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- PDB-6fol: Domain II of the human copper chaperone in complex with human Cu,... -

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基本情報

登録情報
データベース: PDB / ID: 6fol
タイトルDomain II of the human copper chaperone in complex with human Cu,Zn superoxide dismutase
要素
  • Copper chaperone for superoxide dismutase
  • Superoxide dismutase [Cu-Zn]
キーワードMETAL BINDING PROTEIN / heterodimer / copper-chaperone / hSOD1 / protein maturation
機能・相同性
機能・相同性情報


superoxide dismutase copper chaperone activity / action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus ...superoxide dismutase copper chaperone activity / action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / protein-disulfide reductase activity / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / protein maturation / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cellular response to oxidative stress / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / cadherin binding / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
類似検索 - ドメイン・相同性
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Copper chaperone for superoxide dismutase / Superoxide dismutase [Cu-Zn]
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: 2.55 Å
データ登録者Sala, F.A. / Wright, G.S.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
資金援助 英国, ブラジル, 5件
組織認可番号国
Motor Neurone Disease AssociationHasnain/Apr15/833-791 英国
Medical Research Council (United Kingdom)MRF-060-0002-RG-HASNA 英国
Sao Paulo Research Fundation2015/00062-1 ブラジル
Sao Paulo Research Fundation2016/24686-7 ブラジル
National Council for Scientific and Technological Development407438/2013-0 ブラジル
引用ジャーナル: Plos Biol. / 年: 2019
タイトル: Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS.
著者: Sala, F.A. / Wright, G.S.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
履歴
登録2018年2月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年1月30日Provider: repository / タイプ: Initial release
改定 1.12019年6月19日Group: Data collection / Database references
カテゴリ: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22024年1月17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
改定 1.32024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Copper chaperone for superoxide dismutase
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Copper chaperone for superoxide dismutase
E: Copper chaperone for superoxide dismutase
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Copper chaperone for superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)127,67619
ポリマ－126,3208
非ポリマー1,35611
水4,864270
1
A: Copper chaperone for superoxide dismutase
B: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,7114
ポリマ－31,5802
非ポリマー1312
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-8 kcal/mol
Surface area14080 Å2
手法PISA
2
C: Superoxide dismutase [Cu-Zn]
D: Copper chaperone for superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,4526
ポリマ－31,5802
非ポリマー8724
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area13970 Å2
手法PISA
3
E: Copper chaperone for superoxide dismutase
F: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,8035
ポリマ－31,5802
非ポリマー2233
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area13910 Å2
手法PISA
4
G: Superoxide dismutase [Cu-Zn]
H: Copper chaperone for superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,7114
ポリマ－31,5802
非ポリマー1312
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-9 kcal/mol
Surface area13930 Å2
手法PISA
単位格子
Length a, b, c (Å)244.689, 244.689, 182.332
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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要素

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タンパク質 , 2種, 8分子 ADEHBCFG

#1: タンパク質
Copper chaperone for superoxide dismutase / Superoxide dismutase copper chaperone


分子量: 15816.517 Da / 分子数: 4 / 変異: Truncation of Domains: I and III / 由来タイプ: 組換発現
詳細: hCCS Domain II with additional residues (GA) from HISTAG
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CCS / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: O14618
#2: タンパク質
Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


分子量: 15763.432 Da / 分子数: 4 / 変異: C57A; C146A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SOD1 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P00441, superoxide dismutase

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非ポリマー , 4種, 281分子

#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn
#4: 化合物 ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / オクタエチレングリコ-ル


分子量: 370.436 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C16H34O9
#5: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H8O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 270 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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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: 4.15 Å3/Da / 溶媒含有率: 70.38 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 25% (w/v) PEG 1500 and 0.1 M PCTP buffer pH 7.0 (sodium propionate, sodium cacodylate, and BIS-TRIS propane in the molar ratios 2:1:2, respectively)

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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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.97857 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年9月26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: 0.97857 Å / 相対比: 1
反射解像度: 2.55→49.4 Å / Num. obs: 64704 / % possible obs: 95.7 % / 冗長度: 6.8 % / Biso Wilson estimate: 39.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.053 / Rrim(I) all: 0.14 / Net I/σ(I): 9.5
反射 シェル解像度: 2.55→2.69 Å / 冗長度: 6.7 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2 / Num. unique obs: 9558 / CC1/2: 0.409 / Rpim(I) all: 0.335 / Rrim(I) all: 0.877 / % possible all: 97.2

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)精密化
iMOSFLMデータ削減
SCALAデータスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1DO5, 2C9V

1do5

2c9v


解像度: 2.55→46.974 Å / SU ML: 0.4 / 交差検証法: THROUGHOUT / σ(F): 1.38 / 位相誤差: 27.37 / 詳細: TLS and NCS were used
Rfactor反射数%反射
Rfree0.2482 3136 4.85 %
Rwork0.208 --
obs0.2099 64691 95.26 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.55→46.974 Å
タンパク質核酸リガンド溶媒全体
原子数8841 0 64 270 9175
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0039136
X-RAY DIFFRACTIONf_angle_d0.47412338
X-RAY DIFFRACTIONf_dihedral_angle_d7.9585380
X-RAY DIFFRACTIONf_chiral_restr0.0481327
X-RAY DIFFRACTIONf_plane_restr0.0031699
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.58990.39451520.34622826X-RAY DIFFRACTION97
2.5899-2.63240.38291570.34572819X-RAY DIFFRACTION97
2.6324-2.67780.37771400.32812820X-RAY DIFFRACTION97
2.6778-2.72640.33131300.32162829X-RAY DIFFRACTION97
2.7264-2.77890.36931560.3112816X-RAY DIFFRACTION97
2.7789-2.83560.27031510.30012815X-RAY DIFFRACTION97
2.8356-2.89720.31971510.30132815X-RAY DIFFRACTION96
2.8972-2.96460.28981440.28762830X-RAY DIFFRACTION97
2.9646-3.03880.32771410.28172763X-RAY DIFFRACTION95
3.0388-3.12090.29871320.26232798X-RAY DIFFRACTION95
3.1209-3.21270.29511500.24072825X-RAY DIFFRACTION96
3.2127-3.31640.27291310.23152797X-RAY DIFFRACTION96
3.3164-3.43490.26291250.22232806X-RAY DIFFRACTION96
3.4349-3.57240.25791290.21622824X-RAY DIFFRACTION96
3.5724-3.73490.22041680.19922763X-RAY DIFFRACTION95
3.7349-3.93170.22551360.18272772X-RAY DIFFRACTION94
3.9317-4.17790.20461450.16032769X-RAY DIFFRACTION94
4.1779-4.50020.22241180.14362800X-RAY DIFFRACTION94
4.5002-4.95270.19851450.14152787X-RAY DIFFRACTION94
4.9527-5.66830.18981560.15922743X-RAY DIFFRACTION93
5.6683-7.13740.20531530.17292748X-RAY DIFFRACTION93
7.1374-46.98170.18341260.1492790X-RAY DIFFRACTION91
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)
11.33331.58950.2535.5799-4.78037.6508-0.2703-0.0474-0.26050.2999-0.3581-0.3105-0.0945-0.44880.60140.5162-0.0811-0.2210.38120.0680.6362-61.659216.0268-43.6382
22.4805-0.3119-1.39783.9461.08238.56030.1650.20640.2886-0.20940.12140.5094-0.3054-0.2277-0.3190.4367-0.0605-0.13280.37270.01030.6092-63.849910.3657-45.3397
31.0782-0.10920.57334.9005-0.09391.4996-0.04560.13010.1569-0.1204-0.0427-0.3035-0.09950.00480.0820.4013-0.0918-0.0690.37440.08230.539-55.4632.9619-46.0998
41.66580.4193-1.99053.2237-3.63596.78840.00450.4828-0.0918-0.6818-0.254-0.18250.75680.46590.17430.4979-0.0987-0.11660.37390.10390.7613-44.773423.6306-49.1794
51.3949-0.1121-0.46692.8251-0.16193.80740.1163-0.00910.0747-0.1611-0.03010.4273-0.376-0.1039-0.09910.5439-0.1502-0.070.39310.08210.7404-50.022832.2172-44.7356
67.12141.3562-6.12598.7592-1.24235.58240.1162-0.64251.11710.46870.25111.1602-0.6911.001-0.20740.5509-0.0618-0.12640.52430.01150.8653-50.237939.4462-38.448
72.57190.7872-1.01542.6319-1.57453.8087-0.02980.22640.2153-0.21850.08280.365-0.4504-0.0992-0.04530.5688-0.1137-0.12990.39560.06020.6605-48.572333.9962-46.9561
83.2964-1.0836-1.64731.0781-0.18245.1954-0.2856-0.1850.0790.00450.2966-0.01291.03840.6533-0.11190.576-0.1267-0.10770.36320.07990.5078-57.4786-6.7812-12.7544
92.0696-0.63560.81230.3585-0.72613.39480.1871-0.2773-0.3645-0.1030.17-0.08871.0795-0.8798-0.39630.6614-0.2677-0.17010.43040.09280.7233-64.3078-11.5382-16.0588
101.9443-0.778-2.86295.69391.19624.61780.2432-0.4137-0.63950.17090.09460.15140.0726-0.6968-0.33880.4899-0.1374-0.07070.67840.19390.7107-72.38132.0849-14.4477
115.5374-0.5135-6.34492.6592-0.0287.41890.688-0.31830.26590.0667-0.47722.11090.8736-1.2178-0.23810.6082-0.2702-0.15670.7150.07050.7399-76.755-6.3149-19.0401
124.0822.025-0.88272.4168-1.7434.19020.1814-0.286-0.20040.09010.22170.23150.5935-1.1229-0.38610.5641-0.2212-0.18310.6440.12080.6685-69.1519-8.8278-13.6405
132.7758-0.93453.24982.2046-1.4073.55490.0149-0.8476-0.28620.26250.18680.07060.0492-1.4754-0.19650.5296-0.1904-0.09830.71560.06490.4744-68.0633-2.9611-10.2829
143.70114.11360.99417.65812.89783.58130.8499-0.3129-0.2090.2215-0.0394-0.38830.74330.6005-1.03760.5331-0.1473-0.00620.5386-0.01750.4706-54.318410.2525-11.1258
152.17540.4701-0.06523.6979-1.21813.59070.0298-0.06040.26640.5426-0.00130.0983-0.52120.42480.0590.5417-0.1403-0.09230.4666-0.02390.591-50.294416.3095-13.6896
166.86590.6061-5.08257.1243-1.81194.127-0.3757-0.25470.3629-0.31380.4732-0.23610.80060.5525-0.21040.6489-0.1375-0.05510.40550.01320.7347-47.34-1.5284-15.6166
174.76452.0524-1.56757.2824-2.9537.8082-0.1005-0.41190.4155-0.1846-0.00990.1017-0.03410.54530.1720.4314-0.0605-0.08810.4660.03530.6482-41.826911.4217-25.2624
183.46910.8613-0.35632.774-0.51044.5169-0.0507-0.19890.08880.2767-0.0284-0.2377-0.23650.55130.06970.4985-0.1329-0.13140.4380.02140.6248-44.129113.282-16.7452
194.24091.68042.50592.4758-2.44148.1086-0.136-0.85130.42070.0546-0.06160.8274-0.6955-1.23250.030.33310.0074-0.05280.43680.11350.9091-18.133164.6181-42.8079
205.312-0.1762-1.87812.48251.1442.67980.0047-0.06610.7723-0.32040.10.333-0.13140.4546-0.12080.4132-0.0818-0.04350.38610.18550.7142-22.738561.1815-47.3538
219.8190.19794.99940.9179-0.71893.62240.20171.4323-0.3731-0.43860.34340.7071.03820.5781-0.28450.5679-0.2235-0.19280.44750.15180.5052-27.797152.0627-53.9623
223.38411.8507-0.53213.3773.75377.7303-0.73220.8549-1.3269-0.51110.94970.90071.6345-0.2675-0.0960.6563-0.1184-0.02780.57940.00760.9018-13.365945.3605-49.2978
234.60151.04590.64720.66540.23921.6916-0.0774-0.14750.0259-0.11370.05470.20320.3082-0.21050.02490.4502-0.0832-0.04060.37060.14080.6578-28.78848.8348-41.4695
243.62131.57770.25791.7462-0.23681.6508-0.2030.02350.5253-0.21530.08550.4092-0.0665-0.09930.11680.4346-0.0588-0.06250.37370.12090.6311-27.711352.8794-46.0926
254.5205-0.42560.9055-0.0276-0.87837.4432-0.28880.4938-0.1182-0.8170.3766-0.24910.44570.1726-0.10550.3503-0.0375-0.05640.30690.13680.6377-21.151148.883-49.5817
266.52075.2926-5.33138.501-5.90395.39-0.36410.29160.0856-0.41060.32010.0930.5518-0.67750.1430.451-0.01660.01150.3283-0.07690.5445-2.700450.4135-49.7585
275.4390.9479-4.96513.5741-2.46667.3895-0.1563-0.5442-0.59350.07490.064-0.17291.25860.61860.0920.38050.064-0.05710.34140.05110.65622.397547.3834-39.7589
289.27191.0159-3.49065.0618-1.19662.3267-0.43440.3628-0.4028-0.2859-0.0014-0.77470.18010.39120.50190.3378-0.00370.02050.3411-0.02930.38537.639457.417-52.6584
294.62510.61831.60552.2895-1.83462.3176-0.14640.26580.8981-0.7270.42561.1756-0.4134-1.3399-0.35240.5096-0.0402-0.11610.55120.11240.7479-5.065766.2136-46.1673
309.7169-4.1932-2.04912.8046-0.0886.2191-0.1619-1.28-0.38060.6247-0.1268-0.8539-0.24840.62090.19880.2747-0.01220.05480.5121-0.01680.34498.391565.2908-36.7542
314.36350.7848-1.44672.93020.40973.4658-0.0348-0.1156-0.0095-0.03490.0532-0.09670.21170.2732-0.02640.34260.0234-0.03810.32460.00360.42156.673557.8067-44.2614
329.51170.40880.89133.8273-0.32576.2112-0.01160.22580.653-0.1917-0.05640.7053-0.7073-0.3675-0.17010.3904-0.0620.04210.36150.05220.43949.235470.3032-48.2133
334.62942.7936-1.51443.3521-1.46065.22870.07340.05860.3097-0.58020.03080.6910.70620.0209-0.22850.3726-0.0069-0.06320.37030.02850.5156-5.352153.6882-48.0417
344.7720.3952-3.12674.9972-3.40553.8168-0.0504-0.7746-0.54660.647-0.28190.1525-0.0885-0.56430.20380.5978-0.18680.04960.82980.06050.591-37.195749.9854-14.2007
353.51510.418-3.92353.4173-3.81988.44690.0653-0.14360.00750.24310.08160.77890.1935-0.9536-0.30550.4686-0.2280.05730.8080.03480.8273-42.483851.2087-23.182
368.9321-2.34340.11023.74770.76365.1285-0.86050.8757-1.09990.3160.56320.2165-0.4183-0.46870.24230.689-0.0160.1570.6453-0.01520.6559-38.418560.2597-9.5354
373.89390.84161.93277.85984.48928.79280.06470.09130.61380.0004-0.1304-0.0094-0.753-0.17410.00880.6082-0.05070.09730.6277-0.01690.8549-38.341468.6482-18.081
387.41852.40621.30847.61152.47564.5482-0.0871-0.7051.1331-0.2047-0.7419-0.0846-0.3404-1.15460.75750.5758-0.05020.08820.7545-0.02130.7933-44.090767.3803-21.3929
392.8251-2.4468-2.80692.07821.42248.02770.0548-0.0193-0.2710.40350.15750.4979-0.075-0.5543-0.22890.5064-0.13290.1230.7935-0.00390.8872-42.803657.6634-15.6561
402.6235-4.1625-0.13157.1328-1.28854.161-0.287-0.80120.91320.86090.4709-0.4357-1.4061-0.6622-0.32181.02230.06880.27050.8380.01140.8072-45.261672.8149-10.3605
411.9975-4.4425-1.99379.96676.20088.811-0.5069-0.03430.01520.72930.62850.89320.530.4887-0.00310.6073-0.1650.10870.7180.0280.5736-33.53152.6461-14.0522
429.1003-7.00095.56998.9028-4.92693.4560.2936-0.3651-0.72330.20670.51540.6192-0.04690.2083-0.77610.5657-0.14210.00430.9048-0.06850.6035-20.063153.884-11.3897
431.7753-1.4385-1.37492.6583-1.2767.00640.314-1.1406-0.13760.3349-0.036-0.0912-0.4260.6716-0.28150.5191-0.2462-0.05531.2423-0.03440.6201-12.631152.2787-13.2712
441.5324-0.8813-1.32641.65850.75713.56660.0327-0.9802-0.44970.3495-0.02980.06280.37330.26560.02980.6332-0.1652-0.08691.07170.20360.6589-14.603344.6073-17.7411
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 85 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 232 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 22 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 75 )
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 85 )
7X-RAY DIFFRACTION7chain 'B' and (resid 86 through 153 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 21 )
9X-RAY DIFFRACTION9chain 'C' and (resid 22 through 47 )
10X-RAY DIFFRACTION10chain 'C' and (resid 48 through 75 )
11X-RAY DIFFRACTION11chain 'C' and (resid 76 through 85 )
12X-RAY DIFFRACTION12chain 'C' and (resid 86 through 132 )
13X-RAY DIFFRACTION13chain 'C' and (resid 133 through 153 )
14X-RAY DIFFRACTION14chain 'D' and (resid 85 through 99 )
15X-RAY DIFFRACTION15chain 'D' and (resid 100 through 132 )
16X-RAY DIFFRACTION16chain 'D' and (resid 133 through 142 )
17X-RAY DIFFRACTION17chain 'D' and (resid 143 through 162 )
18X-RAY DIFFRACTION18chain 'D' and (resid 163 through 232 )
19X-RAY DIFFRACTION19chain 'E' and (resid 83 through 93 )
20X-RAY DIFFRACTION20chain 'E' and (resid 94 through 120 )
21X-RAY DIFFRACTION21chain 'E' and (resid 121 through 132 )
22X-RAY DIFFRACTION22chain 'E' and (resid 133 through 142 )
23X-RAY DIFFRACTION23chain 'E' and (resid 143 through 173 )
24X-RAY DIFFRACTION24chain 'E' and (resid 174 through 216 )
25X-RAY DIFFRACTION25chain 'E' and (resid 217 through 232 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 21 )
27X-RAY DIFFRACTION27chain 'F' and (resid 22 through 36 )
28X-RAY DIFFRACTION28chain 'F' and (resid 37 through 48 )
29X-RAY DIFFRACTION29chain 'F' and (resid 49 through 65 )
30X-RAY DIFFRACTION30chain 'F' and (resid 66 through 75 )
31X-RAY DIFFRACTION31chain 'F' and (resid 76 through 131 )
32X-RAY DIFFRACTION32chain 'F' and (resid 132 through 142 )
33X-RAY DIFFRACTION33chain 'F' and (resid 143 through 153 )
34X-RAY DIFFRACTION34chain 'G' and (resid 1 through 22 )
35X-RAY DIFFRACTION35chain 'G' and (resid 23 through 36 )
36X-RAY DIFFRACTION36chain 'G' and (resid 37 through 56 )
37X-RAY DIFFRACTION37chain 'G' and (resid 57 through 75 )
38X-RAY DIFFRACTION38chain 'G' and (resid 76 through 85 )
39X-RAY DIFFRACTION39chain 'G' and (resid 86 through 125 )
40X-RAY DIFFRACTION40chain 'G' and (resid 126 through 142 )
41X-RAY DIFFRACTION41chain 'G' and (resid 143 through 153 )
42X-RAY DIFFRACTION42chain 'H' and (resid 85 through 99 )
43X-RAY DIFFRACTION43chain 'H' and (resid 100 through 132 )
44X-RAY DIFFRACTION44chain 'H' and (resid 133 through 232 )

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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