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- PDB-5ibk: Skp1-F-box in complex with a ubiquitin variant -

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基本情報

登録情報
データベース: PDB / ID: 5ibk
タイトルSkp1-F-box in complex with a ubiquitin variant
要素
  • F-box/WD repeat-containing protein 7
  • Polyubiquitin-B
  • S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
キーワードPROTEIN BINDING / phage display / SCF inhibitors / Fbxw7 / Fbxw11 / ?-Trcp / ubiquitin
機能・相同性
機能・相同性情報


negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / regulation of cell migration involved in sprouting angiogenesis / negative regulation of hepatocyte proliferation / positive regulation of epidermal growth factor-activated receptor activity / regulation of lipid storage / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin recycling / ubiquitin-protein transferase activator activity / F-box domain binding ...negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / regulation of cell migration involved in sprouting angiogenesis / negative regulation of hepatocyte proliferation / positive regulation of epidermal growth factor-activated receptor activity / regulation of lipid storage / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin recycling / ubiquitin-protein transferase activator activity / F-box domain binding / regulation of mitophagy / phosphothreonine residue binding / regulation of cell cycle G1/S phase transition / negative regulation of osteoclast development / PcG protein complex / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / 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 / positive regulation of proteasomal protein catabolic process / vasculature development / positive regulation of ubiquitin-dependent protein catabolic process / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein targeting to mitochondrion / sister chromatid cohesion / positive regulation of protein monoubiquitination / SCF ubiquitin ligase complex / positive regulation of ubiquitin-protein transferase activity / 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 / lipid homeostasis / Association of TriC/CCT with target proteins during biosynthesis / male meiosis I / cullin family protein binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of Notch signaling pathway / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / vasculogenesis / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / energy homeostasis / regulation of neuron apoptotic process / Notch signaling pathway / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / 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 / cyclin binding / 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 / neuron projection morphogenesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / molecular function activator activity / Translesion synthesis by REV1
類似検索 - 分子機能
Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain ...Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Monooxygenase / 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 / SKP1/BTB/POZ domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-B / S-phase kinase-associated protein 1 / F-box/WD repeat-containing protein 7
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: 2.503 Å
データ登録者Orlicky, S. / Sicheri, F.
資金援助 カナダ, 米国, 3件
組織認可番号国
Canadian Institutes of Health Research (CIHR)MOP-126129 カナダ
Canadian Institutes of Health Research (CIHR)(MOP-136956 カナダ
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2016
タイトル: Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface.
著者: Gorelik, M. / Orlicky, S. / Sartori, M.A. / Tang, X. / Marcon, E. / Kurinov, I. / Greenblatt, J.F. / Tyers, M. / Moffat, J. / Sicheri, F. / Sidhu, S.S.
履歴
登録2016年2月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年3月30日Provider: repository / タイプ: Initial release
改定 1.12016年4月13日Group: Data collection
改定 1.22017年9月13日Group: Advisory / Author supporting evidence / Derived calculations
カテゴリ: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.32019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年9月27日Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
B: F-box/WD repeat-containing protein 7
F: Polyubiquitin-B
C: Polyubiquitin-B
D: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
E: F-box/WD repeat-containing protein 7


分子量 (理論値)分子数
合計 (水以外)66,6126
ポリマ－66,6126
非ポリマー00
水68538
1
A: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
B: F-box/WD repeat-containing protein 7
C: Polyubiquitin-B


分子量 (理論値)分子数
合計 (水以外)33,3063
ポリマ－33,3063
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-32 kcal/mol
Surface area13620 Å2
手法PISA
2
F: Polyubiquitin-B
D: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
E: F-box/WD repeat-containing protein 7


分子量 (理論値)分子数
合計 (水以外)33,3063
ポリマ－33,3063
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-35 kcal/mol
Surface area13430 Å2
手法PISA
単位格子
Length a, b, c (Å)63.368, 98.015, 107.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21chain D
12chain B
22chain E
13chain C
23chain F

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUchain AAA-1 - 1561 - 144
21METMETCYSCYSchain DDE1 - 1603 - 148
12GLNGLNARGARGchain BBB277 - 32217 - 62
22GLNGLNARGARGchain EEF275 - 32215 - 62
13GLYGLYARGARGchain CCD-1 - 743 - 78
23SERSERARGARGchain FFC0 - 744 - 78

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質 S-phase kinase-associated protein 1,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: 16981.295 Da / 分子数: 2
断片: UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG
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 BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P63208
#2: タンパク質 F-box/WD repeat-containing protein 7 / Archipelago homolog / hAgo / F-box and WD-40 domain-containing protein 7 / F-box protein FBX30 / ...Archipelago homolog / hAgo / F-box and WD-40 domain-containing protein 7 / F-box protein FBX30 / SEL-10 / hCdc4


分子量: 7513.756 Da / 分子数: 2 / 断片: UNP residues 263-323 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FBXW7, FBW7, FBX30, SEL10 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q969H0
#3: タンパク質 Polyubiquitin-B


分子量: 8811.088 Da / 分子数: 2 / 断片: UNP residues 75-150
Mutation: L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F
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 BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0CG47
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 38 / 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: 2.51 Å3/Da / 溶媒含有率: 51.01 %
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: 4.5 / 詳細: 100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol

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データ収集

回折平均測定温度: 100 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: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2013年8月7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: 0.9795 Å / 相対比: 1
反射解像度: 2.5→47.709 Å / Num. obs: 23666 / % possible obs: 99.4 % / 冗長度: 4.4 % / Biso Wilson estimate: 64.87 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.024 / Rrim(I) all: 0.052 / Χ2: 0.43 / Net I/av σ(I): 19.63 / Net I/σ(I): 5.6 / Num. measured all: 103319
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.563.90.657199.1
2.56-2.624.50.557199.8
2.62-2.694.60.4631100
2.69-2.774.50.3691100
2.77-2.864.50.263199.6
2.86-2.964.50.2199.3
2.96-3.084.20.161199.6
3.08-3.224.20.119199
3.22-3.394.60.082199.8
3.39-3.614.50.064199.8
3.61-3.884.40.05199.1
3.88-4.274.20.037198.5
4.27-4.894.50.029199.8
4.89-6.164.20.03198.5
6.16-504.20.021198.8

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解析

ソフトウェア
名称バージョン分類
SCALEPACKデータスケーリング
PHENIX1.8.2_1309精密化
PDB_EXTRACT3.2データ抽出
HKL-2000データ削減
精密化構造決定の手法: 分子置換
開始モデル: 2OVR, 1UBQ

2ovr

1ubq


解像度: 2.503→47.709 Å / SU ML: 0.41 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 25.53
Rfactor反射数%反射
Rfree0.2399 1210 5.12 %
Rwork0.1997 --
obs0.2016 23612 99.25 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 218.53 Å2 / Biso mean: 80.85 Å2 / Biso min: 22.36 Å2
精密化ステップサイクル: final / 解像度: 2.503→47.709 Å
タンパク質核酸リガンド溶媒全体
原子数4246 0 0 38 4284
Biso mean---51.21 -
残基数----526
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0044314
X-RAY DIFFRACTIONf_angle_d0.8795830
X-RAY DIFFRACTIONf_chiral_restr0.035680
X-RAY DIFFRACTIONf_plane_restr0.003742
X-RAY DIFFRACTIONf_dihedral_angle_d13.2771649
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1206X-RAY DIFFRACTION8.694TORSIONAL
12D1206X-RAY DIFFRACTION8.694TORSIONAL
21B434X-RAY DIFFRACTION8.694TORSIONAL
22E434X-RAY DIFFRACTION8.694TORSIONAL
31C680X-RAY DIFFRACTION8.694TORSIONAL
32F680X-RAY DIFFRACTION8.694TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5027-2.60290.39411390.30912420255998
2.6029-2.72140.34611400.269624432583100
2.7214-2.86480.29551370.246724592596100
2.8648-3.04430.30621290.25382465259499
3.0443-3.27930.29191140.24362489260399
3.2793-3.60920.24471360.211524752611100
3.6092-4.13120.19391540.18322467262199
4.1312-5.20390.19311240.159725562680100
5.2039-47.7180.24151370.18812628276599
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)
12.76741.7679-7.18472.6011-7.86713.5245-0.1291-0.2657-1.6375-0.7919-0.8509-2.12360.78140.13040.930.5178-0.13290.0340.65720.00070.5718-18.5207-23.2401-9.4032
22.2055-3.4806-0.10585.94893.18869.74270.28060.192-0.68470.0158-0.10710.45570.9406-0.9298-0.19820.2415-0.020.00960.39470.01880.5446-19.3166-25.8332-3.9125
32.54141.35120.33327.37-2.53896.59070.16030.0368-0.159-0.0177-0.09990.3035-0.1622-0.3501-0.05630.20160.02440.0250.3537-0.0590.3025-18.2198-18.7314-3.4546
45.72432.05580.27917.35821.29995.20851.6733-2.90480.29212.1959-1.48821.5121.9161-1.74910.01690.756-0.17820.04291.28090.25460.838-11.8041-26.736512.9617
53.5203-1.09971.82765.44541.93816.8485-0.1542-0.30150.16580.3240.4142-0.7392-0.57830.6309-0.27570.3347-0.03030.02790.43190.00460.383-3.2181-13.27158.3286
67.9435-2.2734-1.42734.8575-0.35034.0449-0.32710.61360.5919-0.8112-0.34-1.3032-2.37131.0701-0.9981.403-0.6553-0.00731.3895-0.08750.88475.39625.747310.9589
72.6965-1.1668-2.74690.54610.86026.14450.6861-0.3092-0.3943-0.36010.50790.16891.89980.038-1.24111.9027-0.6016-0.08241.6242-0.18811.05654.80868.590823.5847
82.12463.5857-2.22961.0788-0.52580.5480.78220.53080.9440.37810.0251-0.6764-0.58950.8067-0.32220.5016-0.05060.03890.6716-0.12860.5082-3.4418-0.68594.9192
99.18040.3457-0.25367.81841.1965.90610.1504-0.98530.52931.5228-0.2499-0.4425-1.04630.6006-0.12630.7826-0.0614-0.01140.6627-0.12670.4404-4.863-5.292617.9778
109.2698-2.10451.86472.16430.51042.05530.6815-0.74120.26940.5331-0.73020.312-1.9295-0.28120.0820.9719-0.20920.08440.9034-0.21760.5884-5.92421.585518.4712
118.0618-5.46431.45159.24791.01212.7948-0.21771.69431.3351-0.8982-0.45180.3996-1.5637-0.38430.5011.32860.1364-0.03450.73290.38820.875-11.820910.9606-23.3172
122.84450.7038-0.66915.3699-4.68014.05070.87180.4785-0.655-1.8578-1.74062.47192.4543-0.31660.7572.52940.53860.46880.82250.1691.8484-16.736423.3933-16.9762
136.1957-1.12133.40862.1068-8.03952.17910.1414-0.10770.7729-0.21190.17890.4118-2.1598-0.5793-0.40061.25330.08480.24560.5660.00710.8412-13.444211.1387-11.3807
146.5338-6.1828-3.89486.05222.98252.14220.53110.4032.4409-1.07061.0428-1.24710.6986-0.9505-0.99021.457-0.0750.27450.83610.42641.0889-4.380820.6942-13.5861
155.38081.0482-0.69998.29184.08842.337-0.38280.6840.7099-0.35340.57470.3041-0.1896-0.6302-0.49731.909-0.06230.28921.00820.43831.4626-8.535622.5996-22.4471
167.3745-3.17944.60027.6244-1.98372.05630.10360.19420.5521-0.24130.23120.1523-1.8226-0.5162-0.81880.8488-0.07540.0480.375-0.01250.5436-5.94188.1909-11.2675
177.77642.23183.24970.65210.15395.1187-1.1293-0.96921.04541.32390.46751.1776-1.6762-1.32820.27650.87270.33770.28340.8316-0.1280.943-28.84651.44796.2669
182.08575.18-4.98185.32682.78859.27890.43680.49161.3716-1.0689-1.04831.4004-2.0859-0.0162-0.17370.74940.34620.02910.55560.01641.1105-26.19944.2677-2.5588
192.36192.0235-1.23512.7001-2.84213.160.03490.04590.70280.06110.41731.8198-0.6134-0.7354-0.15220.55540.23420.05120.74910.09691.0507-31.5143-4.1894-4.1275
203.0958-1.4931-1.94077.20912.8316.81080.93340.0681.8050.42940.04290.7175-0.7328-0.7529-0.91930.59760.15880.09740.73280.04810.8114-31.0788-4.19191.0572
212.15343.4552-5.78252.53271.94543.91971.1665-3.1994-1.4380.6288-1.7732-1.742-0.23351.8560.29780.6148-0.14860.05221.2580.21170.7037.5559-0.6227-4.9595
229.6008-0.3048-0.05092.87830.86177.11320.2726-0.25120.3049-0.0469-0.2992-1.1763-0.91861.5862-0.03280.6131-0.18120.09910.78130.11460.59436.5692-0.0893-11.8322
238.03223.73482.64268.21084.34971.9886-1.1262.50960.4458-1.04020.00380.64451.19932.9235-0.41220.82780.14470.16261.250.06720.727711.594-9.0473-26.662
249.6712-5.01311.97427.84895.77152.0289-0.34461.1565-0.0357-0.0610.4632-1.88412.46911.56650.35751.09550.43840.22131.05780.04040.8385.2944-17.6928-21.0058
257.72830.70840.38676.131.84668.4097-0.07370.78320.1204-0.15160.3767-0.2438-0.42130.8069-0.16330.46130.08850.11680.62740.1280.3127-3.0963-6.8138-17.4739
269.40662.97890.5575.54381.55436.9939-0.11951.074-0.0713-1.67270.1147-0.06780.23941.4424-0.22780.90060.14710.13820.68290.08910.4177-1.4189-11.5163-26.7313
272.10112.75344.8065.83290.05761.614-0.56361.3318-0.7866-1.20920.47950.63171.188-0.906-0.17531.3544-0.2174-0.26970.8807-0.11350.7446-17.1776-21.8716-28.0148
287.96830.143.00754.87490.76596.63470.67670.83480.6249-0.3992-0.66170.25091.38960.3986-0.19261.62580.0006-0.5411.24380.07451.1999-24.6211-15.7542-39.8797
292.01823.663-5.64760.8745-1.31012.14760.47451.5538-0.8951-0.45810.1851.02430.5492-1.8659-0.87981.0818-0.221-0.2521.14890.10760.7419-22.855-13.7652-19.3535
306.40254.4061-6.17248.2936-2.34537.0242-0.62651.17940.4015-0.77510.1244-0.05720.3147-0.19280.40880.75030.0634-0.06960.59210.09540.335-10.3261-7.6383-26.1106
310.5673-0.26662.346.2688-2.25529.7194-1.10522.6613-1.9273-1.29940.5366-0.2232.55120.46870.84011.4427-0.0331-0.01961.4689-0.38730.5301-12.906-16.3022-37.4411
327.4424-4.5387.63917.7653-8.73892.4030.1870.39650.5145-0.1933-0.9186-0.3678-0.57360.09481.00061.08360.0064-0.14150.7224-0.14120.5942-17.8719-8.6143-33.4293
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 12 )A-1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 23 )A13 - 23
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 64 )A24 - 64
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 86 )A65 - 86
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 139 )A87 - 139
6X-RAY DIFFRACTION6chain 'A' and (resid 140 through 146 )A140 - 146
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 156 )A147 - 156
8X-RAY DIFFRACTION8chain 'B' and (resid 277 through 285 )B277 - 285
9X-RAY DIFFRACTION9chain 'B' and (resid 286 through 306 )B286 - 306
10X-RAY DIFFRACTION10chain 'B' and (resid 307 through 322 )B307 - 322
11X-RAY DIFFRACTION11chain 'F' and (resid 0 through 17 )F0 - 17
12X-RAY DIFFRACTION12chain 'F' and (resid 18 through 22 )F18 - 22
13X-RAY DIFFRACTION13chain 'F' and (resid 23 through 44 )F23 - 44
14X-RAY DIFFRACTION14chain 'F' and (resid 45 through 56 )F45 - 56
15X-RAY DIFFRACTION15chain 'F' and (resid 57 through 65 )F57 - 65
16X-RAY DIFFRACTION16chain 'F' and (resid 66 through 74 )F66 - 74
17X-RAY DIFFRACTION17chain 'C' and (resid -1 through 22 )C-1 - 22
18X-RAY DIFFRACTION18chain 'C' and (resid 23 through 34 )C23 - 34
19X-RAY DIFFRACTION19chain 'C' and (resid 35 through 56 )C35 - 56
20X-RAY DIFFRACTION20chain 'C' and (resid 57 through 74 )C57 - 74
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 12 )D1 - 12
22X-RAY DIFFRACTION22chain 'D' and (resid 13 through 64 )D13 - 64
23X-RAY DIFFRACTION23chain 'D' and (resid 65 through 86 )D65 - 86
24X-RAY DIFFRACTION24chain 'D' and (resid 87 through 96 )D87 - 96
25X-RAY DIFFRACTION25chain 'D' and (resid 97 through 112 )D97 - 112
26X-RAY DIFFRACTION26chain 'D' and (resid 113 through 127 )D113 - 127
27X-RAY DIFFRACTION27chain 'D' and (resid 128 through 146 )D128 - 146
28X-RAY DIFFRACTION28chain 'D' and (resid 147 through 160 )D147 - 160
29X-RAY DIFFRACTION29chain 'E' and (resid 275 through 279 )E275 - 279
30X-RAY DIFFRACTION30chain 'E' and (resid 280 through 295 )E280 - 295
31X-RAY DIFFRACTION31chain 'E' and (resid 296 through 306 )E296 - 306
32X-RAY DIFFRACTION32chain 'E' and (resid 307 through 322 )E307 - 322

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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