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- PDB-7kzr: Structure of the human Fanconi Anaemia Core-UBE2T-ID complex -

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基本情報

登録情報
データベース: PDB / ID: 7kzr
タイトルStructure of the human Fanconi Anaemia Core-UBE2T-ID complex
要素
  • (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 / 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 K27-linked ubiquitination / regulation of regulatory T cell differentiation / protein K29-linked ubiquitination / homologous chromosome pairing at meiosis / male meiotic nuclear division / double-strand break repair involved in meiotic recombination / gamete generation ...regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / protein K29-linked ubiquitination / homologous chromosome pairing at meiosis / male meiotic nuclear division / double-strand break repair involved in meiotic recombination / gamete generation / neuronal stem cell population maintenance / replication-born double-strand break repair via sister chromatid exchange / protein K6-linked ubiquitination / brain morphogenesis / protein K11-linked ubiquitination / myeloid cell homeostasis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / E2 ubiquitin-conjugating enzyme / female gonad development / protein monoubiquitination / germ cell development / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / spermatid development / negative regulation of double-strand break repair via homologous recombination / positive regulation of double-strand break repair via homologous recombination / protein autoubiquitination / protein K48-linked ubiquitination / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / ovarian follicle development / removal of superoxide radicals / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / response to gamma radiation / mitochondrion organization / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / Fanconi Anemia Pathway / 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 / DNA damage response / chromatin binding / ubiquitin protein ligase binding / chromatin / nucleolus / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
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 / 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 2 / FANCL, UBC-like domain 3 / 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 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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
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)
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: 4.4 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
改定 1.22024年3月6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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low

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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-23087
  • 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

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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
M: 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
U: Fanconi anemia, complementation group I
V: Fanconi anemia group D2 protein
X: Ubiquitin-conjugating enzyme E2 T
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,470,67422
ポリマ－1,470,34717
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
#11: 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 LMUX

#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 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
#12: 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

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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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非ポリマー , 1種, 5分子

#13: 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 sequence of FAAP20 is MEAARRPRLGLSRRRPPPAGGPSGGRPWFLLGGDERERLWAELLRTVSPELILDHEVPSL ...The complete sequence of FAAP20 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 complex / タイプ: COMPLEX / Entity ID: #1-#12 / 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 mMBicineC6H13NO41
2150 mMsodium chlorideNaCl1
31 mMDithiothreitolC4H10O2S21
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: 60 e/Å2 / 検出モード: SUPER-RESOLUTION
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k 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: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 114249 / 対称性のタイプ: POINT
精密化解像度: 4.4→4.4 Å / Cor.coef. Fo:Fc: 0.967 / SU B: 114.471 / SU ML: 0.615 / ESU R: 0.735
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
Rwork0.31228 --
obs0.31228 623501 100 %
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: 79.835 Å2
Baniso -1Baniso -2Baniso -3
1--5.84 Å24.59 Å22.14 Å2
2--6.49 Å28.29 Å2
3----0.65 Å2
精密化ステップサイクル: 1 / 合計: 86745
拘束条件
Refine-IDタイプDev idealDev ideal target数
ELECTRON MICROSCOPYr_bond_refined_d0.0120.01388489
ELECTRON MICROSCOPYr_bond_other_d0.0130.01786047
ELECTRON MICROSCOPYr_angle_refined_deg1.561.632119890
ELECTRON MICROSCOPYr_angle_other_deg1.611.571198197
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.608510913
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.70722.0784356
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.0091515704
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.24915579
ELECTRON MICROSCOPYr_chiral_restr0.0810.211498
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0298196
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0219810
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_it2.77812.35443976
ELECTRON MICROSCOPYr_mcbond_other2.77812.35443975
ELECTRON MICROSCOPYr_mcangle_it5.15354781
ELECTRON MICROSCOPYr_mcangle_other5.15354782
ELECTRON MICROSCOPYr_scbond_it2.03312.43244513
ELECTRON MICROSCOPYr_scbond_other2.03312.43244514
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.14665110
ELECTRON MICROSCOPYr_long_range_B_refined14.202276938
ELECTRON MICROSCOPYr_long_range_B_other14.202276938
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→4.309 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0 0 -
Rwork0.468 46230 -
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)
12.6717-2.9431.949116.68535.05555.3109-0.2935-0.4656-0.47381.39330.01871.58510.2056-0.54410.27491.0958-0.21780.15730.95280.23050.659378.387206.27886.489
23.2192-3.3279-1.84695.67460.81943.6117-0.23830.00990.17650.56870.12630.03990.7445-0.36790.11190.8296-0.1543-0.00230.91660.13290.737690.29199.80976.225
34.60121.0081-1.95053.72182.9314.0622-0.2171-0.14920.43330.5744-0.20980.64320.6539-0.04490.42680.8330.12540.01540.94690.07680.903486.585215.64685.645
41.6128-2.8952-0.67216.9688-0.46472.02540.0187-0.09450.15920.0269-0.0181-0.22760.1409-0.0912-0.00070.7812-0.03720.03641.05380.09980.821593.071208.61972.521
52.6464-1.4006-2.50361.76453.08735.481-0.1031-0.07680.14610.16070.2141-0.14570.11670.277-0.1110.8015-0.0250.0420.85750.14391.0802104.516217.17172.521
62.72155.7173-0.006124.99356.44933.31390.0632-0.015-0.125-0.096-0.2058-0.2479-0.07480.21120.14270.70760.038-0.01581.0310.16990.784103.869196.31851.161
725.36184.3764-12.66040.8459-2.14386.35750.0774-2.3018-0.30910.1455-0.0218-0.1280.05751.3195-0.05570.80450.4481-0.44911.7795-0.29131.6923107.974182.08854.35
81.83110.34370.4890.64170.40350.9867-0.0698-0.04020.1760.12340.00490.0776-0.0611-0.01940.06480.70390.07880.01740.89410.12720.885278.739190.46852.923
91.0091-0.2023-1.35890.08940.22892.3107-0.1012-0.031-0.1363-0.1333-0.12660.01460.2008-0.07090.22790.74040.1296-0.09690.95670.11971.084262.702179.82933.555
105.22846.1384-4.45557.2285-5.23213.79850.2462-0.2137-0.19120.3737-0.3721-0.2282-0.22910.18080.12590.959-0.0124-0.00221.0551-0.06841.114156.435165.35343.322
1112.302-1.4699-6.27838.56733.3724.0253-0.20160.4226-0.2631-0.02710.05260.1230.0635-0.21180.14890.6572-0.0425-0.10240.94540.07990.986959.554178.59745.104
124.5897-3.71611.39577.258-1.51740.4731-0.11470.5922-0.00040.75050.08510.5638-0.06810.16590.02960.6048-0.0228-0.07871.09020.01281.027445.809184.29836.008
130.66211.21920.81752.31691.5821.0921-0.02710.0699-0.1186-0.032-0.0396-0.0039-0.0278-0.11410.06660.56190.04740.15611.09430.01341.070437.882184.47544.699
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1050.10360.4327-0.12781.9207-0.59770.53850.0016-0.0807-0.03370.10.01850.14740.7055-0.4034-0.02021.7825-0.26960.2651.80370.20621.872179.88871.178235.93
1065.18954.5342-1.36924.835-0.23962.789-0.2467-0.2778-0.8164-0.06340.3065-0.11760.0853-0.2957-0.05980.5981-0.29190.2911.76470.93111.197854.82193.991256.326
1072.76941.2965-0.02992.06450.04830.19630.0829-0.1662-0.25090.13790.0534-0.0413-0.05450.029-0.13620.8281-0.04590.16141.04730.15320.639783.062113.676247.214
1084.81911.9478-1.45713.9748-0.77922.6287-0.0855-0.012-0.1160.28140.1991-0.4116-0.3464-0.0009-0.11360.63490.15570.36471.62340.38180.619799.256126.83238.319
1092.78830.9482-0.36081.7214-0.97752.9347-0.11440.1226-0.5071-0.2067-0.0328-0.0294-0.17270.3390.14730.4111-0.27570.23881.94340.20160.6704122.625129.453207.622
1102.952-1.11053.15961.1782-2.00624.4255-0.32331.01050.61140.45110.0190.0836-0.94311.10340.30430.7456-0.54430.42311.96270.25170.9485146.793148.728207.829
1113.47470.5406-0.08120.8877-0.15941.212-0.0579-0.00920.09240.13620.09650.011-0.04370.2704-0.03850.7329-0.06090.01571.02090.07740.7605141.887140.025229.298
1122.0624-0.46620.81210.16350.05553.9210.2559-0.69540.2961-0.01830.09150.0518-0.22870.195-0.34740.9553-0.30570.06371.8183-0.09490.8204133.498144.259250.079
1130.58421.32130.29663.46840.53290.2831-0.1195-0.19010.3189-0.2845-0.11320.344-0.1560.03220.23261.04680.00880.17981.0278-0.13690.8907114.069152.299260.54
1140.60980.18780.55850.07170.19980.57360.1522-0.23230.0539-0.0662-0.077-0.0573-0.0993-0.157-0.07511.09250.00560.35990.9859-0.02510.899598.708155.744263.551
1154.4381-0.77130.9563.58051.06161.52060.30320.36810.1397-0.08780.2022-0.9405-0.31630.2711-0.50540.32380.15130.37951.4350.25940.8019132.893126.771172.69
1162.8428-1.6534-0.78632.27933.00786.98720.10330.10410.0696-0.31190.035-0.0747-0.49170.4341-0.13840.63480.12030.0711.02980.19080.48109.517132.002179.83
1172.08911.79750.02384.5180.89214.12380.2802-0.00880.0307-0.2467-0.1287-0.1469-0.2541-0.1761-0.15160.58440.14050.2040.90160.22180.667892.798132.137192.359
1182.00460.5841-0.24161.5309-0.77641.66260.12160.0180.06540.0751-0.01580.0501-0.0705-0.0486-0.10570.6750.04860.10520.90520.21060.713380.446124.783208.692
1192.00961.4894-1.29461.3978-0.84531.7557-0.0899-0.0779-0.1253-0.06220.09390.0110.18790.0006-0.00410.7038-0.07680.04020.95860.24830.717363.092104.251230.073
1201.4443-0.3219-0.38625.16910.05460.2722-0.1030.2035-0.5454-0.7662-0.28961.3-0.1004-0.49230.39260.92650.133-0.31051.8233-0.10441.739428.283106.378230.905
1210.2314-0.4719-0.27571.06470.65130.41030.21210.3441-0.3163-0.3667-0.48470.5205-0.2601-0.18020.27261.41370.2306-0.03832.32270.24551.510732.161120.968205.288
1220.014-0.011-0.00530.00910.00550.00750.11460.06570.0721-0.0967-0.0283-0.0666-0.05420.0412-0.08621.10720.12140.52481.6353-0.02671.223232.654147.515205.008
1230.0005-0.0004-0.00020.0035-0.0070.0162-0.01070.02830.00630.06920.01840.0058-0.1187-0.1079-0.00761.7294-0.0590.66932.19870.09521.100448.491164.889206.465
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1C1 - 14
2ELECTRON MICROSCOPY2C15 - 49
3ELECTRON MICROSCOPY3C50 - 70
4ELECTRON MICROSCOPY4C71 - 94
5ELECTRON MICROSCOPY5C95 - 144
6ELECTRON MICROSCOPY6C145 - 169
7ELECTRON MICROSCOPY7C170 - 178
8ELECTRON MICROSCOPY8C179 - 326
9ELECTRON MICROSCOPY9C327 - 378
10ELECTRON MICROSCOPY10C379 - 390
11ELECTRON MICROSCOPY11C391 - 400
12ELECTRON MICROSCOPY12C401 - 425
13ELECTRON MICROSCOPY13C426 - 483
14ELECTRON MICROSCOPY14C484 - 558
15ELECTRON MICROSCOPY15E12 - 25
16ELECTRON MICROSCOPY16E26 - 47
17ELECTRON MICROSCOPY17E48 - 59
18ELECTRON MICROSCOPY18E60 - 72
19ELECTRON MICROSCOPY19E73 - 83
20ELECTRON MICROSCOPY20E84 - 104
21ELECTRON MICROSCOPY21E105 - 120
22ELECTRON MICROSCOPY22E121 - 130
23ELECTRON MICROSCOPY23E131 - 142
24ELECTRON MICROSCOPY24E143 - 154
25ELECTRON MICROSCOPY25E155 - 181
26ELECTRON MICROSCOPY26F1 - 183
27ELECTRON MICROSCOPY27F184 - 355
28ELECTRON MICROSCOPY28L1 - 103
29ELECTRON MICROSCOPY29L104 - 197
30ELECTRON MICROSCOPY30L198 - 296
31ELECTRON MICROSCOPY31L297 - 402
32ELECTRON MICROSCOPY32M1 - 103
33ELECTRON MICROSCOPY33M104 - 197
34ELECTRON MICROSCOPY34M198 - 296
35ELECTRON MICROSCOPY35M297 - 402
36ELECTRON MICROSCOPY36G12 - 342
37ELECTRON MICROSCOPY36S32 - 55
38ELECTRON MICROSCOPY37G343 - 611
39ELECTRON MICROSCOPY37S19 - 31
40ELECTRON MICROSCOPY38S56 - 246
41ELECTRON MICROSCOPY39S265 - 524
42ELECTRON MICROSCOPY40S542 - 627
43ELECTRON MICROSCOPY41S648 - 1033
44ELECTRON MICROSCOPY42S1043 - 1215
45ELECTRON MICROSCOPY43S1216 - 1443
46ELECTRON MICROSCOPY44H12 - 386
47ELECTRON MICROSCOPY44A29 - 55
48ELECTRON MICROSCOPY45H387 - 611
49ELECTRON MICROSCOPY45A19 - 28
50ELECTRON MICROSCOPY46A56 - 248
51ELECTRON MICROSCOPY47A262 - 401
52ELECTRON MICROSCOPY48A402 - 524
53ELECTRON MICROSCOPY49A648 - 1034
54ELECTRON MICROSCOPY49A2001 - 2107
55ELECTRON MICROSCOPY50A1043 - 1215
56ELECTRON MICROSCOPY51A1216 - 1443
57ELECTRON MICROSCOPY52B7 - 254
58ELECTRON MICROSCOPY53B255 - 369
59ELECTRON MICROSCOPY54B385 - 476
60ELECTRON MICROSCOPY55B477 - 493
61ELECTRON MICROSCOPY56B494 - 502
62ELECTRON MICROSCOPY57B503 - 511
63ELECTRON MICROSCOPY58B512 - 518
64ELECTRON MICROSCOPY59B519 - 531
65ELECTRON MICROSCOPY60B532 - 574
66ELECTRON MICROSCOPY61B575 - 601
67ELECTRON MICROSCOPY62B602 - 612
68ELECTRON MICROSCOPY63B613 - 634
69ELECTRON MICROSCOPY64B635 - 644
70ELECTRON MICROSCOPY65B645 - 663
71ELECTRON MICROSCOPY66B664 - 687
72ELECTRON MICROSCOPY67B688 - 735
73ELECTRON MICROSCOPY68B736 - 770
74ELECTRON MICROSCOPY69B771 - 837
75ELECTRON MICROSCOPY70B838 - 859
76ELECTRON MICROSCOPY71P5 - 86
77ELECTRON MICROSCOPY72P87 - 130
78ELECTRON MICROSCOPY73P131 - 155
79ELECTRON MICROSCOPY74P156 - 217
80ELECTRON MICROSCOPY75P218 - 280
81ELECTRON MICROSCOPY76P281 - 346
82ELECTRON MICROSCOPY77P347 - 371
83ELECTRON MICROSCOPY78P372 - 418
84ELECTRON MICROSCOPY79P419 - 433
85ELECTRON MICROSCOPY80P434 - 457
86ELECTRON MICROSCOPY81P458 - 509
87ELECTRON MICROSCOPY82P510 - 531
88ELECTRON MICROSCOPY83P532 - 548
89ELECTRON MICROSCOPY84P549 - 557
90ELECTRON MICROSCOPY85P558 - 584
91ELECTRON MICROSCOPY86P585 - 593
92ELECTRON MICROSCOPY87P594 - 605
93ELECTRON MICROSCOPY88P606 - 636
94ELECTRON MICROSCOPY89P637 - 654
95ELECTRON MICROSCOPY90P655 - 709
96ELECTRON MICROSCOPY91P710 - 754
97ELECTRON MICROSCOPY92P755 - 768
98ELECTRON MICROSCOPY93P769 - 784
99ELECTRON MICROSCOPY94P785 - 808
100ELECTRON MICROSCOPY95P809 - 836
101ELECTRON MICROSCOPY96P837 - 881
102ELECTRON MICROSCOPY97O7 - 369
103ELECTRON MICROSCOPY98O391 - 432
104ELECTRON MICROSCOPY98Q449 - 500
105ELECTRON MICROSCOPY99O471 - 655
106ELECTRON MICROSCOPY100O656 - 749
107ELECTRON MICROSCOPY100Q669 - 685
108ELECTRON MICROSCOPY101O750 - 859
109ELECTRON MICROSCOPY101Q823 - 881
110ELECTRON MICROSCOPY102Q5 - 435
111ELECTRON MICROSCOPY103Q501 - 668
112ELECTRON MICROSCOPY104Q701 - 822
113ELECTRON MICROSCOPY105X1 - 153
114ELECTRON MICROSCOPY106U1 - 169
115ELECTRON MICROSCOPY107U170 - 305
116ELECTRON MICROSCOPY108U306 - 398
117ELECTRON MICROSCOPY109U411 - 684
118ELECTRON MICROSCOPY110U696 - 791
119ELECTRON MICROSCOPY111U801 - 934
120ELECTRON MICROSCOPY112U949 - 1039
121ELECTRON MICROSCOPY113U1040 - 1154
122ELECTRON MICROSCOPY114U1155 - 1280
123ELECTRON MICROSCOPY115V45 - 187
124ELECTRON MICROSCOPY116V188 - 254
125ELECTRON MICROSCOPY117V255 - 311
126ELECTRON MICROSCOPY118V337 - 465
127ELECTRON MICROSCOPY119V466 - 623
128ELECTRON MICROSCOPY120V624 - 839
129ELECTRON MICROSCOPY121V916 - 1145
130ELECTRON MICROSCOPY122V1150 - 1250
131ELECTRON MICROSCOPY123V1251 - 1376

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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://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