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- PDB-5w6d: Crystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with F... -

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基本情報

登録情報
データベース: PDB / ID: 5w6d
タイトルCrystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with Fabs 35022 and 9H/109L
要素
  • (BG505-SOSIP.v4.1-GT1-N137A ...) x 2
  • 109L FAB light chain
  • 35022 FAB heavy chain
  • 35022 FAB light chain
  • 9H FAB heavy chain
キーワードVIRAL PROTEIN/Immune System / HIV-1 broadly neutralizing antibody / VIRAL PROTEIN-Immune System complex
機能・相同性
機能・相同性情報


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
類似検索 - 分子機能
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / 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: 3.202 Å
データ登録者Garces, F. / Stanfield, R.L. / Wilson, I.A.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657 米国
引用ジャーナル: J. Exp. Med. / 年: 2017
タイトル: Design and crystal structure of a native-like HIV-1 envelope trimer that engages multiple broadly neutralizing antibody precursors in vivo.
著者: Medina-Ramirez, M. / Garces, F. / Escolano, A. / Skog, P. / de Taeye, S.W. / Del Moral-Sanchez, I. / McGuire, A.T. / Yasmeen, A. / Behrens, A.J. / Ozorowski, G. / van den Kerkhof, T.L.G.M. / ...著者: Medina-Ramirez, M. / Garces, F. / Escolano, A. / Skog, P. / de Taeye, S.W. / Del Moral-Sanchez, I. / McGuire, A.T. / Yasmeen, A. / Behrens, A.J. / Ozorowski, G. / van den Kerkhof, T.L.G.M. / Freund, N.T. / Dosenovic, P. / Hua, Y. / Gitlin, A.D. / Cupo, A. / van der Woude, P. / Golabek, M. / Sliepen, K. / Blane, T. / Kootstra, N. / van Breemen, M.J. / Pritchard, L.K. / Stanfield, R.L. / Crispin, M. / Ward, A.B. / Stamatatos, L. / Klasse, P.J. / Moore, J.P. / Nemazee, D. / Nussenzweig, M.C. / Wilson, I.A. / Sanders, R.W.
履歴
登録2017年6月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年7月5日Provider: repository / タイプ: Initial release
改定 1.12017年9月13日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
改定 1.22017年9月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
改定 2.12023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
改定 2.22024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
G: BG505-SOSIP.v4.1-GT1-N137A gp120
B: BG505-SOSIP.v4.1-GT1-N137A gp41
L: 109L FAB light chain
H: 9H FAB heavy chain
D: 35022 FAB heavy chain
E: 35022 FAB light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)176,22718
ポリマ－168,3796
非ポリマー7,84712
水00
1
G: BG505-SOSIP.v4.1-GT1-N137A gp120
B: BG505-SOSIP.v4.1-GT1-N137A gp41
L: 109L FAB light chain
H: 9H FAB heavy chain
D: 35022 FAB heavy chain
E: 35022 FAB light chain
ヘテロ分子

G: BG505-SOSIP.v4.1-GT1-N137A gp120
B: BG505-SOSIP.v4.1-GT1-N137A gp41
L: 109L FAB light chain
H: 9H FAB heavy chain
D: 35022 FAB heavy chain
E: 35022 FAB light chain
ヘテロ分子

G: BG505-SOSIP.v4.1-GT1-N137A gp120
B: BG505-SOSIP.v4.1-GT1-N137A gp41
L: 109L FAB light chain
H: 9H FAB heavy chain
D: 35022 FAB heavy chain
E: 35022 FAB light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)528,68054
ポリマ－505,13818
非ポリマー23,54136
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area88950 Å2
ΔGint81 kcal/mol
Surface area201920 Å2
手法PISA
単位格子
Length a, b, c (Å)126.952, 126.952, 315.199
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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BG505-SOSIP.v4.1-GT1-N137A ... , 2種, 2分子 GB

#1: タンパク質 BG505-SOSIP.v4.1-GT1-N137A gp120


分子量: 53350.699 Da / 分子数: 1 / 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)
細胞株 (発現宿主): 293S freestyle / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6*PLUS
#2: タンパク質 BG505-SOSIP.v4.1-GT1-N137A gp41


分子量: 17146.482 Da / 分子数: 1 / 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)
細胞株 (発現宿主): 293S freestyle / 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 109L FAB light chain


分子量: 23426.996 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): 293 freestyle / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 9H FAB heavy chain


分子量: 25353.307 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): 293 freestyle / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 35022 FAB heavy chain


分子量: 25783.057 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): 293 freestyle / 発現宿主: Homo sapiens (ヒト)
#6: 抗体 35022 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) / 細胞株 (発現宿主): 293 freestyle / 発現宿主: Homo sapiens (ヒト)

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糖 , 7種, 12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 / 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 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 / 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
#9: 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-(1-6)-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 / 分子量: 1397.245 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[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g6-h1WURCSPDB2Glycan 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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#10: 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 / 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
#11: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-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
#12: 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: 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
#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


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
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

Has protein modificationY

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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: 4.46 Å3/Da / 溶媒含有率: 72.44 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4.5 / 詳細: 0.2M NaCl, 34% PEG 300, 0.1M NaOAc

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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: 23-ID-D / 波長: 1.03322 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2016年2月14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: 1.03322 Å / 相対比: 1
反射解像度: 3.2→49.433 Å / Num. obs: 47220 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 12.9 % / Biso Wilson estimate: 97 Å2 / CC1/2: 0.89 / Rpim(I) all: 0.077 / Rsym value: 0.174 / Χ2: 1.14 / Net I/av σ(I): 11 / Net I/σ(I): 11
反射 シェル解像度: 3.2→3.26 Å / 冗長度: 13.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2375 / CC1/2: 0.52 / Rpim(I) all: 0.77 / Rsym value: 1 / Χ2: 1.22 / % possible all: 100

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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
DENZOデータ削減
SCALEPACK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: 5cez

5cez


解像度: 3.202→49.433 Å / SU ML: 0.55 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 34.03 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2673 2409 5.12 %
Rwork0.2424 --
obs0.2437 47083 99.8 %
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: 3.202→49.433 Å
タンパク質核酸リガンド溶媒全体
原子数11206 0 522 0 11728
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00512061
X-RAY DIFFRACTIONf_angle_d0.75416511
X-RAY DIFFRACTIONf_dihedral_angle_d16.5914502
X-RAY DIFFRACTIONf_chiral_restr0.0671974
X-RAY DIFFRACTIONf_plane_restr0.0062021
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2015-3.26690.4141420.41022636X-RAY DIFFRACTION100
3.2669-3.33790.46461590.37832615X-RAY DIFFRACTION100
3.3379-3.41550.39781490.37722582X-RAY DIFFRACTION100
3.4155-3.50090.41811430.34852611X-RAY DIFFRACTION100
3.5009-3.59550.35821360.34122625X-RAY DIFFRACTION100
3.5955-3.70130.34081550.30982596X-RAY DIFFRACTION100
3.7013-3.82070.37171320.30942638X-RAY DIFFRACTION100
3.8207-3.95720.33871160.28832673X-RAY DIFFRACTION100
3.9572-4.11560.30161300.27122616X-RAY DIFFRACTION100
4.1156-4.30280.24041270.24562653X-RAY DIFFRACTION100
4.3028-4.52950.24631660.21622609X-RAY DIFFRACTION100
4.5295-4.81310.25641360.20632607X-RAY DIFFRACTION100
4.8131-5.18440.19551410.19932635X-RAY DIFFRACTION100
5.1844-5.70540.23841460.21562645X-RAY DIFFRACTION100
5.7054-6.52940.25341330.23742630X-RAY DIFFRACTION100
6.5294-8.22020.25781360.21512663X-RAY DIFFRACTION100
8.2202-49.43850.1951620.17982640X-RAY DIFFRACTION99
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)
10.350.1566-0.47030.4333-0.97845.39890.00030.2176-0.1457-0.0811-0.1205-0.039-0.12820.2775-0.11350.6772-0.0570.08730.73380.0540.80781.333828.4772131.5457
21.00670.3273-0.63790.623-0.67673.6953-0.1254-0.0614-0.1748-0.1561-0.2016-0.23680.49830.72910.10580.74750.1450.16710.73360.10240.905192.623319.6977132.6811
30.1719-0.7172-0.04576.3076-4.07324.41330.08050.14090.13631.2548-0.9337-0.3482-0.56981.36960.53390.6844-0.31940.02461.07150.07980.714182.912927.4225170.4268
42.87191.5803-0.40953.85850.41780.19681.23271.30230.1719-0.7049-0.5685-0.5158-0.359-1.0042-0.46911.43840.67910.20071.53650.2130.904170.581340.435143.2157
54.87990.5029-2.13315.1332-2.7262.6670.4886-0.2604-0.5252-1.0263-0.264-0.06361.04840.8161-0.06170.54170.1149-0.06151.03610.0110.726867.437531.2253156.3613
60.1783-0.7108-0.47133.31292.56662.04260.2873-0.820.94871.30.13660.4975-0.7573-0.1101-0.16310.69850.34210.20481.4942-0.13740.787164.008828.4953175.3566
77.52332.9807-4.02645.6693-2.70973.8342-0.6391-1.1084-0.4356-0.00391.20211.53651.6383-1.07060.20181.1438-0.32-0.04231.41810.16610.896767.473717.3925179.9326
86.92491.5798-1.85016.95861.53185.1028-0.61830.4157-1.41040.53890.067-0.00881.85310.2992-0.08820.9003-0.0380.2720.69070.12330.911377.192311.8494174.8723
93.67880.4796-0.29197.0275-0.90683.38120.24040.5111-0.71540.03360.05411.75890.777-0.94220.41280.6699-0.79060.06972.28750.24530.928560.255317.7076174.1063
104.89313.16050.83722.5142-1.1867.25811.94990.31140.31060.2401-0.01260.82290.1563-0.7844-0.6322.15280.53550.22843.22040.561.332150.856729.3466185.6607
113.0704-1.5909-1.63512.6064-1.52235.20041.1129-0.8518-0.09830.3655-0.2092-0.0553-0.4163-0.5396-0.17671.3844-0.1420.07481.20970.09631.2047114.942454.389188.1774
121.91550.6933-2.41720.2865-0.91423.05240.66120.53591.2377-1.10040.0023-0.16570.36660.856-0.86190.96970.3474-0.00781.4259-0.05930.9489108.070340.177497.9158
130.5002-0.28780.85180.84120.13141.99250.20860.51280.1265-1.16740.0485-0.1706-0.1585-0.2184-0.46031.0812-0.11320.29381.08480.06880.9698122.072742.058286.6234
144.6403-1.1686-1.74928.11721.3991.1008-1.1401-0.41460.20510.11370.5106-0.44850.4741-0.34780.18090.962-0.2990.03611.0899-0.05580.871119.965343.4745100.5807
154.019-0.5879-2.66981.7304-2.04336.8065-0.1266-0.43880.2952-0.2387-0.0160.21-0.16861.57520.05050.6158-0.17180.11130.7108-0.04970.9447120.2949.397589.5146
162.3333-0.5502-1.58640.20630.67523.0203-0.38990.25210.30140.38590.5403-0.3641-0.39690.33010.12210.7474-0.07170.22781.04750.1161.1074108.558434.166792.5929
171.641.4932-1.4311.11-1.23021.79450.3669-0.67030.51520.352-0.488-0.23630.3490.93090.40.8433-0.0279-0.11651.02630.15040.9955126.117759.523374.2491
189.45421.2567-0.06516.47010.16694.93560.26770.3419-0.6279-0.56920.5845-0.36970.36550.103-0.58091.62020.10730.29171.37280.20491.398133.925948.830744.8343
195.1125-0.5624-3.18212.29081.61173.0525-0.4558-0.21060.4146-0.4348-0.20610.1478-0.37450.99050.78770.94450.03980.13860.89090.08471.0229126.402259.680861.7296
204.90140.8161-0.99744.1851.08975.6839-1.3448-0.01730.3988-0.7105-0.465-0.0272-0.41511.32510.53380.7411-0.21840.10480.85050.00381.1982124.064257.320262.191
215.4730.34860.79265.39132.10155.3504-0.24031.0143-0.0423-2.10420.40891.0162-0.1471.4548-0.4611.3986-0.0896-0.01151.19240.02381.3106127.302155.658550.3798
221.82461.0898-0.32122.1692-0.59984.5374-0.1920.6839-0.311-0.43090.12641.1819-0.3048-0.6806-0.18341.2433-0.15690.16560.93250.08331.2622129.087465.517755.4233
230.9217-1.3362-0.32812.2582-0.99242.6515-0.3853-0.1707-0.5580.0792-0.2604-0.14870.89870.01010.2431.8689-0.15270.51971.14520.02671.1941123.88827.533871.3897
242.20970.33510.94490.1829-0.58313.0584-0.0339-0.523-1.3923-0.63840.1352-0.61180.34681.23780.15090.79760.40670.27771.44370.32251.5024127.914922.480582.2381
255.86830.6209-0.83354.47990.28215.9337-0.1207-0.00460.0715-0.6126-0.460.08231.74870.50620.1751.20660.09610.11110.74830.15990.9841116.739830.940681.3246
260.6846-0.36451.35878.60490.65443.3731-1.8421-0.876-0.78441.29880.79420.21311.99750.11320.1691.6404-0.06260.45590.99830.20831.1442114.340620.379882.0973
273.33372.22360.45763.01751.93923.5836-0.70480.4795-0.94810.22160.67490.13450.7340.6297-0.19611.07830.05030.46910.67170.09811.1835120.708426.076277.0225
280.5558-0.3024-0.91842.4315-1.00264.65920.2627-0.0546-0.3755-0.00770.2979-0.14370.00010.2146-0.20231.12510.02380.23971.34320.19971.025114.747428.0214100.4927
291.98562.2264-0.87644.3096-1.22392.7072-0.1264-0.68920.0432-0.70640.0206-0.29960.77490.1736-0.09571.12760.28150.33641.06940.02611.1786132.17343.946359.3817
304.28120.75880.1043.01381.81513.636-0.2990.38720.336-0.30830.4119-0.43760.76081.03050.01091.33090.04120.19061.39690.27091.2227135.148342.558263.2926
315.3337-0.2439-0.42584.09020.99461.26430.2319-0.2318-0.74560.3603-0.0083-0.96190.38080.34230.11980.9306-0.00370.27871.1829-0.02941.1738136.632946.980359.9146
325.42582.8194-0.43114.4531-0.63950.6046-1.13810.3983-0.61160.09810.0797-0.73642.08380.09890.81511.6771-0.09820.90271.5909-0.29991.8741139.183139.700255.0987
338.7037-3.52663.45224.2494-1.04772.73790.75170.20560.27-0.2948-0.03140.02630.2479-0.4362-0.4131.25950.0689-0.02270.95340.32771.1485106.4627-7.3307175.0535
340.93220.5997-0.06422.74390.29312.46330.14170.32030.0699-0.0588-0.1273-0.27180.37250.6466-0.11130.86220.1610.10661.12090.31141.0317102.1492.6887178.2865
351.2886-1.72080.89523.1054-0.23583.02590.46981.0992-0.66080.59450.9853-0.92631.2821-0.9194-0.86981.83960.27190.37982.0449-0.10251.7382107.1141-30.049177.1745
364.31344.11322.23954.07872.09971.81620.23020.8819-0.40180.224-0.73710.29390.952-1.0718-0.70791.8840.41610.30391.5652-0.15641.8896101.7734-28.0354177.3389
370.65421.3254-0.62086.34331.01242.1758-0.17650.9626-0.6894-0.18390.69641.15611.03911.2788-0.93851.83910.34960.17611.4638-0.18351.9049100.2532-26.4316180.1725
381.59053.08091.55976.87023.17331.6070.44192.2365-0.9111-1.5355-0.61030.67230.762-0.9835-0.8432.1742-0.2298-0.37522.3771-1.15852.057789.4981-36.1971173.3838
393.1974-0.6073.06543.077-3.03334.9998-1.69010.5645-0.4658-0.6411-1.6511.4673-0.9301-2.47662.00861.62160.61660.18482.8081-0.87732.1806103.6053-27.1599168.828
402.80072.02631.06145.47830.60221.00960.0451-0.7185-0.22961.4982-0.28380.36720.19380.38720.39691.70730.14670.2241.40.17681.408290.5624-5.2676202.7804
413.10890.31960.48992.4847-0.98992.5881-0.5291-0.4496-0.31390.55960.29570.23260.2198-0.2590.33391.49450.22790.19541.3030.31681.171190.1670.9965194.8075
421.1579-0.0591-0.22256.72171.18061.38430.1394-0.1541-0.80271.7893-1.16551.1693-0.5234-0.4120.49912.67990.34630.62821.160.50471.883385.3662-21.6718199.1637
431.28851.50880.24132.6768-0.88581.67450.40111.0385-0.1255-0.0231-0.386-0.9471-0.70420.6386-0.34272.1562-0.09290.30041.67360.04622.4303105.574-40.8265181.5126
440.36760.0639-0.49920.10130.00891.69320.5234-0.6264-0.81691.13730.26040.027-0.59460.2722-0.04022.14480.29760.05141.56820.38152.116997.7846-33.0242193.5726
450.61771.2912-0.52473.0159-0.62852.61260.19880.0863-0.88010.6717-0.9075-0.45410.90310.46490.07732.09210.185-0.00791.67050.00962.270199.8929-30.6098193.5797
461.5074-0.0856-0.27960.0146-0.21612.77691.305-0.5274-0.1937-0.27241.00761.2545-1.32140.2859-0.60441.68420.38450.38721.40220.1652.4948106.995-38.3886188.832
473.08991.20950.23351.1172-1.23242.9221.0605-0.5159-1.13630.0366-0.3991-0.07880.26750.6863-0.58032.6683-0.00210.35331.46560.30893.047898.971-43.059194.695
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 32 through 235 )
2X-RAY DIFFRACTION2chain 'G' and (resid 236 through 506 )
3X-RAY DIFFRACTION3chain 'B' and (resid 518 through 544 )
4X-RAY DIFFRACTION4chain 'B' and (resid 545 through 569 )
5X-RAY DIFFRACTION5chain 'B' and (resid 570 through 595 )
6X-RAY DIFFRACTION6chain 'B' and (resid 596 through 600 )
7X-RAY DIFFRACTION7chain 'B' and (resid 601 through 615 )
8X-RAY DIFFRACTION8chain 'B' and (resid 616 through 638 )
9X-RAY DIFFRACTION9chain 'B' and (resid 639 through 650 )
10X-RAY DIFFRACTION10chain 'B' and (resid 651 through 664 )
11X-RAY DIFFRACTION11chain 'L' and (resid 6 through 22 )
12X-RAY DIFFRACTION12chain 'L' and (resid 23 through 33 )
13X-RAY DIFFRACTION13chain 'L' and (resid 34 through 48 )
14X-RAY DIFFRACTION14chain 'L' and (resid 49 through 71 )
15X-RAY DIFFRACTION15chain 'L' and (resid 72 through 89 )
16X-RAY DIFFRACTION16chain 'L' and (resid 90 through 101 )
17X-RAY DIFFRACTION17chain 'L' and (resid 102 through 119 )
18X-RAY DIFFRACTION18chain 'L' and (resid 120 through 130 )
19X-RAY DIFFRACTION19chain 'L' and (resid 131 through 151 )
20X-RAY DIFFRACTION20chain 'L' and (resid 152 through 172 )
21X-RAY DIFFRACTION21chain 'L' and (resid 173 through 188 )
22X-RAY DIFFRACTION22chain 'L' and (resid 189 through 210 )
23X-RAY DIFFRACTION23chain 'H' and (resid 1 through 17 )
24X-RAY DIFFRACTION24chain 'H' and (resid 18 through 32 )
25X-RAY DIFFRACTION25chain 'H' and (resid 33 through 51 )
26X-RAY DIFFRACTION26chain 'H' and (resid 52 through 72 )
27X-RAY DIFFRACTION27chain 'H' and (resid 73 through 96 )
28X-RAY DIFFRACTION28chain 'H' and (resid 97 through 101 )
29X-RAY DIFFRACTION29chain 'H' and (resid 102 through 140 )
30X-RAY DIFFRACTION30chain 'H' and (resid 141 through 163 )
31X-RAY DIFFRACTION31chain 'H' and (resid 164 through 198 )
32X-RAY DIFFRACTION32chain 'H' and (resid 199 through 213 )
33X-RAY DIFFRACTION33chain 'D' and (resid 1 through 17 )
34X-RAY DIFFRACTION34chain 'D' and (resid 18 through 111 )
35X-RAY DIFFRACTION35chain 'D' and (resid 112 through 134 )
36X-RAY DIFFRACTION36chain 'D' and (resid 135 through 154 )
37X-RAY DIFFRACTION37chain 'D' and (resid 155 through 177 )
38X-RAY DIFFRACTION38chain 'D' and (resid 178 through 194 )
39X-RAY DIFFRACTION39chain 'D' and (resid 195 through 211 )
40X-RAY DIFFRACTION40chain 'E' and (resid 2 through 24 )
41X-RAY DIFFRACTION41chain 'E' and (resid 25 through 105 )
42X-RAY DIFFRACTION42chain 'E' and (resid 106 through 117 )
43X-RAY DIFFRACTION43chain 'E' and (resid 118 through 133 )
44X-RAY DIFFRACTION44chain 'E' and (resid 134 through 154 )
45X-RAY DIFFRACTION45chain 'E' and (resid 155 through 175 )
46X-RAY DIFFRACTION46chain 'E' and (resid 176 through 190 )
47X-RAY DIFFRACTION47chain 'E' and (resid 191 through 214 )

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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