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- PDB-5vxn: Structure of two RcsB dimers bound to two parallel DNAs. -

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基本情報

登録情報
データベース: PDB / ID: 5vxn
タイトルStructure of two RcsB dimers bound to two parallel DNAs.
要素
  • DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
  • Transcriptional regulatory protein RcsB
キーワードdna binding protein/dna / Rcs phosphorelay / response regulator / FixJ/NarL / Center for Structural Genomics of Infectious Diseases / CSGID / DNA-binding protein / dna binding protein-dna complex
機能・相同性
機能・相同性情報


regulation of capsule organization / regulation of carbohydrate catabolic process / single-species biofilm formation on inanimate substrate / cellular stress response to acidic pH / regulation of bacterial-type flagellum-dependent cell motility / positive regulation of cell projection organization / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / transcription regulator complex ...regulation of capsule organization / regulation of carbohydrate catabolic process / single-species biofilm formation on inanimate substrate / cellular stress response to acidic pH / regulation of bacterial-type flagellum-dependent cell motility / positive regulation of cell projection organization / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / transcription regulator complex / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol
類似検索 - 分子機能
Transcriptional regulatory protein RcsB / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain ...Transcriptional regulatory protein RcsB / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Transcriptional regulatory protein RcsB
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 解像度: 3.375 Å
データ登録者Filippova, E.V. / Minasov, G. / Pshenychnyi, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 米国
引用ジャーナル: MBio / 年: 2018
タイトル: Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB.
著者: Filippova, E.V. / Zemaitaitis, B. / Aung, T. / Wolfe, A.J. / Anderson, W.F.
履歴
登録2017年5月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年3月7日Provider: repository / タイプ: Initial release
改定 1.12018年3月14日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
改定 1.22019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32024年3月13日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Transcriptional regulatory protein RcsB
B: Transcriptional regulatory protein RcsB
E: DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
F: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')
C: Transcriptional regulatory protein RcsB
D: Transcriptional regulatory protein RcsB
G: DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
H: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')


分子量 (理論値)分子数
合計 (水以外)116,8538
ポリマ－116,8538
非ポリマー00
水21612
1
A: Transcriptional regulatory protein RcsB
B: Transcriptional regulatory protein RcsB
E: DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
F: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')


分子量 (理論値)分子数
合計 (水以外)58,4264
ポリマ－58,4264
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-59 kcal/mol
Surface area23490 Å2
手法PISA
2
C: Transcriptional regulatory protein RcsB
D: Transcriptional regulatory protein RcsB
G: DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
H: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')


分子量 (理論値)分子数
合計 (水以外)58,4264
ポリマ－58,4264
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-61 kcal/mol
Surface area23710 Å2
手法PISA
単位格子
Length a, b, c (Å)74.116, 113.231, 76.868
Angle α, β, γ (deg.)90.00, 115.37, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Transcriptional regulatory protein RcsB / Capsular synthesis regulator component B


分子量: 23699.600 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rcsB, b2217, JW2205 / プラスミド: pCA24n / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 DE3 magic / 参照: UniProt: P0DMC7
#2: DNA鎖 DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')


分子量: 5562.653 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli (大腸菌)
#3: DNA鎖 DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')


分子量: 5464.577 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli (大腸菌)
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 12 / 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: 2.49 Å3/Da / 溶媒含有率: 50.68 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 / 詳細: 0.2 M Sodium Chloride, 0.1 M HEPES, 25% PEG3350

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 21-ID-G / 波長: 0.97857 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2016年6月16日 / 詳細: beryllium lenses
放射モノクロメーター: C(111) / 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: 3.37→113.23 Å / Num. obs: 15089 / % possible obs: 93 % / 冗長度: 4.3 % / Biso Wilson estimate: 103 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
反射 シェル解像度: 3.37→3.39 Å / 冗長度: 4.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / Num. unique all: 163 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10_2155: ???)精密化
XDSdata processing
XDSデータスケーリング
PHASER位相決定
BLU-MAXデータ収集
Cootモデル構築
精密化解像度: 3.375→56.615 Å / SU ML: 0.5 / σ(F): 1.36 / 位相誤差: 29.84 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2683 794 5.28 %
Rwork0.1985 --
obs0.202 15041 92.76 %
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: 3.375→56.615 Å
タンパク質核酸リガンド溶媒全体
原子数6141 1464 0 12 7617
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0037854
X-RAY DIFFRACTIONf_angle_d0.55610912
X-RAY DIFFRACTIONf_dihedral_angle_d18.4864584
X-RAY DIFFRACTIONf_chiral_restr0.0411314
X-RAY DIFFRACTIONf_plane_restr0.0031118
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3755-3.58690.3267940.28341874X-RAY DIFFRACTION74
3.5869-3.86380.32191320.26732559X-RAY DIFFRACTION99
3.8638-4.25250.31751090.22852270X-RAY DIFFRACTION88
4.2525-4.86760.27921160.19712548X-RAY DIFFRACTION99
4.8676-6.13140.27261970.20072486X-RAY DIFFRACTION99
6.1314-56.62340.22011460.15592510X-RAY DIFFRACTION96
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)
10.4249-0.3804-0.71740.9705-0.12921.4549-1.6904-0.29330.0045-1.08880.0171-0.0285-0.17060.2304-0.05120.51070.0393-0.08341.177-0.28850.922721.6213-33.146586.4114
26.5274-3.3668-0.20784.0963-0.02550.00060.4770.55851.193-0.37280.55550.53011.9831-2.32620.32960.9853-0.0485-0.06141.390.21150.685523.1362-25.709780.67
31.144-0.7527-1.43322.5441.60373.0516-0.2976-0.0684-0.22780.0167-0.44310.5994-0.0993-0.5751-1.34390.4963-0.0610.04061.14480.06290.494723.2006-32.165392.2953
43.1308-0.308-2.25674.843-0.2273.04940.0123-1.7622-2.8021-0.2996-1.28541.06710.55231.2234-1.73450.5698-0.29810.58390.92531.1081-0.244528.6266-40.23395.1987
51.4609-0.4446-0.33890.40820.68620.61440.5432-0.0091-0.57310.154-0.65711.14071.11410.0806-0.00010.9224-0.04770.15961.0208-0.05450.903333.6249-39.554182.1954
60.24880.46060.03330.7137-0.04230.00470.2532-0.3236-0.9261.03391.4548-2.25792.6193-0.18350.13030.9556-0.2007-0.5211.5043-0.39812.706626.1303-47.449979.123
70.4547-0.07250.13460.9827-0.89260.75510.91682.4619-1.3505-3.30550.63881.97312.68920.67450.06591.41-0.20620.17351.0911-0.20721.449642.8889-44.036677.3289
81.44671.1830.06770.8022-0.00370.32930.9595-2.47820.1866-2.0533-0.09890.48731.4161-1.05260.0082-1.80032.5775-1.8455-0.41441.6969-0.507331.6882-14.717969.7349
92.53780.1515-1.72243.5779-1.15834.4586-0.18120.7774-2.7291-1.3048-0.12350.43480.7329-1.1689-1.29630.1171-0.1789-0.17061.11720.07021.210227.6102-21.756974.1546
101.21580.24070.70191.2798-0.30170.5488-0.50210.98880.91170.22560.32210.2619-0.0787-0.9081-00.79720.1771-0.00890.93910.13880.673833.4871-14.813766.1849
111.39620.06540.51620.0627-0.1560.9103-0.07120.73370.5175-0.3480.37610.7203-0.3028-0.0320.00060.84060.10850.06750.93130.160.765547.7165-14.585271.203
120.69450.52710.39720.32740.17690.09851.11380.3271-0.42180.1032-1.5251-0.6103-0.19990.9938-0.03770.79930.20480.3480.88650.14051.116539.0598-8.8372.0288
130.7280.26910.00061.8331-2.14072.9346-1.0523-1.1438-0.7191.72122.22690.5819-2.40111.1660.05251.5433-0.07750.65961.2617-0.40261.988744.0329-12.107186.2788
145.36094.7339-3.75667.3419-8.53662.01790.2061-0.30892.5472-1.84250.2270.29680.8338-0.94140.26811.16540.01770.35850.7152-0.11530.778738.2512-7.158479.9567
153.25772.61225.31612.46394.20568.92232.4485-0.58210.93830.1145-0.77410.57111.2585-0.47971.19340.85630.64270.33361.2171-0.0921.585128.0374-9.764580.6802
160.91120.28940.3050.24490.09980.0914-2.8365-0.693-0.4749-0.34630.31560.37290.0668-0.7083-0.09091.43330.45150.10521.629-0.62231.838933.139-4.92489.1043
170.1474-0.11380.23850.0479-0.17910.3911-1.46130.58311.4487-1.31281.1824-0.0683-0.56020.10970.00051.6467-0.0272-0.21781.05920.22441.468169.0165-50.083292.3429
180.247-0.0491-1.070.20830.86942.31770.4864-0.6715-0.32760.1337-0.4438-3.3557-0.6030.28370.00971.0726-0.0948-0.16011.0083-0.16611.643371.9477-28.150386.3891
190.0333-0.0350.06730.0304-0.0111-0.00910.3093-0.18863.95560.4073-1.3957-0.2743-0.6302-0.7794-0.00041.4185-0.0208-0.12531.0984-0.08872.125872.5467-5.385983.6818
200.0884-0.25620.21650.5334-0.5650.35310.74490.6283-0.13831.1338-1.2605-0.0667-0.1587-0.81530.00271.2305-0.2720.12430.8406-0.09491.507766.4654-11.223482.1079
21-0.115-0.26570.08491.7817-1.19522.11671.0162-0.2727-0.48060.7754-0.9228-2.6416-0.53510.694-0.02530.9530.0213-0.00361.0221-0.08211.405172.0924-32.688686.7328
220.031-0.05520.1360.0331-0.09760.07471.4761-1.1499-0.9056-0.7199-0.93460.1096-0.5690.7861-0.00331.46790.0010.07211.14040.02641.482873.2633-55.543887.3815
230.6182-0.4846-1.0140.94620.07331.78680.01490.4343-0.51020.2814-0.31940.10040.46150.4930.00060.9362-0.17770.1440.8002-0.04511.105911.5406-30.2952120.6757
241.5876-1.9499-0.88872.4291-0.05294.2313-0.04760.0431-0.42710.7588-0.16540.84830.4798-0.2702-0.00091.0063-0.17670.14230.6948-0.07740.713815.0095-36.4383129.7908
250.36240.4328-0.21090.78680.33830.3773-0.29010.63170.8194-0.88710.64072.5193-0.24040.49370.00250.8306-0.15690.10440.88320.05480.803930.5312-40.2737122.6961
26-0.140.13050.14130.10890.27540.3484-0.20420.7954-0.25130.5784-0.04570.03170.82480.3648-0.01680.6948-0.1409-0.11090.8441-0.08030.589118.3954-41.6269115.1885
275.49842.904-3.93657.0806-6.52676.41271.25351.68480.2085-2.1651.1941-1.35011.81071.59731.90881.23110.05840.05020.9236-0.38911.033233.3307-44.0935113.3265
280.28080.1674-0.49530.22290.34221.6261-0.01470.6835-0.1269-0.5342-0.15490.4750.1609-0.9994-0.51480.63170.0217-0.08791.00450.43310.807818.3192-18.9846110.4563
290.40920.4522-0.64851.79730.12312.53770.72331.63341.2184-0.5499-0.89711.1555-0.8171-1.0925-0.22150.94090.4582-0.3750.86080.5353-0.126720.4982-15.8093105.3135
302.37711.2191-0.79690.25780.12371.44950.2710.795-0.0704-0.56740.0224-0.121-0.54720.003-00.7981-0.0940.02790.77160.1210.719532.0136-13.328107.4417
311.5761-0.5396-0.8599-0.1722-0.00120.65350.0606-0.06731.0820.30190.70330.6739-0.93570.320.04821.01820.17160.11550.4610.02730.997431.1647-11.2775118.7071
320.35120.1307-0.22910.2373-0.72831.93020.17110.11560.8646-0.123-0.09240.573-0.0069-1.0707-0.00620.83910.10650.08590.59250.04970.88920.7267-10.5454120.2198
332.14371.18540.99690.64880.50840.4278-0.24261.2671-0.16960.43291.5032.0625-0.45930.78160.0141.37750.24340.00460.92820.01851.317224.2909-2.2724123.5423
343.83693.6975-4.09323.7965-3.39875.737-0.0583-1.1473-0.31151.2931-0.5651.413-1.55190.79520.05621.16950.2215-0.3660.9460.1021.25259.6766-49.7694125.869
350.86950.0252-0.33870.0684-0.33010.1024-0.83570.72611.2583-0.4327-0.3534-2.46190.22570.0979-0.00490.99320.11550.1240.88520.05811.559962.8748-36.3538115.3363
360.1373-0.20690.49840.6786-0.87070.80520.3024-0.9285-0.0744-1.3019-0.6931-1.606-1.0438-0.22690.00451.1305-0.0924-0.23490.8977-0.11781.380860.7922-19.6329122.9426
370.3882-0.2666-0.98830.23220.50923.34891.4321-0.32070.2763.3173-3.2945-1.6318-1.15780.2617-0.10921.8331-0.0744-0.38471.0895-0.17852.383762.1203-5.4131116.2296
380.0420.2704-0.14990.6-0.274-0.00031.099-1.1372-0.52870.48840.3444-1.60110.55510.68770.0141.3581-0.1688-0.08840.9044-0.05241.710255.6673-11.3115.6728
390.3765-0.1301-0.40910.06720.20640.14780.14220.670.59170.5302-0.489-2.5686-0.5830.78810.01631.157-0.1229-0.19831.17240.0092.01765.9827-24.6965120.842
400.5766-1.03561.24481.3671-1.73631.9621-0.383-0.0377-1.23370.12820.627-1.20460.19440.44790.16510.8377-0.0715-0.14370.7246-0.20461.292857.8155-41.0208117.6117
41-0.02590.0380.03840.56720.37160.2217-0.17450.6518-2.4092-0.97590.0856-0.4823-0.9321-0.105-0.00451.08140.23150.02141.23410.12011.374363.132-55.464120.428
423.5637-3.2425-0.09822.3872-0.160.6343-0.1694-0.10360.60840.46410.4522-1.0339-0.09880.08640.01250.5465-0.1857-0.05870.4878-0.0960.845646.4936-18.2352120.1058
432.31471.6151.52298.4356-4.83125.80060.0012-1.10440.13261.50561.05430.72251.41861.07263.04531.0454-0.00620.02690.7119-0.15230.631543.1854-23.4488132.2163
444.1319-0.3844-3.48082.67462.62635.5634-1.6167-0.584-1.28421.844-0.137-0.53581.9497-1.9632-1.08580.84850.3568-0.3260.94940.14840.547355.1094-44.822397.0499
450.30551.12810.05923.64860.0181-0.01790.4058-1.77430.5027-0.31590.0348-1.8522-0.8572-0.0399-0.06971.33610.09-0.24960.8622-0.04640.867865.6855-38.7822100.8414
460.9333-0.40451.7951.3163-0.00192.6962-0.1763-1.0207-1.2922-0.02120.30470.30890.058-0.6867-0.00030.82030.15360.04250.94420.04250.954955.2933-39.80790.1885
477.49793.4791-5.21362.4427-1.51874.71110.5514-0.36531.82520.59312.02230.5656-2.12451.07165.08010.29880.403-0.62160.4733-0.07230.482252.5053-15.508585.3228
480.3776-0.27450.04320.72670.55430.5396-0.2097-0.04271.8807-0.61561.07630.1724-0.21820.06310.00710.50120.0483-0.05630.772-0.00040.881758.0185-22.939678.0614
496.8434-1.40380.24871.8414-1.11510.8097-1.105-3.39330.76790.3096-0.2928-0.4826-1.75920.2105-5.70561.0163-0.1363-0.23050.579-0.57221.053556.3659-19.960692.2374
508.7034.71043.93935.29162.23621.7175-0.283-3.13490.62680.8677-0.02520.8672-0.0920.7786-0.59210.74750.21970.08281.24440.5420.199646.398-44.5271132.4015
510.14440.1938-0.15490.3032-0.05970.1476-0.3443-2.8497-0.01821.25420.7145-0.62720.35361.3773-0.00141.1050.2572-0.221.1295-0.11650.986357.3807-38.3349134.4699
527.74281.93080.45131.56320.2853-0.00210.30931.2153-1.4643-0.7703-0.5743-0.7901-0.0161-0.392-0.04780.83280.2268-0.08540.81710.14530.368251.0834-43.4876124.4822
530.2819-0.10640.52080.8228-1.4473.10360.7327-0.57080.35310.17120.74831.3758-1.557-2.10.08080.91330.00920.06790.736-0.01370.63839.8531-36.7675126.3919
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 131 )
7X-RAY DIFFRACTION7chain 'A' and (resid 132 through 141 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 12 )
9X-RAY DIFFRACTION9chain 'B' and (resid 13 through 23 )
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 55 )
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 87 )
13X-RAY DIFFRACTION13chain 'B' and (resid 88 through 101 )
14X-RAY DIFFRACTION14chain 'B' and (resid 102 through 108 )
15X-RAY DIFFRACTION15chain 'B' and (resid 109 through 124 )
16X-RAY DIFFRACTION16chain 'B' and (resid 125 through 139 )
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 5 )
18X-RAY DIFFRACTION18chain 'E' and (resid 6 through 15 )
19X-RAY DIFFRACTION19chain 'E' and (resid 16 through 18 )
20X-RAY DIFFRACTION20chain 'F' and (resid 20 through 24 )
21X-RAY DIFFRACTION21chain 'F' and (resid 25 through 34 )
22X-RAY DIFFRACTION22chain 'F' and (resid 35 through 37 )
23X-RAY DIFFRACTION23chain 'C' and (resid 2 through 24 )
24X-RAY DIFFRACTION24chain 'C' and (resid 25 through 87 )
25X-RAY DIFFRACTION25chain 'C' and (resid 88 through 101 )
26X-RAY DIFFRACTION26chain 'C' and (resid 102 through 131 )
27X-RAY DIFFRACTION27chain 'C' and (resid 132 through 143 )
28X-RAY DIFFRACTION28chain 'D' and (resid 3 through 23 )
29X-RAY DIFFRACTION29chain 'D' and (resid 24 through 45 )
30X-RAY DIFFRACTION30chain 'D' and (resid 46 through 77 )
31X-RAY DIFFRACTION31chain 'D' and (resid 78 through 101 )
32X-RAY DIFFRACTION32chain 'D' and (resid 102 through 123 )
33X-RAY DIFFRACTION33chain 'D' and (resid 124 through 140 )
34X-RAY DIFFRACTION34chain 'G' and (resid 1 through 5 )
35X-RAY DIFFRACTION35chain 'G' and (resid 6 through 10 )
36X-RAY DIFFRACTION36chain 'G' and (resid 11 through 15 )
37X-RAY DIFFRACTION37chain 'G' and (resid 16 through 18 )
38X-RAY DIFFRACTION38chain 'H' and (resid 20 through 24 )
39X-RAY DIFFRACTION39chain 'H' and (resid 25 through 29 )
40X-RAY DIFFRACTION40chain 'H' and (resid 30 through 34 )
41X-RAY DIFFRACTION41chain 'H' and (resid 35 through 37 )
42X-RAY DIFFRACTION42chain 'K' and (resid 148 through 193 )
43X-RAY DIFFRACTION43chain 'K' and (resid 194 through 208 )
44X-RAY DIFFRACTION44chain 'L' and (resid 149 through 164 )
45X-RAY DIFFRACTION45chain 'L' and (resid 165 through 178 )
46X-RAY DIFFRACTION46chain 'L' and (resid 179 through 209 )
47X-RAY DIFFRACTION47chain 'M' and (resid 150 through 163 )
48X-RAY DIFFRACTION48chain 'M' and (resid 164 through 178 )
49X-RAY DIFFRACTION49chain 'M' and (resid 179 through 207 )
50X-RAY DIFFRACTION50chain 'N' and (resid 149 through 164 )
51X-RAY DIFFRACTION51chain 'N' and (resid 165 through 178 )
52X-RAY DIFFRACTION52chain 'N' and (resid 179 through 193 )
53X-RAY DIFFRACTION53chain 'N' and (resid 194 through 209 )

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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