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- PDB-8onh: Variant Surface Glycoprotein VSG11wt-Oil -

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基本情報

登録情報
データベース: PDB / ID: 8onh
タイトルVariant Surface Glycoprotein VSG11wt-Oil
要素Variant surface glycoprotein
キーワードMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation
機能・相同性Trypanosome variant surface glycoprotein, B-type, N-terminal domain / Trypanosomal VSG domain / plasma membrane / alpha-D-glucopyranose / Variant surface glycoprotein
機能・相同性情報
生物種Trypanosoma brucei brucei (トリパノソーマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.59 Å
データ登録者Zeelen, J.P. / Stebbins, C.E. / Foti, K. / Gkeka, A. / Vlachou, E.P.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Plos Negl Trop Dis / 年: 2023
タイトル: A structural classification of the variant surface glycoproteins of the African trypanosomey.
著者: Dakovic, S. / Zeelen, J.P. / Gkeka, A. / Chandra, M. / van Straaten, M. / Foti, K. / Zhong, J. / Vlachou, E.P. / Aresta-Branco, F. / Verdi, J.P. / Papavasiliou, F.N. / Stebbins, C.E.
履歴
登録2023年4月3日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年9月13日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Variant surface glycoprotein
B: Variant surface glycoprotein
C: Variant surface glycoprotein
D: Variant surface glycoprotein
E: Variant surface glycoprotein
F: Variant surface glycoprotein
G: Variant surface glycoprotein
H: Variant surface glycoprotein
I: Variant surface glycoprotein
J: Variant surface glycoprotein
K: Variant surface glycoprotein
L: Variant surface glycoprotein
M: Variant surface glycoprotein
N: Variant surface glycoprotein
O: Variant surface glycoprotein
P: Variant surface glycoprotein
Q: Variant surface glycoprotein
R: Variant surface glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)809,34950
ポリマ－796,35518
非ポリマー12,99432
水5,116284
1
A: Variant surface glycoprotein
B: Variant surface glycoprotein
C: Variant surface glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,8379
ポリマ－132,7263
非ポリマー3,1116
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint41 kcal/mol
Surface area44660 Å2
手法PISA
2
D: Variant surface glycoprotein
E: Variant surface glycoprotein
F: Variant surface glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)134,0748
ポリマ－132,7263
非ポリマー1,3485
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-4 kcal/mol
Surface area36700 Å2
手法PISA
3
G: Variant surface glycoprotein
H: Variant surface glycoprotein
I: Variant surface glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,1708
ポリマ－132,7263
非ポリマー2,4445
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint22 kcal/mol
Surface area41470 Å2
手法PISA
4
J: Variant surface glycoprotein
K: Variant surface glycoprotein
L: Variant surface glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,1619
ポリマ－132,7263
非ポリマー3,4356
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint44 kcal/mol
Surface area44940 Å2
手法PISA
5
M: Variant surface glycoprotein
N: Variant surface glycoprotein
O: Variant surface glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)134,3988
ポリマ－132,7263
非ポリマー1,6725
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint7 kcal/mol
Surface area39640 Å2
手法PISA
6
P: Variant surface glycoprotein
Q: Variant surface glycoprotein
R: Variant surface glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)133,7098
ポリマ－132,7263
非ポリマー9835
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-8 kcal/mol
Surface area34550 Å2
手法PISA
単位格子
Length a, b, c (Å)131.880, 210.771, 133.754
Angle α, β, γ (deg.)90.000, 104.537, 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

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要素

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タンパク質 / 非ポリマー , 2種, 302分子 ABCDEFGHIJKLMNOPQR

#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 284 / 由来タイプ: 天然 / 式: H2O
#1: タンパク質
Variant surface glycoprotein


分子量: 44241.941 Da / 分子数: 18 / 由来タイプ: 組換発現
由来: (組換発現) Trypanosoma brucei brucei (トリパノソーマ)
遺伝子: Tb427.BES126.15
発現宿主: Trypanosoma brucei brucei (トリパノソーマ)
参照: UniProt: B3GVS7

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糖 , 8種, 32分子

#2: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 / 分子量: 1072.964 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 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
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a3-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 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
DManpb1-4DGlcpNAcb1-3DGlcpNAcb1-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/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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 / 分子量: 586.542 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
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
#6: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-3DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a3-b1_b3-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 / 分子量: 910.823 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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-D-Manp]{}}}}LINUCSPDB-CARE
#8: 糖
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / α-D-グルコピラノ-ス


タイプ: D-saccharide, alpha linking / 分子量: 180.156 Da / 分子数: 17 / 由来タイプ: 組換発現 / 式: C6H12O6 / タイプ: SUBJECT OF INVESTIGATION
識別子タイププログラム
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: 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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 4 / 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: 2.26 Å3/Da / 溶媒含有率: 45.57 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6 / 詳細: 19 % (w/v) PEG2000MME 0.2 M NaCl 0.1 M MES/NaOH

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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: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2019年10月19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: 1 Å / 相対比: 1
反射解像度: 2.59→48.81 Å / Num. obs: 217669 / % possible obs: 99.42 % / 冗長度: 6.8 % / Biso Wilson estimate: 66.93 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.56
反射 シェル解像度: 2.59→2.683 Å / Num. unique obs: 20848 / CC1/2: 0.545

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
xia2データ削減
Aimlessデータスケーリング
PHENIX位相決定
Coot0.9.8.7 ELモデル構築
精密化構造決定の手法: 分子置換 / 解像度: 2.59→48.81 Å / SU ML: 0.4058 / 交差検証法: FREE R-VALUE / σ(F): 1.15 / 位相誤差: 29.9449
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2695 10882 5 %
Rwork0.2292 409034 -
obs0.2312 217644 99.42 %
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 mean: 66.92 Å2
精密化ステップサイクル: LAST / 解像度: 2.59→48.81 Å
タンパク質核酸リガンド溶媒全体
原子数42850 0 848 284 43982
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003444279
X-RAY DIFFRACTIONf_angle_d0.599160174
X-RAY DIFFRACTIONf_chiral_restr0.04137371
X-RAY DIFFRACTIONf_plane_restr0.00467768
X-RAY DIFFRACTIONf_dihedral_angle_d16.705616098
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.620.35145450.36110438X-RAY DIFFRACTION75.57
2.62-2.650.36687160.360413625X-RAY DIFFRACTION99.87
2.65-2.680.36357300.343213840X-RAY DIFFRACTION99.87
2.68-2.710.34737200.325213708X-RAY DIFFRACTION99.8
2.71-2.750.35147330.323513882X-RAY DIFFRACTION99.88
2.75-2.790.33727130.317613700X-RAY DIFFRACTION99.84
2.79-2.830.34817230.305113717X-RAY DIFFRACTION99.85
2.83-2.870.33357280.306213867X-RAY DIFFRACTION99.88
2.87-2.910.33897260.310713774X-RAY DIFFRACTION99.91
2.91-2.960.34747310.307313800X-RAY DIFFRACTION99.88
2.96-3.010.33587180.31413684X-RAY DIFFRACTION99.88
3.01-3.070.34147330.304813864X-RAY DIFFRACTION99.89
3.07-3.130.31537160.279813704X-RAY DIFFRACTION99.88
3.13-3.190.30247300.27613837X-RAY DIFFRACTION99.92
3.19-3.260.32137220.278113663X-RAY DIFFRACTION99.87
3.26-3.330.29497260.265913819X-RAY DIFFRACTION99.78
3.33-3.420.32847200.266313748X-RAY DIFFRACTION99.81
3.42-3.510.31797270.267613772X-RAY DIFFRACTION99.61
3.51-3.610.30537200.248213755X-RAY DIFFRACTION99.69
3.61-3.730.27837200.232713699X-RAY DIFFRACTION99.74
3.73-3.860.26877260.22713760X-RAY DIFFRACTION99.72
3.86-4.020.2657200.217313715X-RAY DIFFRACTION99.3
4.02-4.20.23587140.199613604X-RAY DIFFRACTION99.02
4.2-4.420.22427260.188213780X-RAY DIFFRACTION99.77
4.42-4.70.22257290.186713743X-RAY DIFFRACTION99.68
4.7-5.060.23427300.188213732X-RAY DIFFRACTION99.73
5.06-5.570.28487200.20213763X-RAY DIFFRACTION99.6
5.57-6.370.25597220.208513671X-RAY DIFFRACTION99.09
6.37-8.030.21727180.19213679X-RAY DIFFRACTION99.45
8.03-48.810.21867200.185213691X-RAY DIFFRACTION99.16
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)
12.574502535610.1696422960510.2829644530543.42935395876-1.728861426972.381710844950.0323050547764-0.11494439278-0.301954232135-0.2933470621640.151367638208-0.3521548167390.75156405382-0.114877625988-0.2834943070920.5468900426710.00408832314622-0.01422206323910.315393006215-0.03114424188440.54742505510246.051-13.6536.775
26.6806908302-1.128804732837.748530917320.552228999362-0.891997006618.427540696990.5389549720510.7034062931770.423226740484-0.359021909476-0.401184191651-0.1394902302010.735695657050.93881503572-0.1129195009910.7697307899760.06309222433640.0817352440530.7319916768040.1362736479120.57506191092530.671-0.0220.711
33.627981935-2.503805740240.356196507513.500973686031.639091648683.406056422180.2392336283080.3951257520440.526778162719-0.2597612366970.0112935400199-0.384902708468-0.4756531016360.338770385781-0.2287123700870.881362233487-0.002029809012020.1122109279810.8561452996580.2301223612620.70099753115622.38715.927-15.335
44.571583188010.0201564434653-0.4830885941444.251075861940.3554554704878.990871535810.1120839795850.748710483454-0.179577907142-0.33368357352-0.3017455248220.258172149101-0.878053463771-1.180013892050.1666311732270.7903763391080.2118137003330.002836437321390.9688061122610.2111548110770.66403353390414.6441.421-16.122
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1041.9166103655-0.09806270012010.6020395207123.081443066571.002948153413.46024023019-0.3693372841410.261115431633-0.535805079376-0.1309292598230.172962847766-1.414902775030.08915631445070.7529031860470.1438437169270.575302900704-0.1534204175540.2093959778710.9195102991880.05933465538811.55912738268101.49853.70830.103
1054.396380418240.8976034654791.636674487763.537862577980.824074838060.895097692868-0.30665400960.327973484157-0.321780001812-0.3647236405110.300890641573-0.7702525103830.0233329517777-0.08846724453650.09345967402420.798163714793-0.1215879721880.2845605809720.6987186203210.03681663350270.74144499959590.18959.3522.595
1064.782421986831.348670987731.278630985284.318879614131.409699252170.664175742503-0.1559334426210.328575548973-1.2830663602-1.158840374020.371013270491-0.9885500616380.352610883837-0.734189982269-0.1481689892190.77421044754-0.1712798731090.28322940680.878097484887-0.1158111217060.97898418084183.96945.84620.509
1071.41230434487-0.1043740172462.61249593353-0.25940602862-0.05154292592174.03481210251-0.198550524401-0.504784636413-0.1151529596180.3744611355170.366045516983-0.233116146861-0.127683809555-0.4752282129940.1385385374431.192190485340.110872555008-0.09270749565271.1245063990.1537609434011.5337189892898.70647.75752.534
1084.354388515980.442789558919-2.431866255834.071795565020.5424286876592.0311966971-0.4496841863660.355259766018-0.228742271075-0.454564731159-0.269289194440.0603449311193-0.224476577885-1.25714926140.8067992209640.5653968478250.0286828176961-0.01890995181310.534633721993-0.03738195427870.62571326604769.39962.75434.49
1091.64530163277-1.065462647892.38317235410.620089271011-1.671365195442.98669008858-0.393280687465-0.333564966165-0.0961550506-0.01579897007670.122692370539-0.5926659520430.01743568224670.2605453238250.3719187573011.385031062030.0384155894095-0.1871397613961.671413805010.3005781714751.1110181995885.89954.80285.382
1103.59907261865-0.0151031230050.4123845565522.485977469780.77233808763.83066561927-0.0356448008978-0.2751838577380.103177749007-0.0167277649689-0.1390150661440.0451060573865-0.548733275757-0.2087484068450.1788299981180.654444687896-0.05144098937150.02054438189440.5332999321630.006625113009180.41895554405371.62171.36639.92
111-0.08314251261450.04398881056170.3933230693110.3856658308380.2605062792191.70317410889-0.208889008136-0.406471228641-0.3457559608820.8333402488910.6898778158870.139509715111-0.369748812139-0.0342738593803-0.4856723473531.059096736960.196060010748-0.0435512995641.215094056780.2177077962110.90312619043186.85857.44763.826
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:43 )A24 - 43
2X-RAY DIFFRACTION2( CHAIN A AND RESID 44:70 )A44 - 70
3X-RAY DIFFRACTION3( CHAIN A AND RESID 71:136 )A71 - 136
4X-RAY DIFFRACTION4( CHAIN A AND RESID 137:159 )A137 - 159
5X-RAY DIFFRACTION5( CHAIN A AND RESID 160:185 )A160 - 185
6X-RAY DIFFRACTION6( CHAIN A AND RESID 186:344 )A186 - 344
7X-RAY DIFFRACTION7( CHAIN A AND RESID 345:389 )A345 - 389
8X-RAY DIFFRACTION8( CHAIN B AND RESID 24:43 )B24 - 43
9X-RAY DIFFRACTION9( CHAIN B AND RESID 44:70 )B44 - 70
10X-RAY DIFFRACTION10( CHAIN B AND RESID 71:159 )B71 - 159
11X-RAY DIFFRACTION11( CHAIN B AND RESID 160:185 )B160 - 185
12X-RAY DIFFRACTION12( CHAIN B AND RESID 186:367 )B186 - 367
13X-RAY DIFFRACTION13( CHAIN B AND RESID 368:389 )B368 - 389
14X-RAY DIFFRACTION14( CHAIN C AND RESID 24:43 )C24 - 43
15X-RAY DIFFRACTION15( CHAIN C AND RESID 44:71 )C44 - 71
16X-RAY DIFFRACTION16( CHAIN C AND RESID 72:136 )C72 - 136
17X-RAY DIFFRACTION17( CHAIN C AND RESID 137:172 )C137 - 172
18X-RAY DIFFRACTION18( CHAIN C AND RESID 173:344 )C173 - 344
19X-RAY DIFFRACTION19( CHAIN C AND RESID 345:389 )C345 - 389
20X-RAY DIFFRACTION20( CHAIN D AND RESID 24:43 )D24 - 43
21X-RAY DIFFRACTION21( CHAIN D AND RESID 44:68 )D44 - 68
22X-RAY DIFFRACTION22( CHAIN D AND RESID 69:159 )D69 - 159
23X-RAY DIFFRACTION23( CHAIN D AND RESID 160:185 )D160 - 185
24X-RAY DIFFRACTION24( CHAIN D AND RESID 186:344 )D186 - 344
25X-RAY DIFFRACTION25( CHAIN D AND RESID 345:381 )D345 - 381
26X-RAY DIFFRACTION26( CHAIN E AND RESID 24:43 )E24 - 43
27X-RAY DIFFRACTION27( CHAIN E AND RESID 44:146 )E44 - 146
28X-RAY DIFFRACTION28( CHAIN E AND RESID 147:172 )E147 - 172
29X-RAY DIFFRACTION29( CHAIN E AND RESID 173:313 )E173 - 313
30X-RAY DIFFRACTION30( CHAIN E AND RESID 314:366 )E314 - 366
31X-RAY DIFFRACTION31( CHAIN E AND RESID 367:385 )E367 - 385
32X-RAY DIFFRACTION32( CHAIN F AND RESID 24:43 )F24 - 43
33X-RAY DIFFRACTION33( CHAIN F AND RESID 44:151 )F44 - 151
34X-RAY DIFFRACTION34( CHAIN F AND RESID 152:172 )F152 - 172
35X-RAY DIFFRACTION35( CHAIN F AND RESID 173:300 )F173 - 300
36X-RAY DIFFRACTION36( CHAIN F AND RESID 301:330 )F301 - 330
37X-RAY DIFFRACTION37( CHAIN F AND RESID 331:365 )F331 - 365
38X-RAY DIFFRACTION38( CHAIN F AND RESID 366:381 )F366 - 381
39X-RAY DIFFRACTION39( CHAIN G AND RESID 24:43 )G24 - 43
40X-RAY DIFFRACTION40( CHAIN G AND RESID 44:71 )G44 - 71
41X-RAY DIFFRACTION41( CHAIN G AND RESID 72:136 )G72 - 136
42X-RAY DIFFRACTION42( CHAIN G AND RESID 137:172 )G137 - 172
43X-RAY DIFFRACTION43( CHAIN G AND RESID 173:199 )G173 - 199
44X-RAY DIFFRACTION44( CHAIN G AND RESID 200:286 )G200 - 286
45X-RAY DIFFRACTION45( CHAIN G AND RESID 287:344 )G287 - 344
46X-RAY DIFFRACTION46( CHAIN G AND RESID 345:388 )G345 - 388
47X-RAY DIFFRACTION47( CHAIN H AND RESID 24:57 )H24 - 57
48X-RAY DIFFRACTION48( CHAIN H AND RESID 58:172 )H58 - 172
49X-RAY DIFFRACTION49( CHAIN H AND RESID 173:344 )H173 - 344
50X-RAY DIFFRACTION50( CHAIN H AND RESID 345:386 )H345 - 386
51X-RAY DIFFRACTION51( CHAIN I AND RESID 25:43 )I25 - 43
52X-RAY DIFFRACTION52( CHAIN I AND RESID 44:61 )I44 - 61
53X-RAY DIFFRACTION53( CHAIN I AND RESID 63:136 )I63 - 136
54X-RAY DIFFRACTION54( CHAIN I AND RESID 137:158 )I137 - 158
55X-RAY DIFFRACTION55( CHAIN I AND RESID 159:183 )I159 - 183
56X-RAY DIFFRACTION56( CHAIN I AND RESID 184:246 )I184 - 246
57X-RAY DIFFRACTION57( CHAIN I AND RESID 247:344 )I247 - 344
58X-RAY DIFFRACTION58( CHAIN I AND RESID 345:391 )I345 - 391
59X-RAY DIFFRACTION59( CHAIN J AND RESID 24:70 )J24 - 70
60X-RAY DIFFRACTION60( CHAIN J AND RESID 71:159 )J71 - 159
61X-RAY DIFFRACTION61( CHAIN J AND RESID 160:365 )J160 - 365
62X-RAY DIFFRACTION62( CHAIN J AND RESID 366:389 )J366 - 389
63X-RAY DIFFRACTION63( CHAIN K AND RESID 24:43 )K24 - 43
64X-RAY DIFFRACTION64( CHAIN K AND RESID 44:90 )K44 - 90
65X-RAY DIFFRACTION65( CHAIN K AND RESID 91:136 )K91 - 136
66X-RAY DIFFRACTION66( CHAIN K AND RESID 137:172 )K137 - 172
67X-RAY DIFFRACTION67( CHAIN K AND RESID 173:366 )K173 - 366
68X-RAY DIFFRACTION68( CHAIN K AND RESID 367:389 )K367 - 389
69X-RAY DIFFRACTION69( CHAIN L AND RESID 24:43 )L24 - 43
70X-RAY DIFFRACTION70( CHAIN L AND RESID 44:71 )L44 - 71
71X-RAY DIFFRACTION71( CHAIN L AND RESID 72:102 )L72 - 102
72X-RAY DIFFRACTION72( CHAIN L AND RESID 103:136 )L103 - 136
73X-RAY DIFFRACTION73( CHAIN L AND RESID 137:172 )L137 - 172
74X-RAY DIFFRACTION74( CHAIN L AND RESID 173:233 )L173 - 233
75X-RAY DIFFRACTION75( CHAIN L AND RESID 234:344 )L234 - 344
76X-RAY DIFFRACTION76( CHAIN L AND RESID 345:389 )L345 - 389
77X-RAY DIFFRACTION77( CHAIN M AND RESID 24:43 )M24 - 43
78X-RAY DIFFRACTION78( CHAIN M AND RESID 44:144 )M44 - 144
79X-RAY DIFFRACTION79( CHAIN M AND RESID 145:172 )M145 - 172
80X-RAY DIFFRACTION80( CHAIN M AND RESID 173:213 )M173 - 213
81X-RAY DIFFRACTION81( CHAIN M AND RESID 214:366 )M214 - 366
82X-RAY DIFFRACTION82( CHAIN M AND RESID 367:387 )M367 - 387
83X-RAY DIFFRACTION83( CHAIN N AND RESID 24:43 )N24 - 43
84X-RAY DIFFRACTION84( CHAIN N AND RESID 44:172 )N44 - 172
85X-RAY DIFFRACTION85( CHAIN N AND RESID 173:344 )N173 - 344
86X-RAY DIFFRACTION86( CHAIN N AND RESID 345:381 )N345 - 381
87X-RAY DIFFRACTION87( CHAIN O AND RESID 24:43 )O24 - 43
88X-RAY DIFFRACTION88( CHAIN O AND RESID 44:137 )O44 - 137
89X-RAY DIFFRACTION89( CHAIN O AND RESID 138:159 )O138 - 159
90X-RAY DIFFRACTION90( CHAIN O AND RESID 160:184 )O160 - 184
91X-RAY DIFFRACTION91( CHAIN O AND RESID 185:224 )O185 - 224
92X-RAY DIFFRACTION92( CHAIN O AND RESID 225:266 )O225 - 266
93X-RAY DIFFRACTION93( CHAIN O AND RESID 267:344 )O267 - 344
94X-RAY DIFFRACTION94( CHAIN O AND RESID 345:386 )O345 - 386
95X-RAY DIFFRACTION95( CHAIN P AND RESID 24:43 )P24 - 43
96X-RAY DIFFRACTION96( CHAIN P AND RESID 44:58 )P44 - 58
97X-RAY DIFFRACTION97( CHAIN P AND RESID 59:172 )P59 - 172
98X-RAY DIFFRACTION98( CHAIN P AND RESID 173:199 )P173 - 199
99X-RAY DIFFRACTION99( CHAIN P AND RESID 200:250 )P200 - 250
100X-RAY DIFFRACTION100( CHAIN P AND RESID 251:344 )P251 - 344
101X-RAY DIFFRACTION101( CHAIN P AND RESID 345:380 )P345 - 380
102X-RAY DIFFRACTION102( CHAIN Q AND RESID 24:61 )Q24 - 61
103X-RAY DIFFRACTION103( CHAIN Q AND RESID 62:161 )Q62 - 161
104X-RAY DIFFRACTION104( CHAIN Q AND RESID 162:213 )Q162 - 213
105X-RAY DIFFRACTION105( CHAIN Q AND RESID 214:300 )Q214 - 300
106X-RAY DIFFRACTION106( CHAIN Q AND RESID 301:344 )Q301 - 344
107X-RAY DIFFRACTION107( CHAIN Q AND RESID 345:378 )Q345 - 378
108X-RAY DIFFRACTION108( CHAIN R AND RESID 24:43 )R24 - 43
109X-RAY DIFFRACTION109( CHAIN R AND RESID 44:159 )R44 - 159
110X-RAY DIFFRACTION110( CHAIN R AND RESID 160:346 )R160 - 346
111X-RAY DIFFRACTION111( CHAIN R AND RESID 347:381 )R347 - 381

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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。

-
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