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- PDB-7kzv: Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex ... -

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基本情報

登録情報
データベース: PDB / ID: 7kzv
タイトルStructure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in closed state
要素
  • (DNA (29-MER)) x 2
  • (Fanconi anemia core complex-associated protein ...) x 2
  • (Fanconi anemia group ...) x 7
  • E3 ubiquitin-protein ligase FANCL
  • Fanconi anemia, complementation group I
  • Ubiquitin-conjugating enzyme E2 T
キーワードLIGASE/DNA / Complex / LIGASE / LIGASE-DNA complex
機能・相同性
機能・相同性情報


regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / protein K29-linked ubiquitination / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / homologous chromosome pairing at meiosis / gamete generation ...regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / protein K29-linked ubiquitination / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / homologous chromosome pairing at meiosis / gamete generation / replication-born double-strand break repair via sister chromatid exchange / neuronal stem cell population maintenance / protein K6-linked ubiquitination / protein K11-linked ubiquitination / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / myeloid cell homeostasis / E2 ubiquitin-conjugating enzyme / female gonad development / protein monoubiquitination / germ cell development / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / spermatid development / protein autoubiquitination / negative regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / protein K48-linked ubiquitination / DNA polymerase binding / ovarian follicle development / condensed chromosome / removal of superoxide radicals / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondrion organization / nucleotide-excision repair / Fanconi Anemia Pathway / response to gamma radiation / TP53 Regulates Transcription of DNA Repair Genes / RING-type E3 ubiquitin transferase / response to radiation / PKR-mediated signaling / protein polyubiquitination / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / nuclear envelope / chromosome / regulation of cell population proliferation / cellular response to oxidative stress / regulation of inflammatory response / protein-containing complex assembly / damaged DNA binding / nuclear body / intracellular membrane-bounded organelle / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / chromatin binding / chromatin / nucleolus / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
Fanconi anaemia group C protein / Fanconi anemia-associated protein of 100kDa / Fanconi anemia group B protein / Fanconi anemia group G protein / Fanconi anaemia group C protein / Fanconi anemia-associated / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group F protein / FANCF, C-terminal domain superfamily / Fanconi anemia group E protein ...Fanconi anaemia group C protein / Fanconi anemia-associated protein of 100kDa / Fanconi anemia group B protein / Fanconi anemia group G protein / Fanconi anaemia group C protein / Fanconi anemia-associated / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group F protein / FANCF, C-terminal domain superfamily / Fanconi anemia group E protein / Fanconi anemia group F protein (FANCF) / Fanconi Anaemia group E protein FANCE / Fanconi anaemia group A protein / Fanconi anaemia group A protein, N-terminal domain / Fanconi anaemia group A protein / Fanconi anaemia group A protein N terminus / 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 / Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 4 / FANCI helical domain 1 / FANCI helical domain 2 / Fanconi anaemia protein FANCD2 / Fanconi anaemia protein FancD2 nuclease / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Fanconi anemia, complementation group I / Fanconi anemia group G protein / Fanconi anemia group A protein / Fanconi anemia group C protein / Fanconi anemia core complex-associated protein 100 / Fanconi anemia group B protein / Fanconi anemia group D2 protein / Fanconi anemia group E protein ...DNA / DNA (> 10) / Fanconi anemia, complementation group I / Fanconi anemia group G protein / Fanconi anemia group A protein / Fanconi anemia group C protein / Fanconi anemia core complex-associated protein 100 / Fanconi anemia group B protein / Fanconi anemia group D2 protein / Fanconi anemia group E protein / Ubiquitin-conjugating enzyme E2 T / Fanconi anemia group F protein / E3 ubiquitin-protein ligase FANCL
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
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: 4.2 Å
データ登録者Wang, S.L. / Pavletich, N.P.
資金援助 米国, 1件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
引用ジャーナル: Nat Struct Mol Biol / 年: 2021
タイトル: Structure of the FA core ubiquitin ligase closing the ID clamp on DNA.
著者: Shengliu Wang / Renjing Wang / Christopher Peralta / Ayat Yaseen / Nikola P Pavletich /
要旨: The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates ...The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates the FANCI-FANCD2 (ID) DNA clamp. The 3.1 Å structure of the 1.1-MDa human FA core complex, described here, reveals an asymmetric assembly with two copies of all but the FANCC, FANCE and FANCF subunits. The asymmetry is crucial, as it prevents the binding of a second FANCC-FANCE-FANCF subcomplex that inhibits the recruitment of the UBE2T ubiquitin conjugating enzyme, and instead creates an ID binding site. A single active site then ubiquitinates FANCD2 and FANCI sequentially. We also present the 4.2-Å structures of the human core-UBE2T-ID-DNA complex in three conformations captured during monoubiquitination. They reveal the core-UBE2T complex remodeling the ID-DNA complex, closing the clamp on the DNA before ubiquitination. Monoubiquitination then prevents clamp opening after release from the core.
履歴
登録2020年12月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年3月10日Provider: repository / タイプ: Initial release
改定 1.12021年3月24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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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-23090
  • 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
A: Fanconi anemia group A protein
B: Fanconi anemia group B protein
C: Fanconi anemia group C protein
E: Fanconi anemia group E protein
F: Fanconi anemia group F protein
G: Fanconi anemia group G protein
H: Fanconi anemia group G protein
L: E3 ubiquitin-protein ligase FANCL
O: Fanconi anemia group B protein
P: Fanconi anemia core complex-associated protein 100
Q: Fanconi anemia core complex-associated protein 100
S: Fanconi anemia group A protein
W: Fanconi anemia core complex-associated protein 20
M: E3 ubiquitin-protein ligase FANCL
X: Ubiquitin-conjugating enzyme E2 T
U: Fanconi anemia, complementation group I
V: Fanconi anemia group D2 protein
Y: DNA (29-MER)
Z: DNA (29-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,506,42724
ポリマ－1,506,10019
非ポリマー3275
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: microscopy
タイプ名称対称操作数
identity operation1_5551

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要素

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Fanconi anemia group ... , 7種, 10分子 ASBOCEFGHV

#1: タンパク質 Fanconi anemia group A protein / Protein FACA


分子量: 165513.016 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCA, FAA, FACA, FANCH / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O15360
#2: タンパク質 Fanconi anemia group B protein / Protein FACB / Fanconi anemia-associated polypeptide of 95 kDa / FAAP95


分子量: 100640.172 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCB / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8NB91
#3: タンパク質 Fanconi anemia group C protein / Protein FACC


分子量: 66290.359 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCC, FAC, FACC / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q00597
#4: タンパク質 Fanconi anemia group E protein / Protein FACE


分子量: 61026.086 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCE, FACE / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9HB96
#5: タンパク質 Fanconi anemia group F protein / Protein FACF


分子量: 45108.297 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCF / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9NPI8
#6: タンパク質 Fanconi anemia group G protein / Protein FACG / DNA repair protein XRCC9


分子量: 70873.727 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCG, XRCC9 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O15287
#12: タンパク質 Fanconi anemia group D2 protein / Protein FACD2


分子量: 164325.516 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCD2, FACD
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9BXW9

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タンパク質 , 3種, 4分子 LMXU

#7: タンパク質 E3 ubiquitin-protein ligase FANCL / Fanconi anemia group L protein / Fanconi anemia-associated polypeptide of 43 kDa / FAAP43 / RING- ...Fanconi anemia group L protein / Fanconi anemia-associated polypeptide of 43 kDa / FAAP43 / RING-type E3 ubiquitin transferase FANCL


分子量: 45203.953 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCL, PHF9 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9NW38, RING-type E3 ubiquitin transferase
#10: タンパク質 Ubiquitin-conjugating enzyme E2 T / Cell proliferation-inducing gene 50 protein / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier ...Cell proliferation-inducing gene 50 protein / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier protein T / Ubiquitin-protein ligase T


分子量: 22553.873 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2T, HSPC150, PIG50 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9NPD8, E2 ubiquitin-conjugating enzyme
#11: タンパク質 Fanconi anemia, complementation group I


分子量: 149512.078 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FANCI
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: B7ZMF2

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Fanconi anemia core complex-associated protein ... , 2種, 3分子 PQW

#8: タンパク質 Fanconi anemia core complex-associated protein 100 / Fanconi anemia-associated protein of 100 kDa


分子量: 96513.898 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FAAP100, C17orf70 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q0VG06
#9: タンパク質・ペプチド Fanconi anemia core complex-associated protein 20


分子量: 4041.667 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト)

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DNA鎖 , 2種, 2分子 YZ

#13: DNA鎖 DNA (29-MER)


分子量: 18036.518 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#14: DNA鎖 DNA (29-MER)


分子量: 17716.326 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 1種, 5分子

#15: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 5 / 由来タイプ: 合成 / 式: Zn

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詳細

研究の焦点であるリガンドがあるかN
配列の詳細The complete FAAP20 sequence is MEAARRPRLGLSRRRPPPAGGPSGGRPWFLLGGDERERLWAELLRTVSPELILDHEVPSL ...The complete FAAP20 sequence is MEAARRPRLGLSRRRPPPAGGPSGGRPWFLLGGDERERLWAELLRTVSPELILDHEVPSL PAFPGQEPRCGPEPTEVFTVGPKTFSWTPFPPDLWGPGRSYRLLHGAGGHLESPARSLPQ RPAPDPCRAPRVEQQPSVEGAAALRSCPMCQKEFAPRLTQLDVDSHLAQCLAESTEDVTW

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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: Human Fanconi Anaemia Core-UBE2T-ID-DNA complex / タイプ: COMPLEX / Entity ID: #1-#14 / 由来: RECOMBINANT
分子量値: 1.4 MDa / 実験値: NO
由来(天然)生物種: Homo sapiens (ヒト)
由来(組換発現)生物種: Homo sapiens (ヒト)
緩衝液pH: 8
緩衝液成分
ID濃度名称式Buffer-ID
120 mMtrisC4H11NO31
2100 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
45 mMAdenosine triphosphateC10H16N5O13P31
試料濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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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
撮影電子線照射量: 36.5 e/Å2 / 検出モード: SUPER-RESOLUTION / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

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解析

ソフトウェア名称: REFMAC / バージョン: 5.8.0267 / 分類: 精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 4.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 74481 / 対称性のタイプ: POINT
精密化解像度: 4.2→40 Å / Cor.coef. Fo:Fc: 0.906 / SU B: 91.931 / SU ML: 0.487 / ESU R: 0.777
立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射
Rwork0.3283 --
obs0.3283 630967 99.88 %
溶媒の処理イオンプローブ半径: 0.9 Å / 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 94.302 Å2
Baniso -1Baniso -2Baniso -3
1-5.06 Å22.11 Å2-0.3 Å2
2---2.09 Å2-3.88 Å2
3----2.97 Å2
精密化ステップサイクル: 1 / 合計: 88227
拘束条件
Refine-IDタイプDev idealDev ideal target数
ELECTRON MICROSCOPYr_bond_refined_d0.010.01390115
ELECTRON MICROSCOPYr_bond_other_d0.0340.01787060
ELECTRON MICROSCOPYr_angle_refined_deg2.0921.625122324
ELECTRON MICROSCOPYr_angle_other_deg2.4371.582200575
ELECTRON MICROSCOPYr_dihedral_angle_1_deg10.558510944
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.22522.0614377
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.4091515788
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.99715585
ELECTRON MICROSCOPYr_chiral_restr0.0950.211704
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0299197
ELECTRON MICROSCOPYr_gen_planes_other0.010.0220192
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it4.22614.34244103
ELECTRON MICROSCOPYr_mcbond_other4.22614.34244102
ELECTRON MICROSCOPYr_mcangle_it7.43754938
ELECTRON MICROSCOPYr_mcangle_other7.43754939
ELECTRON MICROSCOPYr_scbond_it2.87914.86846012
ELECTRON MICROSCOPYr_scbond_other2.87914.86746011
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other5.63267386
ELECTRON MICROSCOPYr_long_range_B_refined14.029100531
ELECTRON MICROSCOPYr_long_range_B_other14.029100532
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS精密化 シェル解像度: 4.2→4.308 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0 0 -
Rwork0.456 46393 -
obs--100 %
精密化 TLS

手法: refined / Refine-ID: ELECTRON MICROSCOPY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.20181.5167-0.03813.6040.8521.06570.2647-0.47950.16190.3149-0.1864-0.06080.2004-0.071-0.07830.55820.23960.19981.36470.42530.764397.0283197.058765.6155
24.2467-2.2628-0.37016.02820.49231.720.1268-0.36730.3861-0.262-0.43140.55940.0817-0.31320.30460.46520.13310.19221.22240.2290.894670.2239181.428949.3532
34.289-1.0063-0.59050.9746-0.75131.68050.12110.0771-0.4281-0.2696-0.18190.5210.0617-0.31210.06080.62860.28640.03811.18040.00041.543149.7774184.501540.5031
42.8637-1.73491.62694.74521.81185.21690.32430.0821-0.45370.13460.08960.0440.098-0.2897-0.41390.65090.26550.1110.90440.50580.958290.1667162.39348.2294
52.349-0.9383-0.31475.5213-0.33052.1501-0.0158-0.23180.582-0.19930.301-0.3533-0.35620.1818-0.28520.39060.05580.29641.02940.27411.1847107.6135216.897755.157
66.5143-5.6832-0.62555.04360.43323.16180.2782-0.02420.4667-0.3278-0.1317-0.28740.0940.21-0.14650.31530.36620.37361.02670.43821.1697136.5835190.032243.5968
72.44163.62950.31027.35292.78511.9863-0.4963-0.44390.106-0.022-0.479-0.589-0.3933-0.31850.97520.7050.5851-0.17870.76170.40691.2277108.8352145.411568.8617
811.9314-9.44471.91779.1894-4.80267.82770.13180.0664-0.6350.14620.40430.94290.0353-0.1899-0.53610.47210.36060.15860.91390.36060.685682.6618137.562739.1428
96.1704-1.07792.665610.5418-0.90936.6453-0.4322-0.01090.3945-1.15770.09670.1450.25440.17190.33551.02650.5609-0.04520.90090.17090.552172.4206166.126821.09
102.99132.49322.56453.44411.94482.3734-0.3751.0419-0.9454-1.99481.0811-1.3538-0.32850.3411-0.7062.73710.23180.40512.52820.07542.4496103.686172.388728.0824
119.006-0.27162.67395.5834-1.13388.2478-0.0965-0.2634-0.15920.4824-0.0328-0.11140.1459-0.62120.12940.66560.32220.62411.01570.35680.648875.368691.3643159.0201
122.3976-1.0831-2.20667.46630.896621.12560.04580.2972-0.0149-0.37970.504-0.0715-1.4190.375-0.54980.40320.00920.35321.54880.51641.0561114.18788.4937181.2536
136.0317-2.21472.88780.9915-0.99461.56960.21761.06420.5568-0.1563-0.3354-0.71630.09611.10520.11781.09970.16680.1692.24410.07471.5356118.350796.4674215.247
144.12483.3266-2.05222.9549-1.67051.022-0.08970.1954-0.71490.1938-0.3028-1.15230.0451-0.06530.39252.70770.85530.1482.98730.03892.58396.266695.6017226.011
152.51861.3739-0.02934.7227-1.73450.94280.6925-0.6004-0.78770.0368-0.5613-0.56880.14620.0672-0.13120.62660.2850.03461.42920.99810.9075173.0491110.888264.5419
162.2809-0.80760.7225.92711.18020.9462-0.0443-0.07860.16740.1615-0.1927-0.2639-0.01260.0950.2370.66120.49420.44221.13380.66990.6783164.8006157.494148.2595
173.28382.9978-0.1152.7481-0.10320.047-0.56560.57420.1103-0.56580.56680.20290.15150.2427-0.00110.81630.5622-0.25291.7750.16591.4689216.6269128.479570.2718
181.88260.12210.08121.28591.35621.45470.13440.2427-0.2163-0.10710.196-0.3896-0.06810.146-0.33040.760.38970.20681.64910.77551.1388254.902131.929598.2214
1911.5739-3.756.75972.5783-0.37916.4235-0.7504-0.68670.5772-0.31620.3355-0.176-1.17830.02620.4150.89380.39520.34441.5050.85960.8579257.5535153.6755157.0515
201.24020.2661-0.17082.7317-1.65625.2634-0.31340.27150.1074-0.22460.0332-0.00470.14670.25750.28020.53490.58250.33441.27780.62490.7593242.7009126.5393139.8621
212.35261.56560.49132.13461.43224.87080.5676-0.2564-0.3710.480.0247-0.4224-0.31050.2028-0.59230.5380.58960.2851.61650.86210.7015265.3465130.5026181.3633
222.3231.40720.69583.21390.03120.3098-0.19520.1344-0.19070.31140.0579-0.7133-0.2390.18550.13730.78920.01680.33432.02750.59210.9488283.7469154.0745177.2021
234.0423.4151-0.34096.7359-0.82080.59210.1077-0.27270.24290.8161-0.4557-0.68640.1670.34060.3480.47550.43390.04631.27860.94711.1925141.291281.2842139.6315
2410.8406-0.2283-3.10844.4005-1.21794.44210.0986-0.4959-0.3549-0.6428-0.68230.54440.3711-0.57150.58370.2390.45120.16081.71990.38970.8081181.6212101.1456164.5927
251.40190.52411.24777.49082.5933.46160.253-0.38930.0517-0.4682-0.059-0.7631-0.5197-0.0832-0.19410.40820.16350.22680.95060.45231.5568153.521126.6007126.2158
260.17020.22140.01860.5197-0.62411.88870.3434-0.2086-0.12610.4835-0.26-0.2527-0.1416-0.0941-0.08341.00250.112-0.16911.3269-0.15861.7425153.8565151.9546151.7049
270.4790.2514-0.46990.1605-0.23780.46410.0717-1.0968-0.5081-0.2236-0.5377-0.3064-0.14711.10210.4662.4394-0.36990.09273.11110.34041.6726157.6169164.2515178.4005
281.83531.2767-0.4583.1146-0.0290.375-0.2187-0.53440.824-0.188-0.0680.70920.09330.55940.28681.05020.49950.05391.33280.50011.2736226.2886149.4276178.0079
294.73142.21110.50333.44751.17790.49490.0105-0.3661-0.47650.3676-0.108-0.33990.21250.03310.09750.54820.77090.48231.3890.82650.8606240.296103.5189175.1821
306.99032.8865-0.89222.3938-0.72791.4390.08660.4684-0.60860.10120.0951-0.1980.2432-0.3806-0.18170.40380.53160.27531.26210.5151.0594216.504188.1119165.6967
313.2569-0.2675-0.63385.27441.27561.9380.00680.2433-0.54450.18530.01820.29420.32010.0073-0.02510.65530.61060.37511.13930.59970.644114.134293.174847.2949
322.58520.78515.25552.84472.711712.1372-0.11560.03840.07160.3548-0.58350.56320.71260.19270.69910.72450.33870.29781.0580.38130.7943104.6339126.426858.9655
334.25780.96730.59935.85090.38254.32340.04770.60760.3368-0.6359-0.247-0.47310.45530.43640.19920.58190.59530.43831.31270.72960.6854118.8425107.299796.8931
347.5390.39040.25363.7312-0.48848.39740.3579-0.0393-0.4377-0.1573-0.4825-0.61130.06180.37470.12460.37610.46310.24350.94370.45570.985123.787393.2347119.3708
352.8254-0.04491.70966.69242.48393.61750.18-0.13650.66590.211-0.1714-0.1707-0.14710.5884-0.00860.47870.1730.15221.14120.3751.1157128.3382129.6643130.3109
364.30071.54110.5983.32230.3740.30590.02090.2693-0.0232-0.0554-0.0347-0.0390.03650.02390.01380.45580.52270.3371.20770.54760.7251140.1663121.477445.7271
371.18140.29640.1343.2996-0.92077.5249-0.09510.24570.9693-0.2949-0.02710.1463-0.2971-0.51050.12220.38420.55830.22541.1970.59311.0837105.5764121.7502104.5423
382.6493-1.60871.06754.81742.80123.6191-0.0014-0.38250.6949-0.2798-0.64770.1411-0.3532-0.81980.64910.56420.52490.52451.26750.24281.4178107.7483136.0247128.5395
391.3276-0.29350.08133.3134-1.5692.263-0.04040.2199-0.31690.045-0.1721-0.2030.1332-0.20730.21260.52450.32520.21091.04360.65141.0357109.980737.0654161.3463
408.0552-3.37497.08192.9699-2.35326.92440.0824-0.4269-0.0944-0.18530.1268-0.57570.4181-0.5018-0.20920.64970.44340.49991.0910.49340.881895.659980.2658155.0654
417.6790.61041.29194.011.09594.67340.04490.2282-0.4115-0.0689-0.13880.41230.75480.06920.09390.59310.34450.37630.990.32280.780892.589683.4849114.7612
423.72961.30831.9044.4791-0.00924.3409-0.67151.2112-0.3679-0.79280.29780.38050.63550.13180.37371.12440.23220.34521.45010.1720.655495.448786.124388.2543
432.67110.7045-0.30660.83470.13930.1458-0.8673-0.4223-0.8388-0.41040.48780.6661-0.09030.31750.37950.90770.0332-0.07771.61260.3421.845759.428995.778893.72
442.790.1405-0.39175.2362-0.6032.59630.1704-0.1229-0.43050.3574-0.35720.5204-0.273-0.08350.18680.44190.50830.39980.98230.57590.802978.956755.8659173.4983
450.62670.68641.14716.5389-2.77797.2774-0.22630.01110.2592-0.0585-0.18890.639-0.0413-0.36050.41520.41180.34020.30481.2580.35231.125684.0986103.6469117.7865
462.25551.0234-0.25861.9170.65820.451-0.39390.20670.2074-0.3735-0.04630.7955-0.072-0.08550.44010.61190.302-0.22011.66030.57271.5262.9341114.3767104.089
470.10220.17860.25450.32410.45480.67650.0323-0.12960.0393-0.0035-0.260.158-0.0429-0.17140.22771.17360.0673-0.05081.33560.24211.157164.438787.9467268.8358
486.33380.0561-0.00522.2342.30682.72820.6392-0.5847-0.12490.3039-0.62920.14150.374-0.2907-0.011.26290.49520.24771.30580.45860.623581.9502114.292251.4687
491.85643.6330.09967.47270.52262.3822-0.0374-0.27410.0674-0.0756-0.08430.06080.02690.09370.12170.99790.82660.37131.29810.35440.621292.3997130.2432238.5275
5011.0037-4.6998-3.53032.6181-0.00765.75130.1258-0.30290.4724-0.04360.4004-0.3385-0.0399-0.0995-0.52620.96180.59660.37781.07610.07761.0395102.9428128.3379225.7651
5110.1833-0.41.42168.553-1.83070.8075-0.51080.7307-0.078-0.67620.6315-0.45010.15710.3539-0.12071.1610.4390.58671.4314-0.02840.5749113.6965128.9256207.7883
523.19914.41310.31836.8216-1.24113.9322-0.67411.2211-0.8714-0.92711.4819-0.9429-0.26470.3371-0.80781.05610.39420.80381.9736-0.06480.7613128.3512143.4147202.1982
533.10264.25922.155.90422.96751.4944-0.81760.22430.2708-0.94730.60170.4782-0.51940.23960.2161.54840.15730.61082.10010.26360.3813128.8705163.0201205.2503
544.47265.37441.91356.88622.24785.032-0.17850.0003-0.1082-0.6097-0.1119-0.0036-0.33690.54650.29040.99820.68710.33891.61540.27920.4751124.8388159.5337227.4555
550.78250.71781.03880.97861.32281.9067-0.2129-0.08-0.1080.07760.22330.1751-0.20050.4408-0.01051.31460.38740.51321.6024-0.10150.8886111.1577165.6091244.6705
561.06370.23970.82062.6745-0.19080.8025-0.0001-0.24650.56450.0483-0.55390.5709-0.06360.0950.5541.19610.79220.57281.64270.0361.408488.036164.1846250.7495
570.37370.8130.33882.0380.91810.4350.1449-0.10390.37240.0605-0.09230.3101-0.0103-0.0286-0.05251.19040.67280.361.4071-0.14781.763271.3144162.4292246.3841
585.3570.5681-2.27960.722-1.07092.4186-0.1117-0.157-0.44070.20440.0442-0.4888-0.49840.29830.06750.46750.41910.43661.9703-0.17851.4709128.665128.1245175.0403
596.15760.57432.4831.7412-0.120410.1769-0.1538-0.4229-0.6152-0.19990.5806-0.3481-1.02820.1321-0.42680.75990.48960.53581.17790.27260.5913104.9644132.1598181.6224
606.40281.7453-2.62517.40633.86676.24360.4560.19720.1367-0.4963-0.58560.1093-0.451-0.61530.12961.02090.46150.43821.05030.46350.54588.2669131.4787193.9775
617.598-2.2884-2.15478.1304-3.65573.22980.12610.1014-0.2039-0.3401-0.11950.4447-0.0630.2428-0.00661.13390.33050.20651.2380.44650.499977.1599122.3366210.666
626.99824.1019-1.17795.9609-1.44220.925-0.01140.5299-0.59270.2880.50990.3556-0.01990.0633-0.49841.08730.77910.30130.98150.36810.934463.353497.276229.1493
632.85581.5613-0.19111.25241.24845.2534-0.2282-0.62010.1242-0.2188-0.38650.4389-0.1638-0.5420.61471.15070.8828-0.00681.17260.26551.266531.683297.7471244.035
640.17420.26270.0920.40870.15510.0795-0.13730.0180.3822-0.1701-0.05620.5272-0.0723-0.16650.19341.31870.806-0.19041.66110.46621.753529.2296123.4764227.5157
650.02740.04010.02570.10310.04790.0524-0.01380.02190.2303-0.2365-0.18260.3303-0.14410.08180.19631.30920.6844-0.02921.52980.1351.948935.1793149.8234.2665
661.53721.59021.38671.66851.45741.2789-0.1124-0.24860.7542-0.2431-0.35850.6176-0.1671-0.25610.47091.37461.13340.141.52780.25912.297454.1935164.89235.3841
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1C1 - 247
2ELECTRON MICROSCOPY2C248 - 343
3ELECTRON MICROSCOPY2E151 - 181
4ELECTRON MICROSCOPY3C344 - 558
5ELECTRON MICROSCOPY4E12 - 150
6ELECTRON MICROSCOPY5F1 - 183
7ELECTRON MICROSCOPY6F184 - 355
8ELECTRON MICROSCOPY7L1 - 103
9ELECTRON MICROSCOPY8L104 - 197
10ELECTRON MICROSCOPY9L198 - 296
11ELECTRON MICROSCOPY10L297 - 402
12ELECTRON MICROSCOPY11M1 - 103
13ELECTRON MICROSCOPY12M104 - 197
14ELECTRON MICROSCOPY13M198 - 296
15ELECTRON MICROSCOPY14M297 - 402
16ELECTRON MICROSCOPY15G12 - 342
17ELECTRON MICROSCOPY15S32 - 55
18ELECTRON MICROSCOPY16G343 - 701
19ELECTRON MICROSCOPY16S19 - 31
20ELECTRON MICROSCOPY17S56 - 246
21ELECTRON MICROSCOPY18S265 - 524
22ELECTRON MICROSCOPY19S542 - 627
23ELECTRON MICROSCOPY20S648 - 1033
24ELECTRON MICROSCOPY20S2001 - 2107
25ELECTRON MICROSCOPY21S1043 - 1215
26ELECTRON MICROSCOPY22S1216 - 1443
27ELECTRON MICROSCOPY23H12 - 386
28ELECTRON MICROSCOPY23A29 - 55
29ELECTRON MICROSCOPY24H387 - 610
30ELECTRON MICROSCOPY24A19 - 28
31ELECTRON MICROSCOPY25A56 - 248
32ELECTRON MICROSCOPY26A262 - 401
33ELECTRON MICROSCOPY26B811 - 827
34ELECTRON MICROSCOPY27A402 - 524
35ELECTRON MICROSCOPY28A648 - 1034
36ELECTRON MICROSCOPY29A1043 - 1215
37ELECTRON MICROSCOPY30A1216 - 1443
38ELECTRON MICROSCOPY31B7 - 369
39ELECTRON MICROSCOPY32B385 - 431
40ELECTRON MICROSCOPY32P446 - 500
41ELECTRON MICROSCOPY33B471 - 655
42ELECTRON MICROSCOPY34B656 - 749
43ELECTRON MICROSCOPY34P672 - 685
44ELECTRON MICROSCOPY35B750 - 783
45ELECTRON MICROSCOPY35B828 - 859
46ELECTRON MICROSCOPY35P823 - 881
47ELECTRON MICROSCOPY36P5 - 435
48ELECTRON MICROSCOPY37P501 - 659
49ELECTRON MICROSCOPY38P701 - 822
50ELECTRON MICROSCOPY39O7 - 369
51ELECTRON MICROSCOPY40O385 - 432
52ELECTRON MICROSCOPY40Q449 - 500
53ELECTRON MICROSCOPY41O471 - 655
54ELECTRON MICROSCOPY42O656 - 749
55ELECTRON MICROSCOPY42Q669 - 685
56ELECTRON MICROSCOPY43O750 - 859
57ELECTRON MICROSCOPY43Q823 - 881
58ELECTRON MICROSCOPY44Q5 - 435
59ELECTRON MICROSCOPY45Q501 - 668
60ELECTRON MICROSCOPY46Q701 - 822
61ELECTRON MICROSCOPY47U1 - 169
62ELECTRON MICROSCOPY48U170 - 305
63ELECTRON MICROSCOPY49U306 - 399
64ELECTRON MICROSCOPY50U408 - 476
65ELECTRON MICROSCOPY51U477 - 550
66ELECTRON MICROSCOPY52U575 - 684
67ELECTRON MICROSCOPY53U696 - 800
68ELECTRON MICROSCOPY54U801 - 934
69ELECTRON MICROSCOPY55U949 - 1039
70ELECTRON MICROSCOPY56U1040 - 1154
71ELECTRON MICROSCOPY57U1155 - 1297
72ELECTRON MICROSCOPY58V45 - 187
73ELECTRON MICROSCOPY59V188 - 254
74ELECTRON MICROSCOPY60V255 - 311
75ELECTRON MICROSCOPY61V337 - 465
76ELECTRON MICROSCOPY62V466 - 623
77ELECTRON MICROSCOPY63V624 - 841
78ELECTRON MICROSCOPY64V916 - 1145
79ELECTRON MICROSCOPY65V1150 - 1250
80ELECTRON MICROSCOPY66V1251 - 1400

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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

他の情報も見る