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- PDB-6x5u: Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and NM5M2-Asn -

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基本情報

登録情報
データベース: PDB / ID: 6x5u
タイトルHuman Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and NM5M2-Asn
要素Alpha-(1,6)-fucosyltransferase
キーワードTRANSFERASE / Glycosyl transferase / Fucosyl transferase / GT-B fold / Inverting
機能・相同性
機能・相同性情報


glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / : / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / L-fucose catabolic process / N-glycan processing ...glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / : / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / L-fucose catabolic process / N-glycan processing / regulation of cellular response to oxidative stress / : / respiratory gaseous exchange by respiratory system / fibroblast migration / protein N-linked glycosylation / Golgi cisterna membrane / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / SH3 domain binding / regulation of gene expression / Maturation of spike protein / in utero embryonic development / viral protein processing / Golgi membrane / Golgi apparatus / extracellular exosome / membrane
類似検索 - 分子機能
Alpha-(1,6)-fucosyltransferase / Alpha-(1,6)-fucosyltransferase, SH3 domain / Alpha-(1,6)-fucosyltransferase, N- and catalytic domain / Alpha-(1,6)-fucosyltransferase N- and catalytic domains / Glycosyltransferase family 23 (GT23) domain / Glycosyltransferase family 23 (GT23) domain profile. / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
類似検索 - ドメイン・相同性
ASPARAGINE / GUANOSINE-5'-DIPHOSPHATE / Alpha-(1,6)-fucosyltransferase
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Kadirvelraj, R. / Wood, Z.A.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)R01GM130915, P41GM103390 and P01GM107012 米国
引用ジャーナル: J.Biol.Chem. / 年: 2020
タイトル: Characterizing human alpha-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases.
著者: Boruah, B.M. / Kadirvelraj, R. / Liu, L. / Ramiah, A. / Li, C. / Zong, G. / Bosman, G.P. / Yang, J.Y. / Wang, L.X. / Boons, G.J. / Wood, Z.A. / Moremen, K.W.
履歴
登録2020年5月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年10月7日Provider: repository / タイプ: Initial release
改定 1.12020年10月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22020年12月23日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.32023年10月18日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Alpha-(1,6)-fucosyltransferase
B: Alpha-(1,6)-fucosyltransferase
C: Alpha-(1,6)-fucosyltransferase
D: Alpha-(1,6)-fucosyltransferase
E: Alpha-(1,6)-fucosyltransferase
F: Alpha-(1,6)-fucosyltransferase
G: Alpha-(1,6)-fucosyltransferase
H: Alpha-(1,6)-fucosyltransferase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)506,34726
ポリマ－494,7628
非ポリマー11,58518
水4,702261
1
A: Alpha-(1,6)-fucosyltransferase
B: Alpha-(1,6)-fucosyltransferase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,7347
ポリマ－123,6902
非ポリマー3,0435
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
C: Alpha-(1,6)-fucosyltransferase
D: Alpha-(1,6)-fucosyltransferase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,7347
ポリマ－123,6902
非ポリマー3,0435
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
G: Alpha-(1,6)-fucosyltransferase
ヘテロ分子

E: Alpha-(1,6)-fucosyltransferase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,2776
ポリマ－123,6902
非ポリマー2,5874
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
手法PISA
4
H: Alpha-(1,6)-fucosyltransferase
ヘテロ分子

F: Alpha-(1,6)-fucosyltransferase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,6026
ポリマ－123,6902
非ポリマー2,9114
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation6_654x-y+1,x,z-1/61
手法PISA
単位格子
Length a, b, c (Å)154.020, 154.020, 466.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
Alpha-(1,6)-fucosyltransferase / Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6- ...Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6-fucosyltransferase / GDP-fucose--glycoprotein fucosyltransferase / Glycoprotein 6-alpha-L-fucosyltransferase


分子量: 61845.219 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FUT8 / Cell (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase

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糖 , 4種, 8分子

#2: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(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: 1114.016 Da / 分子数: 3 / 由来タイプ: 天然
記述子タイププログラム
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 3 / 由来タイプ: 天然
記述子タイププログラム
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-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]/1-2-3-1-3/a4-b1_b3-c1_b6-e1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#4: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 天然
記述子タイププログラム
DGlcpNAcb1-2DManpa1-3DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-1/a4-b1_b3-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#5: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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: 951.875 Da / 分子数: 1 / 由来タイプ: 天然
記述子タイププログラム
DGlcpNAcb1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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]/1-1-2-3-1/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE

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非ポリマー , 3種, 271分子

#6: 化合物
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: GDP, エネルギー貯蔵分子*YM
#7: 化合物 ChemComp-ASN / ASPARAGINE / アスパラギン


タイプ: L-peptide linking / 分子量: 132.118 Da / 分子数: 2 / 由来タイプ: 天然 / 式: C4H8N2O3 / タイプ: SUBJECT OF INVESTIGATION
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 261 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY
非ポリマーの詳細NM5M2-Asn was purified as a glycosylated peptide, and proteolyzed to the asparagine-linked oligosaccharide
由来についての詳細NM5M2-Asn was purified from egg yolk powder

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.3 Å3/Da / 溶媒含有率: 63 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 10% PEG 3350, 0.2 M Ammonium chloride / Temp details: Room temperature

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年3月1日
放射モノクロメーター: Si (111) Rosenbaum-Rock double crystal
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: 3.2→87.842 Å / Num. obs: 102079 / % possible obs: 99.3 % / 冗長度: 3.6 % / Biso Wilson estimate: 64.1 Å2 / CC1/2: 0.985 / Rrim(I) all: 0.259 / Net I/σ(I): 5.7
反射 シェル解像度: 3.2→3.28 Å / 冗長度: 3.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7647 / CC1/2: 0.509 / Rrim(I) all: 1.4 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6X5H

6x5h


解像度: 3.2→87.84 Å / 交差検証法: FREE R-VALUE / σ(F): 1.81 / 位相誤差: 30.28 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2359 5072 4.97 %
Rwork0.1902 --
obs0.1943 102078 99.37 %
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: 3.2→87.84 Å
タンパク質核酸リガンド溶媒全体
原子数30408 0 768 264 31440
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00232067
X-RAY DIFFRACTIONf_angle_d0.5543609
X-RAY DIFFRACTIONf_dihedral_angle_d19.21919169
X-RAY DIFFRACTIONf_chiral_restr0.0394731
X-RAY DIFFRACTIONf_plane_restr0.0035504
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.25530.3472480.27354900X-RAY DIFFRACTION95
3.2553-3.31450.29662360.26264867X-RAY DIFFRACTION95
3.3145-3.37830.33422510.2464856X-RAY DIFFRACTION95
3.3783-3.44720.30172600.24224867X-RAY DIFFRACTION95
3.4472-3.52220.27812430.23884873X-RAY DIFFRACTION95
3.5222-3.60410.30242550.22344895X-RAY DIFFRACTION95
3.6041-3.69430.26892690.20724806X-RAY DIFFRACTION94
3.6943-3.79420.26312560.20734843X-RAY DIFFRACTION94
3.7942-3.90580.21832420.20354862X-RAY DIFFRACTION95
3.9058-4.03190.24342440.18424878X-RAY DIFFRACTION95
4.0319-4.1760.20742660.18044833X-RAY DIFFRACTION94
4.176-4.34320.18942450.17364761X-RAY DIFFRACTION93
4.3432-4.54080.19112480.16144892X-RAY DIFFRACTION95
4.5408-4.78020.1952700.15174849X-RAY DIFFRACTION95
4.7802-5.07970.212540.16364860X-RAY DIFFRACTION95
5.0797-5.47180.2252560.16814850X-RAY DIFFRACTION95
5.4718-6.02240.23332580.17474846X-RAY DIFFRACTION94
6.0224-6.89350.21322500.17814874X-RAY DIFFRACTION95
6.8935-8.68390.18652470.15684774X-RAY DIFFRACTION93
8.6839-87.840.25722520.20694834X-RAY DIFFRACTION93
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)
10.40530.0784-0.0510.3640.34590.9842-0.11880.137-0.0316-0.05810.01140.03120.1956-0.19040.00940.73130.06230.03890.7776-0.03690.192120.781287.2394-2.5338
20.721-0.6859-0.5520.69550.51840.41870.0016-0.1387-0.06740.0324-0.0656-0.07450.21210.1185-0.00120.5587-0.040.0130.6631-0.01450.175329.842189.078724.9949
31.453-1.2477-0.06862.81030.02011.34820.08450.4049-0.2327-0.3203-0.40950.3150.14480.02840.17080.5841-0.1079-0.01420.5718-0.03640.1962-57.075932.7421-9.6682
41.40580.69580.89160.90870.39610.6526-0.16510.2017-0.3379-0.03890.02010.00650.0797-0.13220.0730.780.03140.06860.6402-0.09760.1646-42.473837.46860.4617
51.36060.167-0.08670.58780.07170.7988-0.01260.0890.18220.05130.0062-0.1633-0.05540.07710.0140.6119-0.0397-0.01790.6625-0.03610.2339-23.331553.00498.2493
60.57990.06810.27540.42470.20620.9364-0.1005-0.13220.1281-0.06260.0070.0666-0.1401-0.01340.04520.6849-0.007-0.00540.7038-0.06030.1797-38.766551.26214.8591
70.94150.13120.37320.81870.04880.77690.1176-0.1217-0.11620.1629-0.2197-0.0530.05550.0350.040.591-0.06790.10440.6534-0.01790.20975.97865.1993-45.3044
82.9735-1.8873-1.08981.91221.06281.1062-0.23580.01910.59180.0670.3804-0.3328-0.44970.2067-0.11210.8629-0.07950.12230.45170.01790.303558.151197.0625-40.3575
91.0255-0.17860.05420.06060.18011.2070.39150.14570.01380.0397-0.58860.2416-0.37-0.06260.01070.73150.04680.14040.86460.01450.395935.809192.6018-34.0744
100.3864-0.1354-0.48650.53880.72681.94150.21610.15360.2246-0.114-0.13120.1467-0.4909-0.5114-0.11680.77810.14080.16970.8490.02410.276640.495992.1744-33.7072
111.2775-0.1909-0.73271.7514-0.43271.62620.0497-0.3879-0.1658-0.1772-0.32520.14360.2137-0.08710.08310.6908-0.10560.26480.7606-0.06940.41352.445370.9313-25.141
120.3715-0.1541-0.07340.3910.30870.7636-0.0711-0.03-0.10660.1625-0.02770.0750.1880.07670.07590.78060.00830.09840.636-0.08230.208557.863673.6532-20.9125
130.3664-0.556-0.20221.06370.17991.0531-0.01010.2665-0.0546-0.1237-0.02110.08020.1291-0.4802-0.00340.66730.04080.09140.7853-0.00760.21752.547178.296-35.6179
140.3721-0.09380.2760.3207-0.19910.34680.05540.5303-0.1922-0.2967-0.22340.10210.1623-0.2921-0.02040.6444-0.10390.08930.7493-0.12680.247250.904965.851-54.2658
151.0513-0.6855-0.12860.7423-0.00870.04360.14950.5223-0.1236-0.1009-0.3660.1924-0.211-0.29480.06130.89230.1350.09950.92760.03180.290748.943482.8463-50.5789
160.91220.41-0.76171.089-0.48361.022-0.04630.1921-0.0383-0.01330.03320.1054-0.0578-0.14210.02250.6136-0.0204-0.08640.5290.05150.1416-30.716799.08884.9075
170.2401-0.4801-0.03940.95820.07760.00710.2262-0.0413-0.1413-0.2257-0.24480.23160.1828-0.2368-0.15170.5955-0.0925-0.06020.82150.23860.4546-53.265681.462215.7186
181.43560.3297-0.43860.8786-0.38151.3222-0.04830.0664-0.00520.1014-0.01180.0265-0.00020.10280.04950.5333-0.0345-0.00890.49540.04880.1829-28.489794.079712.4485
190.64960.0569-0.19570.2609-0.05480.8587-0.028-0.1098-0.0109-0.24860.0880.02830.1321-0.0035-0.05530.6428-0.04-0.02680.58290.0680.2141-28.152890.37913.7487
201.836-0.38590.08161.3951-0.10810.5-0.1948-0.1013-0.1152-0.11910.1777-0.00720.3261-0.12140.00850.7429-0.1166-0.03590.58170.1120.2423-19.0045101.8765-12.3758
210.5482-0.15870.22261.20470.2560.3544-0.05720.05540.3465-0.0792-0.03240.1339-0.2928-0.04670.08770.5582-0.0136-0.04010.54430.07930.2734-21.9468146.6228-21.3655
221.2137-0.0033-0.62911.60840.01720.6024-0.0043-0.13510.1689-0.0703-0.0569-0.1519-0.20920.03740.01480.6613-0.1904-0.01020.5939-0.02070.3137-10.7254154.135-13.669
231.2569-0.13830.36211.4805-0.37271.17110.0440.10340.11090.0025-0.0805-0.03430.1616-0.07740.05280.6583-0.0244-0.0370.53980.04230.1635-20.3859126.9497-27.4911
240.2415-0.10.18420.8147-0.34350.92240.0565-0.03860.00340.0749-0.02090.01240.00160.0727-0.0360.5712-0.0555-0.03470.61230.05860.1527-11.9251127.1112-19.9475
251.27270.7223-0.09092.8226-0.49461.5361-0.26570.45160.17820.02370.50750.1050.0346-0.28160.13720.4427-0.0386-0.01710.73-0.00960.1776-12.616165.9888-51.6822
261.5255-0.08790.57270.3-0.26160.6426-0.1106-0.0744-0.1599-0.03170.13330.00370.054-0.2345-0.00110.7269-0.0543-0.03480.6393-0.08590.1972-1.027658.5929-37.2711
271.08510.0002-0.45690.351-0.58171.15430.0795-0.0352-0.1869-0.2481-0.1426-0.10470.0450.22530.03810.45970.0437-0.06880.74970.01870.340929.286850.0282-26.5067
280.2850.2731-0.0541.0120.58340.72950.08620.0265-0.0872-0.12670.0418-0.24590.29550.3278-0.04320.6140.1786-0.07330.7704-0.10550.280330.28551.0759-18.6092
291.7249-0.7588-0.05130.46390.39371.11440.00980.2078-0.35820.4035-0.1083-0.25120.19410.86720.01520.69060.0588-0.01780.7184-0.16510.490838.395946.2086-33.366
302.0269-0.10880.03531.8564-0.34841.90830.08230.4922-0.2651-0.41960.1460.02510.09650.1509-0.04180.80570.0224-0.08140.6803-0.08580.28718.596447.4364-40.1381
310.7564-0.32350.50990.89710.32291.2523-0.0373-0.10250.07990.0324-0.0260.082-0.2899-0.07620.10560.6447-0.0308-0.08950.65530.01690.1858.393966.2437-25.1911
321.42820.3430.26740.21430.15980.3567-0.04270.06880.16650.01240.0743-0.0289-0.21490.14080.12850.7075-0.0418-0.05570.6371-0.03260.167112.961373.4918-19.117
330.2993-0.09250.22520.208-0.27740.5879-0.10390.239-0.0895-0.16540.0577-0.07730.05360.1439-0.02660.6229-0.0534-0.00520.7917-0.09840.211313.955160.495-44.9438
340.4459-0.86390.20121.7904-0.54731.0306-0.11380.1290.07310.34120.0623-0.3127-0.08070.16690.14110.52550.0187-0.07170.7179-0.06650.1950.459164.4325-47.7214
351.5721-0.4102-0.02240.1120.04450.3029-0.04660.1983-0.3483-0.02110.1084-0.37880.07680.3631-0.0290.6807-0.0246-0.0320.7171-0.02050.176-12.353954.9224-56.764
361.1365-0.57060.03230.5027-0.15111.62580.18490.1103-0.2005-0.1475-0.00890.25770.07930.3286-0.08790.56040.0098-0.0380.6268-0.10870.3188-44.372543.6843-65.9587
371.66230.0012-0.18870.5966-0.08240.8383-0.026-0.1462-0.27260.03850.0280.0640.05240.0803-0.02660.5723-0.0466-0.02410.5481-0.00980.1906-35.53449.2973-62.6301
380.97050.43030.64680.3591-0.2111.90620.21120.10990.094-0.151-0.0935-0.03040.01330.3479-0.01880.6059-0.08790.03920.834-0.10070.2411-12.143559.8772-71.1591
391.05941.044-0.08631.1405-0.35740.66370.17430.3301-0.0084-0.1297-0.008-0.0432-0.08740.0003-0.05290.6461-0.02520.0270.7302-0.06410.2262-25.405157.7804-81.0165
400.09560.02430.22040.36130.02740.5105-0.0442-0.06830.01990.05870.0072-0.0021-0.02370.0450.09950.6259-0.0283-0.00880.6921-0.08810.1669-25.913656.5386-62.1453
410.40060.1656-0.08570.6901-0.35370.6447-0.0095-0.30840.12470.0829-0.0193-0.0296-0.35490.0446-0.01150.7194-0.0350.0030.6692-0.04330.2238-25.683371.7459-45.1207
420.63320.56630.38791.4947-0.04790.3916-0.07640.21450.19660.69170.16790.0820.26820.03010.09480.60780.02120.02340.7056-0.01160.2781-30.395554.8539-46.5829
430.830.49910.19790.35550.3430.89690.08360.0390.0898-0.0566-0.1628-0.0832-0.09370.06060.09990.662-0.072-0.00720.67610.00580.129226.5516168.3032-14.2365
440.83280.29790.11661.1529-0.1931.2189-0.0938-0.0904-0.22740.0182-0.0786-0.04020.4072-0.04450.07850.798-0.09640.13860.6304-0.11710.266817.3086135.8834-29.3295
450.6143-0.0452-0.07890.38450.49110.9535-0.10250.0493-0.0694-0.04330.00890.00980.0729-0.04270.03750.5919-0.07140.04490.5617-0.04550.183212.9341157.8896-22.989
460.7181-0.3762-0.54030.87230.19531.2253-0.01080.0418-0.0519-0.116-0.0391-0.0582-0.03450.04330.04050.522-0.00180.02050.5891-0.05140.167533.401795.206314.7154
471.2841-0.89090.37041.02670.16130.8934-0.1355-0.2397-0.19170.3260.1449-0.1950.26510.27960.03980.62750.04330.09850.60680.07310.349349.306880.234118.4773
480.7055-0.2451-0.1060.0946-0.00680.2209-0.05450.1515-0.0248-0.374-0.074-0.13930.05050.04510.02070.605-0.01020.10680.6272-0.06480.202530.741790.44873.7897
490.32080.015-0.01160.44450.72181.17880.012-0.07390.0632-0.3687-0.0561-0.0133-0.0804-0.2897-0.00360.66530.0680.05510.6638-0.0670.201816.416199.22397.6992
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 411 through 459 )
2X-RAY DIFFRACTION2chain 'F' and (resid 460 through 574 )
3X-RAY DIFFRACTION3chain 'G' and (resid 108 through 139 )
4X-RAY DIFFRACTION4chain 'G' and (resid 140 through 199 )
5X-RAY DIFFRACTION5chain 'G' and (resid 200 through 395 )
6X-RAY DIFFRACTION6chain 'G' and (resid 396 through 574 )
7X-RAY DIFFRACTION7chain 'H' and (resid 108 through 170 )
8X-RAY DIFFRACTION8chain 'H' and (resid 171 through 199 )
9X-RAY DIFFRACTION9chain 'H' and (resid 200 through 237 )
10X-RAY DIFFRACTION10chain 'H' and (resid 238 through 353 )
11X-RAY DIFFRACTION11chain 'H' and (resid 354 through 378 )
12X-RAY DIFFRACTION12chain 'H' and (resid 379 through 459 )
13X-RAY DIFFRACTION13chain 'H' and (resid 460 through 505 )
14X-RAY DIFFRACTION14chain 'H' and (resid 506 through 548 )
15X-RAY DIFFRACTION15chain 'H' and (resid 549 through 574 )
16X-RAY DIFFRACTION16chain 'A' and (resid 108 through 254 )
17X-RAY DIFFRACTION17chain 'A' and (resid 255 through 296 )
18X-RAY DIFFRACTION18chain 'A' and (resid 297 through 410 )
19X-RAY DIFFRACTION19chain 'A' and (resid 411 through 574 )
20X-RAY DIFFRACTION20chain 'B' and (resid 108 through 171 )
21X-RAY DIFFRACTION21chain 'B' and (resid 172 through 267 )
22X-RAY DIFFRACTION22chain 'B' and (resid 268 through 309 )
23X-RAY DIFFRACTION23chain 'B' and (resid 310 through 410 )
24X-RAY DIFFRACTION24chain 'B' and (resid 411 through 574 )
25X-RAY DIFFRACTION25chain 'C' and (resid 108 through 141 )
26X-RAY DIFFRACTION26chain 'C' and (resid 142 through 199 )
27X-RAY DIFFRACTION27chain 'C' and (resid 200 through 237 )
28X-RAY DIFFRACTION28chain 'C' and (resid 238 through 272 )
29X-RAY DIFFRACTION29chain 'C' and (resid 273 through 296 )
30X-RAY DIFFRACTION30chain 'C' and (resid 297 through 322 )
31X-RAY DIFFRACTION31chain 'C' and (resid 323 through 410 )
32X-RAY DIFFRACTION32chain 'C' and (resid 411 through 459 )
33X-RAY DIFFRACTION33chain 'C' and (resid 460 through 574 )
34X-RAY DIFFRACTION34chain 'D' and (resid 108 through 139 )
35X-RAY DIFFRACTION35chain 'D' and (resid 140 through 199 )
36X-RAY DIFFRACTION36chain 'D' and (resid 200 through 267 )
37X-RAY DIFFRACTION37chain 'D' and (resid 268 through 378 )
38X-RAY DIFFRACTION38chain 'D' and (resid 379 through 410 )
39X-RAY DIFFRACTION39chain 'D' and (resid 411 through 458 )
40X-RAY DIFFRACTION40chain 'D' and (resid 459 through 505 )
41X-RAY DIFFRACTION41chain 'D' and (resid 506 through 548 )
42X-RAY DIFFRACTION42chain 'D' and (resid 549 through 574 )
43X-RAY DIFFRACTION43chain 'E' and (resid 108 through 199 )
44X-RAY DIFFRACTION44chain 'E' and (resid 200 through 353 )
45X-RAY DIFFRACTION45chain 'E' and (resid 354 through 574 )
46X-RAY DIFFRACTION46chain 'F' and (resid 108 through 272 )
47X-RAY DIFFRACTION47chain 'F' and (resid 273 through 319 )
48X-RAY DIFFRACTION48chain 'F' and (resid 320 through 378 )
49X-RAY DIFFRACTION49chain 'F' and (resid 379 through 410 )

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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