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- PDB-5utf: Crystal Structure of a Stabilized DS-SOSIP.6mut BG505 gp140 HIV-1... -

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基本情報

登録情報
データベース: PDB / ID: 5utf
タイトルCrystal Structure of a Stabilized DS-SOSIP.6mut BG505 gp140 HIV-1 Env Trimer, Containing Mutations I201C-P433C (DS), L154M, Y177W, N300M, N302M, T320L, I420M in Complex with Human Antibodies PGT122 and 35O22 at 4.3 A
要素
  • (Envelope glycoprotein ...) x 2
  • 35022 Heavy chain
  • 35022 Light Chain
  • PGT122 Heavy chain
  • PGT122 Light chain
キーワードIMMUNE SYSTEM (免疫系) / HIV-1 Env / stabilized Env / near-native mimic of the viral spike
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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / identical protein binding / 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
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 / 分子置換 / 解像度: 3.503 Å
データ登録者Pancera, M. / Chuang, G.-Y. / Xu, K. / Kwong, P.D.
引用ジャーナル: J. Virol. / 年: 2017
タイトル: Structure-Based Design of a Soluble Prefusion-Closed HIV-1 Env Trimer with Reduced CD4 Affinity and Improved Immunogenicity.
著者: Chuang, G.Y. / Geng, H. / Pancera, M. / Xu, K. / Cheng, C. / Acharya, P. / Chambers, M. / Druz, A. / Tsybovsky, Y. / Wanninger, T.G. / Yang, Y. / Doria-Rose, N.A. / Georgiev, I.S. / Gorman, J. ...著者: Chuang, G.Y. / Geng, H. / Pancera, M. / Xu, K. / Cheng, C. / Acharya, P. / Chambers, M. / Druz, A. / Tsybovsky, Y. / Wanninger, T.G. / Yang, Y. / Doria-Rose, N.A. / Georgiev, I.S. / Gorman, J. / Joyce, M.G. / O'Dell, S. / Zhou, T. / McDermott, A.B. / Mascola, J.R. / Kwong, P.D.
履歴
登録2017年2月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年3月29日Provider: repository / タイプ: Initial release
改定 1.12017年5月10日Group: Database references
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 / chem_comp ...atom_site / 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 / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
改定 2.12023年10月4日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
L: PGT122 Light chain
H: PGT122 Heavy chain
D: 35022 Heavy chain
E: 35022 Light Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)180,52427
ポリマ－169,1426
非ポリマー11,38121
水0
1
G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
L: PGT122 Light chain
H: PGT122 Heavy chain
D: 35022 Heavy chain
E: 35022 Light Chain
ヘテロ分子

G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
L: PGT122 Light chain
H: PGT122 Heavy chain
D: 35022 Heavy chain
E: 35022 Light Chain
ヘテロ分子

G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
L: PGT122 Light chain
H: PGT122 Heavy chain
D: 35022 Heavy chain
E: 35022 Light Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)541,57281
ポリマ－507,42718
非ポリマー34,14463
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_485-y-1,x-y+3,z1
crystal symmetry operation3_145-x+y-4,-x-1,z1
単位格子
Length a, b, c (Å)128.380, 128.380, 313.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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要素

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Envelope glycoprotein ... , 2種, 2分子 GB

#1: タンパク質 Envelope glycoprotein gp120 / Gp120 (HIV)


分子量: 54191.680 Da / 分子数: 1 / 変異: L154M, Y177W, N300M, N302M, T320L, I420M / 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: Q2N0S6
#2: タンパク質 Envelope glycoprotein gp41


分子量: 17146.482 Da / 分子数: 1 / 変異: I201C-P433C (DS) / 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: Q2N0S6

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抗体 , 4種, 4分子 LHDE

#3: 抗体 PGT122 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)
#4: 抗体 PGT122 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)
#5: 抗体 35022 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)
#6: 抗体 35022 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)

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糖 , 7種, 21分子

#7: 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-(1-6)-[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: 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[DManpa1-2DManpa1-6[DManpa1-3]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-i1_i2-j1WURCSPDB2Glycan 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]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#8: 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
#9: 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: 9 / 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
#10: 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
#11: 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
#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: 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: 7 / 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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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: 4.13 Å3/Da / 溶媒含有率: 70.25 %
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: 4.5
詳細: 13.2% PEG 400, 6.6% PEG 8000, 0.1M. Sodium acetate/Acetic acid pH 4.5

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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: 2016年3月21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: 3.5→50 Å / Num. obs: 18609 / % possible obs: 63.2 % / 冗長度: 2.3 %
Data reduction details: The overall resolution is 4.3 angstroms, which is the highest resolution for which completeness is greater than 50% with I over sigma(I)greater than 2. DS-SOSIP.6mut ternary ...Data reduction details: The overall resolution is 4.3 angstroms, which is the highest resolution for which completeness is greater than 50% with I over sigma(I)greater than 2. DS-SOSIP.6mut ternary complex crystal diffraction data were assessed for anisotropy with the Diffraction Anisotropy Server (http://services.mbi.ucla.edu/anisoscale/), which indicates the resolution at which F over sigma drops below 3.0 along a, b, and c axes; these were 5.5 angstroms, 5.5 angstroms, 3.5 angstroms, respectively. 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.
Net I/σ(I): 4.3

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)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
精密化構造決定の手法: 分子置換
開始モデル: 4TVP

4tvp


解像度: 3.503→38.982 Å / SU ML: 0.63 / 交差検証法: FREE R-VALUE / σ(F): 1.39 / 位相誤差: 32.56 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2989 949 5.1 %
Rwork0.2155 --
obs0.2198 18600 50.79 %
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: 3.503→38.982 Å
タンパク質核酸リガンド溶媒全体
原子数11210 0 754 0 11964
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00412317
X-RAY DIFFRACTIONf_angle_d0.67616884
X-RAY DIFFRACTIONf_dihedral_angle_d12.0747328
X-RAY DIFFRACTIONf_chiral_restr0.0442060
X-RAY DIFFRACTIONf_plane_restr0.0052043
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5026-3.68710.404370.2795274X-RAY DIFFRACTION5
3.6871-3.91790.3357560.2938950X-RAY DIFFRACTION19
3.9179-4.22010.33211140.26021865X-RAY DIFFRACTION38
4.2201-4.64410.36561420.23772679X-RAY DIFFRACTION54
4.6441-5.31470.31061880.22333421X-RAY DIFFRACTION69
5.3147-6.69050.31212200.24734300X-RAY DIFFRACTION86
6.6905-38.9840.24192220.16434162X-RAY DIFFRACTION83
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)
10.74110.21340.20142.0366-1.20270.9037-0.1231-0.40980.0050.56570.24550.5852-0.0759-0.9553-0.42570.5063-0.35370.60261.3579-0.35460.3476-258.165853.6212-24.1234
21.1989-0.10650.3510.40410.062.71210.1392-0.57220.01570.2871-0.1205-0.1855-0.0438-0.7053-0.01590.7515-0.23260.21450.63570.09110.4942-259.421453.07986.659
31.12280.5020.00271.1961-0.8161.9535-0.3355-0.4517-0.53440.2989-0.0927-0.27680.8111-0.24580.27260.754-0.10270.33730.36340.11530.4539-257.005639.2648-0.3269
40.39070.11570.07540.8284-1.08181.5476-0.10960.20320.089-0.41570.30030.34260.4305-0.3542-0.1640.62970.20880.29530.41680.4590.5219-258.186852.1794-40.2707
53.98830.5358-5.45510.0725-0.75528.02490.3091-0.30040.5451-0.34380.17890.1878-0.5492-1.2157-0.44481.5779-0.30290.23830.6495-0.26990.8205-261.416765.2398-16.5689
61.26550.2342-1.46410.78280.54614.7486-0.1186-0.029-0.3270.4793-0.1447-0.1010.4229-0.08650.04190.636-0.253300.1436-0.28140.5434-252.987568.1822-28.1795
71.4532-0.2493-0.42992.0618-0.24970.9159-0.32670.3171-0.1463-0.580.0887-0.45660.17640.0123-0.30240.7433-0.51750.32520.6177-0.19150.3843-247.07464.9269-48.4243
83.96640.8051-2.75453.0380.86055.29450.63520.71960.6165-1.554-0.0267-1.9848-0.61751.7847-0.64441.01510.17010.47331.996-0.37831.2975-233.31555.3467-47.7841
93.56550.3911.12994.7395-0.1540.3749-0.05130.4097-0.4918-0.28840.5244-1.11130.45631.9618-0.47520.64770.26510.46330.7922-0.12330.7214-240.547947.1101-51.1638
100.62280.22160.50871.8691-0.6752.61960.4155-0.2237-0.27220.3636-0.2913-0.39540.2795-0.08860.18380.7623-0.14040.29180.51920.45250.5675-243.153349.7425-41.9695
112.319-0.92741.26020.5182-0.34830.8592-0.0813-0.12690.11970.1798-0.4811-0.8448-0.10920.26620.34630.3527-0.45860.11750.8331-0.0980.9153-238.07866.0977-43.3161
120.00520-0.00170.00650.00610.0040.19210.08520.08770.10590.052-0.043-0.0983-0.0446-0.13141.6040.00810.51340.895-0.02360.8757-243.306180.6716-54.4929
137.62130.82492.76252.9636-0.00082.8862-0.0725-0.61070.83010.282-0.77570.20870.0214-0.20090.69671.5972-0.21290.36760.6236-0.14390.7013-293.395336.602935.7732
140.86150.4935-0.42850.5619-0.96092.1145-0.00980.48570.1172-0.22750.03460.03630.2905-0.04280.08381.4242-0.35560.63461.03730.29940.7619-291.550126.388434.8287
150.7009-0.13750.48991.36040.99641.255-0.522-0.0253-0.0410.0634-0.13550.30610.24660.1042-0.23860.7883-0.21560.35140.48860.19550.6-288.261832.173738.6412
165.74052.581-6.33061.3428-3.07597.2669-0.18670.69050.3094-0.39110.62550.28660.5339-1.0113-0.33671.4291-0.6330.81161.3017-0.46521.7799-308.575832.67648.3924
173.4284-0.374-0.88341.91041.11341.4901-0.4927-0.2471-0.76750.80820.74840.16190.5360.2442-0.20661.6234-0.12120.08450.48610.03721.1397-307.281528.212274.5235
182.69880.9292-1.17843.9389-2.23832.1447-0.37610.0116-0.9179-0.6868-0.1526-0.3591.1890.17430.52091.42870.06120.44390.46480.23381.0122-303.652127.818263.1923
195.9322-2.7711-1.69387.5013-0.21155.9296-0.5811-1.2987-0.05641.34350.3580.19551.32190.09430.21511.91190.2510.57351.3089-0.35020.9635-311.346529.994781.5751
204.2834-2.69011.3413.4673-1.72691.1909-0.895-0.6614-0.64420.7530.26680.05080.5043-0.31740.49931.19780.57940.46361.06050.1010.9592-316.686230.020472.8353
210.206-0.2740.60852.05091.50654.9062-0.3191-0.3492-0.4760.351-0.3739-0.24841.41120.37980.56211.58870.04260.42351.57650.70461.012-280.26516.234758.0654
221.11751.02920.72281.85572.01382.96740.2858-0.3273-0.9741-0.1078-0.5097-0.89491.35350.37340.37552.04010.13150.80720.82320.3471.4541-276.507910.224248.6694
232.2506-0.6782-1.05946.84371.7255.4983-0.6174-0.5675-1.0503-0.3945-0.3684-0.74491.51790.95280.71280.68670.23390.48791.04840.35790.8761-277.282222.562146.5282
242.0098-0.8364-0.98290.41560.71861.8967-0.0109-0.3592-0.2682-0.5057-0.0005-0.48650.0663-0.17360.071.3026-0.37060.55441.91030.49961.0119-268.813722.739749.3977
254.53322.5198-2.11261.446-0.7435.07970.127-0.5392-0.8231-0.0117-0.1369-0.62370.35750.14330.27981.2064-0.18520.37721.31150.80561.2566-273.150717.754555.3993
260.6625-0.2709-0.04431.5634-0.57160.2424-0.3162-0.553-0.57640.4559-0.01760.21540.23370.15260.2521.3223-0.48140.33340.90240.11540.7685-279.92820.864940.3119
270.899-0.18550.25991.2054-0.0731.35880.01050.0036-0.14070.05620.0536-0.14560.15980.11170.10190.933-0.26040.50851.19350.24750.7533-273.585126.389127.2771
281.68180.54151.80792.55670.14562.0174-0.6012-0.6264-0.02670.24210.07320.7954-0.55940.21340.15651.33120.19770.52681.19190.52270.9268-292.611818.432366.0778
292.0938-1.7586-1.01092.0463-0.2692.8404-0.3757-0.5183-0.56690.36530.05980.49520.31130.58770.3722.5917-0.24610.78060.9485-0.03051.1333-298.071716.976869.409
307.70470.9361-1.65962.5273-1.89983.3542-0.6130.0035-1.42380.24430.03020.4350.5809-0.50990.69051.2922-0.14520.7441.27920.10120.8928-299.782618.99966.1702
316.02341.0283.50134.16221.72493.86260.5138-0.6893-0.31020.2887-0.18141.03470.89520.4584-0.13871.9560.02990.5621.0748-0.02331.0308-308.668711.563668.5962
323.1379-1.83652.25167.3208-0.16143.6360.731-0.2768-1.35190.3662-0.32930.27780.9609-0.176-0.22012.39360.06790.69550.68530.20071.7107-296.73939.196771.6441
332.0864-0.45710.16590.46080.33761.7641-0.06060.2988-0.49320.0586-0.1015-0.22280.9504-0.1460.05421.43390.38260.25710.6679-0.27470.9329-242.8221.4206-42.7517
341.2284-0.6323-0.29863.75790.0880.4727-0.24130.208-0.5883-0.4931-0.02880.45310.35780.00180.31721.7024-0.32170.65920.3061-0.09690.8881-250.328120.4938-52.3237
352.0889-0.9661-1.13153.2644.71727.808-0.14960.1685-0.2942-0.2561-0.22340.01310.1686-0.30520.20141.20190.37170.61780.5834-0.01670.6621-246.314127.6062-36.8138
362.6904-0.74440.45434.29634.65865.6596-0.91110.3518-1.3262-0.19070.88920.2761.61670.20270.10892.0357-0.29180.62531.1801-0.0690.9353-244.091212.6117-52.5018
370.92210.7161-0.79550.5565-0.56292.1662-0.2780.0228-0.4908-0.04950.0653-0.13490.60520.08850.51971.3401-0.10660.80580.4516-0.03240.8265-243.046627.9453-51.0336
384.37151.69566.07784.0882.0318.54020.4519-0.4157-0.5981-0.7210.7629-0.32240.16120.0469-1.04831.4260.0456-0.08690.8076-0.0471.6159-225.2727-0.2267-45.8818
390.51060.2297-0.19410.1128-0.15210.4981.1237-0.3249-0.1668-0.47610.1558-0.5889-0.11170.5092-1.17732.799-0.330.71021.0037-0.05413.0369-205.688510.435-49.5862
403.40875.3380.59318.35140.92720.1018-0.7787-0.26250.3049-0.2880.6169-1.0780.70490.49780.08612.09670.46620.20430.9392-0.31832.3707-220.247211.8863-45.2718
417.3145-3.1268-1.48034.1502-3.56266.7235-0.41820.3845-0.7853-1.12320.8094-1.54641.2120.6376-0.27081.81760.1250.43130.6828-0.03841.996-222.8474.1511-53.3402
421.8722-0.27061.5415.76951.96472.9445-0.80330.04560.1675-0.03580.0847-1.73750.74251.55330.65591.34430.3387-0.25951.8236-0.06683.2714-203.109615.0994-39.5827
437.5441-7.6154.819.0076-2.40529.69720.0724-0.7291-2.5098-0.09160.1197-1.17692.40990.2652-0.09232.0411-0.0150.36990.94770.12162.0074-222.08166.5701-37.8753
442.82620.82893.49958.22023.04124.842-0.48870.9369-1.1235-1.49191.1167-1.3640.59821.2581-0.55193.24030.1335-0.19592.9145-0.7492.3974-197.94086.9859-46.1512
452.5336-1.54980.16782.07510.37474.234-0.09420.807-0.2499-1.2021-0.1977-0.63880.74760.60180.01381.4878-0.04570.76320.8804-0.28191.0513-238.040832.945-66.8186
461.31430.4849-1.20081.7984-1.32583.92810.2848-1.10690.1322-0.8862-0.2239-1.1159-0.23231.59480.03191.94970.09271.09381.22210.09431.3258-231.069930.4863-64.0552
470.7110.30241.02592.1621-1.0792.52510.80351.42860.1102-0.4024-0.9168-1.65620.76941.00690.15811.43460.08810.71351.5642-0.19012.1065-218.805211.0281-61.1521
481.68561.247-0.68461.19560.12821.7630.20970.4944-0.4782-0.4375-0.6916-1.69190.74460.56940.57131.92480.76340.96312.18410.42472.8854-208.59090.3659-61.6168
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 31 through 98 )
2X-RAY DIFFRACTION2chain 'G' and (resid 99 through 258 )
3X-RAY DIFFRACTION3chain 'G' and (resid 259 through 503 )
4X-RAY DIFFRACTION4chain 'B' and (resid 518 through 544 )
5X-RAY DIFFRACTION5chain 'B' and (resid 545 through 572 )
6X-RAY DIFFRACTION6chain 'B' and (resid 573 through 595 )
7X-RAY DIFFRACTION7chain 'B' and (resid 596 through 610 )
8X-RAY DIFFRACTION8chain 'B' and (resid 611 through 615 )
9X-RAY DIFFRACTION9chain 'B' and (resid 616 through 622 )
10X-RAY DIFFRACTION10chain 'B' and (resid 623 through 637 )
11X-RAY DIFFRACTION11chain 'B' and (resid 638 through 650 )
12X-RAY DIFFRACTION12chain 'B' and (resid 651 through 661 )
13X-RAY DIFFRACTION13chain 'L' and (resid 8 through 33 )
14X-RAY DIFFRACTION14chain 'L' and (resid 34 through 69 )
15X-RAY DIFFRACTION15chain 'L' and (resid 70 through 101 )
16X-RAY DIFFRACTION16chain 'L' and (resid 102 through 114 )
17X-RAY DIFFRACTION17chain 'L' and (resid 115 through 162 )
18X-RAY DIFFRACTION18chain 'L' and (resid 163 through 181 )
19X-RAY DIFFRACTION19chain 'L' and (resid 182 through 198 )
20X-RAY DIFFRACTION20chain 'L' and (resid 199 through 210 )
21X-RAY DIFFRACTION21chain 'H' and (resid 1 through 16 )
22X-RAY DIFFRACTION22chain 'H' and (resid 17 through 32 )
23X-RAY DIFFRACTION23chain 'H' and (resid 33 through 56 )
24X-RAY DIFFRACTION24chain 'H' and (resid 57 through 72 )
25X-RAY DIFFRACTION25chain 'H' and (resid 73 through 87 )
26X-RAY DIFFRACTION26chain 'H' and (resid 88 through 100A)
27X-RAY DIFFRACTION27chain 'H' and (resid 100B through 100P)
28X-RAY DIFFRACTION28chain 'H' and (resid 100Q through 132 )
29X-RAY DIFFRACTION29chain 'H' and (resid 133 through 152 )
30X-RAY DIFFRACTION30chain 'H' and (resid 153 through 173 )
31X-RAY DIFFRACTION31chain 'H' and (resid 174 through 191 )
32X-RAY DIFFRACTION32chain 'H' and (resid 192 through 211 )
33X-RAY DIFFRACTION33chain 'D' and (resid 1 through 33 )
34X-RAY DIFFRACTION34chain 'D' and (resid 34 through 71 )
35X-RAY DIFFRACTION35chain 'D' and (resid 72 through 82 )
36X-RAY DIFFRACTION36chain 'D' and (resid 82A through 94 )
37X-RAY DIFFRACTION37chain 'D' and (resid 95 through 111 )
38X-RAY DIFFRACTION38chain 'D' and (resid 112 through 124 )
39X-RAY DIFFRACTION39chain 'D' and (resid 125 through 143 )
40X-RAY DIFFRACTION40chain 'D' and (resid 144 through 166 )
41X-RAY DIFFRACTION41chain 'D' and (resid 167 through 182 )
42X-RAY DIFFRACTION42chain 'D' and (resid 183 through 194 )
43X-RAY DIFFRACTION43chain 'D' and (resid 195 through 210 )
44X-RAY DIFFRACTION44chain 'D' and (resid 211 through 224 )
45X-RAY DIFFRACTION45chain 'E' and (resid 2 through 75 )
46X-RAY DIFFRACTION46chain 'E' and (resid 76 through 91 )
47X-RAY DIFFRACTION47chain 'E' and (resid 92 through 171 )
48X-RAY DIFFRACTION48chain 'E' and (resid 172 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