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- PDB-9egw: HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled) -

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基本情報

登録情報
データベース: PDB / ID: 9egw
タイトルHOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled)
要素
  • Polyubiquitin-C
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
キーワードLIGASE / RBR E3 ubiquitin ligase / enzyme-substrate complex / RING2 domain
機能・相同性
機能・相同性情報


protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / negative regulation of necroptotic process / ubiquitin ligase activator activity / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / Maturation of protein E / Maturation of protein E ...protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / negative regulation of necroptotic process / ubiquitin ligase activator activity / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Deactivation of the beta-catenin transactivating complex / protein sequestering activity / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR1 signaling / EGFR downregulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Degradation of AXIN / Hh mutants are degraded by ERAD
類似検索 - 分子機能
: / : / : / LUBAC thetering domain / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain ...: / : / : / LUBAC thetering domain / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type
類似検索 - ドメイン・相同性
Polyubiquitin-C / RanBP-type and C3HC4-type zinc finger-containing protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.78 Å
データ登録者Wang, X.S. / Lechtenberg, B.C.
資金援助 オーストラリア, 2件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)GNT2016268 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)GNT1182757 オーストラリア
引用
ジャーナル: Life Sci Alliance / 年: 2025
タイトル: The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitro.
著者: Wang, X.S. / Jiou, J. / Cerra, A. / Cobbold, S.A. / Jochem, M. / Mak, K.H.T. / Corcilius, L. / Silke, J. / Payne, R.J. / Goddard-Borger, E.D. / Komander, D. / Lechtenberg, B.C.
#1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2024年11月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年12月11日Provider: repository / タイプ: Initial release
改定 2.02025年3月19日Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal_grow / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal_grow.pdbx_details / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.seq_num / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
改定 2.12025年4月16日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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構造の表示

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: RanBP-type and C3HC4-type zinc finger-containing protein 1
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
C: Polyubiquitin-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,79913
ポリマ－29,0823
非ポリマー71610
水3,423190
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_555x,y,z1
Buried area3450 Å2
ΔGint-87 kcal/mol
Surface area13440 Å2
2
A: RanBP-type and C3HC4-type zinc finger-containing protein 1
C: Polyubiquitin-C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8167
ポリマ－19,4882
非ポリマー3285
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-40 kcal/mol
Surface area8450 Å2
手法PISA
3
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)9,9826
ポリマ－9,5941
非ポリマー3885
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-33 kcal/mol
Surface area5480 Å2
手法PISA
単位格子
Length a, b, c (Å)96.063, 96.063, 187.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDモデル要素
11A-748-

HOH

21A-773-

HOH

31A-785-

HOH

41A-788-

HOH

51B-744-

HOH

61B-778-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 431 through 438 or resid 440...
d_2ens_1(chain "B" and (resid 431 through 438 or resid 440...

NCSドメイン領域:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11THRTHRMETMETAA431 - 4389 - 16
d_12GLNGLNGLNGLNAA44018
d_13GLYGLYCYSCYSAA442 - 46520 - 43
d_14VALVALCYSCYSAA467 - 49345 - 71
d_15CYSCYSHISHISAA495 - 51073 - 88
d_16ZNZNZNZNAD601
d_17ZNZNZNZNAE602
d_21THRTHRMETMETBB431 - 4389 - 16
d_22GLNGLNGLNGLNBB44018
d_23GLYGLYCYSCYSBB442 - 46520 - 43
d_24VALVALCYSCYSBB467 - 49345 - 71
d_25CYSCYSHISHISBB495 - 51073 - 88
d_26ZNZNZNZNBH601
d_27ZNZNZNZNBI602

NCS oper: (Code: givenMatrix: (0.361486263713, 0.924892493272, -0.117904864346), (-0.835854588175, 0.377494052873, 0.398554070951), (0.413128053481, -0.0455205001637, 0.909534548817)ベクター: -26. ...NCS oper: (Code: given
Matrix: (0.361486263713, 0.924892493272, -0.117904864346), (-0.835854588175, 0.377494052873, 0.398554070951), (0.413128053481, -0.0455205001637, 0.909534548817)
ベクター: -26.4811445567, 58.8566663377, 19.4501678376)

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要素

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タンパク質 , 2種, 3分子 ABC

#1: タンパク質 RanBP-type and C3HC4-type zinc finger-containing protein 1 / HBV-associated factor 4 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / Hepatitis B virus X- ...HBV-associated factor 4 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / Hepatitis B virus X-associated protein 4 / RING finger protein 54 / RING-type E3 ubiquitin transferase HOIL-1 / Ubiquitin-conjugating enzyme 7-interacting protein 3


分子量: 9594.109 Da / 分子数: 2 / 変異: C460A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RBCK1, C20orf18, RNF54, UBCE7IP3, XAP3, XAP4 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9BYM8, RBR-type E3 ubiquitin transferase
#2: タンパク質 Polyubiquitin-C


分子量: 9894.270 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: N-terminal 6xHis-tag. The C-terminus is conjugated via an oxyester bond to the C6-OH of the non-reducing sugar of a maltose molecule.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG48

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非ポリマー , 4種, 200分子

#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn
#4: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#5: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 3 / 由来タイプ: 合成 / 式: SO4
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 190 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationN
配列の詳細In our crystal, Macromolecule 2 is a Polyubiquitin-C protein with its C-terminus conjugated to the ...In our crystal, Macromolecule 2 is a Polyubiquitin-C protein with its C-terminus conjugated to the C6-OH of a maltose molecule via an oxyester bond.

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.36 Å3/Da / 溶媒含有率: 63.36 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 / 詳細: 0.02 M MgCl2, 0.05 M MES pH6 and 1.8 M LiSO4

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2023年3月1日
放射モノクロメーター: silicon-based Double Crystal / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9537 Å / 相対比: 1
反射解像度: 1.78→46.86 Å / Num. obs: 42270 / % possible obs: 99.9 % / 冗長度: 13.5 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.032 / Rrim(I) all: 0.119 / Χ2: 0.54 / Net I/σ(I): 12.9 / Num. measured all: 571589
反射 シェル解像度: 1.78→1.82 Å / % possible obs: 98.7 % / 冗長度: 12.9 % / Rmerge(I) obs: 1.449 / Num. measured all: 30180 / Num. unique obs: 2337 / CC1/2: 0.806 / Rpim(I) all: 0.414 / Rrim(I) all: 1.508 / Χ2: 0.46 / Net I/σ(I) obs: 1.3

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.1_5286精密化
Aimless0.7.8データスケーリング
XDSNov 1, 2016 BUILT=20161205データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.78→46.86 Å / SU ML: 0.203 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 17.3171
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.1821 1745 4.13 %
Rwork0.1649 40470 -
obs0.1657 42215 99.84 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 46.33 Å2
精密化ステップサイクル: LAST / 解像度: 1.78→46.86 Å
タンパク質核酸リガンド溶媒全体
原子数1857 0 22 190 2069
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01391955
X-RAY DIFFRACTIONf_angle_d1.21082651
X-RAY DIFFRACTIONf_chiral_restr0.0709287
X-RAY DIFFRACTIONf_plane_restr0.0126351
X-RAY DIFFRACTIONf_dihedral_angle_d13.7315748
Refine LS restraints NCSタイプ: Torsion NCS / Rms dev position: 2.19922679244 Å
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.30651400.26713262X-RAY DIFFRACTION99.01
1.83-1.890.23881440.22583328X-RAY DIFFRACTION99.86
1.89-1.960.21031440.19163347X-RAY DIFFRACTION99.94
1.96-2.040.20981430.18493310X-RAY DIFFRACTION99.68
2.04-2.130.2251440.18133350X-RAY DIFFRACTION99.97
2.13-2.240.15071440.14933330X-RAY DIFFRACTION99.91
2.24-2.380.15291440.13673356X-RAY DIFFRACTION99.97
2.38-2.570.17881460.14583367X-RAY DIFFRACTION99.97
2.57-2.830.16791470.163396X-RAY DIFFRACTION99.94
2.83-3.240.17571460.17213386X-RAY DIFFRACTION100
3.24-4.080.17821480.15783435X-RAY DIFFRACTION99.97
4.08-46.860.17661550.15913603X-RAY DIFFRACTION99.89
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

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)
10.697479665712-0.148623123639-0.1406710950530.2304318530630.1493664740650.1022977190550.03019974674390.2316492057970.5362068442590.0492838733234-0.14724544597-0.218118240116-0.6099661491830.478432514853-0.04187814512960.510657917205-0.16468595836-0.00542168407340.3509168622910.07123060628130.47573508267916.773430491264.3977696287-65.103616088
20.7850102949570.3620448784340.4743318298940.549998552822-0.1467061151910.629889723331-0.06816840215480.0914932979455-0.0777578481006-0.137609165380.030344004614-0.3600396515930.160568198220.58416865299-0.0001022422698880.358413303099-0.02446768412180.02801365729790.311749480986-0.004649261306320.3068668715815.169890390348.46434545-61.5834381023
30.4872183173460.073016626063-0.5803283863461.09218756108-0.3233476278021.069544041720.0157626961529-0.08223161240270.057268431794-0.0360961242956-0.05373853559850.02261337371480.094806530930.1345085026182.66084279634E-50.291397289856-0.01432687374640.01811211959340.202546069783-0.01373754898810.2598639819775.8359553150242.1786430417-62.298740719
40.0726929792702-0.0396147157774-0.02420896235950.02563423561860.01125643110680.061605026173-0.02022664027790.2760929369710.18132560378-0.01460190869290.382716214159-0.8078602387170.3021419358130.665744104171-0.0003031838131470.721242576026-0.08439577970230.1496444987271.31631893333-0.131009773810.71631017405245.676772452841.8835535802-37.2124105157
50.311912908257-0.02125126485040.2280558232560.316837314379-0.1968524674140.2699108586020.1147921771040.6795924592870.14224878313-0.115520407648-0.097370385313-0.03307368970270.2162389455630.1203183513623.34890965025E-50.2486433546520.0346124440869-0.02182028307440.505029089851-0.01721656960480.33968522256134.75594981345.8360394785-31.4110794712
60.903459670042-0.9462898561611.563372018620.990097762463-1.636147192552.703722369860.3558393914270.201679681374-1.46712945171-0.4306547657550.12096239815-0.1719821304730.8201809720890.418011067525-0.0249287558540.3852859413860.0884934973276-0.04724875799460.634476005773-0.1261812676040.46182852827332.713542848936.9868842391-37.4275125779
71.14729989251-0.1718561999080.4159449280320.363880490229-0.1438125497881.029228634020.04405659873870.107630872957-0.0990219726701-0.09435498235730.0442921771622-0.02942031950970.2258428322550.158811642758-8.79976637668E-70.220094561924-0.00679834234514-0.0231976396710.371084086488-0.008669255535320.29471446425622.059789130144.4205683205-36.2563502875
80.00595043045343-0.04232513880470.001115982864750.322108716443-0.00533075940669-0.0001663315448190.0173642626685-0.2728341996480.1574639305880.183609129249-0.246978935836-0.672300028241-0.478929395370.807619308116-0.2918808623760.664776585852-0.429968368715-0.06891339891211.01909349285-0.05563862444350.77702647335130.513896650861.6855324307-51.5196014622
90.0007743911944680.000398696037413-0.000235873233050.001280999745570.000264316721411-2.05712990468E-5-0.0538663151289-0.102249522906-0.1233896703850.111955081349-0.198436621843-0.711927445523-0.2663883615230.912652538668-0.1686637986660.394455633486-0.198627864509-0.0190780051770.9695117671950.1598547845170.70878222796731.272143058852.8393513191-56.8600151939
100.663271645431-0.680868680254-0.2196386518560.7017215940260.1963879521150.416564683975-0.3644891814090.1952657995-0.0866086362966-0.421536903470.0395443277637-0.3902736921840.07322444199850.330515936389-0.04291111339950.628834148683-0.3700131419380.151414706690.92091556180.2051307940290.85783616263532.084326119962.2430559724-65.3576688136
110.2479497211520.02302895426830.1281293141740.3548239899180.2108862989730.1782276077090.116342879841-0.2008680097610.1075300946910.190554878703-0.147629900428-0.465609094295-0.05906186378930.0872230772379-0.5478593526680.790763173678-0.5400734960890.008685692050421.059038169930.04999001336821.1183814345534.846687572868.4390989623-57.9417731183
120.430357794101-0.2364545696910.2429452155360.130554095997-0.1342892830270.138601574755-0.04995964052070.240861262511-0.111118641718-0.555349950829-0.103766906624-0.511014359849-0.3740687453210.760069735216-0.119443354220.417215741436-0.1230198389090.02566145146190.5692227356190.03525081180740.46608558605222.449031697652.2804737443-61.7655741188
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 425 through 445 )AA425 - 4451 - 21
22chain 'A' and (resid 446 through 464 )AA446 - 46422 - 40
33chain 'A' and (resid 465 through 510 )AA465 - 51041 - 86
44chain 'B' and (resid 431 through 441 )BE431 - 4411 - 11
55chain 'B' and (resid 442 through 452 )BE442 - 45212 - 22
66chain 'B' and (resid 453 through 461 )BE453 - 46123 - 31
77chain 'B' and (resid 462 through 510 )BE462 - 51032 - 80
88chain 'C' and (resid 1 through 22 )CI1 - 221 - 22
99chain 'C' and (resid 23 through 44 )CI23 - 4423 - 44
1010chain 'C' and (resid 45 through 55 )CI45 - 5545 - 55
1111chain 'C' and (resid 56 through 65 )CI56 - 6556 - 65
1212chain 'C' and (resid 66 through 76 )CI66 - 7666 - 76

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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

他の情報も見る