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- PDB-8gi4: Crystal structure of human LIMK2 PDZ domain -

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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: 8gi4
タイトルCrystal structure of human LIMK2 PDZ domain
要素LIM domain kinase 2
キーワードSIGNALING PROTEIN / PDZ domain / protein kinase / autoregulation / cofilin
機能・相同性
機能・相同性情報


cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / phosphorylation / EPHB-mediated forward signaling ...cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / phosphorylation / EPHB-mediated forward signaling / mitotic spindle / positive regulation of protein localization to nucleus / actin cytoskeleton organization / spermatogenesis / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / positive regulation of protein phosphorylation / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
類似検索 - 分子機能
: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
LIM domain kinase 2
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: 2.06 Å
データ登録者Casanova Sepulveda, G. / Boggon, T.J.
資金援助 米国, 3件
組織認可番号国
American Heart Association835293 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102262 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138411 米国
引用ジャーナル: Nat Commun / 年: 2023
タイトル: Autoregulation of the LIM kinases by their PDZ domain.
著者: Casanova-Sepulveda, G. / Sexton, J.A. / Turk, B.E. / Boggon, T.J.
履歴
登録2023年3月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年12月6日Provider: repository / タイプ: Initial release
改定 1.12023年12月27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.pdbx_database_id_DOI / _citation_author.identifier_ORCID
改定 1.22024年5月1日Group: Database references / カテゴリ: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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: LIM domain kinase 2
B: LIM domain kinase 2
C: LIM domain kinase 2
D: LIM domain kinase 2
E: LIM domain kinase 2
F: LIM domain kinase 2
G: LIM domain kinase 2
H: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)109,8348
ポリマ－109,8348
非ポリマー00
水4,125229
1
A: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)13,7291
ポリマ－13,7291
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)13,7291
ポリマ－13,7291
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)13,7291
ポリマ－13,7291
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)13,7291
ポリマ－13,7291
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)13,7291
ポリマ－13,7291
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)13,7291
ポリマ－13,7291
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)13,7291
ポリマ－13,7291
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: LIM domain kinase 2


分子量 (理論値)分子数
合計 (水以外)13,7291
ポリマ－13,7291
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)80.950, 83.028, 83.080
Angle α, β, γ (deg.)90.00, 96.58, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
LIM domain kinase 2 / LIMK-2


分子量: 13729.308 Da / 分子数: 8 / 断片: PDZ domain (UNP residues 130-250) / 変異: C173S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LIMK2 / プラスミド: pET / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P53671, non-specific serine/threonine protein kinase
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 229 / 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: 2.57 Å3/Da / 溶媒含有率: 52.2 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 / 詳細: 0.1 M HEPES, pH 7.5, 10% 2-propanol, 20% PEG4000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-E / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2021年10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: 2.05→83.13 Å / Num. obs: 68051 / % possible obs: 98.3 % / 冗長度: 19.5 % / CC1/2: 0.996 / Rpim(I) all: 0.033 / Rrim(I) all: 0.146 / Net I/σ(I): 23.1 / Num. measured all: 1329519
反射 シェル解像度: 2.05→2.16 Å / % possible obs: 88.5 % / 冗長度: 14.4 % / Num. measured all: 127846 / Num. unique obs: 8868 / CC1/2: 0.517 / Rpim(I) all: 0.44 / Rrim(I) all: 1.706 / Net I/σ(I) obs: 1.9

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解析

ソフトウェア
名称バージョン分類
PHENIXv2.8.3精密化
SCALAデータスケーリング
PHASERv2.8.3位相決定
XDSデータ削減
精密化構造決定の手法: 分子置換 / 解像度: 2.06→80.42 Å / SU ML: 0.29 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 29.8 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2338 3197 4.73 %
Rwork0.209 --
obs0.2102 67544 99.8 %
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: 2.06→80.42 Å
タンパク質核酸リガンド溶媒全体
原子数5822 0 0 229 6051
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0025950
X-RAY DIFFRACTIONf_angle_d0.458102
X-RAY DIFFRACTIONf_dihedral_angle_d13.5342250
X-RAY DIFFRACTIONf_chiral_restr0.044978
X-RAY DIFFRACTIONf_plane_restr0.0031070
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.090.35931300.37282682X-RAY DIFFRACTION96
2.09-2.120.38261100.35322826X-RAY DIFFRACTION100
2.12-2.160.34941150.33792778X-RAY DIFFRACTION100
2.16-2.20.31571310.29582817X-RAY DIFFRACTION100
2.2-2.240.35351160.28092814X-RAY DIFFRACTION100
2.24-2.280.34131270.28582779X-RAY DIFFRACTION100
2.28-2.320.27611440.26522805X-RAY DIFFRACTION100
2.32-2.380.27881310.26282812X-RAY DIFFRACTION100
2.38-2.430.29191440.25282756X-RAY DIFFRACTION100
2.43-2.490.29231500.26742768X-RAY DIFFRACTION100
2.49-2.560.29921530.2562775X-RAY DIFFRACTION100
2.56-2.630.27721440.25762794X-RAY DIFFRACTION100
2.63-2.720.2981330.26622823X-RAY DIFFRACTION100
2.72-2.820.27771640.25492758X-RAY DIFFRACTION100
2.82-2.930.30451530.24772779X-RAY DIFFRACTION100
2.93-3.060.27951570.24072799X-RAY DIFFRACTION100
3.06-3.220.25651270.22462831X-RAY DIFFRACTION100
3.22-3.430.27141270.23142806X-RAY DIFFRACTION100
3.43-3.690.21691470.20122814X-RAY DIFFRACTION100
3.69-4.060.20011390.1732807X-RAY DIFFRACTION100
4.06-4.650.1731220.14752847X-RAY DIFFRACTION100
4.65-5.860.22271330.17322843X-RAY DIFFRACTION100
5.86-80.420.18472000.17542834X-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)
13.24263.0644-2.14438.3563-1.93355.1162-0.35870.3888-0.8005-0.5669-0.1672-0.56620.5381-0.17050.45270.6503-0.01460.04660.3770.01580.3564-0.43869.502-27.3352
26.80372.8497-0.94538.42161.82434.3519-0.08690.4712-0.7007-0.08910.0515-0.68320.62950.4478-0.05270.53570.0230.11470.3390.01880.45043.62315.6042-23.8602
35.45345.92235.36817.00664.73337.08160.6914-1.058-0.73141.0877-0.6098-0.01610.9229-0.8565-0.08040.7289-0.0840.10790.44070.0190.4143-1.47118.2012-14.0224
43.35035.6119-1.93239.7447-2.692810.2279-0.15980.2964-1.2482-0.6315-0.4667-1.15890.57330.80810.65860.6664-0.00810.07060.47780.01220.5025.171812.3168-26.846
51.9385-0.5939-2.01885.76283.03244.5951-0.2485-0.1265-0.35080.34860.11510.09910.15780.07530.02150.569-0.00570.01530.4169-0.01260.4179-31.199615.5553-13.9695
63.2486-0.50681.27232.32020.96772.22210.31940.2126-0.4597-1.29910.5421.54640.7532-1.067-0.73240.9115-0.0312-0.04540.56910.06520.6685-38.168418.4231-30.4795
73.9444-3.66532.42134.8373-0.35984.0876-0.136-0.2255-0.9215-1.41280.92211.76562.3309-1.3132-0.81730.5667-0.08640.01920.46550.05560.5002-37.433411.7311-21.9993
87.797-6.8873.64659.0165-4.38398.5865-0.8166-1.4086-0.39551.48740.90050.3503-0.4241-0.39770.08510.7450.07340.08140.62820.07330.4919-32.36939.7025-10.728
97.1416.5929-5.43886.2591-4.52518.9625-0.9051-0.681.8325-1.11750.3611.3841-1.5644-0.49360.38760.90850.06080.02970.3938-0.08450.5781-34.011421.77-20.8605
109.88383.44370.6557.3495.02283.84560.6424-0.6109-0.1015-0.1353-0.0358-0.6914-0.85150.1197-0.59320.6208-0.00410.01050.32460.00550.4204-29.661424.5903-27.3063
118.0174-4.33473.62995.7456-5.40166.14460.41110.8412-0.2518-1.694-0.2762-1.33621.42291.967-0.34110.82770.04470.0160.4221-0.10990.5995-26.80714.9267-28.9979
126.52264.14745.59345.34495.35785.98670.86472.07612.9676-2.0362-0.5518-2.4228-1.18430.9826-0.21850.70670.13190.18590.5791-0.01421.0738-18.737813.0835-20.8676
135.7917-3.8737-3.67567.46861.19694.0807-0.2362-1.59860.34361.40090.18340.0451-1.0695-0.61510.19830.77360.1431-0.00620.4377-0.01760.4664-32.625420.1408-15.9844
143.671-3.33655.69784.0551-5.66269.6488-0.8022-1.06370.241610.78030.4101-0.9396-1.281-0.04330.67360.05180.01620.49280.07870.5405-38.06033.0309-47.8496
154.1635-3.6947-1.87697.52090.19233.8412-0.7648-1.79021.12031.28770.4583-0.6588-0.67740.3880.14770.6410.0738-0.13660.4697-0.07240.4014-26.216-3.9929-32.3935
168.36910.05263.76599.52324.36653.94090.9186-0.3645-1.1260.5634-0.7641.7042.0966-1.5369-0.38440.9971-0.10410.04880.89010.25030.774-44.4195-14.7868-38.6062
177.68272.28825.4778.88872.82228.3423-0.3224-1.3121.33041.1202-0.18020.1033-0.4611-0.15860.39450.66410.1573-0.03070.4098-0.00440.5773-32.69821.801-35.029
189.0121-0.27821.46112.56171.26167.8164-0.5490.40320.54670.73820.2721-0.1632-1.1225-0.46630.26170.74780.1355-0.0690.388-0.0060.642-35.26424.9469-38.5326
197.16824.0489-1.30468.1170.52036.16220.1536-0.2258-0.54270.34990.226-0.83550.5863-0.1457-0.2830.5871-0.0025-0.05430.26630.06160.4343-37.4018-11.3739-45.0735
205.15364.04265.05083.54353.57056.4911.3205-1.644-1.52151.7325-0.5901-0.18951.5752-1.4471-0.66810.8353-0.0395-0.03090.56090.14510.4936-33.7843-14.0936-35.8284
213.5241-1.66253.58917.48033.34727.8299-0.16140.3348-2.00451.0162-0.3645-0.36113.71181.2699-0.04430.71720.0995-0.12790.476-0.01240.6739-23.0279-10.1465-36.927
225.3198-6.74455.52310.0198-7.06985.8477-0.1006-0.81540.32460.07960.6360.911-0.4179-0.9069-0.57670.73220.09010.02150.42180.0070.5709-37.3426-0.0191-44.559
2310.00987.5507-6.08539.9546-5.77269.6159-0.30840.9276-0.0249-0.76590.80160.4820.797-1.2313-0.39170.75660.01220.09190.44480.08350.474-44.4075-15.93455.9231
249.42633.64157.15195.7297-0.07658.2176-0.8040.7278-0.6511-0.99330.365-0.5146-0.20080.62410.4390.6786-0.0110.15940.4403-0.12430.4375-29.5305-8.7994-6.7424
259.3206-2.9663-3.2569.47242.78494.62080.23230.8938-0.3134-1.3777-0.09380.0241-0.1296-0.6251-0.13550.6751-0.09240.02120.53480.02850.3537-41.2274-8.1575-5.131
269.6982-5.8999-1.18616.3971.09292.8482-0.9336-0.0295-1.6277-0.18590.5518-0.31760.8393-0.42820.63550.9819-0.12460.16390.4187-0.10730.758-39.561-17.8614-2.659
273.93724.56833.11965.25033.64313.0718-0.31620.03170.8561-0.64570.51-0.0323-1.235-1.149-0.10960.61820.0250.04570.42580.04020.5193-43.8502-6.62222.7292
289.6179-6.64-4.6046.96083.24354.11460.71760.76251.0396-0.5843-0.4702-0.5118-0.8714-0.1579-0.23420.75040.03570.0930.34580.0510.4892-37.52240.5852-0.8811
299.83116.9275-1.92165.1146-1.57593.73850.1722-0.26940.0581.00170.03610.581-0.0544-0.1534-0.26570.67840.06870.20310.3484-0.03370.5616-41.3048-11.70883.4368
304.9371-4.2795-4.43899.04113.80064.1203-0.7355-0.44150.41410.71540.6366-0.41250.38290.90750.21150.7073-0.0280.07370.6252-0.06390.3714.2667-20.7135-49.1443
313.22071.7642.27183.6828-0.63622.8388-0.8944-0.4962-0.18810.3370.023-0.3972-1.0543-0.90490.54070.66250.01740.09250.6530.01770.5397-11.8509-12.8339-35.673
327.1392.4778-2.72314.4651-0.40684.1610.1533-0.2538-0.01191.0415-0.7671-1.6574-1.5791.23220.47420.7173-0.11440.0030.45250.02220.43525.4228-4.5736-42.9805
338.876-0.6833-5.11267.0555-2.36114.0861-1.0741-0.3201-1.4190.58850.16180.55782.0201-0.00940.73470.70350.00780.13220.46720.06630.5457-6.0446-21.3236-35.736
344.23326.0833-2.61259.2604-2.06378.955-0.5475-0.3723-2.60070.44720.0132-0.58521.6086-0.06970.48740.67840.03770.14680.45180.02340.75821.7629-19.799-39.6054
354.522-3.30285.41114.3515-2.77917.3309-0.06751.43330.4014-1.87660.1397-0.5584-1.54371.83220.05810.874-0.11260.18350.5193-0.0390.41751.5261-10.6953-49.243
366.34355.0896-1.29578.6756-3.19161.32310.35840.0027-0.1789-0.91-0.1128-0.0492-0.704-0.1551-0.25740.8096-0.04150.07970.3887-0.0140.3801-1.7807-3.8773-52.327
377.26692.8256-4.43434.1137-5.26598.45060.7649-0.79430.95492.0919-0.53811.8011-1.6591-0.7582-0.22240.7282-0.05450.13610.479-0.12290.4389-5.4767-1.9577-42.9921
386.40970.8336-4.52039.02890.27255.16571.05261.69832.4763-1.3481-0.24320.4235-2.3731-1.8449-1.04460.67680.19210.14940.80560.07280.5103-14.4929-8.9384-42.1507
395.3612-1.379-5.30118.2858-0.08915.58630.0123-0.2446-1.069-0.3969-0.0608-0.59030.46910.5835-0.10840.66560.00270.10770.4908-0.03990.5320.9606-15.8647-47.6172
407.7726.37614.24719.71814.46444.2483-0.0907-0.55271.09190.0087-0.43951.0986-0.3308-0.67420.59410.6153-0.05210.03340.4078-0.07540.4278-35.7172-34.9717-29.7054
418.53860.09580.89232.2085-2.58122.9153-0.3396-0.53870.48930.96440.530.2078-1.4015-0.56550.09860.64050.047-0.06350.4131-0.00450.596-21.8395-19.8665-20.3229
429.8915.4252-4.94144.5386-1.01065.52120.3794-0.49791.26190.4407-0.09731.6818-0.9223-1.7062-1.09810.72470.09240.12560.47370.0340.4836-36.1106-25.3037-15.3479
436.1183.7164-3.65215.5448-5.53085.90330.2603-0.04140.43190.90330.64351.7738-0.5354-1.0794-0.71090.66840.02370.13630.5316-0.02070.6006-40.4551-30.3803-13.1778
446.20384.6452-0.19874.9082-3.919.6498-0.95210.98560.3811-1.07670.497-1.18090.170.72840.07930.8555-0.0865-0.0260.46690.03410.5143-26.7166-20.5775-29.3922
459.25323.1332-6.8117.2482-1.95876.2888-0.56641.49820.3256-1.73770.51750.0721-0.3018-0.99810.12760.721-0.0682-0.06080.6267-0.05490.5559-34.2529-25.118-28.6357
466.3228-4.94834.16547.7008-3.21244.8811-0.1232-0.3358-2.28131.76740.24481.4851.7232-0.14290.14480.7532-0.06120.13770.3004-0.10740.5124-34.0301-34.715-19.474
477.2811-0.15861.21732.6818-0.24072.35140.41160.47910.210.9228-0.2427-0.61771.4625-0.1405-0.02180.7114-0.05780.07780.3167-0.02780.4869-31.1887-37.4748-12.2213
487.8934.9801-3.99514.0838-3.94894.18680.5611-0.4970.3191.6686-0.2769-0.0504-1.60560.7788-0.08060.7211-0.03540.03560.3892-0.07420.525-28.7972-27.861-9.892
495.0326.3210.80259.35590.43617.1268-0.13140.4107-0.22590.83340.1284-0.435-0.01230.3953-0.11480.65460.0085-0.00080.2765-0.01740.4921-26.6685-30.2964-20.8793
502.93611.99343.32734.57644.14577.563-0.32650.6546-0.1536-0.46940.4001-0.0797-0.12210.47730.08340.6424-0.00510.06670.4503-0.03450.3632-7.7834-5.49080.4323
512.8356-0.26340.10719.329-4.16828.3485-0.1756-0.00740.1136-0.05410.001-0.40160.04830.10870.19980.5384-0.02530.03590.3638-0.08250.3001-5.9724-12.83881.2254
522.1611-3.91762.0858.181-4.33783.4333-0.5773-0.43690.63940.67320.0958-1.1091-0.8091-0.15110.25570.80450.0661-0.00740.46770.06210.52934.4239-38.4802-10.8883
538.08894.21460.72569.1537-0.77157.4109-0.4703-0.2290.7693-0.01680.54110.7008-1.2695-0.60660.09650.64560.1142-0.01860.3817-0.06540.4733-10.0007-24.1033-19.8672
549.53523.5096-4.19062.0883-2.29269.6656-0.5605-1.11020.24470.1903-0.3552-1.74-0.31651.40420.72770.77330.0131-0.01950.47010.09370.74566.1653-25.2832-20.5667
559.0025-2.72750.82946.45821.15355.67781.16920.65081.4926-1.28820.2875-1.7804-1.44970.5218-0.60480.8226-0.12810.10270.42840.15870.7889.6961-27.881-23.764
563.06-2.5703-0.75663.60212.6893.0017-0.666-1.10790.48021.19970.27050.5583-1.2739-1.07950.28890.83680.21050.00770.69030.0120.5144-7.9633-26.9232-10.0501
572.1075-2.4841-2.92834.1462.35074.7184-0.0482-1.6177-0.07930.470.1205-0.0154-0.4997-0.1401-0.01590.82120.0936-0.03390.61810.02120.39380.4088-29.5274-9.3778
588.4674-2.373-1.41085.2064-0.47585.59940.06920.551-0.0479-0.7323-0.3484-0.2536-0.4911-0.05620.1470.65340.04040.1030.36370.04470.33625.2342-35.7308-25.321
594.596-5.9782-2.93679.64221.79457.26161.01730.59951.5323-1.0387-0.5761-1.3086-1.2934-0.0145-0.34740.91660.05060.11550.42450.09320.59851.1639-26.922-28.4894
609.7976-5.30555.24526.652-2.09479.35740.35790.58910.1603-0.2202-0.4024-0.04320.47460.08390.17360.59480.06120.12630.330.02130.3505-2.1892-33.3159-19.1428
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 145 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 239 )
5X-RAY DIFFRACTION5chain 'B' and (resid 145 through 164 )
6X-RAY DIFFRACTION6chain 'B' and (resid 165 through 178 )
7X-RAY DIFFRACTION7chain 'B' and (resid 179 through 185 )
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 202 )
9X-RAY DIFFRACTION9chain 'B' and (resid 203 through 207 )
10X-RAY DIFFRACTION10chain 'B' and (resid 208 through 216 )
11X-RAY DIFFRACTION11chain 'B' and (resid 217 through 225 )
12X-RAY DIFFRACTION12chain 'B' and (resid 226 through 230 )
13X-RAY DIFFRACTION13chain 'B' and (resid 231 through 237 )
14X-RAY DIFFRACTION14chain 'C' and (resid 145 through 155 )
15X-RAY DIFFRACTION15chain 'C' and (resid 156 through 166 )
16X-RAY DIFFRACTION16chain 'C' and (resid 167 through 178 )
17X-RAY DIFFRACTION17chain 'C' and (resid 179 through 194 )
18X-RAY DIFFRACTION18chain 'C' and (resid 195 through 202 )
19X-RAY DIFFRACTION19chain 'C' and (resid 203 through 216 )
20X-RAY DIFFRACTION20chain 'C' and (resid 217 through 225 )
21X-RAY DIFFRACTION21chain 'C' and (resid 226 through 230 )
22X-RAY DIFFRACTION22chain 'C' and (resid 231 through 239 )
23X-RAY DIFFRACTION23chain 'D' and (resid 145 through 155 )
24X-RAY DIFFRACTION24chain 'D' and (resid 156 through 166 )
25X-RAY DIFFRACTION25chain 'D' and (resid 167 through 194 )
26X-RAY DIFFRACTION26chain 'D' and (resid 195 through 202 )
27X-RAY DIFFRACTION27chain 'D' and (resid 203 through 207 )
28X-RAY DIFFRACTION28chain 'D' and (resid 208 through 230 )
29X-RAY DIFFRACTION29chain 'D' and (resid 231 through 237 )
30X-RAY DIFFRACTION30chain 'E' and (resid 145 through 155 )
31X-RAY DIFFRACTION31chain 'E' and (resid 156 through 164 )
32X-RAY DIFFRACTION32chain 'E' and (resid 165 through 185 )
33X-RAY DIFFRACTION33chain 'E' and (resid 186 through 194 )
34X-RAY DIFFRACTION34chain 'E' and (resid 195 through 202 )
35X-RAY DIFFRACTION35chain 'E' and (resid 203 through 207 )
36X-RAY DIFFRACTION36chain 'E' and (resid 208 through 216 )
37X-RAY DIFFRACTION37chain 'E' and (resid 217 through 225 )
38X-RAY DIFFRACTION38chain 'E' and (resid 226 through 230 )
39X-RAY DIFFRACTION39chain 'E' and (resid 231 through 238 )
40X-RAY DIFFRACTION40chain 'F' and (resid 145 through 155 )
41X-RAY DIFFRACTION41chain 'F' and (resid 156 through 164 )
42X-RAY DIFFRACTION42chain 'F' and (resid 165 through 170 )
43X-RAY DIFFRACTION43chain 'F' and (resid 171 through 185 )
44X-RAY DIFFRACTION44chain 'F' and (resid 186 through 194 )
45X-RAY DIFFRACTION45chain 'F' and (resid 195 through 202 )
46X-RAY DIFFRACTION46chain 'F' and (resid 203 through 207 )
47X-RAY DIFFRACTION47chain 'F' and (resid 208 through 216 )
48X-RAY DIFFRACTION48chain 'F' and (resid 217 through 225 )
49X-RAY DIFFRACTION49chain 'F' and (resid 226 through 237 )
50X-RAY DIFFRACTION50chain 'G' and (resid 145 through 164 )
51X-RAY DIFFRACTION51chain 'G' and (resid 165 through 238 )
52X-RAY DIFFRACTION52chain 'H' and (resid 145 through 155 )
53X-RAY DIFFRACTION53chain 'H' and (resid 156 through 164 )
54X-RAY DIFFRACTION54chain 'H' and (resid 165 through 170 )
55X-RAY DIFFRACTION55chain 'H' and (resid 171 through 185 )
56X-RAY DIFFRACTION56chain 'H' and (resid 186 through 194 )
57X-RAY DIFFRACTION57chain 'H' and (resid 195 through 202 )
58X-RAY DIFFRACTION58chain 'H' and (resid 203 through 216 )
59X-RAY DIFFRACTION59chain 'H' and (resid 217 through 225 )
60X-RAY DIFFRACTION60chain 'H' and (resid 226 through 237 )

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万見について

-
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