONENT
詳細: Filaments were purified from Leptospira biflexa wild type cells.
Entity ID: all / 由来: NATURAL
分子量実験値: NO
由来(天然)生物種: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (バクテリア)
細胞内の位置: periplasm / Organelle: flagellar filament
緩衝液pH: 6.8 / 詳細: Tris-HCl or ddH20, pH6.8 with <1% sodium azide as a preservative. FIDUCIAL MARKERS: Prior to vitrification, 1 uL of 6x concentrated Gold Tracer beads (10 nm colloidal gold) were mixed with 2 uL of purified flagella. To each grid, 3 uL of this mixture were applied.
試料濃度: 0.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
詳細: Leptospira biflexa serovar Patoc strain Patoc I wild type, fcpA, and fcpB mutant cells cultured in Ellinghausen-McCullough-Johnson-Harris liquid medium until they reached logarithmic phase at ...詳細: Leptospira biflexa serovar Patoc strain Patoc I wild type, fcpA, and fcpB mutant cells cultured in Ellinghausen-McCullough-Johnson-Harris liquid medium until they reached logarithmic phase at 30C. The cells were pelleted and the periplasmic flagellar filaments were purified as described in Wunder et al., 2016; Wunder et al., 2018.
試料支持詳細: Model 950 Solarus Advanced Plasma System manufactured by GATAN.
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: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 291 K
詳細: 2 minute incubation time; blot time of 6-7.5 seconds; and blot offset of -2 mm

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電子顕微鏡撮影

実験機器
モデル: Tecnai Polara / 画像提供: FEI Company
顕微鏡モデル: FEI POLARA 300
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 / 倍率（公称値）: 15000 X / 倍率（補正後）: 19230 X / 最大 デフォーカス（公称値）: 5000 nm / 最小 デフォーカス（公称値）: 3000 nm / Cs: 2 mm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN / 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC
撮影平均露光時間: 1.2 sec. / 電子線照射量: 1.7 e/Å2 / 検出モード: COUNTING
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
撮影したグリッド数: 1
詳細: Tilt series acquisition. A total of ~35 tilt angles per tilt stack were acquired. The total dose was ~ 60 e/Angstrom2.
画像スキャンサンプリングサイズ: 5 µm / 横: 3710 / 縦: 3838 / 動画フレーム数/画像: 12 / 利用したフレーム数/画像: 1-12

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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詳細
2PEET1.11volume selectionaddModPts
3RELION2.1volume selectionpreprocessing.py MODIFIED
4SerialEM3画像取得
6IMOD4.9.4_RHEL6-64_CUDA8.0CTF補正
7RELION2.1.b1-gcccuda-2016.10-cc37CTF補正CTFFind4
8emClarity1..0CTF補正ctf estimation and 3d correction
11Rosetta3モデルフィッティングFlaB and FcpB
12Situs2.8-foss-2016bモデルフィッティングcolores, FcpA and FcpB
13UCSF Chimera1.12モデルフィッティングcore symmetrization, FlaB1
16RELION2.1.b1-gcccuda-2016.10-cc37最終オイラー角割当3d-autorefinement
17emClarity1最終オイラー角割当averaging/alignment
19emClarity1.1３次元再構成
20Rosetta3モデル精密化FlaB1, FcpA, FcpB
画像処理詳細: Motion correction was performed on movie stacks acquired at each angle in each tilt series using IMOD alignframes. Tilt series were aligned in IMOD eTomo usinf 10 nm fiducial gold markers. ...詳細: Motion correction was performed on movie stacks acquired at each angle in each tilt series using IMOD alignframes. Tilt series were aligned in IMOD eTomo usinf 10 nm fiducial gold markers. CTF estimation with phase flipping was carried out, along with gold bead subtraction in IMOD eTomo. Tilt series were reconstructed using Weighted Back Projection in Tomo3D.
CTF補正詳細: CTF estimation was initially done in IMOD. / タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C1 (非対称)
3次元再構成解像度: 9.83 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 10581 / アルゴリズム: BACK PROJECTION
詳細: emClarity: The two half-dataset volumes were combined with a B-170 factor of 0, and the Gold standard FSC at 0.143 was calculated to be 9.83 A with anisotropic resolutions ranging from 8.89-16.17 Angstrom.
対称性のタイプ: POINT
EM volume selection手法: Manual selection
詳細: Using IMOD 3dmod, filament trajectories were traced by selecting particle points along a single filament. Each continuous filament was a single contour (3dmod). Using the addModPts program in ...詳細: Using IMOD 3dmod, filament trajectories were traced by selecting particle points along a single filament. Each continuous filament was a single contour (3dmod). Using the addModPts program in PEET, particle gaps along each filament trajectory contour were filled in with additional points according to a repeat spacing of 52 angstroms. The x,y,z coordinates were then imported into RELION using a modified version of the RELION preprocessing.py python script described in Bharat et. al. (2015). The script was modified to ensure that particles in one filament would be sorted into the same ODD or EVEN grouping to prevent over-estimation of FSC due to inclusion of the 2 or more overlapping particles in a filament in both half-datasets.
Num. of tomograms: 62 / Num. of volumes extracted: 15000 / Reference model: de novo
原子モデル構築プロトコル: RIGID BODY FIT / 空間: RECIPROCAL / Target criteria: Correlation coefficient
詳細: Eliminate minor clashes between FlaB1, FcpA, and FcpB
原子モデル構築
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameタイプ
15WJT

5wjt

15WJT1PDBexperimental model
26NQW

6nqw

16NQW2PDBexperimental model
36NQZ

6nqz

16NQZ3PDBexperimental 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

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