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- PDB-8gk6: Crystal structure of extracellular domain of CNNM4 from Echinococ... -

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基本情報

登録情報
データベース: PDB / ID: 8gk6
タイトルCrystal structure of extracellular domain of CNNM4 from Echinococcus granulosus
要素Metal transporter CNNM4
キーワードMETAL TRANSPORT / Immunoglobulin-like fold / beta-sandwich / Magnesium transporter
機能・相同性
機能・相同性情報


magnesium ion homeostasis / 生体膜
類似検索 - 分子機能
Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS domain superfamily / CBSドメイン / CBS domain profile.
類似検索 - ドメイン・相同性
Metal transporter CNNM4
類似検索 - 構成要素
生物種Echinococcus granulosus (いりゅうじょうちゅう)
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Shahsavan, A. / Gehring, K.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR) カナダ
引用ジャーナル: Protein Sci. / 年: 2024
タイトル: Dimerization of the CNNM extracellular domain.
著者: Shahsavan, A. / Lee, E.L. / Illes, K. / Kozlov, G. / Gehring, K.
履歴
登録2023年3月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年12月13日Provider: repository / タイプ: Initial release
改定 1.12024年1月31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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年2月7日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _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: Metal transporter CNNM4
B: Metal transporter CNNM4
C: Metal transporter CNNM4
D: Metal transporter CNNM4
E: Metal transporter CNNM4
F: Metal transporter CNNM4
H: Metal transporter CNNM4
G: Metal transporter CNNM4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)128,73519
ポリマ－124,5078
非ポリマー4,22811
水73941
1
A: Metal transporter CNNM4
E: Metal transporter CNNM4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,3616
ポリマ－31,1272
非ポリマー1,2344
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Metal transporter CNNM4
G: Metal transporter CNNM4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,0223
ポリマ－31,1272
非ポリマー8951
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Metal transporter CNNM4
H: Metal transporter CNNM4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,3595
ポリマ－31,1272
非ポリマー1,2323
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Metal transporter CNNM4
F: Metal transporter CNNM4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,9945
ポリマ－31,1272
非ポリマー8673
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)55.338, 120.764, 95.254
Angle α, β, γ (deg.)90.000, 98.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and resid 25 through 152)
d_2ens_1(chain "B" and resid 25 through 152)
d_3ens_1(chain "C" and resid 25 through 152)
d_4ens_1(chain "D" and resid 25 through 152)
d_5ens_1(chain "E" and resid 25 through 152)
d_6ens_1(chain "F" and resid 25 through 152)
d_7ens_1(chain "G" and resid 25 through 152)
d_8ens_1(chain "H" and resid 25 through 152)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNSERA2 - 129
d_21ens_1ASNSERF2 - 129
d_31ens_1ASNSERG1 - 128
d_41ens_1ASNSERK1 - 128
d_51ens_1ASNSERO1 - 128
d_61ens_1ASNSERR1 - 128
d_71ens_1ASNSERX1 - 128
d_81ens_1ASNSERT1 - 128

NCS oper:
IDCodeMatrixベクター
1given(0.532416466111, 0.181972157564, 0.826691502609), (-0.197971718829, 0.976303051974, -0.0874045150423), (-0.823006625221, -0.117125934692, 0.555825161597)-27.3483186775, 33.7263670402, 7.09985852171
2given(0.328752054591, 0.223354205218, 0.917624643094), (0.224423035595, -0.962275331807, 0.153819657034), (0.917363825152, 0.155367579654, -0.366475821161)-26.93614748, -12.9352143963, 42.1984640712
3given(0.968944076795, 0.0573532188047, 0.240536866896), (0.0544868053816, -0.998342052371, 0.018556252483), (0.241202330177, -0.00487388547726, -0.970462611932)-9.82943996633, 22.1336677986, 54.1239612595
4given(0.77389140623, 0.107190153147, 0.6241813538), (0.0210715205038, -0.989385202015, 0.14378078125), (0.632967678785, -0.0981182607957, -0.767935364801)1.53466660851, 2.04205593595, 4.07182650829
5given(0.862614796118, 0.157162520174, 0.480828093783), (-0.0756238346684, 0.97989681712, -0.184616530758), (-0.500176717919, 0.122890886771, 0.857158725558)-7.10639091505, 20.318884259, 50.3540662678
6given(0.94887833351, -0.111873980301, -0.295151013428), (-0.100508350588, -0.993499327201, 0.0534523929518), (-0.299212265219, -0.0210546760121, -0.953954255172)-22.9887242087, 34.9176880923, 8.10356504631
7given(0.871650167279, -0.0702354149916, -0.48507006954), (0.0968091965948, 0.994853357342, 0.0299128206592), (0.480472647855, -0.0730327588557, 0.873963529443)-25.1681641536, -15.2898103022, 38.7670863197

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要素

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タンパク質 / 非ポリマー , 2種, 49分子 ABCDEFHG

#1: タンパク質
Metal transporter CNNM4


分子量: 15563.418 Da / 分子数: 8 / 断片: extracellular domain / 由来タイプ: 組換発現
由来: (組換発現) Echinococcus granulosus (いりゅうじょうちゅう)
遺伝子: EGR_01344
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: W6USS8
#7: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 41 / 由来タイプ: 天然 / 式: H2O

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糖 , 5種, 11分子

#2: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 367.349 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 424.401 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 586.542 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 894.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン / N-アセチルグルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 5 / 由来タイプ: 組換発現 / 式: C8H15NO6 / タイプ: SUBJECT OF INVESTIGATION
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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詳細

研究の焦点であるリガンドがあるかY

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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: 2.53 Å3/Da / 溶媒含有率: 51.4 %
結晶化温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1 M Tris-HCl pH 8.5, 25% (w/v) PEG 6000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: CLSI / ビームライン: 08ID-1 / 波長: 0.95371 Å
検出器タイプ: DECTRIS EIGER2 S 9M / 検出器: PIXEL / 日付: 2022年7月29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: 0.95371 Å / 相対比: 1
反射解像度: 2.7→50 Å / Num. obs: 45839 / % possible obs: 97.4 % / 冗長度: 4.7 % / Biso Wilson estimate: 39.41 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14
反射 シェル解像度: 2.7→2.72 Å / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1246 / CC1/2: 0.622

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX1.20.1_4487位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.7→46.64 Å / SU ML: 0.325 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 26.1186
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2533 3114 6.79 %
Rwork0.1974 42723 -
obs0.2011 45837 68.19 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 46.27 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→46.64 Å
タンパク質核酸リガンド溶媒全体
原子数8067 0 277 41 8385
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00478576
X-RAY DIFFRACTIONf_angle_d0.767511759
X-RAY DIFFRACTIONf_chiral_restr0.0541452
X-RAY DIFFRACTIONf_plane_restr0.00461453
X-RAY DIFFRACTIONf_dihedral_angle_d11.9633025
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.655685866191
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.945101274339
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.613856238836
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.915767015908
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.880948365046
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.06676162039
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS1.05282360295
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.3318370.3172502X-RAY DIFFRACTION17.33
2.74-2.790.3052480.3015661X-RAY DIFFRACTION23.32
2.79-2.830.3483450.2992750X-RAY DIFFRACTION26.53
2.83-2.880.3077770.2726949X-RAY DIFFRACTION32.75
2.88-2.940.3261720.27381137X-RAY DIFFRACTION40.03
2.94-30.3245980.27531276X-RAY DIFFRACTION45.72
3-3.070.30891110.27451537X-RAY DIFFRACTION53.3
3.07-3.140.29091250.25221672X-RAY DIFFRACTION59.15
3.14-3.210.30871350.24481730X-RAY DIFFRACTION61.23
3.22-3.30.2961350.24321841X-RAY DIFFRACTION64.64
3.3-3.40.30571360.22561992X-RAY DIFFRACTION69.66
3.4-3.510.28691590.2392145X-RAY DIFFRACTION75.15
3.51-3.630.2831590.21882221X-RAY DIFFRACTION77.8
3.63-3.780.26861880.2072487X-RAY DIFFRACTION87.85
3.78-3.950.26261880.19332629X-RAY DIFFRACTION91.58
3.95-4.160.21192040.16872693X-RAY DIFFRACTION95.01
4.16-4.420.22091980.15262743X-RAY DIFFRACTION96.14
4.42-4.760.20191990.14452676X-RAY DIFFRACTION95.2
4.76-5.240.20132040.14942765X-RAY DIFFRACTION96.96
5.24-60.26122040.17932786X-RAY DIFFRACTION97.3
6-7.550.26221900.20492730X-RAY DIFFRACTION96.02
7.55-46.640.23612020.20532801X-RAY DIFFRACTION98.11
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)
12.292605474860.176646740673-0.8485261609122.95964578933-0.7775355313270.8875997256790.02283562421870.5291837919640.0645844410452-0.278868030930.02349107803730.02059731260050.0693186321955-0.4881669085-0.01283296059850.1958113094940.01804320339520.0227527360410.3864542827420.02850808341430.132731114879-5.29404644423-0.2596315301967.05065043868
20.986113671202-0.0832791418094-0.7084332571831.2291891802-0.2091073012131.859191147040.08658905515340.2722046904880.164860782436-0.307576887163-0.077846742691-0.2156837930370.06611676314740.0460623177284-0.05713677640990.1639384857990.01307679717380.02420528769040.2687672347620.1477126824820.2422416547923.47649140143-3.3801969922513.6674164426
31.29460049092-0.8941197246871.208701663970.622980344434-0.8416160171261.13550027833-0.377468169767-0.7327420327580.9772435013080.119814224434-0.477331909754-0.69151505718-1.017789916030.5073850323150.3071136258960.496684235-0.0705533889114-0.110648240590.6811030052530.07743843616720.656381355227-5.331696225188.2396134699622.4655873242
40.0386129400260.1309680589420.02592463552230.4477880375010.08536846808090.257052049570.00127402697599-0.0286974430846-0.03998611854420.125303753229-0.169079156943-0.1681895185670.1419491963980.195135109782-4.306749355340.148357015260.01061968243950.05621919404030.1698848105780.1934394122070.2718322092591.42531447789-5.7424730880616.0260505269
50.7705063217390.2949898584850.5299150933871.25163589991-0.4977563656420.793530608142-0.113129462615-0.06007707105140.1341182796660.04499738734550.01119264055850.351069051024-0.0393671542051-0.3086104680220.03922023952530.112992847504-0.04193366671920.05551678962310.4045938827950.01193050835470.349588501569-10.0973214189-0.83169259470217.5049150314
64.09807153144-0.887802756601-1.783470318974.00537534564-1.610082840432.72332991553-0.484464322371-0.4089707839150.711880333680.7386712474190.644641725067-0.0480865126992-0.2070612610530.0460152234349-0.04982564925860.3585651093850.280236095913-0.1070900672050.78169275727-0.003171855142820.6807102777174.544263611643.0118421933132.5120805476
71.87264560852-0.185939345405-1.104261732810.172865546602-0.1689335529581.348317171750.2023296937740.2826368856350.517593459601-0.0384019495321-3.57754960734E-50.237130083399-0.2006912801930.02022414182650.1856738617190.143780750647-0.00878144178281-0.07639650340130.183880031840.04023886094240.229818449895-3.767582211314.8643481916513.0142573774
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552.504942439561.448931267630.107686443311.52773796498-0.858185098811.23252395010.00425105066031-0.0216149808251-0.4269910964550.0738540116867-0.197046529056-0.584486130955-0.2881598144780.3237112951620.4095329826950.455604668287-0.03205702440.2083532546390.2332556350810.06772881860240.536251888925-23.7820737331-20.313563639951.9122618554
563.17855057183-0.6077864537610.2454472402337.49223983307-0.2369839924921.202603561960.08086240446510.5985223183270.0448682636162-0.565485946325-0.3182897181061.021378896750.572662403364-0.7308855567380.1568359623170.517833739465-0.03303383538820.2381290876280.478564539849-0.03854544559490.527863379939-45.8932891641-18.362876149944.7388119489
571.18100048320.62805558191.04364209771.249678515090.02595873627743.72833162469-0.0534555187529-0.06774754431220.315359117690.7889531212280.0497240037921-0.0690941896666-0.463182298117-0.08714090859610.3729001317920.4441072861430.0196966985198-0.01228789943770.1276029614730.01146925666970.655355389783-34.2952051909-13.395171059162.1348901482
581.707593472120.2790948646630.3241439609953.647807291141.148943984770.394827343694-0.0699248454613-0.2767823843860.5972149605820.9079941889580.180494351276-0.0831205332711-0.581546584685-0.2487496772460.2653109098470.6176706327180.15179566962-0.04405000579840.1738152896250.007262005708120.444450629884-38.6047972097-11.014297650965.304198545
590.2468080192570.1254255741170.04068805555610.06358657363070.02078033471340.00672596549899-0.1745001703320.582156249030.4569885825460.0257445525728-0.302879214777-0.31510083816-0.3394772206570.6779653046550.002102523623970.37051133466-0.0475784598-0.1955490114470.5678454707560.3444125996340.956707681043-30.910654682-5.2240488398747.7751223003
602.99594534870.3868680962860.9922987624512.056481314530.3684445132873.38915653847-0.1781706190280.8081055690880.636309379996-0.856227930272-0.3692263253670.53185270090.123810221588-0.7016521220010.1812929477270.5355224836070.03262120099680.06967567739820.4547638904780.03560049932610.428897201254-41.4602522371-16.563729706140.8342604402
611.36953489473-0.1583283590841.258237819521.669029270530.6934437522931.5841456868-0.0234948273414-0.360237319114-0.0646147456232-0.128524220133-0.06650843841160.174044055044-0.0694512283423-0.253415793188-0.3323124707940.2561687691290.0987758542244-0.03780399209150.2238923916940.131132769740.221459485802-30.611293766437.04317090363.50722581344
621.44608130302-0.3789053741230.5022397817482.39705314358-0.7519053067532.02218607964-0.0950563171740.3367786182590.08634849955210.0567312097416-0.348448472436-0.3044463645660.4479623382310.6797796466150.2822354844270.402250743420.128462688782-0.03568223345750.3008421714430.09381255222650.237745148772-22.979094347938.0461075934-6.29409462154
630.267912583877-0.0679949906809-0.3945150933851.73763754623-0.07483097902410.5962175428350.272371727269-0.114193025551-0.765434342664-0.618092964959-0.04388656701950.3087156640990.57951298344-0.221410572992-0.2331145595320.372351493652-0.0461401786281-0.2060057645610.2440763067360.1366296038370.523376078157-34.497102003934.9328593706-12.3056178936
642.0198274889-0.3877525828550.08279969280131.87904730255-0.7237126356742.138363993340.187301887808-0.456288019562-0.319540897973-0.265984042643-0.140742609854-0.03176665357120.04856614067840.138927557308-0.02359172456170.2073205406890.0638678388199-0.0248020348290.295741280960.02610203321930.318060563804-29.991276962839.1305925509-4.77486866302
651.393511497710.1314739907680.6427981726656.17425260741.576194490373.10861872203-0.00399354627269-0.0464011502186-0.447082635345-0.7068270352710.9435087597920.1090965961790.751387517565-0.249075214102-0.5966968301821.298581470310.009935763887-0.04000947471830.7212434798130.08894394970130.43756621401-28.357407732533.3153675373-24.1566881849
660.762697183402-0.1737941873950.05537284738391.1515981612-0.7317559540351.409542483730.101082838532-0.224912777419-0.6315178037640.134087213503-0.0321732313860.06914491198040.5723260424130.1285323586730.4660374538780.6029697682050.00952398400162-0.1189472602570.1648895126370.1028144477830.380349004359-30.954327228131.1246304615-3.29542002363
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 50 )AA24 - 501 - 27
22chain 'A' and (resid 51 through 70 )AA51 - 7028 - 47
33chain 'A' and (resid 71 through 80 )AA71 - 8048 - 57
44chain 'A' and (resid 81 through 104 )AA81 - 10458 - 81
55chain 'A' and (resid 105 through 121 )AA105 - 12182 - 98
66chain 'A' and (resid 122 through 133 )AA122 - 13399 - 110
77chain 'A' and (resid 134 through 152 )AA134 - 152111 - 129
88chain 'B' and (resid 24 through 40 )BF24 - 401 - 17
99chain 'B' and (resid 41 through 51 )BF41 - 5118 - 28
1010chain 'B' and (resid 52 through 59 )BF52 - 5929 - 36
1111chain 'B' and (resid 60 through 70 )BF60 - 7037 - 47
1212chain 'B' and (resid 71 through 80 )BF71 - 8048 - 57
1313chain 'B' and (resid 81 through 90 )BF81 - 9058 - 67
1414chain 'B' and (resid 91 through 103 )BF91 - 10368 - 80
1515chain 'B' and (resid 104 through 121 )BF104 - 12181 - 98
1616chain 'B' and (resid 122 through 133 )BF122 - 13399 - 110
1717chain 'B' and (resid 134 through 141 )BF134 - 141111 - 118
1818chain 'B' and (resid 142 through 153 )BF142 - 153119 - 130
1919chain 'C' and (resid 25 through 70 )CG25 - 701 - 46
2020chain 'C' and (resid 71 through 80 )CG71 - 8047 - 56
2121chain 'C' and (resid 81 through 90 )CG81 - 9057 - 66
2222chain 'C' and (resid 91 through 121 )CG91 - 12167 - 97
2323chain 'C' and (resid 122 through 133 )CG122 - 13398 - 109
2424chain 'C' and (resid 134 through 153 )CG134 - 153110 - 129
2525chain 'D' and (resid 25 through 40 )DK25 - 401 - 16
2626chain 'D' and (resid 41 through 51 )DK41 - 5117 - 27
2727chain 'D' and (resid 52 through 70 )DK52 - 7028 - 46
2828chain 'D' and (resid 71 through 80 )DK71 - 8047 - 56
2929chain 'D' and (resid 81 through 90 )DK81 - 9057 - 66
3030chain 'D' and (resid 91 through 103 )DK91 - 10367 - 79
3131chain 'D' and (resid 104 through 121 )DK104 - 12180 - 97
3232chain 'D' and (resid 122 through 133 )DK122 - 13398 - 109
3333chain 'D' and (resid 134 through 146 )DK134 - 146110 - 122
3434chain 'D' and (resid 147 through 152 )DK147 - 152123 - 128
3535chain 'E' and (resid 25 through 40 )EO25 - 401 - 16
3636chain 'E' and (resid 41 through 70 )EO41 - 7017 - 46
3737chain 'E' and (resid 71 through 90 )EO71 - 9047 - 66
3838chain 'E' and (resid 91 through 121 )EO91 - 12167 - 97
3939chain 'E' and (resid 122 through 133 )EO122 - 13398 - 109
4040chain 'E' and (resid 134 through 152 )EO134 - 152110 - 128
4141chain 'F' and (resid 25 through 33 )FR25 - 331 - 9
4242chain 'F' and (resid 34 through 40 )FR34 - 4010 - 16
4343chain 'F' and (resid 41 through 51 )FR41 - 5117 - 27
4444chain 'F' and (resid 52 through 70 )FR52 - 7028 - 46
4545chain 'F' and (resid 71 through 80 )FR71 - 8047 - 56
4646chain 'F' and (resid 81 through 103 )FR81 - 10357 - 79
4747chain 'F' and (resid 104 through 121 )FR104 - 12180 - 97
4848chain 'F' and (resid 122 through 133 )FR122 - 13398 - 109
4949chain 'F' and (resid 134 through 146 )FR134 - 146110 - 122
5050chain 'F' and (resid 147 through 152 )FR147 - 152123 - 128
5151chain 'H' and (resid 25 through 40 )HT25 - 401 - 16
5252chain 'H' and (resid 41 through 51 )HT41 - 5117 - 27
5353chain 'H' and (resid 52 through 70 )HT52 - 7028 - 46
5454chain 'H' and (resid 71 through 90 )HT71 - 9047 - 66
5555chain 'H' and (resid 91 through 103 )HT91 - 10367 - 79
5656chain 'H' and (resid 104 through 115 )HT104 - 11580 - 91
5757chain 'H' and (resid 116 through 127 )HT116 - 12792 - 103
5858chain 'H' and (resid 128 through 136 )HT128 - 136104 - 112
5959chain 'H' and (resid 137 through 146 )HT137 - 146113 - 122
6060chain 'H' and (resid 147 through 152 )HT147 - 152123 - 128
6161chain 'G' and (resid 25 through 51 )GX25 - 511 - 27
6262chain 'G' and (resid 52 through 70 )GX52 - 7028 - 46
6363chain 'G' and (resid 71 through 90 )GX71 - 9047 - 66
6464chain 'G' and (resid 91 through 121 )GX91 - 12167 - 97
6565chain 'G' and (resid 122 through 133 )GX122 - 13398 - 109
6666chain 'G' and (resid 134 through 152 )GX134 - 152110 - 128

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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