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- EMDB-10294: Structure of the Fanconi anaemia core subcomplex -

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基本情報

登録情報
データベース: EMDB / ID: EMD-10294
タイトルStructure of the Fanconi anaemia core subcomplex
マップデータNone
試料
  • 複合体: Fanconi anaemia core subcomplex
    • タンパク質・ペプチド: x 18種
キーワードFanconi Anaemia core complex / E3 ligase / DNA repair / LIGASE
機能・相同性
機能・相同性情報


PKR-mediated signaling / Fanconi Anemia Pathway in DNA repair / Fanconi Anemia Pathway / Fanconi anaemia nuclear complex / protein monoubiquitination / interstrand cross-link repair / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / DNA repair / DNA damage response ...PKR-mediated signaling / Fanconi Anemia Pathway in DNA repair / Fanconi Anemia Pathway / Fanconi anaemia nuclear complex / protein monoubiquitination / interstrand cross-link repair / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / DNA repair / DNA damage response / nucleoplasm / nucleus
類似検索 - 分子機能
FANCL, UBC-like domain 2 / FANCL, UBC-like domain 3 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 / FANCL UBC-like domain 3 ...FANCL, UBC-like domain 2 / FANCL, UBC-like domain 3 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 / FANCL UBC-like domain 3 / FANCL C-terminal domain / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
類似検索 - ドメイン・相同性
Fanconi anemia protein FANCL
類似検索 - 構成要素
生物種Gallus gallus (ニワトリ)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.6 Å
データ登録者Shakeel S / Rajendra E / Alcon P / He S / Scheres SHW / Passmore LA
資金援助 英国, 1件
OrganizationGrant number国
Medical Research Council (United Kingdom)MC_U105192715 英国
引用ジャーナル: Nature / 年: 2019
タイトル: Structure of the Fanconi anaemia monoubiquitin ligase complex.
著者: Shabih Shakeel / Eeson Rajendra / Pablo Alcón / Francis O'Reilly / Dror S Chorev / Sarah Maslen / Gianluca Degliesposti / Christopher J Russo / Shaoda He / Chris H Hill / J Mark Skehel / ...著者: Shabih Shakeel / Eeson Rajendra / Pablo Alcón / Francis O'Reilly / Dror S Chorev / Sarah Maslen / Gianluca Degliesposti / Christopher J Russo / Shaoda He / Chris H Hill / J Mark Skehel / Sjors H W Scheres / Ketan J Patel / Juri Rappsilber / Carol V Robinson / Lori A Passmore /
要旨: The Fanconi anaemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks, and responds to replication stress. Genetic inactivation of this pathway by mutation ...The Fanconi anaemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks, and responds to replication stress. Genetic inactivation of this pathway by mutation of genes encoding FA complementation group (FANC) proteins impairs development, prevents blood production and promotes cancer. The key molecular step in the FA pathway is the monoubiquitination of a pseudosymmetric heterodimer of FANCD2-FANCI by the FA core complex-a megadalton multiprotein E3 ubiquitin ligase. Monoubiquitinated FANCD2 then recruits additional protein factors to remove the DNA crosslink or to stabilize the stalled replication fork. A molecular structure of the FA core complex would explain how it acts to maintain genome stability. Here we reconstituted an active, recombinant FA core complex, and used cryo-electron microscopy and mass spectrometry to determine its structure. The FA core complex comprises two central dimers of the FANCB and FA-associated protein of 100 kDa (FAAP100) subunits, flanked by two copies of the RING finger subunit, FANCL. These two heterotrimers act as a scaffold to assemble the remaining five subunits, resulting in an extended asymmetric structure. Destabilization of the scaffold would disrupt the entire complex, resulting in a non-functional FA pathway. Thus, the structure provides a mechanistic basis for the low numbers of patients with mutations in FANCB, FANCL and FAAP100. Despite a lack of sequence homology, FANCB and FAAP100 adopt similar structures. The two FANCL subunits are in different conformations at opposite ends of the complex, suggesting that each FANCL has a distinct role. This structural and functional asymmetry of dimeric RING finger domains may be a general feature of E3 ligases. The cryo-electron microscopy structure of the FA core complex provides a foundation for a detailed understanding of its E3 ubiquitin ligase activity and DNA interstrand crosslink repair.
履歴
登録2019年9月5日-
ヘッダ(付随情報) 公開2019年11月6日-
マップ公開2019年11月6日-
更新2024年5月22日-
現状2024年5月22日処理サイト: PDBe / 状態: 公開

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構造の表示

ムービー
  • 表面図（断面を密度値に従い着色）
  • 表面レベル: 0.01
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（半径に従い着色）
  • 表面レベル: 0.01
  • UCSF Chimeraによる作画
  • ダウンロード
  • あてはめたモデルとの重ね合わせ
  • 原子モデル: PDB-6srs
  • 表面レベル: 0.02
  • 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EMマップ:
SurfViewMolmilJmol/JSmol
添付画像

emd_10294.png

ダウンロードとリンク

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マップ

ファイルダウンロード / ファイル: emd_10294.map.gz / 形式: CCP4 / 大きさ: 209.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈None
ボクセルのサイズX=Y=Z: 1.07 Å
密度
表面レベルBy EMDB: 0.005 / ムービー #1: 0.01
最小 - 最大-0.048650622 - 0.0932454
平均 (標準偏差)0.00020497415 (±0.0021153155)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin-190-190-190
サイズ380380380
Spacing380380380
セルA=B=C: 406.6 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z406.600406.600406.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-190-190-190
NC/NR/NS380380380
D min/max/mean-0.0490.0930.000

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添付データ

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マスク #1

ファイルemd_10294_msk_1.map
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軸ZYX

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マスク #2

ファイルemd_10294_msk_2.map
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マスク #3

ファイルemd_10294_msk_3.map
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軸ZYX

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追加マップ: This is the local symmetry map from auto...

ファイルemd_10294_additional_1.map
注釈This is the local symmetry map from auto refinement in Relion with T=100.
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追加マップ: None

ファイルemd_10294_additional_2.map
注釈None
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軸ZYX

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ハーフマップ: This is half1 map from auto refinement in Relion with T=100.

ファイルemd_10294_half_map_1.map
注釈This is half1 map from auto refinement in Relion with T=100.
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軸ZYX

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ハーフマップ: This is half2 map from auto refinement in Relion with T=100.

ファイルemd_10294_half_map_2.map
注釈This is half2 map from auto refinement in Relion with T=100.
投影像・断面図
軸ZYX

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試料の構成要素

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全体 : Fanconi anaemia core subcomplex

全体名称: Fanconi anaemia core subcomplex
要素
  • 複合体: Fanconi anaemia core subcomplex
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (proposed FANCB)
    • タンパク質・ペプチド: Unassigned secondary structure elements (proposed FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (proposed FANCB)
    • タンパク質・ペプチド: Unassigned secondary structure elements (proposed FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (proposed FANCG)
    • タンパク質・ペプチド: Unassigned secondary structure elements (proposed FANCG)
    • タンパク質・ペプチド: Fanconi anaemia protein FANCL
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
    • タンパク質・ペプチド: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)

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超分子 #1: Fanconi anaemia core subcomplex

超分子名称: Fanconi anaemia core subcomplex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1, #10-#18, #2-#9
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 860 KDa

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分子 #1: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 6.485986 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #2: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 2.145636 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #3: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 2.571161 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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分子 #4: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 1.975426 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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分子 #5: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 5 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 783.958 Da
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #6: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 6 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 1.294587 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #7: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 7 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 2.230741 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #8: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 8 / コピー数: 4 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 1.464797 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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分子 #9: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 9 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 3.166895 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #10: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 10 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 1.805216 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)

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分子 #11: Unassigned secondary structure elements (central region, proposed...

分子名称: Unassigned secondary structure elements (central region, proposed FANCB-FAAP100)
タイプ: protein_or_peptide / ID: 11 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 1.549902 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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分子 #12: Unassigned secondary structure elements (proposed FANCB)

分子名称: Unassigned secondary structure elements (proposed FANCB)
タイプ: protein_or_peptide / ID: 12 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 10.230603 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #13: Unassigned secondary structure elements (proposed FAAP100)

分子名称: Unassigned secondary structure elements (proposed FAAP100)
タイプ: protein_or_peptide / ID: 13 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 3.677524 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #14: Unassigned secondary structure elements (proposed FANCB)

分子名称: Unassigned secondary structure elements (proposed FANCB)
タイプ: protein_or_peptide / ID: 14 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 23.762168 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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分子 #15: Unassigned secondary structure elements (proposed FAAP100)

分子名称: Unassigned secondary structure elements (proposed FAAP100)
タイプ: protein_or_peptide / ID: 15 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 23.506855 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)

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分子 #16: Unassigned secondary structure elements (proposed FANCG)

分子名称: Unassigned secondary structure elements (proposed FANCG)
タイプ: protein_or_peptide / ID: 16 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 24.272791 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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分子 #17: Unassigned secondary structure elements (proposed FANCG)

分子名称: Unassigned secondary structure elements (proposed FANCG)
タイプ: protein_or_peptide / ID: 17 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 12.358226 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)

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分子 #18: Fanconi anaemia protein FANCL

分子名称: Fanconi anaemia protein FANCL / タイプ: protein_or_peptide / ID: 18 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Gallus gallus (ニワトリ)
分子量理論値: 10.475292 KDa
組換発現生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
配列文字列:
SLLRQCPLLL PQNREGTAYE GFVSAQGRDF HIRILLPTDS QLKNARIECS WHLKKILHGY QHILKQRLHS CPDLVSFVVE LKTILEIAL KA

UniProtKB: Fanconi anemia protein FANCL

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実験情報

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構造解析

手法クライオ電子顕微鏡法
解析単粒子再構成法
試料の集合状態particle

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試料調製

濃度0.7 mg/mL
緩衝液pH: 8 / 詳細: 50 mM HEPES pH 8.0, ~500 mM NaCl, 1 mM TCEP
グリッドモデル: Quantifoil, UltrAuFoil, R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: PLASMA CLEANING
凍結凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV
詳細: Blot time: 3 to 4.5 s Wait time: 0 s Drain time: 0 s Force: -10 N.

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
撮影フィルム・検出器のモデル: FEI FALCON III (4k x 4k)
検出モード: COUNTING / 実像数: 4145 / 平均電子線量: 40.0 e/Å2
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス（公称値）: -4.0 µm / 最小 デフォーカス（公称値）: -1.8 µm / 倍率（公称値）: 75000
試料ステージ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
ホルダー冷却材: NITROGEN
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

初期モデルモデルのタイプ: OTHER / 詳細: initial model generated in EMAN2.
最終 再構成想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.0)
詳細: Local symmetry was applied for two regions followed by autorefinement was was done with tau_fudge (T)=100. Map was post processed to obtain realistic resolution for the map.
使用した粒子像数: 49423
初期 角度割当タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0)
最終 角度割当タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0)
FSC曲線 (解像度の算出)

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原子モデル構築 1

精密化プロトコル: OTHER
得られたモデル

PDB-6srs:
Structure of the Fanconi anaemia core subcomplex

+
万見について

-
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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