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- PDB-5u7o: Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer B... -

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基本情報

登録情報
データベース: PDB / ID: 5u7o
タイトルCrystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-626529 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom
要素
  • (Envelope glycoprotein ...) x 2
  • 35O22 FAB HEAVY CHAIN
  • 35O22 FAB LIGHT CHAIN
  • PGT122 FAB HEAVY CHAIN
  • PGT122 FAB LIGHT CHAIN
キーワードVIRAL PROTEIN/Immune System (ウイルス性) / HIV-1 entry / small molecule (小分子) / inhibitor (酵素阻害剤) / VIRAL PROTEIN-Immune System complex (ウイルス性)
機能・相同性
機能・相同性情報


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / virus-mediated perturbation of host defense response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / エンベロープ (ウイルス) ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / virus-mediated perturbation of host defense response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / エンベロープ (ウイルス) / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 細胞膜
類似検索 - 分子機能
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Gp120 (HIV) / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 抗体 / Immunoglobulin-like / サンドイッチ / Mainly Beta
類似検索 - ドメイン・相同性
Chem-83J / Envelope glycoprotein gp160
類似検索 - 構成要素
生物種Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 解像度: 3.031 Å
データ登録者Pancera, M. / Lai, Y.-T. / Kwong, P.D.
引用ジャーナル: Nat. Chem. Biol. / 年: 2017
タイトル: Crystal structures of trimeric HIV envelope with entry inhibitors BMS-378806 and BMS-626529.
著者: Pancera, M. / Lai, Y.T. / Bylund, T. / Druz, A. / Narpala, S. / O'Dell, S. / Schon, A. / Bailer, R.T. / Chuang, G.Y. / Geng, H. / Louder, M.K. / Rawi, R. / Soumana, D.I. / Finzi, A. / ...著者: Pancera, M. / Lai, Y.T. / Bylund, T. / Druz, A. / Narpala, S. / O'Dell, S. / Schon, A. / Bailer, R.T. / Chuang, G.Y. / Geng, H. / Louder, M.K. / Rawi, R. / Soumana, D.I. / Finzi, A. / Herschhorn, A. / Madani, N. / Sodroski, J. / Freire, E. / Langley, D.R. / Mascola, J.R. / McDermott, A.B. / Kwong, P.D.
履歴
登録2016年12月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年8月30日Provider: repository / タイプ: Initial release
改定 1.12017年9月6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_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
改定 1.22017年9月20日Group: Structure summary / カテゴリ: struct / Item: _struct.title
改定 1.32017年9月27日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.42017年10月18日Group: Structure summary / カテゴリ: struct / Item: _struct.title
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation

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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
B: Envelope glycoprotein gp160
D: 35O22 FAB HEAVY CHAIN
E: 35O22 FAB LIGHT CHAIN
G: Envelope glycoprotein gp160
H: PGT122 FAB HEAVY CHAIN
L: PGT122 FAB LIGHT CHAIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)181,40934
ポリマ－169,0156
非ポリマー12,39428
水0
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)131.027, 131.027, 311.491
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDモデル要素
11G-603-

SO4

21L-301-

SO4

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要素

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Envelope glycoprotein ... , 2種, 2分子 BG

#1: タンパク質 Envelope glycoprotein gp160


分子量: 17146.482 Da / 分子数: 1 / 断片: UNP residues 509-661 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: env / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S5
#4: タンパク質 Envelope glycoprotein gp160


分子量: 54064.277 Da / 分子数: 1 / 断片: UNP residues 30-510 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: env / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S5

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抗体 , 4種, 4分子 DEHL

#2: 抗体 35O22 FAB HEAVY CHAIN


分子量: 26170.533 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 35O22 FAB LIGHT CHAIN


分子量: 23318.824 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 PGT122 FAB HEAVY CHAIN


分子量: 25434.691 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#6: 抗体 PGT122 FAB LIGHT CHAIN


分子量: 22880.275 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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糖 , 8種, 22分子

#7: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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オリゴ糖 / 分子量: 1235.105 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]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 748.682 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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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オリゴ糖 / 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]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: 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: 8 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#11: 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オリゴ糖 / 分子量: 1072.964 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
DManpa1-2DManpa1-3[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]/1-1-2-3-3-3/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)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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オリゴ糖 / 分子量: 1721.527 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
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1WURCSPDB2Glycan 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)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#13: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#15: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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: 8 / 由来タイプ: 組換発現 / 式: C8H15NO6
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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非ポリマー , 2種, 6分子

#14: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン / 硫酸塩


分子量: 96.063 Da / 分子数: 5 / 由来タイプ: 組換発現 / 式: SO4
#16: 化合物 ChemComp-83J / 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol-1-yl)-1H-pyrrolo[2,3-c]pyridin-3-yl]ethane-1,2-dione / BMS-626529


分子量: 473.484 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C24H23N7O4

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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: 4.28 Å3/Da / 溶媒含有率: 71.28 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5
詳細: 16% ISOPROPANOL, 5.32% PEG1500, 0.2M LISO4, 0.1M SODIUM ACETATE PH 5.5

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: RAYONIX MX300-HS / 検出器: CCD / 日付: 2015年3月13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: 3.02→50 Å / Num. obs: 43880 / % possible obs: 85.6 % / 冗長度: 2.6 % / Net I/σ(I): 2.2

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化解像度: 3.031→41.349 Å / SU ML: 0.58 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 40.62 / 立体化学のターゲット値: ML
詳細: AUTHORS STATE THAT THE OVERALL RESOLUTION WAS DETERMINED AS FOLLOWS: IT IS THE HIGHEST RESOLUTION FOR WHICH THE COMPLETENESS WAS GREATER THAN 50% AND THE I/SIGMAI WAS GREATER THAN 2.0. ...詳細: AUTHORS STATE THAT THE OVERALL RESOLUTION WAS DETERMINED AS FOLLOWS: IT IS THE HIGHEST RESOLUTION FOR WHICH THE COMPLETENESS WAS GREATER THAN 50% AND THE I/SIGMAI WAS GREATER THAN 2.0. CRYSTAL DIFFRACTION DATA WERE THEN ASSESSED FOR ANISOTROPY THROUGH USE OF THE DIFFRACTION ANISOTROPY SERVER (HTTP://SERVICES.MBI.UCLA.EDU/ANISOSCALE/), WHICH INDICATES THE RESOLUTION AT WHICH F/SIGMA DROPS BELOW 3.0 ALONG A, B, AND C AXES; THESE WERE 3.8 A, 3.8 A, 3.0 A. BECAUSE WE SOUGHT TO USE AS MUCH OF THE DATA AS POSSIBLE FOR REFINEMENT, WE USED THE OVERALL RESOLUTION DESCRIBED ABOVE TO DEFINE THE RESOLUTION OF THE A AND B AXES, WITH THE RESOLUTION LIMIT FOR THE C AXIS DEFINED BY THE DIFFRACTION ANISOTROPY SERVER.
Rfactor反射数%反射
Rfree0.3254 1584 5.01 %
Rwork0.2723 --
obs0.2749 31627 54.07 %
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: 3.031→41.349 Å
タンパク質核酸リガンド溶媒全体
原子数11249 0 817 0 12066
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00112415
X-RAY DIFFRACTIONf_angle_d0.38317028
X-RAY DIFFRACTIONf_dihedral_angle_d10.0857351
X-RAY DIFFRACTIONf_chiral_restr0.0382073
X-RAY DIFFRACTIONf_plane_restr0.0042061
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0309-3.12870.4673100.3997158X-RAY DIFFRACTION3
3.1287-3.24040.5194240.3879459X-RAY DIFFRACTION9
3.2404-3.37010.4021460.3696853X-RAY DIFFRACTION17
3.3701-3.52340.3841750.36111354X-RAY DIFFRACTION27
3.5234-3.70910.4111020.33781948X-RAY DIFFRACTION39
3.7091-3.94130.36821280.32362629X-RAY DIFFRACTION52
3.9413-4.24530.36141840.29433488X-RAY DIFFRACTION69
4.2453-4.6720.35722320.27054354X-RAY DIFFRACTION86
4.672-5.34690.29692710.26494948X-RAY DIFFRACTION98
5.3469-6.73180.33962500.28994963X-RAY DIFFRACTION98
6.7318-41.35330.27532620.2284889X-RAY DIFFRACTION96
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3449-0.69820.61020.5518-0.39080.6864-0.0281-0.0548-0.0606-0.0067-0.0488-0.07820.04690.31340.21330.18650.2953-0.40930.22810.03270.5518198.6524284.0359-10.9155
20.64010.22980.42870.23180.36632.0682-0.14560.0920.04850.0401-0.0003-0.02770.0299-0.16440.0905-0.1835-0.2904-0.1648-0.0020.07610.3167193.16270.5258-3.4719
38.7482-1.6719-2.69850.5240.40190.89520.31732.2627-1.8273-0.6565-0.29910.71460.3087-0.8015-0.02630.7732-0.1857-0.41071.0612-0.08110.8557189.3983269.4306-20.683
44.3796-3.45993.1675.2412-0.64025.38750.34930.2588-0.692-1.1272-0.32141.1083-0.59-0.8325-0.02720.6312-0.1469-0.35591.20460.04070.3958181.2655278.0852-25.0041
57.43942.3305-2.07323.1602-2.2352.14750.03522.60791.1471-0.70510.53140.74220.1109-1.407-0.59521.86280.3943-0.74641.35960.08271.0802180.1348291.3944-26.7554
60.1857-0.07570.07040.2849-0.20680.2334-0.068-0.12250.10990.0297-0.03460.1537-0.1687-0.24060.05130.79180.4641-0.61280.6148-0.3320.6543182.148288.3543-17.4876
71.93820.0129-0.79015.73581.48081.36550.08170.2667-0.4411-1.1369-0.08711.1817-0.1802-0.69880.0250.5585-0.1011-0.32651.604-0.04680.8095179.8922267.5995-24.6941
81.19752.3412-0.93457.6806-1.91270.7370.7038-0.4678-0.09811.8671-0.4925-1.0398-1.49250.2297-0.12493.2059-0.3368-0.86411.22870.05731.3416179.4793324.2625-19.7591
92.5364-0.6503-0.15080.7577-0.45350.420.10770.25570.7086-0.03280.0375-0.1112-0.4973-0.14-0.00422.36370.5597-0.77770.6459-0.01580.9445188.1003316.0383-24.3877
100.4445-0.23990.31780.66140.03140.5286-0.23290.30080.5055-1.0513-0.12190.3341-1.0779-0.07170.45771.89350.2522-0.76420.4971-0.37460.96185.4928314.1565-21.5218
110.74070.4219-1.10823.49610.19481.8657-0.15650.07130.67910.20430.36240.8111-1.7857-1.79270.09342.51580.8082-0.78322.1136-0.21331.1595171.1102328.1215-23.0422
120.34760.7266-1.34373.7472-2.46455.2546-0.02430.19430.60990.5771-0.1287-0.9876-0.0681-0.89650.17732.11470.30760.03291.7622-0.14192.3183153.6883326.6969-22.1709
132.5001-1.14771.06530.96280.97815.3820.48730.019-0.0444-0.78910.1520.2998-0.313-0.6833-0.61251.73080.6908-0.20721.1972-0.23112.6219162.1758334.2312-28.4682
141.5511-0.9629-2.30251.25540.944.10760.4198-0.77542.15010.7110.6760.0701-0.92160.0142-1.06462.23710.4520.49211.6793-0.61013.0517153.7656327.9978-13.8182
150.22170.69350.15313.49672.27452.5505-0.02210.77411.1164-0.14740.93640.5222-0.789-0.1336-0.93653.47690.0370.95823.24410.4783.5751137.0338330.7754-21.4879
162.5630.7625-0.37824.5322-3.67793.1281-0.35470.5710.8508-0.10120.40790.6214-0.0834-0.0841-0.06421.88160.7992-0.66251.3401-0.02541.0653172.9826309.881-47.7052
172.2572-0.56031.93950.9999-1.1342.7319-0.2154-1.1980.7399-0.1142-0.5008-0.1343-0.88871.07880.66882.31010.0742-1.14361.65960.04921.6033185.6521307.2182-42.8212
183.0099-1.25372.0792.5877-2.17652.7898-0.1001-0.5865-0.12970.0860.26090.2838-0.1398-0.3961-0.11911.43460.7227-0.67661.31640.1540.9234176.172303.3832-39.1164
193.87090.22493.77833.2033-0.9614.18-0.4515-0.82361.0740.1006-0.34190.4341-0.4523-0.22250.70852.93650.6587-0.81531.335-0.31441.2315170.9402310.7817-40.3093
205.55314.81251.53728.4046.81679.43931.65540.61810.976-0.3263-1.71240.2704-0.0903-1.78270.05981.82880.3755-0.7332.083-0.11842.9482151.7601336.7651-34.2156
216.225-0.6804-2.07243.48285.37768.47670.9369-0.36940.304-2.0489-1.5462-0.2211-1.1396-1.6030.62121.50970.1725-0.42711.2085-0.26142.5174157.667326.0779-34.7597
228.23050.06320.79721.845-1.97112.19851.1634-0.16991.054-1.1804-1.53110.962-2.0642-1.20.33333.46571.2976-0.98862.3715-0.9462.6306145.6544339.925-37.1221
230.5906-0.3484-0.26621.1587-0.39081.1284-0.052-0.1463-0.04310.2728-0.2637-0.5854-0.11510.17410.110.17630.4673-0.00470.5297-0.09260.2338199.6883281.7356-0.0074
240.35290.19620.22750.17240.12440.7808-0.0665-0.23330.21490.0584-0.48770.5402-0.3402-0.2991-0.4892-0.21690.5274-1.56890.4032-0.0099-1.0336197.532288.562225.4347
250.30530.00550.23260.4064-0.19730.43-0.2406-0.16310.7755-0.1014-0.13860.3775-0.6632-0.3851-0.21140.85780.3997-1.32270.3779-0.2199-0.5896200.0465300.269530.6826
261.7452-0.46820.50380.9398-0.4980.3094-0.2981-0.14420.59880.3981-0.0697-0.091-0.4432-0.37270.05880.31260.4552-0.1930.4439-0.10660.3641187.1475293.02854.636
272.61720.8176-0.39582.8459-2.45652.7684-0.060.86990.3999-0.4529-0.17850.12380.06020.23880.21270.95270.6513-0.53521.655-0.51860.9123220.9443322.140881.9092
286.89456.3849-7.57026.1763-6.50929.5523-0.31560.76870.6613-0.95670.18430.9243-1.1347-1.19750.16421.35380.3609-0.67450.9813-0.54781.153217.483328.242272.3889
290.16080.35560.0581.0890.14442.2073-0.395-0.23590.6768-0.2006-0.04940.3875-1.43-0.89520.56081.35960.4911-0.64430.9893-0.28160.492214.4902317.456171.5881
300.16820.85330.2414.22240.59722.6956-0.3755-0.01420.32030.3780.14590.6015-0.844-1.55320.34450.86590.4548-0.2311.2563-0.43540.5555217.5586316.821171.8503
311.44480.5981.90810.31330.72022.9749-0.13540.27960.0668-0.15820.0250.168-0.1132-0.064-0.03670.740.4604-0.73180.668-0.37460.4736222.0678316.021571.7258
326.60571.9511-2.95346.06711.75133.7184-0.47180.2608-0.1494-0.30170.2923-0.5985-0.2617-0.0420.09061.26730.0921-0.42470.4454-0.30780.6338242.7513320.610994.5103
331.0897-0.55610.24990.41830.22751-0.3314-0.02550.77640.36080.0589-0.1092-0.58880.4396-0.1881.2945-0.2519-0.35570.668-0.66630.8601239.8309320.37689.9317
340.07990.001-0.683-0.00130.01135.69950.4011-0.60870.10650.2855-0.3593-0.4806-1.24591.3607-0.05510.7797-0.1255-0.38240.86-0.41071.7244251.74329.596791.9091
352.51983.783.34826.02014.15646.88950.17830.1621.26670.48370.15910.0034-0.65370.4594-0.33221.30570.3807-0.18661.173-0.3161.3805236.619329.058195.5458
361.41940.7520.68760.39680.36620.32070.034-0.0640.13980.2343-0.0427-0.2297-0.32450.52070.04830.5238-0.0345-0.77860.6466-0.56740.7093233.3117308.875460.2866
371.4610.77171.33731.45790.95323.1265-0.18490.14510.00980.06850.1271-0.4195-0.49820.409-0.17090.46120.0507-0.54950.2117-0.47280.3846228.7432305.643660.0725
383.05410.42652.58184.46882.41493.49930.3041.1132-0.7778-0.46150.0252-0.69790.34491.2833-0.31960.84140.27340.28040.68330.05110.9849249.7425306.294974.3141
391.4063-0.54770.35681.5157-0.10040.5074-0.3546-0.273-0.26450.2906-0.10350.2007-0.0344-0.07650.25130.63340.6595-0.31020.4016-0.35390.8818247.7512310.336498.5164
402.0923-0.89270.02231.6730.090.9258-0.2988-0.16070.0312-0.024-0.1102-0.0809-0.1747-0.00940.01480.28940.544-0.22790.2058-0.00490.5958250.3005309.392995.9911
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 518 through 571 )
2X-RAY DIFFRACTION2chain 'B' and (resid 572 through 595 )
3X-RAY DIFFRACTION3chain 'B' and (resid 596 through 600 )
4X-RAY DIFFRACTION4chain 'B' and (resid 601 through 615 )
5X-RAY DIFFRACTION5chain 'B' and (resid 616 through 622 )
6X-RAY DIFFRACTION6chain 'B' and (resid 623 through 638 )
7X-RAY DIFFRACTION7chain 'B' and (resid 639 through 663 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'D' and (resid 18 through 71 )
10X-RAY DIFFRACTION10chain 'D' and (resid 72 through 100E)
11X-RAY DIFFRACTION11chain 'D' and (resid 100F through 124 )
12X-RAY DIFFRACTION12chain 'D' and (resid 125 through 166 )
13X-RAY DIFFRACTION13chain 'D' and (resid 167 through 182 )
14X-RAY DIFFRACTION14chain 'D' and (resid 183 through 210 )
15X-RAY DIFFRACTION15chain 'D' and (resid 211 through 224 )
16X-RAY DIFFRACTION16chain 'E' and (resid 2 through 25 )
17X-RAY DIFFRACTION17chain 'E' and (resid 26 through 37 )
18X-RAY DIFFRACTION18chain 'E' and (resid 38 through 75 )
19X-RAY DIFFRACTION19chain 'E' and (resid 76 through 113 )
20X-RAY DIFFRACTION20chain 'E' and (resid 114 through 161 )
21X-RAY DIFFRACTION21chain 'E' and (resid 162 through 180 )
22X-RAY DIFFRACTION22chain 'E' and (resid 181 through 210 )
23X-RAY DIFFRACTION23chain 'G' and (resid 31 through 82 )
24X-RAY DIFFRACTION24chain 'G' and (resid 83 through 283 )
25X-RAY DIFFRACTION25chain 'G' and (resid 284 through 456 )
26X-RAY DIFFRACTION26chain 'G' and (resid 457 through 505 )
27X-RAY DIFFRACTION27chain 'H' and (resid 1 through 16 )
28X-RAY DIFFRACTION28chain 'H' and (resid 17 through 32 )
29X-RAY DIFFRACTION29chain 'H' and (resid 33 through 76 )
30X-RAY DIFFRACTION30chain 'H' and (resid 77 through 100A)
31X-RAY DIFFRACTION31chain 'H' and (resid 100B through 122 )
32X-RAY DIFFRACTION32chain 'H' and (resid 123 through 148 )
33X-RAY DIFFRACTION33chain 'H' and (resid 149 through 175 )
34X-RAY DIFFRACTION34chain 'H' and (resid 176 through 192 )
35X-RAY DIFFRACTION35chain 'H' and (resid 193 through 211 )
36X-RAY DIFFRACTION36chain 'L' and (resid 8 through 61 )
37X-RAY DIFFRACTION37chain 'L' and (resid 62 through 101 )
38X-RAY DIFFRACTION38chain 'L' and (resid 102 through 116 )
39X-RAY DIFFRACTION39chain 'L' and (resid 117 through 162 )
40X-RAY DIFFRACTION40chain 'L' and (resid 163 through 210 )

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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://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