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- PDB-4c4w: Structure of a rare, non-standard sequence k-turn bound by L7Ae p... -

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基本情報

登録情報
データベース: PDB / ID: 4c4w
タイトルStructure of a rare, non-standard sequence k-turn bound by L7Ae protein
要素
  • 50S RIBOSOMAL PROTEIN L7AE
  • TSKT-23
  • U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
キーワードRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / RNA BINDING PROTEIN / KINK TURN
機能・相同性
機能・相同性情報


U1 snRNP binding / ribonuclease P activity / 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 ...U1 snRNP binding / ribonuclease P activity / 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 / translation / ribonucleoprotein complex / 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 / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / RNA-binding domain superfamily / 50S ribosomal protein L30e-like / 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
DIHYDROGENPHOSPHATE ION / 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)
KNEALLHAZIA SOLENOPSAE (菌類)
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: 2014
タイトル: Structure of a Rare, Non-Standard Sequence K-Turn Bound by L7Ae Protein
著者: Huang, L. / Lilley, D.M.J.
履歴
登録2013年9月9日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02014年2月12日Provider: repository / タイプ: Initial release
改定 1.12014年4月30日Group: Database references
改定 1.22023年12月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
C: 50S RIBOSOMAL PROTEIN L7AE
D: TSKT-23
E: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
G: 50S RIBOSOMAL PROTEIN L7AE
H: TSKT-23
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,59510
ポリマ－96,4018
非ポリマー1942
水00
1
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
C: 50S RIBOSOMAL PROTEIN L7AE
D: TSKT-23
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,2985
ポリマ－48,2014
非ポリマー971
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-26.2 kcal/mol
Surface area21050 Å2
手法PISA
2
E: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
G: 50S RIBOSOMAL PROTEIN L7AE
H: TSKT-23
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,2985
ポリマ－48,2014
非ポリマー971
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-24.6 kcal/mol
Surface area20480 Å2
手法PISA
単位格子
Length a, b, c (Å)135.892, 155.545, 146.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 11740.739 Da / 分子数: 4 / 断片: RRM 1 DOMAIN, RESIDUES 1-102 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PT7 / 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


分子量: 13522.559 Da / 分子数: 2 / 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 TSKT-23


分子量: 11196.685 Da / 分子数: 2 / 断片: KINK TURN MOTIF, RESIDUES 1-35 / 由来タイプ: 合成 / 由来: (合成) KNEALLHAZIA SOLENOPSAE (菌類)
#4: 化合物 ChemComp-2HP / DIHYDROGENPHOSPHATE ION / (りん酸ジ水素)イオン


分子量: 96.987 Da / 分子数: 2 / 由来タイプ: 合成 / 式: H2O4P

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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: 2

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試料調製

結晶マシュー密度: 4.2 Å3/Da / 溶媒含有率: 71 % / 解説: NONE
結晶化pH: 8
詳細: 100 MM TRISHCL 8.5 AND 2.0 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE

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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: ESRF / ビームライン: ID23-1 / 波長: 0.9763
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2012年7月10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→30.46 Å / Num. obs: 31598 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / 冗長度: 6.8 % / Biso Wilson estimate: 77.85 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.9
反射 シェル解像度: 2.95→3.06 Å / 冗長度: 5.3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / % possible all: 93.7

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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
XDS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: 1URN AND 4BW0

1urn

4bw0


解像度: 2.95→30.456 Å / SU ML: 0.37 / σ(F): 1.34 / 位相誤差: 21.69 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2107 1598 5.1 %
Rwork0.167 --
obs0.1692 31541 95.44 %
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: 73.6 Å2
精密化ステップサイクル: LAST / 解像度: 2.95→30.456 Å
タンパク質核酸リガンド溶媒全体
原子数4878 1486 10 0 6374
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0086621
X-RAY DIFFRACTIONf_angle_d1.1749244
X-RAY DIFFRACTIONf_dihedral_angle_d15.292746
X-RAY DIFFRACTIONf_chiral_restr0.0771106
X-RAY DIFFRACTIONf_plane_restr0.005913
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.04510.33511500.29932606X-RAY DIFFRACTION93
3.0451-3.15390.31561500.24692621X-RAY DIFFRACTION93
3.1539-3.280.30711340.23152621X-RAY DIFFRACTION93
3.28-3.42910.21291610.21452617X-RAY DIFFRACTION93
3.4291-3.60960.27121260.19352611X-RAY DIFFRACTION92
3.6096-3.83540.21951310.17032635X-RAY DIFFRACTION92
3.8354-4.13080.20261510.14682678X-RAY DIFFRACTION95
4.1308-4.54530.19691440.13672857X-RAY DIFFRACTION100
4.5453-5.20020.1691510.13322870X-RAY DIFFRACTION100
5.2002-6.5410.18961540.15822881X-RAY DIFFRACTION100
6.541-30.45730.1851460.15712946X-RAY DIFFRACTION98
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)
18.27624.0192-0.93373.4921-2.50582.8394-0.85130.7631.04010.20340.39841.01190.2808-1.2501-0.29970.33430.07290.32850.54950.15560.7052-75.6492-30.6821-23.2905
21.5428-2.21870.12213.2414-0.08330.14550.6434-1.08670.23790.8689-0.75911.23180.0680.25660.05990.5407-0.01540.17730.5242-0.04270.3862-68.6544-20.5855-14.5249
32.5374-0.43344.3660.0884-0.77457.5109-0.5362-0.01460.3501-0.69420.3102-0.54660.1004-1.0652-0.26440.6121-0.07290.23250.3844-0.12291.1292-59.6629-12.593-17.1925
43.8842-0.2176-2.00463.6307-1.9993.14380.3648-0.06761.0086-0.49950.3294-0.6692-0.34770.7644-0.44840.5020.05910.14350.4146-0.10440.5355-57.7744-19.5886-19.8044
51.7180.5022.20371.0071-0.8737.39820.45140.50040.2440.13220.6976-0.0254-0.3131.3695-0.73980.4027-0.0713-0.01160.2761-0.10370.3412-58.8978-29.221-19.946
67.612-1.54822.01343.9655-4.44435.06940.11931.59120.59880.8554-0.1734-0.0528-0.6793-0.06350.03170.44080.06380.10010.52410.01760.4264-62.7424-29.796-26.5822
72.47030.8760.6771.38090.85991.00460.0766-0.2270.42360.11940.0128-0.0106-0.05450.0828-0.10240.37020.06060.11870.35970.04240.4378-68.256-24.3259-20.2359
84.16071.6034-1.12683.1994-1.24314.6645-0.2017-1.94811.0307-0.0058-0.51070.15420.87230.26440.61560.5764-0.00440.1080.459-0.14290.5011-62.0162-22.7505-8.8488
94.5753-0.2785-0.60533.0645-0.21854.75590.41980.25631.03490.3978-0.06930.8376-0.6756-0.6503-0.1510.50430.01620.19940.4206-0.01680.5581-75.1367-25.2377-21.4673
106.65413.34561.26987.054-0.42416.17720.23622.0490.0156-0.05480.16370.30370.3416-0.0751-0.10340.23920.01830.04450.5847-0.03110.5341-74.8324-27.0283-36.3816
112.6019-1.21870.23172.9102-1.54230.86960.3556-0.3042-0.53190.0775-0.6361-0.2930.06810.40640.26630.5973-0.1751-0.19290.5657-0.00010.5372-42.9966-31.0094-7.6235
129.0634-0.88511.22273.5283-1.05561.33190.3409-0.0173-0.4176-0.556-0.1-0.26470.02130.4128-0.16040.5626-0.1223-0.0350.6708-0.04540.3694-45.0368-24.5029-22.9486
135.1906-1.4784-1.75181.8284-0.67452.92070.5633-0.24871.0670.31090.0598-1.2266-1.90740.7101-0.53990.8848-0.2409-0.070.4308-0.04110.4456-50.5763-22.1388-13.4033
140.5177-0.1194-0.02650.6546-0.82671.550.0496-0.19751.32950.9464-0.07230.34210.00210.41030.18590.7158-0.2402-0.06150.6455-0.19340.763-47.1887-21.6334-6.5713
154.7413-1.25941.57841.08131.58145.76-0.9819-0.21040.1286-1.5545-0.0397-0.81470.5773-0.7810.77470.924-0.0553-0.09070.8617-0.14671.1015-34.3948-29.5259-20.2391
160.0931-0.19110.12963.174-2.45512.38660.16910.27270.03482.11110.7328-0.32090.8445-0.9364-0.26270.7726-0.1676-0.05430.6628-0.23170.5222-46.0249-26.9095-2.6531
173.617-1.0560.09891.911-0.7643.09330.5226-0.0459-0.34370.7433-0.3076-0.24520.2297-0.168-0.2770.7393-0.17780.03760.4388-0.08260.4031-52.611-33.7644-12.5159
186.53291.69012.85612.3831-0.90212.9813-0.0535-0.4471-1.0505-0.3280.1176-1.096-0.07870.1534-0.41470.8181-0.2442-0.06850.5350.06410.7048-42.3666-34.5712-5.3481
190.86410.34130.47391.7933-0.32070.40520.2624-0.3757-0.0990.28330.0413-0.15-0.1566-0.05670.2740.6811-0.6515-0.83770.7406-0.42640.4584-32.961-24.4781-5.0309
202.5668-1.4698-1.74836.81760.03171.3485-0.2199-0.44860.24840.6139-0.462-0.8499-1.27350.8714-0.04070.1454-0.5904-0.99151.1182-0.3996-0.4449-31.1116-22.784-12.4734
213.4326-0.233-3.06486.5426-0.893.07411.18720.48751.5111-0.0009-0.1947-0.44430.0732-1.1401-0.38710.94450.14740.13250.8530.3861.1445-40.608128.331-26.4703
227.08930.1564-2.50712.00072.00175.7918-1.33451.4973-0.6256-0.59480.34761.1149-0.26470.60640.67471.10820.44310.03341.20230.18470.8214-45.002618.0096-32.1973
236.85360.97361.1623.4441-0.38328.11110.69531.6036-1.4710.18960.08470.47611.2851-0.567-1.10471.04070.0387-0.07811.25-0.06940.7078-43.9727.5553-32.1949
243.9172-0.70460.57543.41530.6184.01980.50440.46440.2229-0.3003-0.48880.1662-0.65721.0466-0.00740.70940.01060.18570.54580.06610.4758-36.954613.7587-19.1823
256.45963.50250.72114.7971-1.33321.14620.9742-0.07471.64271.42740.1916-2.04280.21351.0856-0.61170.79860.07210.10170.5775-0.04771.0331-34.154520.365-13.2691
265.03230.234-2.02015.5585-3.09284.2825-0.09680.03580.89740.53130.0513-1.2136-0.76670.14090.35230.8235-0.18380.2111.54130.18220.987-25.769718.1735-19.9949
271.2682-0.62150.68673.74971.18681.84260.18320.09160.7313-1.12380.5747-0.58040.3018-0.393-0.20380.9109-0.08010.2180.95610.41870.6996-35.894921.943-24.1639
283.88690.3156-0.33193.70370.73472.3727-0.4450.84010.7132-0.93350.42430.5284-0.2657-0.22050.05990.9950.14840.03330.5709-0.05320.5173-46.978913.78-21.5184
292.3919-0.1547-0.23410.6177-0.69393.076-1.4121.3452-0.8770.07970.95410.02960.9721-0.51470.25961.54990.00720.41441.48340.10780.6546-36.006213.6107-37.0197
301.71740.306-0.30061.3401-0.4930.20340.21950.9183-0.2699-0.48110.1889-0.40490.05160.1261-0.35251.39540.12670.28411.26230.41291.1263-32.366826.822-32.8516
315.40820.73332.06171.9924-1.71357.01710.8118-0.78520.45180.7274-0.1253-0.5450.6924-1.37270.13671.0777-0.1528-0.14351.47520.43750.7821-35.42521.7191-7.2786
321.8097-0.70341.49636.16810.31944.6397-0.28820.2164-0.57930.39610.22681.03750.6659-0.27350.04020.7654-0.00740.03710.5595-0.01150.7309-50.560.2023-13.1096
331.83381.11710.95494.2545-2.38162.9344-0.10170.169-0.11011.0932-0.3560.36080.13550.22890.49051.0514-0.07510.56160.6718-0.16881.126-68.9208-3.5843-6.7265
340.5193-1.02930.36992.54640.45072.05220.9436-0.66790.56410.41060.36880.7689-0.4534-0.0321-0.12110.64050.08720.38870.6101-0.10540.9973-75.592-15.9977-17.0484
354.66483.97554.06074.20321.48568.2079-0.16350.78151.2309-0.05790.10111.011-2.00151.4807-0.02870.96780.18420.31810.98610.11591.1605-71.9806-9.5149-29.2649
360.59940.43940.46820.54270.55080.44550.2225-0.4884-0.2483-0.0655-0.49661.02960.5591-0.22330.22280.9812-0.02180.20870.4805-0.09071.0874-62.84695.0086-12.1359
372.5049-1.0751-0.52670.74930.95522.7274-0.0803-0.6923-0.451-0.1156-0.05480.539-0.43140.1448-0.14980.7741-0.04040.11480.39280.08240.5049-45.4568.3048-11.662
381.13370.62051.39781.1050.18422.33110.3694-0.23820.00541.3508-0.4016-0.0919-0.40240.43170.19020.8665-0.0490.04160.93080.31320.7634-41.7766-5.8004-6.6041
394.2846-1.33181.28942.8678-1.98255.7537-0.38660.83120.1783-0.3792-0.1247-1.38050.37641.7380.50660.20470.0132-0.08530.5934-0.0360.491614.077131.1987-27.5637
401.4468-0.8358-0.95981.06981.00111.3048-0.2496-1.297-0.0931.0824-0.95020.04030.53790.3774-1.1417-0.36610.0027-0.17060.45630.01460.54667.228818.5087-16.6939
413.9210.5602-2.2498.29974.31624.8318-0.48450.2772-0.569-0.61340.91521.1083-0.4838-1.7711-0.22470.3047-0.1184-0.10870.74960.13630.7394-3.558814.4436-18.2014
425.9953-0.0661-1.79121.5862-0.83051.1399-0.06181.11410.1205-0.21850.050.5307-0.4054-0.25010.05660.3418-0.0722-0.0720.41760.08170.2944-2.816124.2999-18.4902
436.60571.21520.40956.71870.77239.1046-0.2119-0.0117-0.5678-0.3485-0.73390.5509-0.3213-0.11070.26170.3990.18370.09260.4034-0.04910.5335-1.521433.2628-21.1757
441.7914-1.51030.49055.1067-0.46161.7515-0.01020.0179-0.8373-0.42470.36730.04560.2818-0.1174-0.21510.2224-0.0335-0.00850.36060.06050.45065.037717.8675-23.64
455.68442.372-0.86491.99874.85422.75540.2721-0.41751.0628-0.1985-1.28331.677-0.3674-0.44020.52830.2943-0.0930.09340.6121-0.17120.65944.363935.2648-27.1683
462.17880.1765-1.08392.689-0.12622.14230.1445-0.3726-0.67380.5998-0.07320.2453-0.10580.48550.02830.2791-0.0555-0.10160.39590.0990.44346.302327.1976-12.4199
473.90950.0080.92652.66230.46762.5145-0.14080.9005-0.0820.6937-0.0848-0.44960.58290.20370.10580.34510.0115-0.01260.3839-0.02040.476310.450425.3685-28.5156
482.74982.41690.80463.047-1.86037.5251-0.03891.1174-0.305-1.0178-0.4252-0.6540.68510.00190.46340.30690.16230.07230.6970.12160.76628.200227.0783-40.8616
493.2731-0.2438-0.06143.7232-0.00831.03270.6887-0.720.44460.5982-0.46980.42410.91910.0152-0.19660.7231-0.09850.18130.7110.12610.4309-12.591730.2693-0.7896
509.24440.7460.21271.3655-0.56182.01690.41940.6149-1.69590.2936-0.6797-0.00450.6916-1.235-0.1630.6076-0.09810.0611.01920.10110.7536-16.497124.276-16.2421
512.7988-0.29920.63711.8122-0.39242.19840.0042-0.4238-0.72630.64440.3240.1693-0.3992-0.676-0.43140.5864-0.00020.17870.60060.15830.5864-7.90621.1666-5.2919
521.3951-1.4226-1.68591.82050.61915.56890.4818-1.0261.2847-0.02970.1044-0.1407-0.7664-0.7009-0.50320.60870.0725-0.30260.98730.06181.2373-22.729328.1387-13.3047
531.75130.9741-1.24215.36842.44122.93540.6722-0.83470.07591.5694-0.06450.7031-0.2317-0.8836-0.33390.7183-0.07480.2850.87770.14550.4749-8.991825.09682.9182
542.0231-0.0667-0.13637.9979-2.28715.07180.1749-0.65550.68151.66160.28650.1768-0.33710.0816-0.60080.7439-0.04210.03690.49920.02290.4889-2.184632.11960.6013
551.5458-0.5931.83163.1279-1.66945.1439-0.27570.8830.30850.4975-0.07960.0024-0.8638-0.65580.09080.3555-0.06420.11710.6110.06610.5433-6.801133.2197-11.3316
564.28141.2992-2.32311.2571-1.31891.95160.2096-0.82430.33160.13720.84520.6323-0.7867-0.2263-0.67731.1267-0.14020.38750.89820.08440.7575-11.053234.0740.7455
571.4291.45120.98481.92230.73080.86010.4673-0.2381-0.07380.81290.3732-0.3309-0.74760.28210.01321.0668-0.1540.40141.9377-0.0210.9522-19.581825.03596.4487
580.78570.58040.84022.3603-0.59991.6599-0.1937-0.49060.167-0.2368-0.21760.48150.3922-0.1234-0.02090.4552-0.30580.31761.51140.62191.1926-24.37921.993-1.5638
592.3505-0.1396-0.08532.96790.40914.17880.22571.0441-1.5605-0.4121-0.52660.0983-0.3189-2.53370.2340.6933-0.17050.02520.8363-0.28110.8321-23.028-22.8025-29.5307
604.8069-1.2881-0.64662.61110.99753.6015-0.78730.8078-0.42510.22130.35990.0091-0.94270.21670.16741.16070.06520.08821.04720.0020.5317-16.8123-6.9673-34.4155
611.1928-1.3495-0.20681.69520.4722.6821-0.1834-0.23510.3663-0.1431-0.39670.2419-0.4770.28060.32090.63090.04850.04230.6442-0.08860.352-23.5554-5.2166-19.7504
622.95130.2767-0.8454.4251.92611.17410.420.6250.6831-0.18180.23770.3271-0.0411-0.69050.09750.8940.1649-0.07760.6185-0.02170.301-29.7869-3.6777-24.8218
637.49290.7831-0.87942.8556-0.27065.10840.50330.4798-1.1617-0.1421-0.0514-0.06710.026-0.4115-0.38970.5999-0.0041-0.0460.3909-0.10550.4249-24.7269-16.0045-22.9084
649.23165.0209-3.42175.8775-0.73167.39110.2060.9628-0.4362-1.03770.7137-0.65960.03990.5031-0.42320.53810.04790.1740.829-0.20620.6355-10.6829-12.1981-26.935
652.592-0.298-0.84965.4654-1.56054.5823-0.23060.5426-0.1089-0.18270.0473-0.5964-0.3487-0.3040.11450.544-0.0020.08820.44750.08380.3674-14.3777-7.9415-23.541
664.88760.0076-0.48553.73581.12912.8057-0.09931.77091.083-0.8599-0.0752-0.72080.09010.22580.44331.52760.0007-0.12430.94120.3370.6586-23.32760.0747-35.7679
670.01020.0748-0.06051.3156-1.23351.13890.01151.44460.9375-0.67050.46260.4325-0.99761.3655-0.27381.2118-0.1764-0.14981.33570.11960.813-25.4447-7.4999-40.5352
682.27460.0174-0.91921.13762.46135.7370.17150.09680.4768-0.29220.20570.005-1.13030.13290.57661.80750.4690.07991.2577-0.47710.2674-29.3959-17.5298-38.5589
697.97514.5346-4.92185.3235-0.55544.86111.0836-0.47130.00282.44310.30410.33991.48881.6051-0.81080.99-0.25950.09880.879-0.14660.5131-23.5354-0.0964-7.5716
705.14940.3777-1.65783.2631.0734.00350.16971.66-0.42020.4288-0.1721-1.1737-1.29110.9188-0.16810.7451-0.1572-0.14810.52670.07730.9419-8.11861.0981-13.7967
713.37191.06632.28766.7155-0.62112.64620.0707-1.88760.4201-0.1096-0.4489-1.29440.19790.17290.38370.4532-0.0115-0.19220.70490.25651.021110.68422.452-10.4748
721.2682-0.6776-0.41244.1180.8352.89660.7101-0.26-1.28480.44140.2664-1.2688-0.01960.0257-0.58430.3138-0.0354-0.07650.52240.05390.72513.024515.7686-23.7849
732.6686-0.0154-0.58974.24920.10910.2714-0.3950.6024-1.8347-0.16540.3552-0.3124-0.3698-0.3656-0.12570.5296-0.0767-0.13420.66430.05990.81376.33735.6087-28.6778
742.00373.06051.66880.78050.34020.51650.9378-1.84980.2417-0.6687-0.5459-0.92910.4315-0.122-0.66150.7539-0.14340.14030.65190.18911.47133.7693-6.4681-14.8053
752.979-0.33280.53895.85510.41334.12230.4664-0.4506-0.4025-0.2243-1.43110.15010.55260.44320.64790.7292-0.1771-0.09490.44990.06130.5293-12.761-6.6557-13.8154
761.34861.50431.57295.3093-0.83913.73920.13530.20920.95821.06450.0475-0.5171-0.49770.8959-0.45731.0234-0.2748-0.06050.7453-0.0780.7242-16.33266.2781-5.5677
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