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- PDB-6bva: Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragme... -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6bva
タイトルUbiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex.
要素
  • Lysine-specific demethylase 2B
  • Polyubiquitin-B
  • S-phase kinase-associated protein 1
キーワードPROTEIN BINDING / Ubiquitination
機能・相同性
機能・相同性情報


fourth ventricle development / initiation of neural tube closure / midbrain-hindbrain boundary morphogenesis / third ventricle development / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / embryonic camera-type eye morphogenesis / lateral ventricle development / negative regulation of neural precursor cell proliferation / F-box domain binding ...fourth ventricle development / initiation of neural tube closure / midbrain-hindbrain boundary morphogenesis / third ventricle development / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / embryonic camera-type eye morphogenesis / lateral ventricle development / negative regulation of neural precursor cell proliferation / F-box domain binding / hindbrain development / unmethylated CpG binding / PcG protein complex / histone H3K36 demethylase activity / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / SCF ubiquitin ligase complex / fat pad development / mitochondrion transport along microtubule / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / female gonad development / seminiferous tubule development / Prolactin receptor signaling / midbrain development / positive regulation of stem cell population maintenance / male meiosis I / cullin family protein binding / histone demethylase activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / forebrain development / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / 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 / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / molecular function activator activity / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / neuron projection morphogenesis / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination
類似検索 - 分子機能
PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Cupin-like domain 8 / Cupin-like domain / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / SKP1 component, dimerisation ...PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Cupin-like domain 8 / Cupin-like domain / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / SKP1/BTB/POZ domain superfamily / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Leucine-rich repeat domain superfamily / Zinc finger, FYVE/PHD-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-B / S-phase kinase-associated protein 1 / Lysine-specific demethylase 2B
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: 2.66 Å
データ登録者Manczyk, N. / Sicheri, F.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR)FDN 143277 カナダ
引用ジャーナル: Structure / 年: 2018
タイトル: A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases.
著者: Gorelik, M. / Manczyk, N. / Pavlenco, A. / Kurinov, I. / Sidhu, S.S. / Sicheri, F.
履歴
登録2017年12月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年7月18日Provider: repository / タイプ: Initial release
改定 1.12018年8月8日Group: Data collection / Database references / Derived calculations
カテゴリ: citation / citation_author ...citation / citation_author / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
改定 1.22018年9月19日Group: Data collection / Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.32020年1月8日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年10月4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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: S-phase kinase-associated protein 1
E: Lysine-specific demethylase 2B
B: Polyubiquitin-B
A: Polyubiquitin-B
C: S-phase kinase-associated protein 1
F: Lysine-specific demethylase 2B


分子量 (理論値)分子数
合計 (水以外)68,9236
ポリマ－68,9236
非ポリマー00
水72140
1
D: S-phase kinase-associated protein 1
E: Lysine-specific demethylase 2B
B: Polyubiquitin-B


分子量 (理論値)分子数
合計 (水以外)34,4613
ポリマ－34,4613
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-35 kcal/mol
Surface area13720 Å2
手法PISA
2
A: Polyubiquitin-B
C: S-phase kinase-associated protein 1
F: Lysine-specific demethylase 2B


分子量 (理論値)分子数
合計 (水以外)34,4613
ポリマ－34,4613
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-37 kcal/mol
Surface area13860 Å2
手法PISA
単位格子
Length a, b, c (Å)65.360, 81.793, 128.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質 S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


分子量: 18808.096 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: SKP1, EMC19, OCP2, SKP1A, TCEB1L / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63208
#2: タンパク質・ペプチド Lysine-specific demethylase 2B / CXXC-type zinc finger protein 2 / F-box and leucine-rich repeat protein 10 / F-box protein FBL10 / ...CXXC-type zinc finger protein 2 / F-box and leucine-rich repeat protein 10 / F-box protein FBL10 / F-box/LRR-repeat protein 10 / JmjC domain-containing histone demethylation protein 1B / Jumonji domain-containing EMSY-interactor methyltransferase motif protein / Protein JEMMA / Protein-containing CXXC domain 2 / [Histone-H3]-lysine-36 demethylase 1B


分子量: 5680.714 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: KDM2B, CXXC2, FBL10, FBXL10, JHDM1B, PCCX2 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q8NHM5, [histone H3]-dimethyl-L-lysine36 demethylase
#3: タンパク質 Polyubiquitin-B


分子量: 9972.468 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: UBB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG47
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 40 / 由来タイプ: 天然 / 式: H2O

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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: 2.5 Å3/Da / 溶媒含有率: 50.71 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000

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データ収集

回折平均測定温度: 93.15 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9791 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年11月21日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9791 Å / 相対比: 1
反射解像度: 2.66→50 Å / Num. obs: 20716 / % possible obs: 99.8 % / 冗長度: 5.3 % / Rsym value: 0.174 / Net I/σ(I): 16.5
反射 シェル解像度: 2.66→2.76 Å / 冗長度: 4.6 % / Mean I/σ(I) obs: 2.2 / Rsym value: 1.067 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1UBQ, 5IBK, 5JH5

1ubq

5ibk

5jh5


解像度: 2.66→47.46 Å / SU ML: 0.35 / 交差検証法: FREE R-VALUE / σ(F): 2.01 / 位相誤差: 28.43 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.263 1060 5.19 %
Rwork0.216 --
obs0.218 20406 99.7 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.66→47.46 Å
タンパク質核酸リガンド溶媒全体
原子数4071 0 0 40 4111
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0064147
X-RAY DIFFRACTIONf_angle_d0.8815661
X-RAY DIFFRACTIONf_dihedral_angle_d8.4112498
X-RAY DIFFRACTIONf_chiral_restr0.062687
X-RAY DIFFRACTIONf_plane_restr0.006719
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.78110.3161260.25032366X-RAY DIFFRACTION100
2.7811-2.92770.28691480.24482373X-RAY DIFFRACTION100
2.9277-3.11110.31921360.24022377X-RAY DIFFRACTION100
3.1111-3.35120.30331270.2492393X-RAY DIFFRACTION100
3.3512-3.68830.27441120.20952417X-RAY DIFFRACTION100
3.6883-4.22180.22051160.19022421X-RAY DIFFRACTION100
4.2218-5.31780.24361590.18642434X-RAY DIFFRACTION100
5.3178-47.46820.25711360.22972565X-RAY DIFFRACTION100
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)
13.0754-1.5272-1.61047.76536.68338.8378-0.6785-0.0362-0.31460.63571.5047-1.2133-0.17521.6481-0.39780.2402-0.0559-0.0470.45560.08070.723826.977816.7573-0.9584
26.56513.8832-3.66573.97450.51236.0485-0.14750.9105-0.58790.3746-0.2796-0.96380.949-0.01470.24570.24330.0461-0.07070.47050.03120.577923.738311.23441.4948
33.5368-0.6777-4.74292.84010.03019.04610.07221.4712-0.312-1.11711.0812-0.6183-0.7563-0.6841-0.69690.4622-0.02310.06720.5628-0.13240.620614.108615.38830.7426
42.13671.0159-3.32556.6833-4.45478.1506-0.21170.27130.8898-0.20460.24370.89360.7586-1.0221-0.32550.4278-0.06340.01740.6123-0.04840.676420.084320.8487-0.7975
59.91513.6918-4.3947.5106-5.46157.4265-0.2685-0.75670.2164-0.42480.1011-0.38590.63940.91340.2920.3810.04910.00410.4522-0.08410.399426.188413.611411.0728
65.4413-6.49122.45537.94-2.49822.0558-1.1497-0.2442-1.7003-0.71570.81411.51161.0926-0.8470.43220.7649-0.08120.32950.4796-0.13232.000213.01435.813611.5749
70.8863-1.0157-1.71542.81221.72177.1872-0.5477-1.599-2.00091.8760.20911.76221.2817-0.54690.28810.90730.01460.2910.95970.30390.93612.54768.486726.1352
87.6782-2.5712-0.00215.7799-0.19352.241-0.0085-1.46160.3130.98940.13330.14180.53580.65850.22970.62810.0707-0.06160.781-0.15250.412422.74317.604818.5589
90.1212-0.0539-0.06064.74515.10376.2805-0.7492-1.91570.51841.35890.335-0.10890.6457-0.0082-0.27460.6890.2243-0.12921.2016-0.32890.476417.307918.769726.8367
101.0247-0.79120.34442.33880.06890.15330.0832-0.6090.63110.26720.5194-0.05960.2571.0081-0.28120.68270.27210.17231.1222-0.58471.020718.829133.377434.4118
110.7739-0.3039-0.15970.11720.06040.0206-0.2229-0.4213-0.32510.18860.15960.3756-0.6294-0.40650.44671.81610.30161.04642.573-0.66370.98455.132329.990143.7777
124.289-1.9422-0.0336.07121.9389.9543-1.04130.05750.1095-0.13310.27550.1462-1.1011-1.30690.20610.63360.185-0.03211.0437-0.3710.480411.712125.07923.7655
135.0518-5.13113.28435.7676-2.30534.0197-0.3618-4.22320.28411.09671.5133-0.3999-0.3466-0.0981-1.06431.67170.31160.16252.002-0.15071.01188.4821.940936.0296
140.75330.4779-0.25390.41630.16020.94680.2496-0.29680.15680.35380.3460.1676-0.35430.16810.85211.76750.6018-0.26271.5196-0.96170.60848.912531.22131.0849
154.98711.24322.11871.83312.97794.83220.20830.0340.05730.53650.52310.36630.2975-1.2706-0.0621.16940.04690.24141.5513-0.21970.66970.696522.295529.3717
166.2129-2.76385.18818.0761-4.05897.0228-0.46-0.06880.3220.04430.910.2901-0.713-0.4731-0.57880.36680.0672-0.01170.6056-0.04660.53994.625526.3851.8427
177.09643.8001-6.2717.9685-3.99786.3604-0.96291.43442.2427-1.12731.06670.1742-0.358-1.5667-0.25830.6154-0.038-0.06210.47510.08110.87227.305538.5865-2.3313
188.6416-4.3547-1.41125.47721.10257.3829-0.11150.43451.84970.14330.2671-0.696-0.35780.6989-0.34660.3164-0.083-0.02870.8368-0.03720.97513.179431.098-3.194
196.6668-1.4272-2.28895.34453.61585.7481-0.8757-1.46870.99760.39670.7054-1.0918-0.6130.1702-0.51980.7405-0.022-0.3883-0.0086-0.24580.611757.352931.44571.8366
209.00753.16427.06276.63275.06697.98080.21821.3105-0.8733-0.7332-0.0368-0.7544-1.0450.8329-0.42420.3703-0.11630.05040.6287-0.02570.373254.655821.628154.4022
219.67052.89224.90392.17071.89422.6164-0.07730.35591.3737-0.3229-0.0859-0.5884-0.8115-0.70050.2180.52690.0118-0.0690.32940.01070.572559.002732.393768.4365
226.3047-1.6756-2.16886.89290.44248.13910.046-0.62562.1059-0.2544-0.02940.1439-0.8820.74870.18240.4509-0.1623-0.03970.3167-0.05460.714752.821838.697566.2797
237.46234.1221-0.31497.65913.77343.9442-0.55640.24681.5803-1.30060.01180.3454-0.5355-0.23830.39870.3001-0.0105-0.02480.44530.18020.512448.727533.172858.8906
249.42783.63623.08783.47435.00088.00240.02830.51751.1957-0.4463-0.41861.0661-0.0591-0.93620.15390.3544-0.0511-0.11850.5341-0.02590.710243.094231.387970.2362
255.24030.31390.83361.34041.35814.97180.169-0.71050.46510.0763-0.56870.3331-0.3451-1.22930.4060.2820.00040.01470.4324-0.12920.432148.405629.938367.8853
267.2161-3.30753.20254.1981-4.29194.5184-0.0163-0.16010.1106-0.29910.3892-0.26740.0413-0.9542-0.32780.28950.07850.03220.3551-0.07630.407234.445517.055965.2144
273.7724-0.7071-0.25615.91911.83943.9548-0.0514-0.37780.07290.10780.0734-0.25240.2780.27680.01190.24160.0230.03870.42970.03080.429839.194514.849660.8596
286.05923.6332-5.29733.4647-1.55076.9374-0.71380.6989-2.1605-0.4926-0.075-0.70950.9310.38170.56850.5061-0.01060.09640.5348-0.18180.546342.55287.922945.2201
290.81490.6945-2.14983.5599-2.95886.0508-0.15580.80440.0797-0.37540.2284-0.1609-0.0111-0.16970.07730.4253-0.10880.02590.83850.13590.275344.624422.915335.4545
307.02360.8787-0.01445.7255-3.296.1735-0.33760.5115-0.6744-0.8107-0.1695-0.3548-0.52560.40570.56850.7207-0.02870.10570.95840.05810.389850.01323.329934.8169
313.94311.1673-2.40698.1701-2.95863.66350.0916-0.434-0.3121-0.32310.2419-1.0416-0.4081.42360.31510.7023-0.13210.10231.20880.16280.39554.098327.698333.9802
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'D' AND (RESID 0 THROUGH 12 )
2X-RAY DIFFRACTION2CHAIN 'D' AND (RESID 13 THROUGH 23 )
3X-RAY DIFFRACTION3CHAIN 'D' AND (RESID 24 THROUGH 31 )
4X-RAY DIFFRACTION4CHAIN 'D' AND (RESID 32 THROUGH 51 )
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID 52 THROUGH 64 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 65 THROUGH 74 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 75 THROUGH 86 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 87 THROUGH 110 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 111 THROUGH 138 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 139 THROUGH 147 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 148 THROUGH 161 )
12X-RAY DIFFRACTION12CHAIN 'E' AND (RESID 1064 THROUGH 1076 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 1077 THROUGH 1087 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 1088 THROUGH 1097 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 1098 THROUGH 1103 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 0 THROUGH 24 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 25 THROUGH 41 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 42 THROUGH 80 )
19X-RAY DIFFRACTION19CHAIN 'A' AND (RESID -2 THROUGH 7 )
20X-RAY DIFFRACTION20CHAIN 'A' AND (RESID 8 THROUGH 18 )
21X-RAY DIFFRACTION21CHAIN 'A' AND (RESID 19 THROUGH 24 )
22X-RAY DIFFRACTION22CHAIN 'A' AND (RESID 25 THROUGH 41 )
23X-RAY DIFFRACTION23CHAIN 'A' AND (RESID 42 THROUGH 51 )
24X-RAY DIFFRACTION24CHAIN 'A' AND (RESID 52 THROUGH 63 )
25X-RAY DIFFRACTION25CHAIN 'A' AND (RESID 64 THROUGH 83 )
26X-RAY DIFFRACTION26CHAIN 'C' AND (RESID 1 THROUGH 12 )
27X-RAY DIFFRACTION27CHAIN 'C' AND (RESID 13 THROUGH 64 )
28X-RAY DIFFRACTION28CHAIN 'C' AND (RESID 65 THROUGH 96 )
29X-RAY DIFFRACTION29CHAIN 'C' AND (RESID 97 THROUGH 161 )
30X-RAY DIFFRACTION30CHAIN 'F' AND (RESID 1064 THROUGH 1087 )
31X-RAY DIFFRACTION31CHAIN 'F' AND (RESID 1088 THROUGH 1103 )

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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