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- PDB-5fj4: Structure of the standard kink turn HmKt-7 as stem loop bound wit... -

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基本情報

登録情報
データベース: PDB / ID: 5fj4
タイトルStructure of the standard kink turn HmKt-7 as stem loop bound with U1A and L7Ae proteins
要素
  • 50S RIBOSOMAL PROTEIN L7AE
  • HMKT-7
  • U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
キーワードTRANSCRIPTION / KINK TURN
機能・相同性
機能・相同性情報


ribonuclease P activity / U1 snRNP binding / tRNA 5'-leader removal / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / ribosome biogenesis ...ribonuclease P activity / U1 snRNP binding / tRNA 5'-leader removal / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
類似検索 - 分子機能
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / RRM (RNA recognition motif) domain / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / : / Ribosomal protein L7Ae/L8/Nhp2 family ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / RRM (RNA recognition motif) domain / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / : / Ribosomal protein L7Ae/L8/Nhp2 family / RNA recognition motif / RNA recognition motif / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / 50S ribosomal protein L30e-like / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
RNA / RNA (> 10) / Large ribosomal subunit protein eL8 / U1 small nuclear ribonucleoprotein A
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
ARCHAEOGLOBUS FULGIDUS (古細菌)
HALOARCULA MARISMORTUI (好塩性)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.95 Å
データ登録者Huang, L. / Lilley, D.M.J.
引用ジャーナル: Nucleic Acids Res. / 年: 2016
タイトル: A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function.
著者: Huang, L. / Wang, J. / Lilley, D.M.J.
履歴
登録2015年10月6日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年5月25日Provider: repository / タイプ: Initial release
改定 1.12016年7月6日Group: Database references
改定 1.22024年1月10日Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
C: 50S RIBOSOMAL PROTEIN L7AE
D: HMKT-7
E: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
G: 50S RIBOSOMAL PROTEIN L7AE
H: HMKT-7


分子量 (理論値)分子数
合計 (水以外)96,5968
ポリマ－96,5968
非ポリマー00
水00
1
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
C: 50S RIBOSOMAL PROTEIN L7AE
D: HMKT-7


分子量 (理論値)分子数
合計 (水以外)48,2984
ポリマ－48,2984
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-12.4 kcal/mol
Surface area24320 Å2
手法PQS
2
E: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
G: 50S RIBOSOMAL PROTEIN L7AE
H: HMKT-7


分子量 (理論値)分子数
合計 (水以外)48,2984
ポリマ－48,2984
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-16 kcal/mol
Surface area24300 Å2
手法PQS
単位格子
Length a, b, c (Å)131.853, 161.226, 149.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
22
/ NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A / U1 SNRNP A / U1-A / U1A


分子量: 11744.777 Da / 分子数: 4 / 断片: RRM 1 DOMAIN, UNP RESIDUES 1-102 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): GOLD PLYSS / 参照: UniProt: P09012
#2: タンパク質 50S RIBOSOMAL PROTEIN L7AE / RIBOSOMAL PROTEIN L8E / AFL7AE


分子量: 13494.545 Da / 分子数: 2 / 断片: RNA BINDING DOMAIN, UNP RESIDUES 5-119 / 由来タイプ: 組換発現 / 由来: (組換発現) ARCHAEOGLOBUS FULGIDUS (古細菌) / 株: DSM 4304 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): GOLD PLYSS / 参照: UniProt: O29494
#3: RNA鎖 HMKT-7


分子量: 11313.805 Da / 分子数: 2 / 断片: KINK TURN MOTIF / 由来タイプ: 合成 / 由来: (合成) HALOARCULA MARISMORTUI (好塩性)

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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: 4.67 Å3/Da / 溶媒含有率: 73.68 % / 解説: NONE
結晶化pH: 8.5
詳細: 0.1 M TRIS HYDROCHLORIDE PH 8.5, 2.0 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE

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データ収集

回折平均測定温度: 173 K
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I03 / 波長: 0.9763
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年1月29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: 0.9763 Å / 相対比: 1
反射解像度: 2.95→84.37 Å / Num. obs: 34011 / % possible obs: 99.9 % / Observed criterion σ(I): 1.1 / 冗長度: 7.5 % / Biso Wilson estimate: 104.08 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.6
反射 シェル解像度: 2.95→3.09 Å / 冗長度: 7.6 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.1 / % possible all: 99.7

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
iMOSFLMデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 4C4W

4c4w


解像度: 2.95→80.613 Å / SU ML: 0.38 / σ(F): 1.35 / 位相誤差: 26.08 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2369 1654 4.9 %
Rwork0.1987 --
obs0.2007 33933 99.91 %
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 mean: 128.18 Å2
精密化ステップサイクル: LAST / 解像度: 2.95→80.613 Å
タンパク質核酸リガンド溶媒全体
原子数4938 1504 0 0 6442
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0146733
X-RAY DIFFRACTIONf_angle_d1.8459406
X-RAY DIFFRACTIONf_dihedral_angle_d16.4683982
X-RAY DIFFRACTIONf_chiral_restr0.0831119
X-RAY DIFFRACTIONf_plane_restr0.013932
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.03690.33591290.32892656X-RAY DIFFRACTION100
3.0369-3.13490.33691250.31112655X-RAY DIFFRACTION100
3.1349-3.24690.34521300.30752683X-RAY DIFFRACTION100
3.2469-3.37690.30051290.2742683X-RAY DIFFRACTION100
3.3769-3.53060.31981310.24482635X-RAY DIFFRACTION100
3.5306-3.71680.22961550.21882681X-RAY DIFFRACTION100
3.7168-3.94960.2371320.20012680X-RAY DIFFRACTION100
3.9496-4.25460.2291400.1822668X-RAY DIFFRACTION100
4.2546-4.68270.20571530.17212687X-RAY DIFFRACTION100
4.6827-5.36010.23981460.17152700X-RAY DIFFRACTION100
5.3601-6.75270.22961410.19682726X-RAY DIFFRACTION100
6.7527-80.64310.21471430.17632825X-RAY DIFFRACTION99
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)
16.1838-2.0782.59091.1191-1.19191.33910.1346-2.376-0.2617-0.9033-0.99772.91130.6909-2.510.83260.7628-0.08090.18180.7319-0.18221.201-45.6397-6.2074-12.4559
23.9144-1.5318-3.283.54161.2322.870.64361.824-0.2996-0.8831-0.2709-0.29121.8755-2.50150.11140.7525-0.0443-0.04091.09470.03190.5594-39.5508-14.8749-23.5189
31.7094-0.56190.56022.3323-1.96063.91710.38240.1863-2.5702-0.29250.32180.11962.2142-0.5016-0.23911.12770.13620.17920.9991-0.06661.0864-31.0551-23.252-23.7722
48.3715-1.7989-1.08743.08554.08087.2958-0.79910.2533-0.7448-0.69290.6249-1.41680.92842.5481-0.17750.7692-0.16630.25521.0360.04520.7142-28.0937-16.2-20.3719
57.16452.09931.04677.18794.95383.35690.8254-0.8294-0.64070.57281.2906-0.86081.64062.90540.0588-0.5672-0.43521.44570.57460.60040.231-28.8895-6.6807-19.1287
66.98130.6753-1.25632.31842.13692.50970.0968-0.30460.0199-0.8514-2.0123-0.66780.0590.58111.27510.7438-0.1178-0.04340.75930.07530.6149-31.4838-7.1615-11.559
73.9554-1.2937-0.7744.6648-2.50394.3156-0.31030.4552-0.2549-0.28080.28840.28430.043-0.58910.04090.504-0.04240.09320.77560.00730.6665-38.2491-11.9867-17.6154
85.4894-0.3963.26884.8419-1.67914.4482-0.57131.6136-0.7693-0.02480.1725-0.515-0.9228-0.3917-0.28030.97360.05470.11571.07770.03430.868-34.097-11.9046-29.9895
96.5238-1.44880.46523.5043-3.72568.2776-0.4343-0.79690.0672-0.86070.60960.56672.2145-2.31020.14620.7696-0.19170.02920.8857-0.09270.8169-44.6237-11.2926-14.9929
103.1354-3.4396-0.17914.8082.77976.89540.2145-1.6704-0.34030.7688-0.15062.30610.527-0.22390.10730.5059-0.01220.15230.75210.04691.031-41.3882-11.5223-0.5409
111.69441.69571.0972.62-1.22443.31820.14960.79060.7303-0.6063-0.1654-0.8041-1.24990.5592-0.3121.12210.24530.47021.14760.06161.0996-14.8473-3.4567-34.1588
120.02720.03270.34732.03671.34053.84080.05190.1375-1.197-0.8013-0.0654-1.70641.14940.08970.93290.97620.15650.12371.44210.06341.1556-14.769-12.4199-18.863
135.1445-0.05621.53723.7044-1.194.04981.30271.4587-1.22050.2864-0.4324-0.96281.68550.47360.9870.85250.12850.92590.67710.341.1721-21.5475-13.541-27.5484
145.85640.72373.15136.17081.08238.44980.28360.51760.1065-1.1826-0.6974-0.4339-0.2069-0.34680.77361.21010.0170.29351.1487-0.13151.112-20.1688-12.7375-34.7894
154.6087-2.29520.45241.99231.61587.84040.85911.35911.26321.4248-0.64770.94591.88852.65990.60191.87430.094-0.0031.70270.0961.5589-7.2401-8.2351-20.8006
164.19172.4958-0.53464.2249-0.4574.52710.32661.96070.348-1.70481.11-0.0733-1.50590.84830.67891.31270.54350.86521.16210.1481.0726-19.1568-6.9608-38.182
176.25530.1067-3.4532.3057-2.45248.59160.1958-0.0480.4154-0.9069-1.20370.0856-0.82532.12770.33670.9809-0.0460.15810.67930.01640.9516-23.8172-1.8252-26.4726
188.1173-1.329-2.13864.56673.95623.87421.58360.9297-0.8027-0.43390.9589-2.7981-1.92970.2601-2.17051.21430.16490.43031.0780.26992.0036-14.7541-0.3334-35.2965
191.98261.02485.52255.7786-4.84528.23470.6848-0.3261-0.4251-1.352.0164-0.2697-1.33322.7395-1.06271.2607-0.03760.85251.5177-0.08331.6801-6.3031-9.9931-37.805
205.11383.35120.23453.74231.12060.63220.36211.5286-1.45681.9985-0.1593-0.45280.04293.07830.31541.6344-0.21570.28071.810.06011.7441-3.405-13.1487-30.2792
217.56310.65616.03013.93430.43295.59332.393-2.9647-2.2352.52210.97262.5215-0.93310.3995-2.08962.4658-0.25940.25251.75330.30971.7549-14.9415-61.1967-12.02
224.0370.90042.60133.79542.84393.0782.209-2.4133-0.5851.93470.57740.94-0.5354-0.0388-2.99991.8607-0.42360.37082.36670.37061.3219-19.681-50.4901-6.5152
234.68070.62482.19322.62682.0912.32880.6986-0.7080.4294-0.5789-1.893-0.2941-0.1405-0.7670.16072.50550.18530.38261.6069-0.08731.0596-18.4606-39.5487-7.3957
244.31330.2481.67673.6587-0.62974.26320.0739-0.988-0.3344-0.0631-0.39350.39540.3248-0.0792-0.14651.5356-0.13390.20271.0667-0.03750.8819-10.4801-47.5669-18.8173
254.4012-0.6144-1.49633.5356-0.33550.60131.1578-0.0464-0.8520.0629-0.7505-0.03761.5051.0876-0.51921.5698-0.00860.19011.0092-0.00981.2105-7.6254-54.914-23.6413
266.75184.38091.75293.02071.73642.4684-1.22241.6477-2.1681-0.2371.5696-2.16130.85530.930.34711.6792-0.2530.18541.333-0.13141.39480.2795-52.8379-16.3396
270.58920.2487-0.33282.40522.54233.2942-0.468-0.26720.72170.99231.17850.2688-0.69691.1555-0.79811.7138-0.0830.19251.1360.1621.0213-10.1028-55.2521-12.9982
286.289-2.16512.14448.5435-1.71523.9758-0.2215-2.3118-1.0063-0.19540.92431.4261-1.1798-0.0802-1.02921.2817-0.14090.28281.141-0.01970.9172-20.6496-47.2619-17.2727
294.4031.298-0.44522.0292-0.09422.57730.0315-2.64631.27843.1815-0.10550.47270.64930.5982-0.18412.5480.3860.28172.72390.06291.4188-10.8938-45.0894-1.1103
302.59390.54560.84570.2068-0.30692.9012-0.4760.52451.11461.2841-0.0067-1.6986-0.92080.8187-0.06391.7305-0.3199-0.00962.01850.48461.7626-7.7842-58.4667-3.3768
316.3859-2.0191-3.67772.5201-0.71314.8650.93190.4379-0.022-0.75910.50850.46991.5291-0.7337-1.19341.4813-0.0790.35831.12090.02770.8214-7.821-37.014-31.3731
321.81711.01451.10353.2806-1.57933.14830.04360.3531-0.6693-0.34070.35480.8526-0.6491-0.226-0.66751.5367-0.06070.14650.9482-0.2031.0884-23.1627-34.4899-27.0824
332.25740.2868-2.60264.6392.56838.0914-1.11973.4602-2.3366-0.5004-2.28760.8246-0.1471-1.08412.79511.2369-0.1536-0.03761.5197-0.4681.4689-41.3436-30.8661-32.9088
343.6306-0.54420.01224.0331-0.07253.170.5270.7837-1.5526-1.52580.03910.85350.52760.404-0.2060.952-0.0761-0.18141.0508-0.08441.1278-46.1433-19.7205-20.6321
354.3968-3.6317-1.14213.5541.69571.1942-0.68780.7917-2.47252.90611.41513.2092.4008-0.35220.08631.3310.07330.00821.1533-0.1321.442-40.3211-27.9543-9.6594
362.58390.65131.55640.28210.75461.29621.22690.5806-0.99290.7626-0.77951.05330.05480.4817-0.5221.3541-0.13370.18280.9233-0.41671.4557-34.5696-39.782-28.1725
375.5791-2.81090.51587.4576-2.95786.47811.0725-0.5946-0.2990.0703-0.95341.37930.3510.3356-0.16991.61810.06220.16830.7986-0.05440.8603-18.3304-42.951-27.3234
384.41511.1421-2.4821.4822-0.84642.02780.6562-0.11140.356-0.2098-0.09531.18710.932-0.549-0.15051.4058-0.01160.33731.0635-0.03561.1071-13.428-29.3495-32.9911
392.8908-2.86773.17134.1673-1.14676.4039-1.9496-1.26670.08970.04650.0378-3.4443-2.44351.38050.78660.4759-0.1179-0.04680.82650.29061.57443.4866-71.3502-10.0727
404.4737-0.24371.55254.80490.80993.7897-0.53361.95270.6602-1.2555-0.5793-1.3272-1.5716-0.20250.62360.91390.1467-0.04150.71240.15440.915135.2946-57.2348-18.099
414.8842-2.70020.13955.2469-4.15956.26260.71-1.35193.51540.05491.31511.0507-0.7335-1.1801-1.2191.10050.26220.16431.01550.03781.133125.1997-53.6785-14.0552
425.965-1.5568-1.06425.26522.14084.00660.3619-0.34371.11270.9752-0.3937-0.6380.0586-0.7186-0.72130.68080.28170.03780.85580.07690.556925.77-63.4734-15.3612
432.272-1.7403-2.41372.64192.26342.6813-0.4699-1.73220.879-0.5036-0.63531.5365-0.40970.49990.51230.7279-0.08580.14510.64180.30940.849427.239-72.9456-14.1804
444.23862.7912-1.22975.0415-0.59965.1581-0.06810.33151.2989-0.01060.10121.1082-0.42090.4207-0.07410.6054-0.0332-0.13210.55410.14080.900834.4162-57.8185-10.7368
452.0111-4.3482-4.91697.2034.15714.488-0.58230.3287-0.18471.3228-0.09350.76731.8121-1.05340.61650.5420.1633-0.20190.7519-0.11451.175734.084-75.3542-9.2509
464.14140.94891.16859.167-0.92656.34660.00730.95230.5547-3.0005-0.4528-1.07570.1204-0.40140.11820.90660.14060.13810.82040.07720.693733.6652-65.6888-22.9872
472.1719-1.0157-0.05350.85840.09345.09630.06050.1680.009-0.5384-0.2457-0.8781-0.83721.26760.31490.66640.05180.08880.80750.1610.908940.4361-65.8542-7.6883
486.11791.73-4.92683.3753-3.22565.6313-1.5001-1.599-1.23230.50272.0235-1.09480.2089-0.5596-1.09630.770.1162-0.1580.9030.18761.062740.224-69.26564.2894
493.32981.6149-1.43734.87030.37094.09630.3731.1111-0.0542-0.216-0.22021.2078-0.9385-1.6409-0.32150.90010.19970.01671.56270.01040.782312.9199-67.458-32.5568
500.8654-0.1291-0.7699.9091-2.2243.17710.219-0.70880.31891.604-1.0321.0970.1483-1.08230.71830.91650.2324-0.05131.96420.01830.894411.8905-63.6698-15.77
514.5045-0.3543-0.36745.4512-0.22897.7061-0.45380.92211.7572-0.9387-0.2031-0.4669-0.9009-1.05130.56250.96240.2861-0.14621.16820.05070.827518.4036-59.1042-26.7236
527.7868-0.3514-0.47382.24433.24154.66751.72581.20780.67762.31950.52220.2744-1.2856-0.1922-1.29621.9930.0539-0.29772.4073-0.00981.10613.7132-67.0778-18.9447
530.65971.1310.25933.85931.98443.9037-0.1561-0.10560.4427-2.5030.09930.8078-0.4888-0.8725-0.26621.25940.4156-0.09721.40650.37310.58615.9708-62.1252-35.0936
541.5246-1.78040.8962.1064-0.9641.01610.8881.0120.3877-1.8166-0.4308-1.55250.24750.64930.88891.50230.28530.34240.95150.21280.919223.3689-69.2556-34.7248
553.3096-1.16641.36696.9550.70143.7730.24930.0765-0.1382-0.5738-1.2936-0.54511.0276-0.92740.6690.7520.1091-0.02660.82980.05450.864320.4686-71.5881-22.5946
569.3819-1.30830.42392.2708-1.61931.6387-0.21030.69970.5722-0.47051.04182.5919-1.2028-1.4740.29761.35160.3118-0.06491.23190.01180.565814.0153-70.7667-34.0304
571.07870.66661.09171.39330.24661.2758-0.62111.97270.5507-0.3179-0.6097-0.1352-1.3534-0.4265-0.30060.55111.129-2.15862.5088-0.60740.54135.2692-62.1388-36.7638
580.2697-0.51910.87125.32981.53535.1961-0.07241.63542.2113-2.6199-2.02561.64260.422-0.71011.3721.36190.7184-0.1371.595-0.13881.01781.7088-59.3241-28.7415
599.5985-0.55640.79396.70392.41522.3318-1.1349-0.91153.09360.3826-0.8192-1.17671.3048-0.69380.31232.45940.2758-0.43911.0578-0.37291.9694.9093-12.4597-5.858
606.6412-0.4932-0.94685.081-2.41726.13480.6687-2.67350.75030.0567-0.31530.4902-0.77912.71390.44972.371-0.3879-0.13142.0002-0.51740.9936.7828-30.0916-1.3504
611.0811-1.42940.08861.7458-0.15111.9174-0.42451.8632-0.1839-0.7511-0.0146-0.5228-0.0464-1.95811.01681.0048-0.0314-0.01061.2367-0.04050.94133.4585-29.6764-17.0405
622.63670.72863.06931.83432.6155.534-2.3976-1.1152-1.3556-1.1195-1.0642-0.9124-0.2673-0.28162.92561.3975-0.07530.32821.6562-0.06721.1307-4.2414-29.9493-13.8587
635.12750.2147-2.44853.0932-2.58153.1246-0.1808-0.09410.50941.0346-0.30710.464-1.2868-0.18150.05271.53180.00140.17661.0885-0.33641.17193.522-18.9246-13.5237
647.71325.42850.38364.0437-0.36631.87061.1653-2.4104-0.3106-0.3059-0.9227-1.95071.12310.3384-0.23821.70170.1635-0.56231.8504-0.45531.495415.5948-25.5046-6.7738
658.0797-5.07891.63483.7421-2.36744.3271-0.6732-1.24530.9122-0.28980.2372-2.03480.5368-1.916-0.31491.67170.05890.0561.073-0.11981.056711.9343-28.7717-11.0945
660.30190.4356-1.02261.2043-1.5943.4681-0.1697-1.23-1.0790.19341.656-1.3419-0.20941.1198-1.21631.77060.1273-0.0932.1565-0.14310.8923-0.976-35.7209-1.8741
676.08330.25390.78930.88990.60610.4842-0.1893-3.0363-1.8594-0.58760.18890.5587-0.9121.06690.21042.05540.18381.00614.1921-1.83360.6652-3.2613-27.98332.7297
685.17540.11385.54862.0985-0.33647.79091.1933-0.711-1.12041.0467-0.3978-0.16242.5349-0.18061.14551.6308-0.0946-0.00132.4954-1.16921.5681-4.3459-17.06710.56
692.8714-2.55760.2068.3718-3.28362.5961.05871.18071.8661-3.37720.7552-2.63840.66310.5726-1.33891.49020.19230.30891.0072-0.08810.82575.4842-34.4869-29.2272
707.1897-0.7672-0.36822.9550.51883.2108-0.8963-0.23031.8440.0349-0.0667-2.15640.45250.30410.79341.24830.093-0.0020.76360.03941.662218.3535-38.3994-19.9739
710.2664-0.5806-0.02131.06170.0881-0.04780.15141.0689-0.1286-1.50.2379-0.78350.3224-0.6180.1171.2128-0.0220.36781.13290.34431.656238.4674-41.1478-22.5405
725.62370.4567-0.20086.8230.84674.24810.28891.18141.4478-0.22710.735-0.9376-0.8652-1.187-1.47360.68380.0430.14680.83320.05931.239842.3422-55.8675-11.4695
736.5071-2.49221.77945.84892.27625.4715-0.3483-4.82042.08290.96141.46120.76722.4601-1.1497-1.34311.584-0.2387-0.04951.46710.10921.674336.7491-46.5864-4.1731
747.9508-2.13052.06564.1325-0.02361.2373-0.57492.47731.97891.2985-0.27931.1206-0.57251.34350.54711.52680.0291-0.40610.99690.32852.679931.6247-32.966-17.5838
753.6496-0.2519-0.1543.5224-0.07033.14640.1749-0.13570.5418-0.3674-1.0984-2.6592-0.71670.07950.67621.48960.20270.020.93320.11511.385915.5483-29.7825-20.2318
764.00780.16240.59887.0942-0.60546.2928-0.7948-0.29020.3999-0.4655-0.3662-0.0909-0.3310.02031.0991.70750.10790.12941.0898-0.01941.121311.1139-42.4005-29.1405
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:11)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 12:18)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 19:24)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 25:30)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 31:36)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 37:42)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 43:73)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 74:82)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 83:92)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 93:101)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 7:18)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 19:24)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 25:34)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 35:46)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 47:52)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 53:69)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 70:82)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 83:88)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 89:96)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 97:102)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 1:12)
22X-RAY DIFFRACTION22(CHAIN C AND RESID 13:19)
23X-RAY DIFFRACTION23(CHAIN C AND RESID 20:27)
24X-RAY DIFFRACTION24(CHAIN C AND RESID 28:56)
25X-RAY DIFFRACTION25(CHAIN C AND RESID 57:64)
26X-RAY DIFFRACTION26(CHAIN C AND RESID 65:69)
27X-RAY DIFFRACTION27(CHAIN C AND RESID 70:77)
28X-RAY DIFFRACTION28(CHAIN C AND RESID 78:98)
29X-RAY DIFFRACTION29(CHAIN C AND RESID 99:111)
30X-RAY DIFFRACTION30(CHAIN C AND RESID 112:117)
31X-RAY DIFFRACTION31(CHAIN D AND RESID 1:4)
32X-RAY DIFFRACTION32(CHAIN D AND RESID 5:9)
33X-RAY DIFFRACTION33(CHAIN D AND RESID 10:13)
34X-RAY DIFFRACTION34(CHAIN D AND RESID 14:17)
35X-RAY DIFFRACTION35(CHAIN D AND RESID 18:21)
36X-RAY DIFFRACTION36(CHAIN D AND RESID 22:27)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 28:31)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 32:35)
39X-RAY DIFFRACTION39(CHAIN E AND RESID 6:10)
40X-RAY DIFFRACTION40(CHAIN E AND RESID 11:21)
41X-RAY DIFFRACTION41(CHAIN E AND RESID 22:26)
42X-RAY DIFFRACTION42(CHAIN E AND RESID 27:34)
43X-RAY DIFFRACTION43(CHAIN E AND RESID 35:39)
44X-RAY DIFFRACTION44(CHAIN E AND RESID 40:59)
45X-RAY DIFFRACTION45(CHAIN E AND RESID 60:65)
46X-RAY DIFFRACTION46(CHAIN E AND RESID 66:82)
47X-RAY DIFFRACTION47(CHAIN E AND RESID 83:96)
48X-RAY DIFFRACTION48(CHAIN E AND RESID 97:102)
49X-RAY DIFFRACTION49(CHAIN F AND RESID 7:18)
50X-RAY DIFFRACTION50(CHAIN F AND RESID 19:24)
51X-RAY DIFFRACTION51(CHAIN F AND RESID 25:46)
52X-RAY DIFFRACTION52(CHAIN F AND RESID 47:52)
53X-RAY DIFFRACTION53(CHAIN F AND RESID 53:66)
54X-RAY DIFFRACTION54(CHAIN F AND RESID 67:72)
55X-RAY DIFFRACTION55(CHAIN F AND RESID 73:82)
56X-RAY DIFFRACTION56(CHAIN F AND RESID 83:87)
57X-RAY DIFFRACTION57(CHAIN F AND RESID 88:93)
58X-RAY DIFFRACTION58(CHAIN F AND RESID 94:102)
59X-RAY DIFFRACTION59(CHAIN G AND RESID 1:10)
60X-RAY DIFFRACTION60(CHAIN G AND RESID 11:28)
61X-RAY DIFFRACTION61(CHAIN G AND RESID 29:39)
62X-RAY DIFFRACTION62(CHAIN G AND RESID 40:46)
63X-RAY DIFFRACTION63(CHAIN G AND RESID 47:79)
64X-RAY DIFFRACTION64(CHAIN G AND RESID 80:85)
65X-RAY DIFFRACTION65(CHAIN G AND RESID 86:97)
66X-RAY DIFFRACTION66(CHAIN G AND RESID 98:103)
67X-RAY DIFFRACTION67(CHAIN G AND RESID 104:111)
68X-RAY DIFFRACTION68(CHAIN G AND RESID 112:117)
69X-RAY DIFFRACTION69(CHAIN H AND RESID 1:4)
70X-RAY DIFFRACTION70(CHAIN H AND RESID 5:9)
71X-RAY DIFFRACTION71(CHAIN H AND RESID 10:13)
72X-RAY DIFFRACTION72(CHAIN H AND RESID 14:18)
73X-RAY DIFFRACTION73(CHAIN H AND RESID 19:22)
74X-RAY DIFFRACTION74(CHAIN H AND RESID 23:26)
75X-RAY DIFFRACTION75(CHAIN H AND RESID 27:31)
76X-RAY DIFFRACTION76(CHAIN H AND RESID 32:35)

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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