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- PDB-3fwc: Sac3:Sus1:Cdc31 complex -

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基本情報

登録情報
データベース: PDB / ID: 3fwc
タイトルSac3:Sus1:Cdc31 complex
要素
  • Cell division control protein 31
  • Nuclear mRNA export protein SAC3
  • Protein SUS1
キーワードcell cycle / transcription / gene gating / complex / Calcium / Cell division / Mitosis / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / Protein transport / Translocation / Transport / Acetylation / Transcription regulation
機能・相同性
機能・相同性情報


half bridge of spindle pole body / actin filament-based process / spindle pole body duplication / DUBm complex / Golgi vesicle transport / mitotic spindle pole body / transcription export complex 2 / nuclear mRNA surveillance / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery ...half bridge of spindle pole body / actin filament-based process / spindle pole body duplication / DUBm complex / Golgi vesicle transport / mitotic spindle pole body / transcription export complex 2 / nuclear mRNA surveillance / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / mRNA 3'-end processing / SAGA complex / poly(A)+ mRNA export from nucleus / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / nuclear pore / enzyme activator activity / protein export from nucleus / transcription elongation by RNA polymerase II / P-body / microtubule cytoskeleton organization / nuclear envelope / regulation of protein localization / protein transport / chromatin organization / mitotic cell cycle / ribosomal small subunit biogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / molecular adaptor activity / cell division / chromatin binding / calcium ion binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
類似検索 - 分子機能
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2880 / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2880 / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / EF hand / Serum Albumin; Chain A, Domain 1 / Proteasome component (PCI) domain / PCI domain profile. / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Helix non-globular / EF-hand, calcium binding motif / Special / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Cell division control protein 31 / Nuclear mRNA export protein SAC3 / Transcription and mRNA export factor SUS1
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 / 分子置換 / 解像度: 2.7 Å
データ登録者Stewart, M. / Jani, D.
引用ジャーナル: Mol.Cell / 年: 2009
タイトル: Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export.
著者: Jani, D. / Lutz, S. / Marshall, N.J. / Fischer, T. / Kohler, A. / Ellisdon, A.M. / Hurt, E. / Stewart, M.
履歴
登録2009年1月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02009年4月14日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22023年9月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Cell division control protein 31
B: Nuclear mRNA export protein SAC3
C: Protein SUS1
D: Protein SUS1
E: Cell division control protein 31
F: Nuclear mRNA export protein SAC3
G: Protein SUS1
H: Protein SUS1
I: Cell division control protein 31
J: Nuclear mRNA export protein SAC3
K: Protein SUS1
L: Protein SUS1
M: Cell division control protein 31
N: Nuclear mRNA export protein SAC3
O: Protein SUS1
P: Protein SUS1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)204,74720
ポリマ－204,36216
非ポリマー3844
水2,198122
1
A: Cell division control protein 31
B: Nuclear mRNA export protein SAC3
C: Protein SUS1
D: Protein SUS1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,1875
ポリマ－51,0914
非ポリマー961
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-93 kcal/mol
Surface area23060 Å2
手法PISA
2
E: Cell division control protein 31
F: Nuclear mRNA export protein SAC3
G: Protein SUS1
H: Protein SUS1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,1875
ポリマ－51,0914
非ポリマー961
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-100 kcal/mol
Surface area23790 Å2
手法PISA
3
I: Cell division control protein 31
J: Nuclear mRNA export protein SAC3
K: Protein SUS1
L: Protein SUS1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,1875
ポリマ－51,0914
非ポリマー961
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-97 kcal/mol
Surface area22740 Å2
手法PISA
4
M: Cell division control protein 31
N: Nuclear mRNA export protein SAC3
O: Protein SUS1
P: Protein SUS1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,1875
ポリマ－51,0914
非ポリマー961
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-92 kcal/mol
Surface area23710 Å2
手法PISA
単位格子
Length a, b, c (Å)73.590, 122.710, 128.710
Angle α, β, γ (deg.)90.000, 95.750, 90.000
Int Tables number4
Space group name H-MP1211
詳細Sac3:Sus1:Cdc31 complex

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要素

#1: タンパク質
Cell division control protein 31 / Nucleoporin CDC31 / Nuclear pore protein CDC31


分子量: 18774.039 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: see publication for complete details
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: CDC31, DSK1, YOR257W / プラスミド: pET / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P06704
#2: タンパク質
Nuclear mRNA export protein SAC3 / Leucine permease transcriptional regulator


分子量: 10127.569 Da / 分子数: 4 / Fragment: residues 723-805 / 由来タイプ: 組換発現 / 詳細: see publication for complete ddetails
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: LEP1, SAC3, YD8358.13, YDR159W / プラスミド: pET / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P46674
#3: タンパク質
Protein SUS1


分子量: 11094.497 Da / 分子数: 8 / 由来タイプ: 組換発現 / 詳細: see publication for complete details
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: SUS1, YBR111W-A / プラスミド: pET / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Bl21(DE3) / 参照: UniProt: Q6WNK7
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 合成 / 式: SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 122 / 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: 2.83 Å3/Da / 溶媒含有率: 56.53 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: ID14-1 / 波長: 0.979 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2008年8月30日
放射モノクロメーター: Si (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: 0.979 Å / 相対比: 1
反射解像度: 2.7→20 Å / Num. all: 61904 / Num. obs: 61904 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 10.8 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 2.8
反射 シェル解像度: 2.7→2.85 Å / 冗長度: 7.4 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.8 / % possible all: 99.1

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
MOSFLMデータ削減
SCALAデータスケーリング
PHASER位相決定
PHENIX精密化
PDB_EXTRACT3.006データ抽出
ADSCQuantumデータ収集
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3FWB

3fwb


解像度: 2.7→19.924 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.12 / Isotropic thermal model: isotropic + TLS / σ(F): 1.91 / 位相誤差: 30.42 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2646 3094 5.02 %
Rwork0.2112 --
obs0.214 61667 98.83 %
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 / Bsol: 60.847 Å2 / ksol: 0.324 e/Å3
原子変位パラメータBiso mean: 99.126 Å2
Baniso -1Baniso -2Baniso -3
1--2.496 Å2-0 Å2-8.506 Å2
2---4.472 Å20 Å2
3---2.352 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→19.924 Å
タンパク質核酸リガンド溶媒全体
原子数13368 0 20 122 13510
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00613549
X-RAY DIFFRACTIONf_angle_d0.86718197
X-RAY DIFFRACTIONf_dihedral_angle_d16.475190
X-RAY DIFFRACTIONf_chiral_restr0.0492057
X-RAY DIFFRACTIONf_plane_restr0.0032342
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74210.39991260.35552693X-RAY DIFFRACTION99
2.7421-2.78690.3331310.29282627X-RAY DIFFRACTION99
2.7869-2.83490.31331300.29392677X-RAY DIFFRACTION99
2.8349-2.88630.38791470.29122622X-RAY DIFFRACTION99
2.8863-2.94160.33161240.29392720X-RAY DIFFRACTION99
2.9416-3.00150.32021180.26872644X-RAY DIFFRACTION99
3.0015-3.06650.31971570.26792664X-RAY DIFFRACTION99
3.0665-3.13760.30511500.26322633X-RAY DIFFRACTION99
3.1376-3.21570.31481460.2472643X-RAY DIFFRACTION99
3.2157-3.30230.30821420.23732655X-RAY DIFFRACTION99
3.3023-3.3990.29341430.22162649X-RAY DIFFRACTION99
3.399-3.50810.27081140.21472722X-RAY DIFFRACTION99
3.5081-3.63280.28121510.21662608X-RAY DIFFRACTION99
3.6328-3.77730.26291530.19852667X-RAY DIFFRACTION99
3.7773-3.9480.2511450.18662679X-RAY DIFFRACTION99
3.948-4.15430.21721480.17672650X-RAY DIFFRACTION99
4.1543-4.4120.20651410.15612666X-RAY DIFFRACTION99
4.412-4.74840.20491370.15732684X-RAY DIFFRACTION99
4.7484-5.21840.24821530.17052670X-RAY DIFFRACTION99
5.2184-5.95580.27021400.21792688X-RAY DIFFRACTION99
5.9558-7.43820.27441480.22732681X-RAY DIFFRACTION99
7.4382-19.92470.21331500.16842631X-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)
11.20612.241-0.14895.0842-0.5614-0.26631.09630.2453-0.84691.4903-0.36460.3435-0.0145-0.0794-0.69890.7985-0.0073-0.48790.49750.02520.873921.33193.8061-3.6854
21.39960.2229-2.42071.192.112-1.604-0.0537-0.463-0.1484-0.29060.30140.00831.22670.8428-0.14530.8361-0.0749-0.20350.369-0.03760.150430.7574.275611.7191
3-0.09510.1348-1.76910.29192.39225.6842-0.03910.0365-0.0046-0.15750.4056-0.07420.20910.0786-0.26840.6810.047-0.28930.3477-0.10670.271837.91574.45164.9424
43.3904-1.17380.94050.57410.88644.7993-0.2363-0.4988-1.51880.18020.23370.2501-0.48720.7067-0.22320.4638-0.0739-0.24170.5760.35560.859715.5291-11.266411.8242
55.3696-1.5949-3.9037-2.41883.98715.5018-1.0957-0.2973-1.591-0.1953-0.56330.5553-0.12860.33731.36631.0579-0.0061-0.11040.95420.29671.5630.8628-6.198316.4058
64.49450.66573.57835.7931-0.26661.7406-0.31380.1327-1.99470.7918-0.1620.3521-0.45610.44770.54030.7890.1439-0.67260.7133-0.54722.11717.6404-13.15116.6492
70.09421.0321-0.2906-4.67487.62040.15550.19850.04-0.5340.20270.17832.04740.41170.0582-0.34070.85660.3926-0.0640.56640.15061.72899.20110.316471.8251
81.78682.50381.4132.06311.11081.29960.5770.08270.25180.0682-0.6579-0.30281.43440.1240.0050.6660.00820.1070.3047-0.13170.573477.28388.737958.8568
95.9868-1.79363.03420.80760.63832.59550.917-0.14520.4018-0.7605-1.0016-0.04340.1728-0.169-0.01460.8729-0.0792-0.22270.7687-0.20290.712455.55936.072144.6274
108.91962.93895.94872.04721.1952-0.2514-0.1359-0.87910.1945-0.0619-0.217-0.06740.091-0.63090.46120.831-0.2069-0.11380.60960.01830.500241.932.593934.4333
110.3068-0.7004-0.77870.1724-3.67740.59380.6485-1.1210.04150.9835-0.25690.03770.37490.9121-0.3621.0364-0.119-0.25720.8995-0.2280.312827.38921.295421.7043
12-0.4294-0.3575-0.03793.5324-3.68190.84840.2963-0.2414-0.30650.52930.14270.8331-0.3619-0.1542-0.40970.9378-0.1078-0.31610.79230.15850.881510.1426-1.742310.1672
136.70794.80995.43992.00696.2011.6308-0.90241.05120.66110.56920.06861.15770.32870.98760.87940.8558-0.0338-0.1230.89680.56250.945554.173711.889632.8354
146.30054.5309-0.6495.15942.1065-4.4181-0.1021.4220.0539-0.48510.56-0.06470.4909-0.1333-0.42971.27040.0009-0.18820.60860.01540.339848.4061-2.07927.0202
157.78193.9962.6601-1.8633-4.42413.36821.1195-0.5259-0.92750.1169-1.1754-0.18570.9206-0.5122-0.09711.1024-0.5822-0.13920.5529-0.02840.577329.4446-7.375930.7297
169.09079.1251.52537.66498.01642.0197-0.236-2.76532.10940.4991-0.48941.57140.5817-0.26680.85470.54890.1538-0.07321.2697-0.35530.928923.61966.161630.9769
177.1983-1.4779-2.27041.45791.1274-5.8031-0.5407-2.178-0.1331.33790.2780.42230.48210.13060.19421.1668-0.3111-0.09260.72770.5536-0.950140.2095-6.423439.9239
18-4.6599-7.3461-2.89321.99988.03678.98161.1978-0.12340.0252-0.05950.4952-2.6865-1.863-0.6042-0.94120.84350.006-0.42410.04430.14550.128155.996-1.087836.2179
19-0.32211.6566-3.2304-2.8126-3.0385-0.50280.35070.00190.65470.34341.29080.6864-0.85620.2801-1.58050.9979-0.0048-0.12280.3795-0.27211.032992.038714.003278.8786
201.2643-1.73322.42853.6036-0.85735.2630.9101-0.2416-0.552-0.1740.0824-1.47030.367-0.1878-0.92830.3229-0.0347-0.08320.31630.1040.760386.854621.473468.3775
213.51610.0790.3655.2339-0.9681-0.27850.30650.2945-0.3004-0.4672-0.3484-1.07370.2510.2371-0.14670.62360.06450.25530.2083-0.26750.320379.26746.876249.8502
221.0691-1.85621.15799.35162.77120.8691-1.04830.09730.52751.0140.59882.8714-0.1889-0.03430.32390.8038-0.1752-0.00550.2179-0.18950.876266.3196-3.209156.6715
238.84630.9071-0.2570.88941.08252.95570.7939-0.7175-2.39280.6402-0.976-2.72070.45751.0565-0.3859-0.11430.84310.4238-0.5484-0.36640.723888.55637.747158.4797
244.9957-6.8427-0.51631.99976.94132.0458-0.8522-0.1142-0.3025-0.4677-1.6481-0.5355-0.1287-0.10692.60980.62930.1346-0.13410.42520.36331.509298.59922.143770.5786
252.3591-3.094-1.0534-1.0716-1.29664.1503-0.7457-0.43670.6397-0.1921-0.13160.04131.39540.2460.85260.64390.0760.04860.3795-0.16120.820346.428528.495622.8509
26-4.21353.41250.69792.34770.36071.6822-0.15570.56741.0161-0.14730.70040.74-0.6128-2.32060.00430.1447-0.15130.02740.4633-0.31180.552140.581534.711813.886
277.94851.1455-2.92191.5433-2.5953.78760.26811.8899-0.85640.45150.267-0.0564-0.3266-1.1389-0.52850.2830.01130.1290.7026-0.05050.278751.525338.769220.3566
288.31837.43647.84526.8292.37566.2799-0.97120.75462.0293-0.1897-1.45531.3271-0.02030.27190.9786-0.10.32840.5372-0.4427-1.4996-1.419545.02747.914439.0786
292.93070.16530.11823.64283.7926-4.36250.2784-1.1050.28352.1157-1.09880.05710.7440.51690.68581.1343-0.43940.0421.25380.28930.502647.247441.304951.724
306.1921-1.52746.42359.59292.74591.7635-0.34650.2930.37840.51360.3847-0.9808-0.1487-0.8040.01120.4311-0.2623-0.04130.54960.11650.527853.718448.508542.755
311.8559-5.82193.59525.6236-4.75068.83360.0454-0.39640.7995-1.2792-0.237-0.86190.6758-0.490.2450.92420.0472-0.00120.55360.06490.5268-40.808329.5871-10.5607
320.9461.80222.2811.36012.20895.16210.69490.76060.26190.20060.5097-0.58120.19771.03-1.18430.3776-0.12280.0280.634-0.25960.7538-19.379530.42782.0131
333.81480.95093.771-0.54860.09040.50150.3805-2.30030.2534-0.19920.2486-0.6534-0.2826-0.5461-0.59120.3756-0.34040.22191.3785-0.52821.04062.909933.451814.5082
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 13:19)
2X-RAY DIFFRACTION2(chain A and resid 20:59)
3X-RAY DIFFRACTION3(chain A and resid 60:89)
4X-RAY DIFFRACTION4(chain A and resid 90:112)
5X-RAY DIFFRACTION5(chain A and resid 113:150)
6X-RAY DIFFRACTION6(chain A and resid 151:161)
7X-RAY DIFFRACTION7(chain B and resid 722:728)
8X-RAY DIFFRACTION8(chain B and resid 729:754)
9X-RAY DIFFRACTION9(chain B and resid 755:764)
10X-RAY DIFFRACTION10(chain B and resid 765:776)
11X-RAY DIFFRACTION11(chain B and resid 777:790)
12X-RAY DIFFRACTION12(chain B and resid 791:805)
13X-RAY DIFFRACTION13(chain C and resid 6:13)
14X-RAY DIFFRACTION14(chain C and resid 14:32)
15X-RAY DIFFRACTION15(chain C and resid 33:47)
16X-RAY DIFFRACTION16(chain C and resid 48:68)
17X-RAY DIFFRACTION17(chain C and resid 69:83)
18X-RAY DIFFRACTION18(chain C and resid 84:95)
19X-RAY DIFFRACTION19(chain D and resid 3:12)
20X-RAY DIFFRACTION20(chain D and resid 13:27)
21X-RAY DIFFRACTION21(chain D and resid 28:53)
22X-RAY DIFFRACTION22(chain D and resid 54:60)
23X-RAY DIFFRACTION23(chain D and resid 61:87)
24X-RAY DIFFRACTION24(chain D and resid 88:95)
25X-RAY DIFFRACTION25(chain E and resid 13:41)
26X-RAY DIFFRACTION26(chain E and resid 42:81)
27X-RAY DIFFRACTION27(chain E and resid 82:93)
28X-RAY DIFFRACTION28(chain E and resid 94:113)
29X-RAY DIFFRACTION29(chain E and resid 114:147)
30X-RAY DIFFRACTION30(chain E and resid 148:161)
31X-RAY DIFFRACTION31(chain F and resid 722:734)
32X-RAY DIFFRACTION32(chain F and resid 735:754)
33X-RAY DIFFRACTION33(chain F and resid 755:769)
34X-RAY DIFFRACTION34(chain F and resid 770:778)
35X-RAY DIFFRACTION35(chain F and resid 779:788)
36X-RAY DIFFRACTION36(chain F and resid 789:805)
37X-RAY DIFFRACTION37(chain G and resid 6:28)
38X-RAY DIFFRACTION38(chain G and resid 29:38)
39X-RAY DIFFRACTION39(chain G and resid 39:49)
40X-RAY DIFFRACTION40(chain G and resid 50:63)
41X-RAY DIFFRACTION41(chain G and resid 64:81)
42X-RAY DIFFRACTION42(chain G and resid 82:95)
43X-RAY DIFFRACTION43(chain H and resid 3:11)
44X-RAY DIFFRACTION44(chain H and resid 12:22)
45X-RAY DIFFRACTION45(chain H and resid 23:31)
46X-RAY DIFFRACTION46(chain H and resid 32:57)
47X-RAY DIFFRACTION47(chain H and resid 58:83)
48X-RAY DIFFRACTION48(chain H and resid 84:95)
49X-RAY DIFFRACTION49(chain I and resid 13:30)
50X-RAY DIFFRACTION50(chain I and resid 31:73)
51X-RAY DIFFRACTION51(chain I and resid 74:94)
52X-RAY DIFFRACTION52(chain I and resid 95:126)
53X-RAY DIFFRACTION53(chain I and resid 127:149)
54X-RAY DIFFRACTION54(chain I and resid 150:161)
55X-RAY DIFFRACTION55(chain J and resid 722:730)
56X-RAY DIFFRACTION56(chain J and resid 731:754)
57X-RAY DIFFRACTION57(chain J and resid 755:767)
58X-RAY DIFFRACTION58(chain J and resid 768:778)
59X-RAY DIFFRACTION59(chain J and resid 779:789)
60X-RAY DIFFRACTION60(chain J and resid 790:805)
61X-RAY DIFFRACTION61(chain K and resid 6:15)
62X-RAY DIFFRACTION62(chain K and resid 16:29)
63X-RAY DIFFRACTION63(chain K and resid 30:44)
64X-RAY DIFFRACTION64(chain K and resid 45:59)
65X-RAY DIFFRACTION65(chain K and resid 60:78)
66X-RAY DIFFRACTION66(chain K and resid 79:95)
67X-RAY DIFFRACTION67(chain L and resid 6:16)
68X-RAY DIFFRACTION68(chain L and resid 17:30)
69X-RAY DIFFRACTION69(chain L and resid 31:52)
70X-RAY DIFFRACTION70(chain L and resid 53:60)
71X-RAY DIFFRACTION71(chain L and resid 61:86)
72X-RAY DIFFRACTION72(chain L and resid 87:95)
73X-RAY DIFFRACTION73(chain M and resid 13:18)
74X-RAY DIFFRACTION74(chain M and resid 19:55)
75X-RAY DIFFRACTION75(chain M and resid 56:81)
76X-RAY DIFFRACTION76(chain M and resid 82:93)
77X-RAY DIFFRACTION77(chain M and resid 94:148)
78X-RAY DIFFRACTION78(chain M and resid 149:161)
79X-RAY DIFFRACTION79(chain N and resid 722:738)
80X-RAY DIFFRACTION80(chain N and resid 739:754)
81X-RAY DIFFRACTION81(chain N and resid 755:765)
82X-RAY DIFFRACTION82(chain N and resid 766:778)
83X-RAY DIFFRACTION83(chain N and resid 779:787)
84X-RAY DIFFRACTION84(chain N and resid 788:805)
85X-RAY DIFFRACTION85(chain O and resid 6:15)
86X-RAY DIFFRACTION86(chain O and resid 16:29)
87X-RAY DIFFRACTION87(chain O and resid 30:47)
88X-RAY DIFFRACTION88(chain O and resid 48:69)
89X-RAY DIFFRACTION89(chain O and resid 70:78)
90X-RAY DIFFRACTION90(chain O and resid 79:95)
91X-RAY DIFFRACTION91(chain P and resid 3:18)
92X-RAY DIFFRACTION92(chain P and resid 19:29)
93X-RAY DIFFRACTION93(chain P and resid 30:49)
94X-RAY DIFFRACTION94(chain P and resid 50:55)
95X-RAY DIFFRACTION95(chain P and resid 56:69)
96X-RAY DIFFRACTION96(chain P and resid 70:95)

+
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://pdbjlc1.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