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- PDB-6d6i: Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13 -

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基本情報

登録情報
データベース: PDB / ID: 6d6i
タイトルUbe2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13
要素
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-conjugating enzyme E2 variant 1
  • Ubv.V1.1
キーワードTRANSFERASE / Ubiquitin / Ubiquitin conjugating enzyme / Ubiquitin variant / Ube2V1
機能・相同性
機能・相同性情報


error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / ubiquitin conjugating enzyme binding / postreplication repair / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair ...error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / ubiquitin conjugating enzyme binding / postreplication repair / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / regulation of DNA repair / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / negative regulation of TORC1 signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / antiviral innate immune response / activated TAK1 mediates p38 MAPK activation / positive regulation of DNA repair / ubiquitin binding / double-strand break repair via homologous recombination / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / Nonhomologous End-Joining (NHEJ) / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / positive regulation of NF-kappaB transcription factor activity / G2/M DNA damage checkpoint / FCERI mediated NF-kB activation / Interleukin-1 signaling / Aggrephagy / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / T cell receptor signaling pathway / Processing of DNA double-strand break ends / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / : ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 1 / UBC protein
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: 2.551 Å
データ登録者Ceccarelli, D.F. / Garg, P. / Keszei, A. / Sidhu, S. / Sicheri, F.
資金援助 カナダ, 2件
組織認可番号国
Canadian Institutes of Health Research (CIHR)MOP-136956 カナダ
Canadian Institutes of Health Research (CIHR)MOP-126129 カナダ
引用ジャーナル: J.Mol.Biol. / 年: 2020
タイトル: Structural and Functional Analysis of Ubiquitin-based Inhibitors That Target the Backsides of E2 Enzymes.
著者: Garg, P. / Ceccarelli, D.F. / Keszei, A.F.A. / Kurinov, I. / Sicheri, F. / Sidhu, S.S.
履歴
登録2018年4月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年7月17日Provider: repository / タイプ: Initial release
改定 1.12019年11月6日Group: Data collection / Database references / カテゴリ: citation / citation_author
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
改定 1.22020年1月8日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32020年3月11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.title / _citation.year / _citation_author.name
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 / 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: Ubiquitin-conjugating enzyme E2 variant 1
B: Ubiquitin-conjugating enzyme E2 N
C: Ubv.V1.1
D: Ubiquitin-conjugating enzyme E2 variant 1
E: Ubiquitin-conjugating enzyme E2 N
F: Ubv.V1.1


分子量 (理論値)分子数
合計 (水以外)87,0836
ポリマ－87,0836
非ポリマー00
水00
1
A: Ubiquitin-conjugating enzyme E2 variant 1
B: Ubiquitin-conjugating enzyme E2 N
C: Ubv.V1.1


分子量 (理論値)分子数
合計 (水以外)43,5423
ポリマ－43,5423
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Ubiquitin-conjugating enzyme E2 variant 1
E: Ubiquitin-conjugating enzyme E2 N
F: Ubv.V1.1


分子量 (理論値)分子数
合計 (水以外)43,5423
ポリマ－43,5423
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)91.444, 91.444, 92.446
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 12 through 133 or (resid 134...
21(chain D and (resid 12 through 25 or (resid 26...
12(chain B and (resid 3 through 25 or (resid 26...
22(chain E and (resid 3 or (resid 4 and (name...
13(chain C and (resid 1 or (resid 2 and (name...
23(chain F and (resid 1 through 19 or (resid 20...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROASNASN(chain A and (resid 12 through 133 or (resid 134...AA12 - 1338 - 129
121METMETLEULEU(chain A and (resid 12 through 133 or (resid 134...AA134 - 136130 - 132
131PROPROASNASN(chain A and (resid 12 through 133 or (resid 134...AA12 - 1478 - 143
141PROPROASNASN(chain A and (resid 12 through 133 or (resid 134...AA12 - 1478 - 143
151PROPROASNASN(chain A and (resid 12 through 133 or (resid 134...AA12 - 1478 - 143
161PROPROASNASN(chain A and (resid 12 through 133 or (resid 134...AA12 - 1478 - 143
211PROPROGLNGLN(chain D and (resid 12 through 25 or (resid 26...DD12 - 258 - 21
221LYSLYSLYSLYS(chain D and (resid 12 through 25 or (resid 26...DD2622
231PROPROASNASN(chain D and (resid 12 through 25 or (resid 26...DD12 - 1478 - 143
241PROPROASNASN(chain D and (resid 12 through 25 or (resid 26...DD12 - 1478 - 143
251PROPROASNASN(chain D and (resid 12 through 25 or (resid 26...DD12 - 1478 - 143
261PROPROASNASN(chain D and (resid 12 through 25 or (resid 26...DD12 - 1478 - 143
112GLYGLYALAALA(chain B and (resid 3 through 25 or (resid 26...BB3 - 256 - 28
122GLUGLUGLUGLU(chain B and (resid 3 through 25 or (resid 26...BB2629
132GLYGLYASNASN(chain B and (resid 3 through 25 or (resid 26...BB3 - 1506 - 153
142GLYGLYASNASN(chain B and (resid 3 through 25 or (resid 26...BB3 - 1506 - 153
152GLYGLYASNASN(chain B and (resid 3 through 25 or (resid 26...BB3 - 1506 - 153
162GLYGLYASNASN(chain B and (resid 3 through 25 or (resid 26...BB3 - 1506 - 153
212GLYGLYGLYGLY(chain E and (resid 3 or (resid 4 and (name...EE36
222LEULEULEULEU(chain E and (resid 3 or (resid 4 and (name...EE47
232GLYGLYASNASN(chain E and (resid 3 or (resid 4 and (name...EE3 - 1506 - 153
242GLYGLYASNASN(chain E and (resid 3 or (resid 4 and (name...EE3 - 1506 - 153
252GLYGLYASNASN(chain E and (resid 3 or (resid 4 and (name...EE3 - 1506 - 153
262GLYGLYASNASN(chain E and (resid 3 or (resid 4 and (name...EE3 - 1506 - 153
113METMETMETMET(chain C and (resid 1 or (resid 2 and (name...CC113
123GLNGLNGLNGLN(chain C and (resid 1 or (resid 2 and (name...CC214
133METMETLEULEU(chain C and (resid 1 or (resid 2 and (name...CC1 - 7313 - 85
143METMETLEULEU(chain C and (resid 1 or (resid 2 and (name...CC1 - 7313 - 85
153METMETLEULEU(chain C and (resid 1 or (resid 2 and (name...CC1 - 7313 - 85
163METMETLEULEU(chain C and (resid 1 or (resid 2 and (name...CC1 - 7313 - 85
213METMETPROPRO(chain F and (resid 1 through 19 or (resid 20...FF1 - 1913 - 31
223SERSERSERSER(chain F and (resid 1 through 19 or (resid 20...FF2032
233METMETLEULEU(chain F and (resid 1 through 19 or (resid 20...FF1 - 7313 - 85
243METMETLEULEU(chain F and (resid 1 through 19 or (resid 20...FF1 - 7313 - 85
253METMETLEULEU(chain F and (resid 1 through 19 or (resid 20...FF1 - 7313 - 85

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質 Ubiquitin-conjugating enzyme E2 variant 1 / UEV-1 / CROC-1 / TRAF6-regulated IKK activator 1 beta Uev1A


分子量: 16138.480 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: UBE2V1, CROC1, UBE2V, UEV1, P/OKcl.19 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q13404
#2: タンパク質 Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


分子量: 17358.951 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: UBE2N, BLU / プラスミド: Pet28 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: タンパク質 Ubv.V1.1


分子量: 10044.318 Da / 分子数: 2 / Mutation: Q62H, K63W, H68L, V70W, L71W, R74L, G75I, G76A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: Uba52 / プラスミド: ProEx / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q96H31

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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: 2.77 Å3/Da / 溶媒含有率: 55.58 %
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: 8.5 / 詳細: 0.2M LiSO4, 25% PEG3350, 0.1 M Tris-HCl pH 8.5

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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: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2015年2月5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: 0.9792 Å / 相対比: 1
反射解像度: 2.55→50 Å / Num. obs: 28109 / % possible obs: 99.8 % / 冗長度: 5.1 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.032 / Rrim(I) all: 0.072 / Χ2: 0.913 / Net I/σ(I): 7.6 / Num. measured all: 143038
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.55-2.594.90.9513980.5720.4770.42499.9
2.59-2.6450.79614090.6660.3920.43799.80.889
2.64-2.695.10.66414120.7480.3270.48199.80.741
2.69-2.7550.56313770.8480.280.44599.80.63
2.75-2.814.60.40514040.8840.2080.46799.60.456
2.81-2.874.90.37914170.8930.1890.46199.90.424
2.87-2.945.30.29314230.9490.1390.49799.90.325
2.94-3.025.30.22314070.9660.1060.52499.70.247
3.02-3.115.30.19313980.9720.0930.54199.80.214
3.11-3.215.20.14113650.9860.0680.5699.90.157
3.21-3.335.10.11214450.990.0550.6481000.125
3.33-3.464.60.09613870.9910.050.73699.80.108
3.46-3.625.10.07214350.9950.0350.7751000.08
3.62-3.815.40.06214130.9960.030.87399.90.069
3.81-4.055.20.05813940.9970.0281.09799.90.064
4.05-4.365.10.05214150.9970.0251.22899.90.057
4.36-4.84.90.0513970.9970.0241.58799.40.056
4.8-5.495.40.05313860.9970.0251.71999.90.059
5.49-6.9250.05814110.9960.0292.06499.80.065
6.92-505.30.04914160.9980.0232.51399.40.054

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
HKL-2000716.1データ削減
HKL-2000716.1データスケーリング
PHASER2.8.1位相決定
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 5AIT

5ait


解像度: 2.551→45.722 Å / SU ML: 0.74 / 交差検証法: THROUGHOUT / σ(F): 1.99 / 位相誤差: 39.95 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2963 1423 5.07 %
Rwork0.2635 26649 -
obs0.2651 28072 99.73 %
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
原子変位パラメータBiso max: 327.28 Å2 / Biso mean: 114.7371 Å2 / Biso min: 42.11 Å2
精密化ステップサイクル: final / 解像度: 2.551→45.722 Å
タンパク質核酸リガンド溶媒全体
原子数5118 0 0 0 5118
残基数----697
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1300X-RAY DIFFRACTION5.429TORSIONAL
12D1300X-RAY DIFFRACTION5.429TORSIONAL
21B1139X-RAY DIFFRACTION5.429TORSIONAL
22E1139X-RAY DIFFRACTION5.429TORSIONAL
31C620X-RAY DIFFRACTION5.429TORSIONAL
32F620X-RAY DIFFRACTION5.429TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5506-2.64170.4781230.432326782801100
2.6417-2.74750.51531380.372326452783100
2.7475-2.87250.40211470.353926742821100
2.8725-3.02390.36021540.313726662820100
3.0239-3.21330.3531290.32726412770100
3.2133-3.46140.30641260.309627132839100
3.4614-3.80950.28281760.273426692845100
3.8095-4.36040.2881480.252326552803100
4.3604-5.49220.28981290.219226552784100
5.4922-45.72930.24861530.22572653280699
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)
13.5605-0.51130.35652.2850.31096.94350.56010.8905-0.4122-0.5494-0.42340.2785-0.0418-1.6619-0.13430.51790.1773-0.07180.72510.12850.9162-30.4221-38.872-17.0894
29.61451.66692.56097.75580.43899.43580.33120.2602-1.91390.8658-0.266-0.83271.626-1.3799-0.22440.7872-0.1553-0.08720.9730.23541.0695-29.7071-46.437-6.691
33.3616-1.55712.75213.31271.59626.88-0.16110.92710.1189-0.5326-0.0163-0.9778-0.18411.3631-0.34740.39640.04080.0340.88060.18860.8967-13.1274-34.8125-17.9866
44.9304-0.50941.19653.89671.09398.95690.2312-0.32220.38570.04210.0991-0.2527-0.48860.772-0.20050.35590.02660.03110.53030.02920.8743-18.2697-32.9633-7.1309
58.1969-2.54712.47863.8562-1.08087.9049-0.05650.16951.049-0.5711-0.42880.1912-2.63820.03620.09150.81480.0085-0.09280.55270.15881.0757-20.6193-23.2527-7.2167
64.73480.32031.15835.06191.95872.18150.31720.13190.2668-1.0579-0.26230.0955-1.7449-0.6292-0.04830.76290.17760.09490.64490.1730.9203-23.5178-27.4405-15.9574
76.3932-1.85780.29123.09981.06188.1881-0.52310.57070.49650.28810.4194-0.8602-0.88921.8181-0.35570.5003-0.18650.19561.1438-0.06141.3272-5.7783-31.9088-11.511
84.5999-0.3291.5253.02492.27462.42350.418-1.0841-0.59020.5981-0.34440.14960.8635-1.55010.51590.6116-0.08910.06272.68390.24450.9726-55.7075-37.0534-8.6549
94.1539-0.0392-1.81043.01591.95462.93420.54320.34860.23750.2668-0.5283-0.34731.2082-2.18770.0520.8533-0.798-0.10941.8320.09820.7404-45.4657-47.898-10.8789
103.5145-0.4596-1.39022.22281.32891.14270.47370.9226-0.05660.4993-1.17610.10880.3137-1.6262-0.11880.9577-0.678-0.0812.5377-0.14180.9955-52.781-48.4589-17.9952
114.83180.86211.5870.36310.9822.930.2828-0.2024-0.48140.5483-0.5830.15831.103-1.22020.27351.3984-0.311-0.6761.1751-0.80062.537-45.2357-62.6274-16.8808
121.3106-2.0744-2.9453.33034.66926.6175-0.22850.4406-0.77450.0402-0.007-0.13830.5042-1.31730.36541.8745-0.3678-0.1040.7950.05181.9643-37.833-68.0202-14.0852
134.87091.253-0.87821.812-1.17771.6430.2016-0.6605-0.56050.7073-0.4861-0.67890.9233-0.48430.03381.8595-1.1488-0.30721.87810.38161.1231-41.5861-61.8123-1.1197
143.8531-1.68651.80592.8986-1.7212.29950.46960.7485-0.1838-0.8737-0.17630.53950.6168-0.46640.00070.82960.6119-0.1171.4192-0.04450.6488-22.8292-45.0636-32.1094
157.09640.6689-0.94875.9714-0.03322.3547-0.36350.5033-1.30120.0039-0.0221-0.48110.7255-0.29040.28441.9762-0.1469-0.84880.7621-0.22792.1598-22.4232-59.4274-26.9648
168.5354-0.88580.30473.75693.8644.16350.27581.9224-0.6628-1.0587-0.4938-0.28610.48040.6553-0.19790.74340.4008-0.12610.9264-0.32191.3879-14.6138-53.1065-32.8326
170.0078-0.1364-0.01661.22860.0780.0020.42840.82950.2669-0.3604-0.1281-0.34150.02930.47320.13760.16251.9385-0.08161.9477-0.18370.7571-10.1018-47.5668-28.0357
185.35973.24271.48062.12371.15780.83760.83160.2811-1.547-0.1463-0.4963-0.22191.71360.7929-0.43561.0750.39710.02150.80460.1441.0246-17.3403-50.9047-18.9381
199.40441.4219-1.6034.34633.95844.53650.36060.5801-2.51950.7243-0.6612-0.47241.7369-0.5436-0.10091.09370.0395-0.10340.80890.02551.4597-26.008-53.7158-21.4211
204.426-2.64333.95912.8786-2.073.61050.54841.6895-0.1941-0.5851-0.5471-0.60530.16040.9001-0.46860.63070.42490.01761.00510.11420.8424-14.1664-42.359-26.5185
214.6432-1.0483-1.40542.9743-0.0364.7559-0.3366-1.303-0.8960.32610.1604-0.05251.56281.2240.24340.75390.2899-0.24220.7432-0.01631.0994-17.067-49.604715.496
221.2752-0.2544-1.51153.5610.34635.8516-0.2033-0.85140.15690.71620.5049-0.13490.93740.2082-0.20550.40370.0278-0.06110.7612-0.11550.8928-21.1145-39.117620.9909
238.16380.10441.26711.9742-1.37199.7578-0.3670.1449-0.2121-0.35020.64331.51281.6516-0.736-0.13331.00160.0507-0.31290.6289-0.02751.0437-25.2891-48.9086.9436
245.3324-0.8717-0.56494.5521-0.89068.74010.0277-0.75541.05790.7912-0.2470.2253-1.4472-0.5149-0.3790.75130.1961-0.16480.6548-0.10070.8588-23.5362-28.734118.213
254.8968-0.833-1.06264.6758-0.36968.79730.399-0.17910.0478-0.70870.15060.1037-0.46660.0322-0.21210.43970.119-0.02280.4099-0.00670.7967-19.3911-35.06728.0246
262.7098-1.6167-3.2084.7244-2.29548.6151-0.1003-0.33531.46680.2612-0.1918-0.7297-1.61050.7896-0.73740.68530.006-0.2140.4078-0.08261.0923-14.5976-26.83236.4568
273.7006-0.778-1.84514.7048-2.46573.15570.345-1.1038-0.46180.2167-0.2128-0.5731-0.21781.5662-0.08830.39270.0117-0.17210.877-0.18640.872-12.053-34.130316.2419
285.2261-2.4967-1.26074.8024-0.47118.62090.39450.60990.44151.04870.4385-0.13-1.66750.2584-0.45641.0860.17740.24260.5696-0.06291.1797-25.1001-21.003311.8634
291.21491.2675-1.13421.8002-1.85571.854-0.53940.3741-0.4123-0.94120.263-0.32552.26610.76960.46042.2250.90670.00071.2252-0.03441.015-4.331-66.96338.999
302.38850.598-0.79862.618-2.00482.1253-1.71350.34780.2794-1.35370.82170.44861.6803-0.4488-0.0362.3494-0.2151-0.11060.7181-0.11141.0984-19.9579-67.63875.2132
313.4695-1.8563-0.47263.1188-0.5913.497-0.0682-0.8521-0.1931-0.25220.61440.17021.9280.35520.68692.29630.368-0.23910.46260.11450.8894-18.5694-61.381813.6803
326.9615-2.3631-2.00682.8402-0.67982.6883-1.1286-0.9644-0.0637-0.01210.95210.44022.06920.35030.36932.65390.40510.19980.76690.08581.0741-15.728-69.719118.5726
331.7728-0.8742-0.97932.25322.5382.8777-0.1434-0.1819-1.1319-0.58750.39360.46782.6293-0.98030.01811.5855-0.7887-0.03831.54160.62611.4321-36.288-67.834915.9801
341.5706-1.3491.17543.6796-0.44263.2481-0.66350.81130.0656-0.95480.93221.68051.5983-1.0884-0.39392.7935-0.4758-0.34581.12690.13281.1713-32.6356-67.10121.3628
355.9059-1.91070.14621.7130.47920.8361-0.2146-1.1647-0.51910.45590.00810.43250.487-0.1237-0.28180.47970.52260.03241.71570.2240.7997-27.6069-42.230732.4022
361.5339-2.37181.28544.1376-1.33691.9934-1.217-0.9246-0.20690.28911.01622.05840.5552-1.75650.1580.8822-0.4314-0.28051.0060.04161.5689-40.5305-49.519827.0866
373.7415-1.5291-0.4471.80971.44351.5953-0.2598-0.71080.27840.47720.140.4353-0.0673-0.67270.12640.34390.78020.44881.31450.43571.6759-38.9572-39.37632.9964
382.26870.1642-1.06550.0121-0.06610.5029-0.278-0.86570.69080.91840.74970.3488-0.8065-0.8264-0.27550.9020.79030.14951.98740.20130.8902-35.817-32.671928.2708
390.58840.15640.25743.973-2.57041.9247-0.3836-0.6043-0.5984-0.13271.20911.82820.1056-1.93-0.32590.54310.0212-0.08081.35120.05831.2058-35.1102-40.606119.3433
405.07891.0438-2.86622.00051.60457.2676-1.0744-0.6408-0.54940.79081.07261.98421.1152-0.7626-0.24420.64650.148-0.14481.12770.11761.2045-31.333-42.362124.4249
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 37 )A12 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 46 )A38 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 63 )A47 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 99 )A64 - 99
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 109 )A100 - 109
6X-RAY DIFFRACTION6chain 'A' and (resid 110 through 129 )A110 - 129
7X-RAY DIFFRACTION7chain 'A' and (resid 130 through 147 )A130 - 147
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 38 )B3 - 38
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 86 )B39 - 86
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 113 )B87 - 113
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 124 )B114 - 124
12X-RAY DIFFRACTION12chain 'B' and (resid 125 through 132 )B125 - 132
13X-RAY DIFFRACTION13chain 'B' and (resid 133 through 150 )B133 - 150
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 16 )C1 - 16
15X-RAY DIFFRACTION15chain 'C' and (resid 17 through 22 )C17 - 22
16X-RAY DIFFRACTION16chain 'C' and (resid 23 through 34 )C23 - 34
17X-RAY DIFFRACTION17chain 'C' and (resid 35 through 44 )C35 - 44
18X-RAY DIFFRACTION18chain 'C' and (resid 45 through 55 )C45 - 55
19X-RAY DIFFRACTION19chain 'C' and (resid 56 through 65 )C56 - 65
20X-RAY DIFFRACTION20chain 'C' and (resid 66 through 73 )C66 - 73
21X-RAY DIFFRACTION21chain 'D' and (resid 12 through 26 )D12 - 26
22X-RAY DIFFRACTION22chain 'D' and (resid 27 through 37 )D27 - 37
23X-RAY DIFFRACTION23chain 'D' and (resid 38 through 46 )D38 - 46
24X-RAY DIFFRACTION24chain 'D' and (resid 47 through 63 )D47 - 63
25X-RAY DIFFRACTION25chain 'D' and (resid 64 through 89 )D64 - 89
26X-RAY DIFFRACTION26chain 'D' and (resid 90 through 109 )D90 - 109
27X-RAY DIFFRACTION27chain 'D' and (resid 110 through 129 )D110 - 129
28X-RAY DIFFRACTION28chain 'D' and (resid 130 through 147 )D130 - 147
29X-RAY DIFFRACTION29chain 'E' and (resid 3 through 39 )E3 - 39
30X-RAY DIFFRACTION30chain 'E' and (resid 44 through 57 )E44 - 57
31X-RAY DIFFRACTION31chain 'E' and (resid 58 through 86 )E58 - 86
32X-RAY DIFFRACTION32chain 'E' and (resid 87 through 113 )E87 - 113
33X-RAY DIFFRACTION33chain 'E' and (resid 114 through 132 )E114 - 132
34X-RAY DIFFRACTION34chain 'E' and (resid 133 through 150 )E133 - 150
35X-RAY DIFFRACTION35chain 'F' and (resid 1 through 16 )F1 - 16
36X-RAY DIFFRACTION36chain 'F' and (resid 17 through 22 )F17 - 22
37X-RAY DIFFRACTION37chain 'F' and (resid 23 through 34 )F23 - 34
38X-RAY DIFFRACTION38chain 'F' and (resid 35 through 44 )F35 - 44
39X-RAY DIFFRACTION39chain 'F' and (resid 45 through 55 )F45 - 55
40X-RAY DIFFRACTION40chain 'F' and (resid 56 through 73 )F56 - 73

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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