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基本情報

登録情報
データベース: PDB / ID: 5fyk
タイトルCrystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade B JR-FL SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01
要素
  • (35O22) x 2
  • (PGT122) x 2
  • JR-FL, GP120 ENV ECTODOMAIN
  • JR-FL, GP41 ENV ECTODOMAIN
  • VRC01
キーワードVIRAL PROTEIN / HIV / ENVELOPE / GLYCAN / TRIMER
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 / 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: 3.107 Å
データ登録者Stewart-Jones, G.B.E. / Zhou, T. / Thomas, P.V. / Kwong, P.D.
引用ジャーナル: Cell(Cambridge,Mass.) / 年: 2016
タイトル: Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B and G
著者: Stewart-Jones, G.B.E. / Soto, C. / Lemmin, T. / Chuang, G.Y. / Druz, A. / Kong, R. / Thomas, P.V. / Wagh, K. / Zhou, T. / Behrens, A.J. / Bylund, T. / Choi, C.W. / Davison, J.R. / Georgiev, I. ...著者: Stewart-Jones, G.B.E. / Soto, C. / Lemmin, T. / Chuang, G.Y. / Druz, A. / Kong, R. / Thomas, P.V. / Wagh, K. / Zhou, T. / Behrens, A.J. / Bylund, T. / Choi, C.W. / Davison, J.R. / Georgiev, I.S. / Joyce, M.G. / Kwon, Y.D. / Pancera, M. / Taft, J. / Yang, Y. / Zhang, B. / Shivatare, S.S. / Shivatare, V.S. / Lee, C.C.D. / Wu, C.Y. / Bewley, C.A. / Burton, D.R. / Koff, W.C. / Connors, M. / Crispin, M. / Korber, B.T. / Wong, C.H. / Mascola, J.R. / Kwong, P.D.
履歴
登録2016年3月8日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年4月27日Provider: repository / タイプ: Initial release
改定 1.12016年5月4日Group: Database references
改定 1.22016年5月11日Group: Database references
改定 1.32016年5月18日Group: Database references
改定 1.42016年7月20日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
改定 1.52016年8月3日Group: Structure summary
改定 1.62017年7月12日Group: Derived calculations / カテゴリ: struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.pdbx_PDB_ins_code / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 2.12024年1月10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
改定 2.22024年11月13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

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集合体

登録構造単位
B: JR-FL, GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: JR-FL, GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)246,32533
ポリマ－222,9498
非ポリマー23,37625
水00
1
B: JR-FL, GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: JR-FL, GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
ヘテロ分子

B: JR-FL, GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: JR-FL, GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
ヘテロ分子

B: JR-FL, GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: JR-FL, GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)738,97499
ポリマ－668,84624
非ポリマー70,12875
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area130110 Å2
ΔGint239.5 kcal/mol
Surface area248470 Å2
手法PISA
単位格子
Length a, b, c (Å)130.780, 130.780, 314.620
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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タンパク質 , 3種, 3分子 BGH

#1: タンパク質 JR-FL, GP41 ENV ECTODOMAIN


分子量: 18074.541 Da / 分子数: 1 / 断片: GP41 ENV ECTODOMAIN / 変異: YES / 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)
Cell: T-CELL / 遺伝子: ENV / プラスミド: PVRC8400 / 細胞株 (発現宿主): HEK-293T GNTI- / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q6BC19, UniProt: Q75760*PLUS
#4: タンパク質 JR-FL, GP120 ENV ECTODOMAIN


分子量: 53732.043 Da / 分子数: 1 / 断片: GP120 ENV ECTODOMAIN / 変異: YES / 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)
Cell: T-CELL / 遺伝子: ENV / プラスミド: PVRC8400 / 細胞株 (発現宿主): HEK-293T GNTI- / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q75760
#5: タンパク質 PGT122


分子量: 26465.877 Da / 分子数: 1 / 断片: PGT122 ANTIBODY FAB HEAVY CHAIN / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / Cell: B-CELL / プラスミド: PVRC8400 / 細胞株 (発現宿主): HEK-293T GNTI- / 発現宿主: HOMO SAPIENS (ヒト)

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抗体 , 4種, 5分子 DELUV

#2: 抗体 35O22


分子量: 26170.533 Da / 分子数: 1 / 断片: 35O22 ANTIBODY FAB HEAVY CHAIN / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / Cell: B-CELL / プラスミド: PVRC8400 / 細胞株 (発現宿主): HEK-293T / 発現宿主: HOMO SAPIENS (ヒト)
#3: 抗体 35O22


分子量: 23318.824 Da / 分子数: 1 / 断片: 35O22 ANTIBODY FAB LIGHT CHAIN / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / Cell: B-CELL / プラスミド: PVRC8400 / 細胞株 (発現宿主): HEK-293T / 発現宿主: HOMO SAPIENS (ヒト)
#6: 抗体 PGT122


分子量: 22880.275 Da / 分子数: 1 / 断片: PGT122 ANTIBODY FAB LIGHT CHAIN / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / Cell: B-CELL / プラスミド: PVRC8400 / 細胞株 (発現宿主): HEK-293T GNTI- / 発現宿主: HOMO SAPIENS (ヒト)
#7: 抗体 VRC01


分子量: 26153.303 Da / 分子数: 2 / 断片: VRC01 ANTIBODY FAB HEAVY CHAIN / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / Cell: B-CELL / プラスミド: PVRC8400 / 細胞株 (発現宿主): HEK-293T GNTI- / 発現宿主: HOMO SAPIENS (ヒト)

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糖 , 17種, 25分子

#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 / 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 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
#10: 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-(1-3)-[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: 1559.386 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[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/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-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]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#11: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...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: 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
DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d3-e1_d6-g1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-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-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...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: 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
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d3-e1_d6-f1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#13: 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: 2 / 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
#14: 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-(1-3)-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: 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[DManpa1-3DManpa1-6]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_g3-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]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#15: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 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
#16: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(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: 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
DManpa1-2DManpa1-3DManpa1-6[DManpa1-2DManpa1-3]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-f1_d2-e1_f3-g1_g2-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]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#17: 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 / 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
#18: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D- ...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: 1235.105 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]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-f1_d2-e1_f6-g1WURCSPDB2Glycan 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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#19: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: 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
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-3]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-e1_e3-f1_e6-g1_g2-h1WURCSPDB2Glycan 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]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#20: 多糖 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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: 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
DManpa1-3DManpa1-6[DManpa1-3]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-e1_e3-f1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#21: 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: 2 / 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
#22: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1072.964 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d3-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#23: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...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: 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
DManpa1-6DManpa1-6[DManpa1-3]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-e1_e6-f1WURCSPDB2Glycan 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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#24: 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: 5 / 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

-
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: 3.48 Å3/Da / 溶媒含有率: 64.69 % / 解説: NONE
結晶化pH: 4.5
詳細: 4.95% ISOPROPANOL, 8.25% PEG 3350, 0.2M AMMONIUM CITRATE PH 4.5

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データ収集

回折平均測定温度: 77 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
検出器タイプ: MAR / 検出器: CCD / 日付: 2014年8月15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: 3.1→50 Å / Num. obs: 55001 / % possible obs: 86.2 % / Observed criterion σ(I): 2 / 冗長度: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.76

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE: 1.9_1692)精密化
HKL-2000データ削減
SCALEPACKデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 4TVP

4tvp


解像度: 3.107→42.808 Å / σ(F): 1.39 / 位相誤差: 34.31 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.303 1654 5.2 %
Rwork0.2456 --
obs0.2488 31882 58.33 %
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: 3.107→42.808 Å
タンパク質核酸リガンド溶媒全体
原子数13259 0 1565 0 14824
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00515290
X-RAY DIFFRACTIONf_angle_d1.05920999
X-RAY DIFFRACTIONf_dihedral_angle_d15.5555920
X-RAY DIFFRACTIONf_chiral_restr0.0412717
X-RAY DIFFRACTIONf_plane_restr0.0042433
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1435-3.24490.3627170.294296X-RAY DIFFRACTION6
3.2449-3.36080.3604340.3189631X-RAY DIFFRACTION13
3.3608-3.49520.4357530.3371976X-RAY DIFFRACTION20
3.4952-3.6540.3116760.31861467X-RAY DIFFRACTION30
3.654-3.84640.31191120.32282073X-RAY DIFFRACTION43
3.8464-4.0870.31751490.29752848X-RAY DIFFRACTION60
4.087-4.40180.29362000.26223823X-RAY DIFFRACTION80
4.4018-4.84350.27132340.23284484X-RAY DIFFRACTION93
4.8435-5.54140.29052370.23064531X-RAY DIFFRACTION95
5.5414-6.97020.3672290.25884570X-RAY DIFFRACTION95
6.9702-32.52160.28052420.21284570X-RAY DIFFRACTION94
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)
18.49421.4149-0.35434.00525.87139.4392-0.2846-0.512-1.1217-0.09710.1045-0.84871.19640.17550.16331.55060.35710.15120.7065-0.28251.024747.947225.3925.1489
22.16991.5982-1.23232.60151.49684.7680.0206-0.3067-0.54680.3081-0.1542-0.09310.8705-0.34540.15962.0526-0.0294-0.2051.7338-0.00571.815465.1397231.5841
34.0801-1.8091-1.16813.19850.42290.33610.19890.8076-0.3926-0.6342-0.17170.09040.0415-0.0929-0.01180.17330.208-0.30410.3888-0.221.053158.843837.253510.3555
42.00290.965-0.21492.00080.30061.11070.0555-0.16860.46580.2621-0.47880.3459-0.3946-0.34960.0581.15750.54770.18370.7768-0.8830.986848.71845.805331.5623
52.4319-1.438-3.06531.09511.41324.52260.4012-0.01940.04680.2426-0.03430.61830.21490.0838-0.42251.4055-0.63570.01272.2166-0.2781.47598.022921.969428.0296
62.81641.2879-1.92338.31330.39341.5294-0.54630.0113-0.40440.28950.59760.58020.2067-0.6311-0.00961.415-0.91060.29282.7901-0.58921.330219.251122.023734.2869
73.051.5867-0.6424.851-0.97590.2367-0.37130.2585-0.4589-0.85650.30150.06770.3525-0.03030.06981.992-0.95970.11212.1883-0.57051.344220.006418.555928.1538
80.9054-0.3028-1.03542.0710.04581.2253-0.2665-0.04640.0952-0.59720.3351.08150.4912-0.437-0.00831.6859-0.80470.04872.7039-0.74121.669210.330422.102334.8394
91.4965-0.53050.51230.9537-1.121.31960.20850.5672-0.28360.0282-0.37220.107-0.044-0.09970.13922.5250.0418-0.24912.8907-0.19852.7642-11.034941.932629.9949
102.908-1.90861.7711.4845-1.69362.3086-0.04390.11450.1828-0.0568-0.00890.235-0.18950.03240.06122.608-0.0851-0.13782.4429-0.25182.8913-11.727841.457230.4875
113.1908-0.2071-0.07770.01180.007-0.00150.18040.3903-0.284-0.0741-0.16060.2357-0.335-0.0927-0.00812.3478-0.1395-0.32863.1685-0.14292.8317-16.842.672926.7137
122.6689-0.8649-2.8771.89471.99698.24410.0844-0.96560.56450.42530.24050.51520.3220.1861-0.38341.0047-0.21120.12662.6615-0.63291.312319.489634.253950.2651
130.151-0.1374-0.42720.10980.3921.19470.1267-0.0713-0.2097-0.15230.0480.1597-0.2785-0.3255-0.16791.672-0.149-0.02973.214-0.26682.9779-16.273541.956344.0289
142.48931.33851.07771.60820.11122.3367-0.34940.5532-0.6131-0.5806-0.258-0.0920.9655-0.15450.54851.04570.5732-0.29530.9514-0.49191.267748.297326.51988.6507
152.06810.9317-1.07832.67650.07132.3465-0.13310.42240.1907-0.89890.2061-0.33470.1825-0.3903-0.10870.2373-0.0023-0.30060.8708-0.52851.235548.235325.2532-22.4488
161.98990.79710.34911.67590.72572.4679-0.04460.32590.0211-0.08-0.01610.23860.343-0.68040.10570.4091-0.5798-0.19431.4697-0.86111.159633.729618.5461-19.5725
172.5244-0.981-0.35681.1828-0.78235.7222-0.07470.13530.08880.47760.35090.141-0.61690.3333-0.0115-0.16510.1572-0.58530.3-0.56031.084145.44734.613916.9005
181.5013-0.2460.50252.41010.76964.33230.25490.6469-0.3348-0.8941-0.14720.70850.68220.416-0.08791.6812-0.2843-0.22662.2533-0.63231.214124.2595-11.9789-69.0268
192.0003-2.8211-6.60742.70122.92246.90280.329-0.75030.33970.2073-0.30120.34930.4083-0.3637-0.07081.59280.1792-0.18452.4226-0.55471.059834.2118-6.9409-63.7464
205.02920.293-2.95227.2112-1.25891.89790.3833-0.15840.3542-0.7569-0.23451.1266-0.0718-0.3493-0.14911.6227-0.0535-0.2192.5949-0.83691.361125.67190.8296-63.5479
211.20911.07841.03814.55381.81082.0025-0.12280.38010.0437-0.93970.1660.6621-0.0794-0.0279-0.01821.40620.0636-0.23812.1846-0.57771.229726.0592-4.9959-71.5135
222.76652.79862.10953.13792.26432.86040.98230.4307-0.26480.4378-0.35980.21252.6233-1.0102-0.60911.2398-0.1312-0.30652.1417-0.68471.326631.1495-9.1635-55.2262
232.6649-0.573-0.30350.12160.09796.32810.1840.6391-0.1311-0.1713-0.10830.57510.6102-0.309-0.05831.6344-0.51040.13652.1062-0.62191.190532.7016-3.0164-45.9138
243.6512.3746-0.2655.11824.17375.302-0.10930.4691-0.3693-0.2067-0.08480.2467-0.5201-0.42750.17451.0960.2589-0.42062.1572-0.66381.268334.622-16.0019-84.8474
253.3338-0.58890.3691.71360.04010.52810.1523-0.3703-0.47370.6253-0.1890.69970.1264-0.82550.12210.81420.0650.28392.1883-0.42821.462838.0517-31.4028-83.7814
266.0337-1.5545-0.56714.206-4.04424.6588-0.26470.31350.05190.2683-0.3797-0.0331-0.5881-0.23640.6050.9265-0.2896-0.06942.2732-0.70111.08742.8801-21.6369-87.0152
271.9999-3.0406-4.65514.0842-2.71992-1.3411-2.1955-0.27450.74810.66670.16491.75852.83640.67061.19740.1214-0.02352.3088-0.28651.232940.3143-45.9793-81.7709
281.6353-0.1539-2.50330.1012-0.05374.75790.3243-0.3198-0.6394-0.2449-0.0660.63060.1242-0.2546-0.25640.9387-0.4309-0.0282.1602-0.60411.900130.5714-33.7694-87.7458
292.262-2.6841-1.70033.47932.38282.1881-0.19180.018-0.19210.1605-0.18240.29371.32490.01070.27621.954-0.4556-0.03481.4772-0.69291.168345.7186-13.6169-52.1461
306.9326-1.190.69438.4843-1.41412.4074-0.24090.10480.0920.1028-0.5510.43760.8313-0.69960.78880.9136-0.0870.07451.2821-0.28010.720552.8704-30.2268-86.0425
315.24531.59684.3432.07491.57826.10630.27670.78630.2828-0.5375-0.13490.8199-0.1201-0.2481-0.13341.91420.185-0.21822.39370.10852.5423.668949.942-33.1211
320.70411.32730.23862.86051.31752.2085-0.1540.07080.682-0.23670.3959-0.1344-0.4028-0.2728-0.23541.13430.5303-0.0541.8447-0.20522.237133.571345.4125-23.6497
330.20310.514-0.94766.381-0.17175.3744-0.0486-0.26980.6222-0.01490.08560.105-0.2084-0.2754-0.05851.06310.3492-0.62981.94190.13441.979421.426241.3826-21.3999
346.1913-0.45630.30532.7930.4661.6844-0.03040.0389-0.5979-0.2636-0.13450.278-0.2489-0.44430.16131.44670.2914-0.32031.54740.09791.875526.513839.0612-28.323
357.45174.19358.2632.36054.65359.1604-0.1895-0.3488-0.0342-0.17570.1632-0.43910.15610.35860.02461.29980.3568-0.62712.1511-0.2632.412217.849645.4288-28.5492
360.0063-0.00530.025-0.00190.00220.0646-0.21810.6230.1221-0.56660.00270.25330.03620.51290.21791.64520.4351-0.3241.3526-0.42312.089824.786248.7624-17.8069
374.991-0.7544-2.73620.11380.41371.49720.09620.3195-0.15060.04750.06360.1448-0.305-0.1648-0.14881.95240.3589-0.26752.1112-0.21782.89355.215758.9008-7.8631
382.72791.4554-1.0241.11860.31692.5521-0.42920.09710.01660.22930.43760.4210.00950.0901-0.0021.76050.46370.20082.1053-0.35442.764311.976947.0285-4.9256
394.18611.12562.13863.9341.24751.21690.0581-0.4405-0.09440.3326-0.08730.12820.1206-0.24730.03061.93950.47760.14092.7016-0.2712.854816.809961.1617-18.3606
400.0073-0.10740.15991.5764-2.34993.50240.4080.80710.18640.1845-0.2539-1.4586-0.15080.7387-0.15432.00010.32950.14842.7698-0.32022.960620.986957.558-16.4947
414.48583.105-3.08242.1491-2.13372.1179-0.0253-0.10230.226-0.15080.025-0.90720.04480.61130.00451.50170.2719-0.16622.009-0.51772.660121.724452.0195-3.9874
423.87710.33630.35482.52941.19926.23970.6011-0.01270.1013-0.6442-0.4319-0.027-0.5633-0.1376-0.17251.20660.2256-0.13631.7527-0.44232.351423.304355.9044-1.9092
431.8071-2.3544-1.49594.41721.52771.7133-0.1873-0.0066-0.1069-0.12560.01760.21940.0376-0.27260.15242.15560.16260.36772.1232-0.22042.421715.277555.24461.1873
440.00240.3223-0.03961.9999-5.11250.63380.1411-0.5788-0.64891.39130.41261.4446-0.121-0.6886-0.55762.7779-0.0009-0.07862.6755-0.2973.015111.923755.1585-1.5683
452.56150.4586-0.19640.8931.86156.111.37020.9923-0.8731-0.3076-1.0108-0.2255-0.2070.0754-0.35981.63020.3901-0.01931.7293-0.27912.476812.652765.4223-10.146
461.8811-0.6872-2.77787.8587-0.18634.2927-0.33090.00590.5414-0.22870.26591.5016-0.942-1.18110.07061.17560.4037-0.20161.8445-0.26522.400813.573645.3473-11.8668
472.47540.16810.58250.02490.20742.22430.08080.0855-0.0614-0.12840.019-0.16880.30010.091-0.09712.45770.0637-0.12212.8575-0.17072.97056.44762.8442-15.9856
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 514 THROUGH 545 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 546 THROUGH 569 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 570 THROUGH 595 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 596 THROUGH 664 )
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID 1 THROUGH 25 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 26 THROUGH 56 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 57 THROUGH 77 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 78 THROUGH 119 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 120 THROUGH 165 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 166 THROUGH 197 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 198 THROUGH 224 )
12X-RAY DIFFRACTION12CHAIN 'E' AND (RESID 2 THROUGH 102 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 103 THROUGH 210 )
14X-RAY DIFFRACTION14CHAIN 'G' AND (RESID 31 THROUGH 98 )
15X-RAY DIFFRACTION15CHAIN 'G' AND (RESID 99 THROUGH 258 )
16X-RAY DIFFRACTION16CHAIN 'G' AND (RESID 259 THROUGH 475 )
17X-RAY DIFFRACTION17CHAIN 'G' AND (RESID 476 THROUGH 508 )
18X-RAY DIFFRACTION18CHAIN 'H' AND (RESID 1 THROUGH 32 )
19X-RAY DIFFRACTION19CHAIN 'H' AND (RESID 33 THROUGH 51 )
20X-RAY DIFFRACTION20CHAIN 'H' AND (RESID 52 THROUGH 72 )
21X-RAY DIFFRACTION21CHAIN 'H' AND (RESID 73 THROUGH 88 )
22X-RAY DIFFRACTION22CHAIN 'H' AND (RESID 89 THROUGH 100A )
23X-RAY DIFFRACTION23CHAIN 'H' AND (RESID 100B THROUGH 101 )
24X-RAY DIFFRACTION24CHAIN 'H' AND (RESID 102 THROUGH 121 )
25X-RAY DIFFRACTION25CHAIN 'H' AND (RESID 122 THROUGH 166 )
26X-RAY DIFFRACTION26CHAIN 'H' AND (RESID 167 THROUGH 180 )
27X-RAY DIFFRACTION27CHAIN 'H' AND (RESID 181 THROUGH 184 )
28X-RAY DIFFRACTION28CHAIN 'H' AND (RESID 185 THROUGH 211 )
29X-RAY DIFFRACTION29CHAIN 'L' AND (RESID 6 THROUGH 101 )
30X-RAY DIFFRACTION30CHAIN 'L' AND (RESID 102 THROUGH 210 )
31X-RAY DIFFRACTION31CHAIN 'U' AND (RESID 1 THROUGH 17 )
32X-RAY DIFFRACTION32CHAIN 'U' AND (RESID 18 THROUGH 33 )
33X-RAY DIFFRACTION33CHAIN 'U' AND (RESID 34 THROUGH 59 )
34X-RAY DIFFRACTION34CHAIN 'U' AND (RESID 60 THROUGH 82 )
35X-RAY DIFFRACTION35CHAIN 'U' AND (RESID 82A THROUGH 95 )
36X-RAY DIFFRACTION36CHAIN 'U' AND (RESID 96 THROUGH 111 )
37X-RAY DIFFRACTION37CHAIN 'V' AND (RESID 3 THROUGH 19 )
38X-RAY DIFFRACTION38CHAIN 'V' AND (RESID 20 THROUGH 36 )
39X-RAY DIFFRACTION39CHAIN 'V' AND (RESID 37 THROUGH 41 )
40X-RAY DIFFRACTION40CHAIN 'V' AND (RESID 42 THROUGH 46 )
41X-RAY DIFFRACTION41CHAIN 'V' AND (RESID 47 THROUGH 51 )
42X-RAY DIFFRACTION42CHAIN 'V' AND (RESID 52 THROUGH 56 )
43X-RAY DIFFRACTION43CHAIN 'V' AND (RESID 57 THROUGH 70 )
44X-RAY DIFFRACTION44CHAIN 'V' AND (RESID 71 THROUGH 75 )
45X-RAY DIFFRACTION45CHAIN 'V' AND (RESID 76 THROUGH 86 )
46X-RAY DIFFRACTION46CHAIN 'V' AND (RESID 87 THROUGH 101 )
47X-RAY DIFFRACTION47CHAIN 'V' AND (RESID 102 THROUGH 106 )

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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