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- PDB-5oki: Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in compl... -

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基本情報

登録情報
データベース: PDB / ID: 5oki
タイトルCrystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon
要素
  • Chromosome transmission fidelity protein 18
  • Chromosome transmission fidelity protein 8
  • DNA polymerase epsilon catalytic subunit A
  • Sister chromatid cohesion protein DCC1
キーワードREPLICATION / Clamp loader DNA-binding protein DNA polymerase Winged-helix domain
機能・相同性
機能・相同性情報


maintenance of mitotic sister chromatid cohesion / gene conversion / DNA replication initiation / epsilon DNA polymerase complex / Ctf18 RFC-like complex / maintenance of DNA trinucleotide repeats / SUMO binding / DNA clamp loader activity / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity ...maintenance of mitotic sister chromatid cohesion / gene conversion / DNA replication initiation / epsilon DNA polymerase complex / Ctf18 RFC-like complex / maintenance of DNA trinucleotide repeats / SUMO binding / DNA clamp loader activity / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドデオキシリボヌクレアーゼ / single-stranded DNA helicase activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / mitotic sister chromatid cohesion / leading strand elongation / nuclear replication fork / chromosome, centromeric region / Dual incision in TC-NER / DNA replication initiation / error-prone translesion synthesis / base-excision repair, gap-filling / replication fork / double-strand break repair via homologous recombination / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / mitotic cell cycle / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / mRNA binding / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / ATP binding / nucleus
類似検索 - 分子機能
Chromosome transmission fidelity protein 8 / Ctf8 / Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1 / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / : / DNA polymerase family B, thumb domain ...Chromosome transmission fidelity protein 8 / Ctf8 / Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1 / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / : / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribonuclease H superfamily / Ribonuclease H-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
DNA polymerase epsilon catalytic subunit A / Sister chromatid cohesion protein DCC1 / Chromosome transmission fidelity protein 8 / Chromosome transmission fidelity protein 18
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 解像度: 4.5 Å
データ登録者Grabarczyk, D.B. / Kisker, C.
資金援助 ドイツ, 1件
組織認可番号国
Alexander von Humboldt Foundation ドイツ
引用ジャーナル: Structure / 年: 2018
タイトル: Structural Basis for the Recruitment of Ctf18-RFC to the Replisome.
著者: Grabarczyk, D.B. / Silkenat, S. / Kisker, C.
履歴
登録2017年7月25日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年12月20日Provider: repository / タイプ: Initial release
改定 1.12018年1月10日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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: DNA polymerase epsilon catalytic subunit A
B: DNA polymerase epsilon catalytic subunit A
C: Sister chromatid cohesion protein DCC1
D: Chromosome transmission fidelity protein 8
E: Chromosome transmission fidelity protein 18
G: Sister chromatid cohesion protein DCC1
H: Chromosome transmission fidelity protein 8
I: Chromosome transmission fidelity protein 18


分子量 (理論値)分子数
合計 (水以外)244,4898
ポリマ－244,4898
非ポリマー00
水00
1
A: DNA polymerase epsilon catalytic subunit A
G: Sister chromatid cohesion protein DCC1
H: Chromosome transmission fidelity protein 8
I: Chromosome transmission fidelity protein 18


分子量 (理論値)分子数
合計 (水以外)122,2444
ポリマ－122,2444
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: DNA polymerase epsilon catalytic subunit A
C: Sister chromatid cohesion protein DCC1
D: Chromosome transmission fidelity protein 8
E: Chromosome transmission fidelity protein 18


分子量 (理論値)分子数
合計 (水以外)122,2444
ポリマ－122,2444
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)121.678, 145.826, 378.752
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain D
21chain H
12chain E
22chain I
13chain C
23chain G
14chain A
24chain B

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain DD2 - 132
211chain HH2 - 132
112chain EE715 - 740
212chain II715 - 740
113chain CC2 - 380
213chain GG2 - 380
114chain AA31 - 524
214chain BB27 - 524

NCSアンサンブル:
ID
1
2
3
4

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要素

#1: タンパク質 DNA polymerase epsilon catalytic subunit A / DNA polymerase II subunit A


分子量: 59749.184 Da / 分子数: 2 / 変異: D290A. E292A / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: POL2, DUN2, YNL262W, N0825 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P21951, DNA-directed DNA polymerase
#2: タンパク質 Sister chromatid cohesion protein DCC1 / Defective in sister chromatid cohesion protein 1


分子量: 44133.785 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: DCC1, YCL016C, YCL16C / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P25559
#3: タンパク質 Chromosome transmission fidelity protein 8


分子量: 15189.688 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: CTF8, YHR191C / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P38877
#4: タンパク質・ペプチド Chromosome transmission fidelity protein 18


分子量: 3171.607 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: CTF18, CHL12, YMR078C, YM9582.03C / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P49956

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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: 3.44 Å3/Da / 溶媒含有率: 64.25 %
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: 6.5
詳細: 12% PEG 10000, 0.1 M MES pH 6.5, 0.2 M ammonium chloride

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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: BESSY / ビームライン: 14.1 / 波長: 0.918 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年4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: 0.918 Å / 相対比: 1
反射解像度: 4.5→47.72 Å / Num. obs: 20450 / % possible obs: 99.9 % / 冗長度: 6.6 % / Biso Wilson estimate: 141.74 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.668 / Rpim(I) all: 0.278 / Rrim(I) all: 0.725 / Net I/σ(I): 3.5 / Num. measured all: 135607 / Scaling rejects: 0
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4.5-4.936.62.5483199048140.3231.0672.7650.8100
11.02-47.725.50.075823914920.9970.0340.08218.998.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
Aimless0.5.32データスケーリング
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHASER位相決定
精密化解像度: 4.5→47.724 Å / SU ML: 0.89 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 37.5 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.3121 1011 4.96 %Random selection
Rwork0.2926 19376 --
obs0.2935 20387 99.84 %-
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 max: 354.28 Å2 / Biso mean: 186.3768 Å2 / Biso min: 65.41 Å2
精密化ステップサイクル: final / 解像度: 4.5→47.724 Å
タンパク質核酸リガンド溶媒全体
原子数15910 0 0 0 15910
残基数----1967
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00416267
X-RAY DIFFRACTIONf_angle_d1.04321979
X-RAY DIFFRACTIONf_chiral_restr0.0422426
X-RAY DIFFRACTIONf_plane_restr0.0062808
X-RAY DIFFRACTIONf_dihedral_angle_d12.176097
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11D1256X-RAY DIFFRACTION9.22TORSIONAL
12H1256X-RAY DIFFRACTION9.22TORSIONAL
21E236X-RAY DIFFRACTION9.22TORSIONAL
22I236X-RAY DIFFRACTION9.22TORSIONAL
31C3496X-RAY DIFFRACTION9.22TORSIONAL
32G3496X-RAY DIFFRACTION9.22TORSIONAL
41A4197X-RAY DIFFRACTION9.22TORSIONAL
42B4197X-RAY DIFFRACTION9.22TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.5001-4.73710.3871450.357427332878100
4.7371-5.03360.38851580.34927062864100
5.0336-5.42180.38151350.363127282863100
5.4218-5.96650.39941540.362827472901100
5.9665-6.82770.39381330.350227852918100
6.8277-8.59390.29341460.292427862932100
8.5939-47.72710.19961400.20372891303199
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)
17.3764-3.02973.96295.92.76895.9630.50611.1461-1.33710.0239-0.0780.45481.07290.5004-0.42142.5375-0.5422-0.22041.8837-0.04812.0723-59.0926-26.21091.5082
20.47930.4459-0.51420.7428-1.16351.31180.49920.0575-0.20030.5197-0.0008-0.09170.87061.1211-0.32252.8982-0.2476-0.45092.1187-0.68442.4002-56.609-17.6274-4.567
32.71710.01790.20435.8932-0.2582.06720.62720.41880.95571.0301-0.61980.38090.47830.2701-0.00383.105-0.63850.32380.930.11371.7063-46.5458-7.913427.6489
46.6046-2.9385-1.56771.65660.69992.4596-0.608-0.3131-0.96040.33590.61610.49391.518-0.8395-0.12062.2061-0.6008-0.07051.64510.0671.8534-22.49371.860884.4081
5-0.2246-0.402-0.22397.78723.25415.27751.2643-1.51450.0674-0.3803-0.323-1.7765-0.4806-0.78-0.68521.2684-0.18-0.14682.403-0.03272.2347-23.289214.256108.6887
63.2166-0.1051.73596.14730.1595.3141-0.31970.3975-0.3388-1.1310.58080.41060.20970.2254-0.20941.1145-0.42840.07531.4026-0.21381.5063-9.530820.364866.3673
74.89070.03152.22681.2036-0.79923.99530.2381-0.8683-1.12980.01340.3308-1.1306-0.3765-0.0817-0.14831.8818-0.7164-0.52761.7856-0.16242.0072-3.250417.55776.363
81.4445-1.62670.73012.9350.31411.225-0.92660.41210.1543-0.03910.1750.14841.46530.50340.87722.9592-0.4013-0.13121.16450.07731.910623.502415.979329.4172
98.33482.6387-4.34395.9988-3.6954.5412-0.46582.44880.7897-0.92680.06830.8991-1.2293-0.69580.60433.09330.0294-0.59892.22090.31981.98462.903-13.194123.0727
103.95-1.84380.45454.0004-3.7419.9480.71760.2899-1.9308-1.30050.0745-0.25680.4386-0.1331-0.84162.7328-0.30280.08391.19010.0882.11361.8375-29.786132.9135
115.6513-0.81120.2610.0481-0.12930.48010.54310.66971.6372-0.2868-0.4228-0.31690.58732.35230.00844.3207-1.3955-0.50390.5625-0.13121.7492-1.5016-22.521342.2869
122.8265-4.8794.04668.5669-6.98755.74851.50560.0093-1.4122-1.57230.9131.41870.5702-0.8796-1.37664.6692-1.0301-0.20521.76930.1052.3326-22.6118-20.415147.2594
134.56680.1251-0.32690.30750.66493.09890.8345-1.3368-0.6253-0.34340.2786-1.7822-3.4067-1.3569-0.2692.4722-1.2997-0.4021.0705-0.16082.1966-13.0917-15.391245.3954
146.43957.0043-3.80599.7389-7.06596.8606-0.8471.0779-0.314-1.89780.04120.5222.2174-0.62580.5833.16180.0171-0.09881.2034-0.41641.205-14.7825-1.075244.5398
158.03733.7051-3.90021.6974-1.84342.06570.7459-2.4605-0.08020.6863-1.25680.36840.21870.95370.29591.7802-0.2893-0.38261.6639-0.17571.6108-10.55844.837150.1571
161.9936-4.45022.02223.7815-3.0117.26031.4417-0.3944-4.0669-1.23710.90272.61711.4667-0.7181-2.01814.0861-1.09220.9755-1.02940.91362.626520.69932.095123.3081
174.55331.6856-2.41527.4014-4.88561.99950.99880.45682.0312-2.82490.8010.4391-0.4334-0.2211-1.36655.6227-0.3641-0.70951.1886-0.42473.334334.93634.9530.594
181.98486.6632-1.12124.681-6.27281.98941.35771.1030.63-2.84030.05670.7955-0.720.2679-1.10232.7358-0.0103-0.64742.00930.41722.179137.130914.879438.1695
192.5118-2.87521.66874.367-1.54781.535-0.04291.8228-0.7701-0.3866-0.7095-1.20620.7197-0.2646-0.09083.2045-0.38020.4610.59640.12912.128325.410529.618528.0962
200.2684-0.5621-0.15161.24720.2790.0611.2211.4412-0.0052-1.23420.54971.32660.5074-0.1515-0.87013.1746-1.1741-1.41034.0392-0.27932.753834.949841.572116.0474
212.0115-8.3458-6.42564.69354.85882.00620.68132.26050.1256-1.9786-2.24181.504-1.3225-1.11311.3822.7833-1.0557-1.05253.5472-0.12971.151235.224130.213915.5447
222.06340.05260.59452.39294.79099.66950.1329-0.46211.0008-0.94490.94740.05862.89930.8982-0.51382.1848-1.1989-0.27981.6198-0.35091.875633.616135.648436.0255
230.05050.4350.18482.00265.1762.47321.03450.7250.0031.9827-1.1038-1.21710.5497-1.1852-0.06042.2456-0.58680.17261.76360.72821.04228.048232.850940.891
246.7949-2.4927-2.07373.2124.57032.0107-0.20160.3491-2.5678-1.40250.3031-0.31330.4174-0.83470.02393.1934-0.13950.61351.16940.13512.335423.965611.737626.6917
255.18-1.8274-1.6091.87181.67071.6114-1.16470.4914-0.4567-0.8634-0.42582.00471.1460.27931.18043.28230.3998-0.77470.60060.54361.89225.507833.028139.4882
261.99882.0036-2.75772.0003-2.140.3661-3.19866.65132.8302-4.29653.2930.35930.5285-0.9273-0.61771.1503-0.4559-0.06791.8387-0.00161.196826.464945.208924.5744
271.99839.09184.18981.9975-1.28375.98681.63370.0592.07080.8619-0.29721.4849-1.7136-3.6071-1.60361.26680.54742.07151.99570.91862.392516.464138.603133.884
286.76537.4537-0.91598.0845-0.97760.1094-1.0229-0.32430.00441.75260.69471.5854-0.86220.20440.52493.7762-0.13150.51371.1486-0.58822.35557.266320.807733.996
299.35839.5059-1.45872.00222.04942.0045-0.3368-0.48481.08210.2255-0.1664-0.91841.1681-0.31120.36542.5629-0.2639-0.38672.0164-0.48321.848811.336110.963420.0059
303.0741.6229-2.19371.2809-1.15372.1265-0.90431.92372.94051.90171.68591.43010.0625-2.60940.23941.4589-1.5538-0.7766-1.12951.0282.5919-61.18124.175864.2732
316.51740.79311.130.29820.82952.9019-0.0153-0.09451.19140.35690.63740.5455-0.18850.1927-0.50981.2374-0.1605-0.45011.45380.58482.769-53.913424.08964.7638
324.8617-2.33842.31885.82340.86355.3034-1.6773-0.88670.58240.81430.71970.77580.4411-1.62220.75021.7502-0.8044-0.45891.69040.24462.7898-91.0953-5.007364.2357
332.0008-6.37387.47396.1616-5.58922.0101-0.194-1.5342-2.7497-1.51590.77683.35953.263-1.1529-0.18362.8303-0.3620.44632.09430.63012.7415-85.6663-28.227647.4308
341.3973-1.1891-1.79822.08460.86991.00220.1285-0.28751.7837-1.2324-0.66550.8064-0.0150.76340.12232.1541-1.07710.25292.26160.27611.9335-82.1088-18.631849.0176
350.1053-0.0702-0.12810.11530.1230.17510.66640.2458-0.23751.5450.2824-0.8148-0.05760.6704-0.10591.436-0.6511.20973.61730.58131.9619-67.3234-18.665349.1643
368.08843.85866.6745.0958-1.31621.9267-1.0604-0.56063.6088-0.1127-1.70160.3970.21791.03522.40531.7066-0.215-0.02173.1861-0.13132.26-63.821-12.686843.8813
372.00321.2472-2.54612.99552.96944.3384-0.17040.16580.5797-0.07070.3441.1795-0.3048-0.7511-0.433-1.2431.5370.47212.48021.24914.0589-70.35317.925470.9017
380.4876-0.17590.84910.28241.04769.8858-0.47010.3201-0.8494-0.4564-0.01640.34571.4191-2.12920.4931.1555-1.3068-0.91512.46950.09224.9905-70.012732.196663.8153
391.46790.39172.04920.09090.5872.85760.20331.34992.59710.0920.5349-0.3905-1.9857-0.43120.1110.8715-2.0944-0.77741.9640.62972.9454-56.824233.556658.6053
408.0335-7.23658.13116.6006-7.38768.2165-0.7119-1.82151.46081.90390.35820.3744-0.8211-1.62120.69272.2937-0.7806-0.77111.434-0.57020.7196-35.997225.074570.5148
416.9849-0.09392.17729.77046.36295.76181.0176-0.3006-3.3261-2.31852.1013-0.95130.034-0.4994-3.01653.79820.1374-1.79152.9603-0.54752.8352-34.448239.824878.6283
426.63486.1918-3.71947.3399-1.45384.7168-0.21050.8586-0.34110.51780.66941.6905-0.02190.1134-0.07443.23-0.5391-1.75561.8984-0.11944.0829-45.173637.301878.8024
433.4472-0.3945-6.37742.4168-0.27581.9710.01260.03480.5104-0.1996-0.21921.1955-0.846-1.52210.10941.113-3.0147-0.8641-1.17641.96233.1043-41.144536.64557.0165
442.05793.01444.25431.9615-1.37641.9689-0.93661.01352.0108-1.13212.57531.2277-0.0311-1.326-0.47792.7036-0.0563-1.7741.31082.1023.2663-38.662732.451955.9709
453.4079-0.8983-5.57762.81912.3092.0017-1.2035-0.85880.29420.53560.7270.8431-0.4096-0.05850.34751.133-1.2096-0.7491.3355-0.16912.6505-59.135422.017963.0627
460.83791.85620.31293.5753-0.15321.4172-0.41460.45431.1012-0.1573-0.69231.1976-1.19990.12490.31311.9868-0.6334-0.83551.86310.18362.5704-51.305525.965762.3265
472.03755.5537-4.71241.9899-3.99082.09990.26050.2113-0.463.97770.21520.2952-1.729-0.0615-0.60372.6144-0.04570.35431.3172-0.14361.9998-31.38625.837764.7348
481.98566.39515.94142.03792.53371.9862-1.3841.62642.11330.18852.72321.9975-1.3081.5184-1.19092.1653-0.31940.03031.5476-0.0061.9155-49.46358.493659.2468
499.13776.9766-4.47877.042-6.94099.3660.4651-1.08421.70983.44240.42932.792-1.4134-1.9425-1.05711.6716-0.48930.61391.48161.34141.4253-59.64069.7373.8748
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 212 )A31 - 212
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 274 )A213 - 274
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 524 )A275 - 524
4X-RAY DIFFRACTION4chain 'B' and (resid 27 through 145 )B27 - 145
5X-RAY DIFFRACTION5chain 'B' and (resid 146 through 248 )B146 - 248
6X-RAY DIFFRACTION6chain 'B' and (resid 249 through 466 )B249 - 466
7X-RAY DIFFRACTION7chain 'B' and (resid 467 through 524 )B467 - 524
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 112 )C2 - 112
9X-RAY DIFFRACTION9chain 'C' and (resid 113 through 167 )C113 - 167
10X-RAY DIFFRACTION10chain 'C' and (resid 168 through 241 )C168 - 241
11X-RAY DIFFRACTION11chain 'C' and (resid 242 through 268 )C242 - 268
12X-RAY DIFFRACTION12chain 'C' and (resid 269 through 286 )C269 - 286
13X-RAY DIFFRACTION13chain 'C' and (resid 287 through 324 )C287 - 324
14X-RAY DIFFRACTION14chain 'C' and (resid 325 through 350 )C325 - 350
15X-RAY DIFFRACTION15chain 'C' and (resid 351 through 380 )C351 - 380
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 8 )D2 - 8
17X-RAY DIFFRACTION17chain 'D' and (resid 9 through 16 )D9 - 16
18X-RAY DIFFRACTION18chain 'D' and (resid 17 through 26 )D17 - 26
19X-RAY DIFFRACTION19chain 'D' and (resid 27 through 44 )D27 - 44
20X-RAY DIFFRACTION20chain 'D' and (resid 45 through 58 )D45 - 58
21X-RAY DIFFRACTION21chain 'D' and (resid 59 through 68 )D59 - 68
22X-RAY DIFFRACTION22chain 'D' and (resid 69 through 87 )D69 - 87
23X-RAY DIFFRACTION23chain 'D' and (resid 88 through 96 )D88 - 96
24X-RAY DIFFRACTION24chain 'D' and (resid 97 through 119 )D97 - 119
25X-RAY DIFFRACTION25chain 'D' and (resid 120 through 132 )D120 - 132
26X-RAY DIFFRACTION26chain 'E' and (resid 715 through 719 )E715 - 719
27X-RAY DIFFRACTION27chain 'E' and (resid 720 through 724 )E720 - 724
28X-RAY DIFFRACTION28chain 'E' and (resid 725 through 734 )E725 - 734
29X-RAY DIFFRACTION29chain 'E' and (resid 735 through 740 )E735 - 740
30X-RAY DIFFRACTION30chain 'G' and (resid 2 through 37 )G2 - 37
31X-RAY DIFFRACTION31chain 'G' and (resid 38 through 112 )G38 - 112
32X-RAY DIFFRACTION32chain 'G' and (resid 113 through 268 )G113 - 268
33X-RAY DIFFRACTION33chain 'G' and (resid 269 through 286 )G269 - 286
34X-RAY DIFFRACTION34chain 'G' and (resid 287 through 324 )G287 - 324
35X-RAY DIFFRACTION35chain 'G' and (resid 325 through 348 )G325 - 348
36X-RAY DIFFRACTION36chain 'G' and (resid 349 through 380 )G349 - 380
37X-RAY DIFFRACTION37chain 'H' and (resid 2 through 8 )H2 - 8
38X-RAY DIFFRACTION38chain 'H' and (resid 9 through 16 )H9 - 16
39X-RAY DIFFRACTION39chain 'H' and (resid 17 through 35 )H17 - 35
40X-RAY DIFFRACTION40chain 'H' and (resid 36 through 44 )H36 - 44
41X-RAY DIFFRACTION41chain 'H' and (resid 45 through 58 )H45 - 58
42X-RAY DIFFRACTION42chain 'H' and (resid 59 through 68 )H59 - 68
43X-RAY DIFFRACTION43chain 'H' and (resid 69 through 84 )H69 - 84
44X-RAY DIFFRACTION44chain 'H' and (resid 85 through 96 )H85 - 96
45X-RAY DIFFRACTION45chain 'H' and (resid 97 through 107 )H97 - 107
46X-RAY DIFFRACTION46chain 'H' and (resid 108 through 132 )H108 - 132
47X-RAY DIFFRACTION47chain 'I' and (resid 715 through 724 )I715 - 724
48X-RAY DIFFRACTION48chain 'I' and (resid 725 through 734 )I725 - 734
49X-RAY DIFFRACTION49chain 'I' and (resid 735 through 740 )I735 - 740

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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://pdbjlvh1.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