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- PDB-5fyj: Crystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1... -

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基本情報

登録情報
データベース: PDB / ID: 5fyj
タイトルCrystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1 Clade G X1193.c1 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01
要素
  • (35O22) x 2
  • (PGT122) x 2
  • GP120 ENV ECTODOMAIN
  • 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 ...: / 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 / 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
CITRIC ACID / 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: 3.11 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18日Group: Database references
改定 1.32016年7月27日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
改定 1.42016年8月3日Group: Structure summary
改定 1.52017年7月12日Group: Advisory / Derived calculations / カテゴリ: database_PDB_caveat / 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_ptnr1_PDB_ins_code / _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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_symm_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.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 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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10月23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: GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: 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)253,21640
ポリマ－223,6698
非ポリマー29,54732
水21612
1
B: GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
ヘテロ分子

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

B: GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: 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)759,648120
ポリマ－671,00624
非ポリマー88,64296
水32418
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)127.160, 127.160, 313.650
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 GP41 ENV ECTODOMAIN


分子量: 17990.371 Da / 分子数: 1 / 断片: GP41 ENV ECTODOMAIN, RESIDUES 510-663 / 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: C6ZIG9
#4: タンパク質 GP120 ENV ECTODOMAIN


分子量: 54536.035 Da / 分子数: 1 / 断片: GP120 ENV ECTODOMAIN, RESIDUES 32-506 / 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: C6ZIG9
#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 GNTI- / 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 GNTI- / 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 FV LIGHT 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 , 15種, 27分子

#8: 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: 4 / 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
#9: 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: 3 / 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
#10: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...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: 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
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]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-f1_d2-e1_f3-g1_f6-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]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#11: 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-(1-2)-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: 1883.668 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[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 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]{[(2+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 / 分子量: 1721.527 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
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#13: 多糖 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
DManpa1-2DManpa1-3[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
#14: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...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: 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[DManpa1-3DManpa1-6]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_f3-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]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#15: 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)]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: 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[DManpa1-2DManpa1-3DManpa1-6]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_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]{}}}}}}}LINUCSPDB-CARE
#16: 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-(1-2)-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: 1559.386 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[DManpa1-2DManpa1-3]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-f1_d2-e1_f3-g1_f6-h1_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]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#17: 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: 3 / 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
#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-(1-3)]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
DManpa1-2DManpa1-3DManpa1-6[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_f2-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]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#19: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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: 1559.386 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[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-3]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-e1_e3-f1_e6-h1_f2-g1_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]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#20: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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: 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
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]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-f1_d2-e1_f3-g1_f6-i1_g2-h1_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]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#21: 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)]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
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]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-g1_d2-e1_e2-f1WURCSPDB2Glycan 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]{}}}}}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: 3 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 3種, 17分子

#22: 化合物 ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C6H8O7
#23: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H6O2
#25: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 12 / 由来タイプ: 天然 / 式: H2O

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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

-
試料調製

結晶マシュー密度: 3.27 Å3/Da / 溶媒含有率: 62.42 % / 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: MARRESEARCH / 検出器: CCD / 日付: 2015年2月8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: 51684 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / 冗長度: 6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.05

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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: 3.11→44.654 Å / σ(F): 1.35 / 位相誤差: 30.67 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2733 2011 4.7 %
Rwork0.2144 --
obs0.2166 42755 83.28 %
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: 3.11→44.654 Å
タンパク質核酸リガンド溶媒全体
原子数13482 0 1982 12 15476
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00515968
X-RAY DIFFRACTIONf_angle_d1.01421973
X-RAY DIFFRACTIONf_dihedral_angle_d14.8366310
X-RAY DIFFRACTIONf_chiral_restr0.0392916
X-RAY DIFFRACTIONf_plane_restr0.0042495
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1314-3.20970.2964180.2873410X-RAY DIFFRACTION11
3.2097-3.29640.3863470.2691006X-RAY DIFFRACTION28
3.2964-3.39330.3557940.26661949X-RAY DIFFRACTION55
3.3933-3.50270.33421550.25613140X-RAY DIFFRACTION87
3.5027-3.62770.26911660.25083371X-RAY DIFFRACTION94
3.6277-3.77280.28481680.23293397X-RAY DIFFRACTION95
3.7728-3.94420.27941650.22763413X-RAY DIFFRACTION95
3.9442-4.15180.26471620.21093420X-RAY DIFFRACTION95
4.1518-4.41140.25261730.19343445X-RAY DIFFRACTION95
4.4114-4.75110.26641690.18573412X-RAY DIFFRACTION95
4.7511-5.22760.24641700.1933413X-RAY DIFFRACTION95
5.2276-5.98020.30951730.21543423X-RAY DIFFRACTION95
5.9802-7.520.31481680.23243449X-RAY DIFFRACTION95
7.52-33.24720.23361750.1923455X-RAY DIFFRACTION95
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.60310.9898-0.94633.46942.00282.5633-0.1612-0.0250.06910.523-0.70321.0424-0.4534-0.4444-0.15460.41570.1096-0.0080.3641-0.15460.443944.298628.8359-24.512
20.10670.433-0.23611.1583-0.99960.6863-0.6165-0.01860.7648-0.2666-0.17410.0581-0.156-0.08290.47890.8461-0.10690.33871.2328-0.05260.975248.706642.8738-4.5755
31.4008-0.8556-2.98051.46092.87989.8134-1.1622-1.4348-0.17761.35931.42840.2790.4318-0.01150.2081-1.1659-2.0165-0.1805-2.5698-0.35430.535659.870830.6028-11.8037
42.23270.05-0.33543.8160.5540.1718-0.454-0.10720.0612-0.54010.0602-1.0951-0.59430.2524-0.2080.3422-0.0272-0.07490.3082-0.18130.279360.941522.8309-34.1947
54.6053-0.8934-0.45573.14330.53051.6244-0.9631-0.7475-0.9640.0673-0.9882-0.27751.32422.2991-0.12970.71790.08440.2227-0.6458-0.49440.340251.34311.6075-30.095
67.6253.2033-2.78344.379-0.73152.7221-1.94821.38070.9359-0.5774-0.0578-0.9333-1.18751.2895-0.2367-0.17150.85290.6774-0.1427-0.6723-0.258674.275923.3793-34.3531
72.97040.6954-0.52392.7496-0.01930.53320.62510.0556-0.9101-0.56690.41070.83220.37671.0233-0.1840.553-0.8566-0.23-1.4572-0.70361.239524.8395-1.7948-31.5552
81.42910.8053-0.54871.8954-0.03441.09570.04410.3653-0.22960.4695-0.11511.13270.1817-0.0554-0.18360.8211-0.1536-0.00650.5187-0.2821.104623.6371-0.3008-33.2572
90.47480.0442-0.34480.01640.02810.1563-0.72330.4987-0.9832-0.3729-0.3401-0.03780.82151.4594-0.41422.4311-0.2891-0.1150.2285-0.70411.617630.1144-31.9952-33.5182
101.8269-0.22430.45241.6135-1.15450.6749-0.082-0.4835-0.4747-0.2943-0.83840.1314-0.10630.6408-0.22961.0097-0.26060.20711.0307-0.04781.640830.9775-32.6802-29.2893
111.9552-0.3108-0.62783.18180.86941.19470.2560.2717-0.5974-1.5707-0.05960.06160.15950.3337-0.36071.2485-0.1732-0.15421.0781-0.43930.913337.1959-0.5139-51.6327
120.34-0.1808-0.02750.31460.08720.0104-0.1834-0.13940.14140.11080.11280.10140.24960.5532-0.03482.10080.1660.07831.308-0.52741.466231.0598-34.8616-41.6497
130.7971-0.31610.14164.7894-1.51210.40190.0159-0.0454-0.8162-0.41340.1838-0.07831.543-1.1594-0.13421.7779-0.0515-0.30910.8384-0.51892.571427.9852-32.4323-47.4202
143.6906-0.7173-1.86860.94930.9991.3620.94230.0203-0.3141-0.25370.47860.6080.13630.2012-0.0082.101-0.11310.25080.66190.01071.859427.3017-44.5651-45.8868
150.6890.16741.0934-0.1081-0.10772.4177-0.2036-0.40550.14210.3428-0.16190.0057-0.09-0.11190.03160.5127-0.03880.14060.4124-0.06620.666646.597927.3407-4.3694
162.069-0.2345-0.64632.5085-0.3962.73030.1081-1.0541-0.50290.84790.50920.3170.0733-0.30230.5131.04570.08320.00171.43960.07230.580940.242728.777242.5901
171.9754-0.0081-0.76492.68220.01820.3971-0.4116-0.6763-0.47780.3981-0.2384-0.0860.1793-0.56410.24280.9778-0.1160.06931.2066-0.11070.614547.515628.35840.7242
180.7323-0.4487-0.99770.8564-1.25250.90250.1214-0.4098-0.26110.226-0.24690.33590.1086-0.5673-0.00430.6933-0.14370.11420.6533-0.10290.53735.536821.32753.9494
191.6155-0.0960.9971.4774-0.94041.0762-1.48290.1861.03680.1039-0.14050.1183-0.5391-1.0309-0.15820.1362-0.60321.5761.5687-0.4681-0.476230.356321.362723.0895
204.41640.07961.58332.0242-0.99432.3011-0.0627-0.2705-0.4947-0.57830.15821.15691.4783-0.3087-0.0621.0013-0.1110.26561.6425-0.28330.792923.484817.834321.2876
211.18061.15341.00191.15380.58230.9872-0.4868-0.3160.08010.9599-0.1457-0.13750.13990.5754-0.00341.127-0.16860.09121.2662-0.10190.41236.591324.18922.0229
222.3469-0.3883-0.38362.58370.78632.3261-0.3197-0.1719-0.61290.5647-0.20610.04390.45220.0670.10750.3025-0.1901-0.0410.2252-0.20220.643944.758413.8109-8.6675
230.9498-0.064-0.02850.2976-0.53521.4168-0.3308-0.3855-0.10450.62660.4590.85830.1532-1.03910.21161.5906-0.70850.35212.3641-0.38390.7614-0.152924.503967.1841
244.5916-1.51042.02946.1512-0.75315.49330.2535-0.3793-0.3602-0.258-0.10850.09161.2242-0.38740.34691.75080.21180.70271.7947-0.65550.49998.54333.843765.2983
252.293-1.44872.29111.2298-1.9333.00670.5891.1031-0.5879-1.8818-0.14610.33341.00260.7328-0.3211.80150.53351.86462.0678-0.34120.16919.89721.557958.4677
260.2923-0.0865-0.57010.01210.26861.04890.02140.1502-1.15650.45691.01260.05410.8696-0.55770.2591.30750.07910.271.9253-0.49350.91449.863925.10457.6997
271.42850.4692-0.31722.396-0.73691.61030.2631.0519-0.0606-0.07880.2453-0.16090.6492-0.1282-0.19831.4735-0.07240.92972.001-1.26120.66290.221335.998179.6829
281.8927-0.19410.97551.93780.21720.5367-0.07150.2994-0.567-0.2714-0.09780.0528-0.04210.3739-0.31211.1871-0.1020.22642.1115-0.30680.7284-10.43445.192684.4645
291.03460.1371-0.3581.7618-1.42730.9523-0.09340.1589-0.05470.1298-0.13590.6415-1.0001-0.9287-0.03851.12430.14930.09971.9017-0.21160.80938.70244.124551.292
304.2799-4.6173-2.99939.55254.17712.31630.0953-0.58140.3720.5768-0.217-0.76840.0720.12330.15241.6521-0.2001-0.30042.4669-0.40330.57251.851259.241264.2938
311.95350.59620.11952.02030.58170.1097-0.03310.33710.0651-0.41560.02410.33270.554-0.19770.08161.7941-0.05430.05072.1588-0.02820.5687-0.705856.558286.1162
326.209-1.4669-0.78937.72771.76290.4606-0.6987-0.4323-0.21060.12940.56740.369-0.25010.10040.03911.40930.00340.021.2949-0.05350.6911-1.650861.475390.8723
335.34552.6608-1.08675.312-2.13730.8460.1454-1.3623-0.32270.8591-0.62980.538-0.50330.44160.54371.14460.4832-0.62551.16930.51020.997461.6042-0.41920.7813
341.99851.0523-4.93352.94450.57571.952-0.34980.0735-0.2562-0.03110.1091-0.2812-0.05080.16860.38341.74660.5648-0.07721.4734-0.05870.673548.557-8.857538.156
352.26020.0158-0.79674.44520.67820.5576-0.2213-0.6227-0.29470.6489-0.03470.28210.023-0.11480.36331.4217-0.07430.49030.62040.24281.307954.20484.345622.0157
361.31640.739-0.71746.37051.16080.79960.0578-0.1887-0.31250.06210.07580.26110.18910.04110.16092.53250.67270.10281.18540.18931.78245.6228-12.374621.3145
376.85-3.5816-0.41535.96014.03733.5978-0.23170.1149-0.12340.1294-0.04150.0403-0.04310.0372-0.0060.7106-0.6230.84770.10211.22081.095945.77197.267219.3142
381.5471.5944-0.9851.6226-1.02430.648-0.4008-0.5308-0.33471.03-0.26040.54190.14720.54060.22591.63720.01570.92771.05280.31870.918437.5352-2.398423.816
394.0050.50120.81286.22482.86781.40310.2574-0.20470.3860.0796-0.38970.25180.1936-0.07320.2241.72160.18050.43411.12660.29180.19349.48675.354228.5497
404.25080.13721.95460.62231.60914.82670.2592-0.0059-0.07970.2113-0.0896-0.3935-0.2620.2959-0.02081.5269-0.2350.90231.15980.26441.767545.1949-11.112931.1008
412.0162-1.210.48591.77430.11732.1181-0.35150.26940.39290.02860.0357-0.2508-0.8261-0.63390.20831.21540.36580.34771.76640.3831.823653.61661.469712.2973
421.83230.1661-0.97524.2712-1.75775.26-0.2678-0.4431-0.7878-0.1183-0.4886-0.67010.05830.87740.79191.64490.12830.2320.80930.26161.042953.2781-6.18119.0148
430.03650.12850.00720.3838-0.0278-0.0098-0.58780.1799-0.06640.09840.01320.298-0.22650.11020.36932.07360.43120.12211.5941-0.1082.487351.1863-24.68985.925
440.24360.4249-0.3290.735-0.31942.46680.44540.3124-0.5598-0.5456-0.1276-0.0042-0.12720.8054-0.77912.0180.5558-0.19381.4974-0.54141.927746.4063-12.67845.9674
454.679-2.84781.60691.7579-0.97910.54650.0156-0.5003-0.0802-0.1687-0.16120.2002-0.5159-0.0040.09561.2831-0.4491-0.20111.23360.27091.721359.3625-13.115214.3113
464.34081.49681.56841.2291-0.92363.5228-0.055-0.14430.2520.16930.2236-0.1589-0.38590.58370.0291.53150.14220.92231.13660.0561.288560.0782-11.11412.2682
471.34270.2252-0.67890.0433-0.12440.3373-0.23720.52-1.0187-0.02060.36510.25570.28770.2111-0.24371.42750.46960.40331.0489-0.37571.584749.1685-16.4207-2.4274
482.2637-0.09510.51180.03350.00890.0816-0.0909-0.2342-0.43670.24330.32590.2675-0.50830.80510.38771.92930.8961-0.24071.28090.08921.402152.7752-16.876710.4748
490.3459-0.28480.95680.2295-0.78882.649-0.622-0.614-0.0270.56010.26970.3139-0.8052-0.79050.40152.0559-0.12910.31012.43280.3491.285656.5327-27.013513.7424
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 512 THROUGH 546 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 547 THROUGH 569 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 570 THROUGH 596 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 597 THROUGH 611 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 612 THROUGH 638 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 639 THROUGH 665 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 1 THROUGH 44 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 45 THROUGH 124 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 125 THROUGH 153 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 154 THROUGH 242 )
11X-RAY DIFFRACTION11CHAIN 'E' AND (RESID 2 THROUGH 106A)
12X-RAY DIFFRACTION12CHAIN 'E' AND (RESID 107 THROUGH 144 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 145 THROUGH 179 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 180 THROUGH 210 )
15X-RAY DIFFRACTION15CHAIN 'G' AND (RESID 31 THROUGH 117 )
16X-RAY DIFFRACTION16CHAIN 'G' AND (RESID 118 THROUGH 168 )
17X-RAY DIFFRACTION17CHAIN 'G' AND (RESID 169 THROUGH 203 )
18X-RAY DIFFRACTION18CHAIN 'G' AND (RESID 204 THROUGH 300 )
19X-RAY DIFFRACTION19CHAIN 'G' AND (RESID 301 THROUGH 373 )
20X-RAY DIFFRACTION20CHAIN 'G' AND (RESID 374 THROUGH 412 )
21X-RAY DIFFRACTION21CHAIN 'G' AND (RESID 413 THROUGH 457 )
22X-RAY DIFFRACTION22CHAIN 'G' AND (RESID 458 THROUGH 510)
23X-RAY DIFFRACTION23CHAIN 'H' AND (RESID 1 THROUGH 33 )
24X-RAY DIFFRACTION24CHAIN 'H' AND (RESID 34 THROUGH 45 )
25X-RAY DIFFRACTION25CHAIN 'H' AND (RESID 46 THROUGH 59 )
26X-RAY DIFFRACTION26CHAIN 'H' AND (RESID 60 THROUGH 100P)
27X-RAY DIFFRACTION27CHAIN 'H' AND (RESID 100Q THROUGH 122 )
28X-RAY DIFFRACTION28CHAIN 'H' AND (RESID 123 THROUGH 211 )
29X-RAY DIFFRACTION29CHAIN 'L' AND (RESID 6 THROUGH 99 )
30X-RAY DIFFRACTION30CHAIN 'L' AND (RESID 100 THROUGH 116 )
31X-RAY DIFFRACTION31CHAIN 'L' AND (RESID 117 THROUGH 172 )
32X-RAY DIFFRACTION32CHAIN 'L' AND (RESID 173 THROUGH 210 )
33X-RAY DIFFRACTION33CHAIN 'U' AND (RESID 1 THROUGH 6 )
34X-RAY DIFFRACTION34CHAIN 'U' AND (RESID 7 THROUGH 18 )
35X-RAY DIFFRACTION35CHAIN 'U' AND (RESID 19 THROUGH 36 )
36X-RAY DIFFRACTION36CHAIN 'U' AND (RESID 37 THROUGH 48 )
37X-RAY DIFFRACTION37CHAIN 'U' AND (RESID 49 THROUGH 55 )
38X-RAY DIFFRACTION38CHAIN 'U' AND (RESID 56 THROUGH 66 )
39X-RAY DIFFRACTION39CHAIN 'U' AND (RESID 67 THROUGH 82 )
40X-RAY DIFFRACTION40CHAIN 'U' AND (RESID 82A THROUGH 91 )
41X-RAY DIFFRACTION41CHAIN 'U' AND (RESID 92 THROUGH 99 )
42X-RAY DIFFRACTION42CHAIN 'U' AND (RESID 100 THROUGH 111 )
43X-RAY DIFFRACTION43CHAIN 'V' AND (RESID 3 THROUGH 23 )
44X-RAY DIFFRACTION44CHAIN 'V' AND (RESID 24 THROUGH 38 )
45X-RAY DIFFRACTION45CHAIN 'V' AND (RESID 39 THROUGH 48 )
46X-RAY DIFFRACTION46CHAIN 'V' AND (RESID 49 THROUGH 62 )
47X-RAY DIFFRACTION47CHAIN 'V' AND (RESID 63 THROUGH 75 )
48X-RAY DIFFRACTION48CHAIN 'V' AND (RESID 76 THROUGH 101 )
49X-RAY DIFFRACTION49CHAIN 'V' AND (RESID 102 THROUGH 106 )

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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