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- PDB-4xr7: Structure of the Saccharomyces cerevisiae PAN2-PAN3 core complex -

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基本情報

登録情報
データベース: PDB / ID: 4xr7
タイトルStructure of the Saccharomyces cerevisiae PAN2-PAN3 core complex
要素
  • PAB-dependent poly(A)-specific ribonuclease subunit PAN2
  • PAB-dependent poly(A)-specific ribonuclease subunit PAN3
キーワードHYDROLASE / RNA degradation / Deadenylation / Pseudokinase
機能・相同性
機能・相同性情報


PAN complex / Deadenylation of mRNA / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / postreplication repair / P-body / mRNA processing / nucleic acid binding ...PAN complex / Deadenylation of mRNA / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / postreplication repair / P-body / mRNA processing / nucleic acid binding / protein kinase activity / DNA repair / RNA binding / ATP binding / metal ion binding / cytoplasm
類似検索 - 分子機能
Helix Hairpins - #3700 / : / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal ...Helix Hairpins - #3700 / : / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Quinoprotein alcohol dehydrogenase-like superfamily / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
PAN2-PAN3 deadenylation complex subunit PAN3 / PAN2-PAN3 deadenylation complex catalytic subunit PAN2
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 / 単波長異常分散 / 解像度: 3.796 Å
データ登録者Schafer, I.B. / Rode, M. / Bonneau, F. / Schussler, S. / Conti, E.
資金援助 ドイツ, 6件
組織認可番号国
European Research Council294371 ドイツ
German Research FoundationSFB646 ドイツ
German Research FoundationSFB1035 ドイツ
German Research FoundationGRK1721 ドイツ
German Research FoundationFOR1680 ドイツ
German Research FoundationCIPSM ドイツ
引用ジャーナル: Nat. Struct. Mol. Biol. / 年: 2014
タイトル: The structure of the Pan2-Pan3 core complex reveals cross-talk between deadenylase and pseudokinase.
著者: Schafer, I.B. / Rode, M. / Bonneau, F. / Schussler, S. / Conti, E.
履歴
登録2015年1月20日登録サイト: RCSB / 処理サイト: PDBE
置き換え2015年1月28日ID: 4Q8J
詳細: D_1000206167 is an updated version of 4Q8J that resolves some issues of the original deposited structure such as cis-peptides and other discrepancies between NCS related chains.
改定 1.02015年1月28日Provider: repository / タイプ: Initial release
改定 1.12024年5月8日Group: Author supporting evidence / Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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
G: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
L: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
K: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
E: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
F: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
D: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
H: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
I: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
J: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
C: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
B: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
A: PAB-dependent poly(A)-specific ribonuclease subunit PAN2


分子量 (理論値)分子数
合計 (水以外)791,69812
ポリマ－791,69812
非ポリマー00
水00
1
G: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
H: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
I: PAB-dependent poly(A)-specific ribonuclease subunit PAN3


分子量 (理論値)分子数
合計 (水以外)197,9253
ポリマ－197,9253
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17070 Å2
ΔGint-108 kcal/mol
Surface area71270 Å2
手法PISA
2
L: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
K: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
J: PAB-dependent poly(A)-specific ribonuclease subunit PAN2


分子量 (理論値)分子数
合計 (水以外)197,9253
ポリマ－197,9253
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17770 Å2
ΔGint-105 kcal/mol
Surface area71780 Å2
手法PISA
3
E: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
F: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
D: PAB-dependent poly(A)-specific ribonuclease subunit PAN2


分子量 (理論値)分子数
合計 (水以外)197,9253
ポリマ－197,9253
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16790 Å2
ΔGint-105 kcal/mol
Surface area70870 Å2
手法PISA
4
C: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
B: PAB-dependent poly(A)-specific ribonuclease subunit PAN3
A: PAB-dependent poly(A)-specific ribonuclease subunit PAN2


分子量 (理論値)分子数
合計 (水以外)197,9253
ポリマ－197,9253
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18650 Å2
ΔGint-113 kcal/mol
Surface area73030 Å2
手法PISA
単位格子
Length a, b, c (Å)131.443, 205.298, 234.410
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
PAB-dependent poly(A)-specific ribonuclease subunit PAN2 / PAB1P-dependent poly(A)-nuclease / PAN deadenylation complex catalytic subunit 2


分子量: 89263.133 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: PAN2, YGL094C / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P53010, poly(A)-specific ribonuclease
#2: タンパク質
PAB-dependent poly(A)-specific ribonuclease subunit PAN3 / PAB1P-dependent poly(A)-nuclease / PAN deadenylation complex subunit 3


分子量: 54330.719 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: PAN3, ECM35, YKL025C / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P36102

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 3.98 Å3/Da / 溶媒含有率: 69.13 %
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 / 詳細: 0.1 M CHES, pH 9.2, 29% v/v PEG400

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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: SLS / ビームライン: X10SA / 波長: 0.97974 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2013年8月26日
放射モノクロメーター: double-channel cut fixed-exit 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: 0.97974 Å / 相対比: 1
反射解像度: 3.79→48.83 Å / Num. obs: 243648 / % possible obs: 99.3 % / 冗長度: 20 % / Rmerge(I) obs: 0.383 / Net I/σ(I): 8.8
反射 シェル解像度: 3.79→3.86 Å / 冗長度: 16.7 % / Rmerge(I) obs: 3.826 / Mean I/σ(I) obs: 0.9 / % possible all: 87.5

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.9_1692)精密化
XDSデータ削減
Aimlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 3.796→48.828 Å / SU ML: 0.61 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 33.07 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射
Rfree0.2994 11988 5.01 %
Rwork0.2855 --
obs0.2862 239257 99.05 %
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: 3.796→48.828 Å
タンパク質核酸リガンド溶媒全体
原子数46471 0 0 0 46471
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00547465
X-RAY DIFFRACTIONf_angle_d1.24164783
X-RAY DIFFRACTIONf_dihedral_angle_d13.01216217
X-RAY DIFFRACTIONf_chiral_restr0.0497512
X-RAY DIFFRACTIONf_plane_restr0.0058406
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7956-3.83870.46952980.39785686X-RAY DIFFRACTION74
3.8387-3.88380.38093820.38357658X-RAY DIFFRACTION100
3.8838-3.93120.39224320.37757555X-RAY DIFFRACTION100
3.9312-3.98090.38913950.3697714X-RAY DIFFRACTION100
3.9809-4.03330.37713750.35397637X-RAY DIFFRACTION100
4.0333-4.08850.35584000.36037665X-RAY DIFFRACTION100
4.0885-4.14690.35654180.35437635X-RAY DIFFRACTION100
4.1469-4.20870.35574320.34887586X-RAY DIFFRACTION100
4.2087-4.27450.36243780.34837708X-RAY DIFFRACTION100
4.2745-4.34450.34473940.34137650X-RAY DIFFRACTION100
4.3445-4.41940.36744430.32967596X-RAY DIFFRACTION100
4.4194-4.49970.35273820.3217689X-RAY DIFFRACTION100
4.4997-4.58620.3224590.31177595X-RAY DIFFRACTION100
4.5862-4.67970.32134150.317649X-RAY DIFFRACTION100
4.6797-4.78140.29593570.29647676X-RAY DIFFRACTION100
4.7814-4.89250.32413720.29547654X-RAY DIFFRACTION100
4.8925-5.01470.29654190.29197612X-RAY DIFFRACTION100
5.0147-5.15020.30823950.30567612X-RAY DIFFRACTION100
5.1502-5.30150.32964040.29837726X-RAY DIFFRACTION100
5.3015-5.47240.31864200.30097621X-RAY DIFFRACTION100
5.4724-5.66780.37683710.3037696X-RAY DIFFRACTION100
5.6678-5.89430.31673890.32727632X-RAY DIFFRACTION100
5.8943-6.16210.30843940.32597637X-RAY DIFFRACTION100
6.1621-6.48630.33924070.3037634X-RAY DIFFRACTION100
6.4863-6.89160.32434020.28937686X-RAY DIFFRACTION100
6.8916-7.4220.30023980.27297659X-RAY DIFFRACTION100
7.422-8.16580.25884060.24537643X-RAY DIFFRACTION100
8.1658-9.34030.21153940.21167663X-RAY DIFFRACTION100
9.3403-11.74070.18054190.16997541X-RAY DIFFRACTION99
11.7407-48.83210.24974380.23577554X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3492-0.0158-1.84040.44470.79092.09310.2899-0.09130.4540.204-0.0972-0.0538-0.2209-0.1122-0.15491.1851-0.1147-0.01511.0695-0.02651.04669.1547-53.7609106.8448
23.0628-1.5532-0.73642.37070.30953.48030.9837-0.24530.1502-0.3365-0.9638-0.9692-0.80842.0607-0.08161.3635-0.14760.14581.6289-0.00181.26247.0201-57.1176124.3091
33.3146-0.584-0.0062.0057-0.64953.0567-0.0715-0.2332-0.70870.3013-0.0027-0.39640.64430.66460.19241.3326-0.1516-0.10061.3285-0.00651.16314.3386-74.9978123.4151
42.71932.074-0.8284.0061-0.41122.4020.4404-0.47710.43480.6138-0.45120.1573-0.5139-0.04050.0931.1918-0.00310.01821.1434-0.10861.0872-6.5792-49.9052122.0285
51.8628-1.17391.33861.5093-0.02611.62690.22070.41711.62930.2954-0.72120.0324-0.3770.0210.58512.4905-0.41740.58721.6814-0.36011.9689-9.5166-26.6483133.7398
62.35412.51721.2315.51682.79172.78930.53280.1442-1.65650.11060.5533-2.88070.7174-0.1226-0.87741.3277-0.0497-0.13281.4412-0.06831.7355-23.5782-51.688875.4043
70.80441.00910.83452.68470.33371.90140.1660.12220.17610.08180.02740.28270.0315-0.0103-0.15220.92740.0737-0.02161.2647-0.09041.1705-49.7705-77.214880.7682
81.6164-1.45941.44463.26760.67563.59850.4055-0.4330.03470.4708-0.1670.43170.7363-0.4-0.25291.0452-0.08050.03680.98580.00411.2066-42.2182-73.417799.5618
93.0097-0.57770.44491.50750.29863.37630.4594-0.084-0.62990.02340.0380.62710.5643-0.7013-0.39091.19670.0155-0.13361.2247-0.04041.3842-48.0002-77.948392.7979
100.6748-0.0795-0.02812.853-1.65513.4233-0.0997-0.0530.11010.2905-0.0846-0.107-0.4769-0.2840.18520.75750.05720.03131.1323-0.13491.1879-35.6829-51.393382.0718
112.23551.5215-1.49584.60671.45695.1367-0.3222-0.61570.3154-0.9408-0.41160.6441-0.6741-0.57280.60031.4010.1929-0.03961.26750.02061.3031-44.359-40.48185.4475
120.90850.137-0.19341.94030.22433.15220.0842-0.27990.24750.4865-0.1220.1379-0.5669-0.25150.01421.00460.1477-0.04221.1022-0.10991.3195-39.3602-43.21188.9584
133.0209-1.34220.74592.2357-0.4832.63990.0462-1.3733-1.0550.66860.8192-0.0001-0.3149-1.047-0.50340.87830.18210.31671.31510.21921.6018-48.66095.7559-34.4354
140.5901-0.47521.17840.5306-0.94132.27080.23450.0150.20120.8501-0.57370.905-1.44-1.71270.53211.72150.0892-0.13911.6598-0.13871.1884-34.67123.4833-13.7373
150.630.67091.36873.05070.41384.14530.1781-0.4788-0.15950.4410.035-0.5230.63540.95940.14561.13440.078-0.10151.52440.081.263-27.4082-8.7852-22.1043
160.88860.21680.69941.977-0.12051.44190.2247-0.6807-0.790.30180.10540.765-0.4291-0.0749-0.18891.2172-0.13360.02961.19270.1151.5475-43.4644-10.0481-29.3707
170.5516-0.4772-0.32440.3510.35770.5606-0.2447-0.61070.7713-0.29180.63240.35050.16110.7343-0.1971.3918-0.1565-0.01421.2250.26651.8367-38.5903-23.2252-27.8336
180.57560.16480.45150.03730.10920.48580.0442-0.4703-0.04010.6746-0.08111.157-0.94870.3604-0.3831.7625-0.30480.40461.56240.09831.9699-59.489-21.5254-28.5214
191.48520.4712-0.04584.1856-1.34412.157-0.1705-0.04750.1361-0.43170.22720.1542-0.41010.0628-0.08580.56640.04620.20941.0446-0.10490.8944-37.760521.5436-38.593
201.6891-0.86661.70840.6809-1.16263.1897-0.19630.74350.80130.1155-0.2158-0.59850.10230.89680.33931.33460.05810.02721.25280.07251.3533-36.116318.0673-51.235
211.11120.05830.04591.16630.44261.97090.11530.5774-0.85280.4994-0.231-0.48860.3913-1.02750.11570.9824-0.0879-0.15791.1875-0.02261.5999-49.019914.4445-68.6864
220.7285-0.1634-0.05371.87590.47881.41740.19710.0186-0.21530.05290.1026-0.00220.3612-0.0576-0.28580.957-0.0980.01081.12540.13611.2282-40.31795.7379-50.31
232.7832-0.82841.97370.2227-0.85582.89080.3098-0.3855-0.18890.38-0.04670.24340.45510.1265-0.23711.5643-0.09910.03731.2089-0.11091.1432-13.594517.6082-8.4355
243.74050.3749-1.25611.74570.75883.2854-0.4032-0.53741.31780.0087-0.2029-0.0581-1.017-0.44030.35321.76760.21210.1011.6226-0.37051.4844-10.541139.67626.7131
251.54540.4560.33164.25660.10542.27020.1611-0.4061-0.15240.9023-0.08530.28410.2108-0.0821-0.031.4243-0.022-0.0541.5133-0.14341.1316-0.710211.87426.3794
262.5388-0.5828-0.10442.2066-0.4622.4361-0.7281-0.2915-1.60891.41250.1572-0.40430.653-0.45160.60712.5871-0.07410.0431.7731-0.00331.71783.6849-15.894612.2223
273.47062.3321-1.71812.3821-1.19746.78730.8406-1.64270.10070.7148-0.4272-0.3732-0.3872.1235-0.59771.0582-0.03-0.03671.4268-0.06151.479944.6995-38.939586.8538
281.3308-0.3676-0.16233.6250.80080.73470.0504-0.17340.36070.13130.0577-0.4171-0.4120.2123-0.11151.0562-0.12940.07311.0766-0.07391.029633.6087-36.388189.2268
295.9775-0.1151-2.32772.3990.87954.5647-0.25261.3175-0.6221-0.6345-0.05741.14580.8175-1.94270.47791.18030.2247-0.00731.199-0.01971.505720.4186-50.691279.6119
300.3954-0.49830.25761.52570.68511.09060.62320.0319-0.3023-0.4506-0.0095-0.3862-0.28950.4594-0.69741.2468-0.16830.13881.2421-0.20091.467646.3289-52.934860.2939
310.1369-0.2145-0.1661.9778-0.25492.20110.07540.08450.1826-0.44960.1909-0.298-0.50840.124-0.19641.0244-0.21760.15261.2588-0.0571.32737.5381-40.424269.5522
321.40981.31930.84921.1890.88070.4054-0.02210.10750.1115-0.19790.04090.1122-0.2271-0.0406-0.01751.60790.16160.08891.2856-0.03641.3354-7.0813-11.575474.0197
332.69011.96991.87051.64621.39514.0247-0.1009-0.0221-0.04440.0701-0.18640.60350.1658-0.35710.04341.3958-0.03550.00111.0315-0.11351.2177-2.77376.817594.8491
341.90321.5234-0.97761.3978-0.24091.9635-0.3442-0.574-0.9260.9778-0.2872-0.63981.24950.46120.04661.8210.04670.01781.4964-0.07711.4345.87990.0221111.7035
350.89730.7752-1.33092.5498-1.21573.2140.0834-0.04620.25230.2666-0.1559-0.2112-0.38020.35010.08551.1863-0.1384-0.26611.35730.01291.397941.298732.762-27.8581
363.40880.81680.85962.86930.19143.2663-0.0858-0.82130.4791.0739-0.24850.2573-0.6608-0.08540.56151.8734-0.2239-0.19731.5599-0.22341.602328.589537.3769-6.3849
370.48640.86250.82582.50771.28614.4046-0.0047-0.2861-0.20970.2413-0.0323-0.43750.73680.21040.06180.89520.0109-0.13571.01740.16020.982733.3343-3.779-46.7444
382.3003-0.05560.37092.15290.9312.2917-0.3404-0.1176-0.1946-0.14050.1911-0.35020.99970.09180.07171.4225-0.0095-0.15111.21670.12151.156731.8733-5.7075-25.5642
392.28391.65170.12791.47570.41792.6505-0.3372-0.0017-0.28140.0540.2215-0.45180.6880.5480.16551.4727-0.074-0.19771.38420.18021.030330.399-4.431-15.2754
401.16420.1348-0.31421.15750.56112.5858-0.0157-0.5031-0.08220.7165-0.0792-0.22110.31290.35980.07381.1311-0.0556-0.15271.12650.06981.139836.91496.1726-24.6351
413.5189-0.4760.67824.81370.9326.16150.52870.23670.4582-0.4282-0.1550.8057-0.3189-2.0030.2470.7936-0.039-0.14510.9460.04161.022223.568710.9645-62.9366
422.91651.8143-1.08822.1749-1.31110.5016-0.001-0.2321-0.13220.17230.01670.05370.01080.08930.09881.1816-0.0156-0.11891.19230.02280.96879.3768-15.4644-42.9656
432.90450.7709-0.73121.6069-0.43291.10920.52620.404-0.3160.7082-0.2274-1.61480.45731.12940.18361.2365-0.013-0.10311.36060.02871.61496.6136-33.6644-45.485
442.24960.13260.03481.2380.31281.5112-0.0040.0813-0.5583-0.1802-0.0897-0.16030.17770.13030.14041.2234-0.0137-0.00831.11660.0441.2555-3.6248-32.2704-43.8864
452.6126-1.02230.56012.06730.55561.8597-0.1702-1.33710.29030.95480.28880.1674-0.8253-1.1136-0.02591.80580.0650.12181.96710.2911.4994-14.0882-38.3972-10.8669
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 340 through 577 )
2X-RAY DIFFRACTION2chain 'G' and (resid 578 through 634 )
3X-RAY DIFFRACTION3chain 'G' and (resid 635 through 742 )
4X-RAY DIFFRACTION4chain 'G' and (resid 743 through 981 )
5X-RAY DIFFRACTION5chain 'G' and (resid 982 through 1087 )
6X-RAY DIFFRACTION6chain 'L' and (resid 228 through 259 )
7X-RAY DIFFRACTION7chain 'L' and (resid 260 through 398 )
8X-RAY DIFFRACTION8chain 'L' and (resid 399 through 431 )
9X-RAY DIFFRACTION9chain 'L' and (resid 432 through 467 )
10X-RAY DIFFRACTION10chain 'L' and (resid 468 through 679 )
11X-RAY DIFFRACTION11chain 'K' and (resid 226 through 294 )
12X-RAY DIFFRACTION12chain 'K' and (resid 295 through 680 )
13X-RAY DIFFRACTION13chain 'E' and (resid 252 through 273 )
14X-RAY DIFFRACTION14chain 'E' and (resid 274 through 314 )
15X-RAY DIFFRACTION15chain 'E' and (resid 315 through 363 )
16X-RAY DIFFRACTION16chain 'E' and (resid 364 through 443 )
17X-RAY DIFFRACTION17chain 'E' and (resid 444 through 489 )
18X-RAY DIFFRACTION18chain 'E' and (resid 490 through 513 )
19X-RAY DIFFRACTION19chain 'E' and (resid 514 through 679 )
20X-RAY DIFFRACTION20chain 'F' and (resid 228 through 294 )
21X-RAY DIFFRACTION21chain 'F' and (resid 295 through 322 )
22X-RAY DIFFRACTION22chain 'F' and (resid 323 through 679 )
23X-RAY DIFFRACTION23chain 'D' and (resid 340 through 636 )
24X-RAY DIFFRACTION24chain 'D' and (resid 637 through 728 )
25X-RAY DIFFRACTION25chain 'D' and (resid 729 through 1008 )
26X-RAY DIFFRACTION26chain 'D' and (resid 1009 through 1088 )
27X-RAY DIFFRACTION27chain 'H' and (resid 250 through 274 )
28X-RAY DIFFRACTION28chain 'H' and (resid 275 through 679 )
29X-RAY DIFFRACTION29chain 'I' and (resid 229 through 259 )
30X-RAY DIFFRACTION30chain 'I' and (resid 260 through 294 )
31X-RAY DIFFRACTION31chain 'I' and (resid 295 through 679 )
32X-RAY DIFFRACTION32chain 'J' and (resid 340 through 981 )
33X-RAY DIFFRACTION33chain 'J' and (resid 982 through 1024 )
34X-RAY DIFFRACTION34chain 'J' and (resid 1025 through 1096 )
35X-RAY DIFFRACTION35chain 'C' and (resid 227 through 494 )
36X-RAY DIFFRACTION36chain 'C' and (resid 495 through 548 )
37X-RAY DIFFRACTION37chain 'C' and (resid 549 through 683 )
38X-RAY DIFFRACTION38chain 'B' and (resid 225 through 336 )
39X-RAY DIFFRACTION39chain 'B' and (resid 337 through 398 )
40X-RAY DIFFRACTION40chain 'B' and (resid 399 through 657 )
41X-RAY DIFFRACTION41chain 'B' and (resid 658 through 680 )
42X-RAY DIFFRACTION42chain 'A' and (resid 340 through 579 )
43X-RAY DIFFRACTION43chain 'A' and (resid 580 through 636 )
44X-RAY DIFFRACTION44chain 'A' and (resid 637 through 997 )
45X-RAY DIFFRACTION45chain 'A' and (resid 998 through 1097 )

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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