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基本情報

登録情報
データベース: PDB / ID: 5t3z
タイトル3.5 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074
要素
  • (Envelope glycoprotein ...) x 2
  • 10-1074 Heavy Chain
  • 10-1074 Light Chain
  • IOMA Heavy Chain
  • IOMA Light Chain
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / HIV / N-linked Glycosylation / Broadly Neutralizing Antibodies / 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: 3.5 Å
データ登録者Gristick, H.B. / Bjorkman, P.J.
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)P01 AI100148 米国
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2016
タイトル: Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site.
著者: Gristick, H.B. / von Boehmer, L. / West, A.P. / Schamber, M. / Gazumyan, A. / Golijanin, J. / Seaman, M.S. / Fatkenheuer, G. / Klein, F. / Nussenzweig, M.C. / Bjorkman, P.J.
履歴
登録2016年8月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年10月5日Provider: repository / タイプ: Initial release
改定 1.12016年10月19日Group: Database references
改定 1.22017年9月20日Group: Derived calculations / カテゴリ: pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
改定 1.32018年2月14日Group: Database references / カテゴリ: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_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.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_atom_id / _struct_conn.ptnr2_label_comp_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12022年4月13日Group: Author supporting evidence / Database references / Structure summary
カテゴリ: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
改定 2.22023年10月4日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 2.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
改定 3.02025年1月15日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / diffrn / entity / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _cell.volume / _diffrn.pdbx_serial_crystal_experiment / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_entity_nonpoly.entity_id / _pdbx_entry_details.has_ligand_of_interest / _pdbx_modification_feature.auth_seq_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns_shell.number_unique_obs / _software.version / _struct_asym.entity_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _symmetry.space_group_name_Hall
解説: Model orientation/position
詳細: Updated CDRH3 using coordinates from a high-resolution Fab structure (7TQG)
Provider: author / タイプ: Coordinate replacement

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)183,74325
ポリマ－167,8226
非ポリマー15,92219
水00
1
B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
ヘテロ分子

B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
ヘテロ分子

B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)551,22975
ポリマ－503,46518
非ポリマー47,76557
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area76070 Å2
ΔGint-56 kcal/mol
Surface area204360 Å2
手法PISA
単位格子
Length a, b, c (Å)217.258, 217.258, 154.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3

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要素

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

#1: タンパク質 Envelope glycoprotein gp160


分子量: 17146.482 Da / 分子数: 1 / 断片: UNP residues 509-611 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: env / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6
#2: タンパク質 Envelope glycoprotein gp160


分子量: 54064.277 Da / 分子数: 1 / 断片: UNP residues 30-508 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: env / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6

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抗体 , 4種, 4分子 HLDE

#3: 抗体 10-1074 Heavy Chain


分子量: 25661.688 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 10-1074 Light Chain


分子量: 23180.760 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 IOMA Heavy Chain


分子量: 25176.416 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#6: 抗体 IOMA Light Chain


分子量: 22591.975 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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糖 , 12種, 19分子

#7: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 367.349 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
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#10: 多糖 beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1990.824 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
DGalpb1-4DGlcpNAcb1-4[DGlcpNAcb1-2]DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-1-4-3-1-4-5/a4-b1_a6-k1_b4-c1_c3-d1_c6-h1_d2-e1_d4-f1_f4-g1_h2-i1_i4-j1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#11: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 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
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#12: 多糖 beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 1479.349 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
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-4-3-1/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1_g2-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#13: 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-ROHGlycam 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
[][D-1-deoxy-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
#14: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(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: 1114.016 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
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+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-(1-6)-[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-ROHGlycam 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
[][D-1-deoxy-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
#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-(1-3)]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-ROHGlycam 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
[][D-1-deoxy-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
#17: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 732.682 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
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#18: 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: 2 / 由来タイプ: 組換発現 / 式: C8H15NO6 / タイプ: SUBJECT OF INVESTIGATION
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

研究の焦点であるリガンドがあるかY
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: 4.19 Å3/Da / 溶媒含有率: 70.67 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 200 mM ammonium citrate tribasic pH 7.0 100 mM imidazole pH 7.0 20% PEG MME 2,000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRL / ビームライン: BL12-2 / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年1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
Reflection twinOperator: k,h,-l / Fraction: 0.13
反射解像度: 3.5→64.631 Å / Num. obs: 34373 / % possible obs: 100 % / 冗長度: 61.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.68 / Rpim(I) all: 0.09 / Net I/σ(I): 12.6
反射 シェル解像度: 3.5→3.67 Å / 冗長度: 59.7 % / Rmerge(I) obs: 9.29 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4992 / CC1/2: 0.4 / Rpim(I) all: 1.21 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.2_5419精密化
Cootモデル構築
Aimlessデータスケーリング
iMOSFLMデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5T3X

5t3x


解像度: 3.5→64.63 Å / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 38.1182
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3061 1755 5.11 %
Rwork0.2645 32611 -
obs0.267 34366 99.99 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 189.8 Å2
精密化ステップサイクル: LAST / 解像度: 3.5→64.63 Å
タンパク質核酸リガンド溶媒全体
原子数11199 0 1066 0 12265
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003812527
X-RAY DIFFRACTIONf_angle_d0.839417048
X-RAY DIFFRACTIONf_chiral_restr0.05472182
X-RAY DIFFRACTIONf_plane_restr0.00532036
X-RAY DIFFRACTIONf_dihedral_angle_d16.10265319
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.35561410.31662486X-RAY DIFFRACTION94.63
3.59-3.70.37621460.31932506X-RAY DIFFRACTION94.49
3.7-3.820.31481430.29952492X-RAY DIFFRACTION94.57
3.82-3.960.41071210.32372540X-RAY DIFFRACTION95.38
3.96-4.110.32241280.28482512X-RAY DIFFRACTION95.15
4.12-4.30.28181350.27032510X-RAY DIFFRACTION94.9
4.3-4.530.27341280.25822532X-RAY DIFFRACTION95.19
4.53-4.810.2611190.25722495X-RAY DIFFRACTION95.45
4.81-5.180.27461360.2412514X-RAY DIFFRACTION94.87
5.18-5.70.33451160.25692529X-RAY DIFFRACTION95.58
5.71-6.530.30271700.28312480X-RAY DIFFRACTION93.58
6.53-8.220.34331230.2632506X-RAY DIFFRACTION95.32
8.23-64.630.28611480.23832510X-RAY DIFFRACTION94.36
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)
14.28790270498-1.09396039965-1.72407946514.52796730062.338317275829.39692379931-0.03628411292841.25147479483-0.216102187796-1.277720177770.3368657185330.9969311331631.11778772268-0.555231670264-0.4644969853261.96796615845-0.289318008229-0.0739939308511.625212113990.05228229502851.05306583073-2.61703042926-18.9649438828-22.3968760495
24.275774011690.209508732558-1.066044731933.454796877090.6360483236122.60165322637-0.6373708588851.091437969720.554037460653-1.243271255180.6411003109940.06506936160250.286875512670.5492667734450.09392624628192.18372071183-0.0926109214498-0.2138408694891.27155381731-0.01773601575590.8835584040615.54710392315-6.88684020008-22.4686049398
32.798007725570.99164809157-0.1134811859294.55967351803-0.7222624955030.7096965780990.346282344335-0.230522176256-0.738341085882-0.129412850364-0.306448152827-0.2258717333740.112839859711.681594303820.05559256766982.366386345020.2234504956850.1866473833652.5042932272-0.3341165767791.1990832148316.6221738159-18.4041470072-31.3837199042
40.158062823181-0.1572456193330.3910764444080.165146225364-0.4271452735441.133410504970.73829575331-0.70162582710.0641538058502-0.0698263426377-0.5269567008890.221831396446-0.908091247197-0.153395535512-0.1766474481892.3760052302-0.5337950941650.5267362617322.62173678488-0.4381367797581.4843933752612.58749407737.0746381575-41.8886238339
51.226346340870.1493190083190.6945713839153.88879919252-2.338097449681.898819613690.06612953075770.341933202236-0.26054298895-0.2906394755130.5745382548190.5460927380980.227294420580.089472072173-0.5823987720611.75493610484-0.226694736523-0.000888295474691.73249482412-0.3515717360391.25921405275-1.47612524843-20.3757172638-10.7092959455
63.54426891725-1.01922844289-1.250812765792.130295302192.489691235955.24165847788-0.229684793351-0.276573332539-0.265346893504-0.02917478356610.3604134491460.2631369806890.3040884973060.0104904091991-0.1228868784010.824122067554-0.135308596217-0.03437494368180.6480980044910.03625393699450.957823906859-2.90509286861-18.079832631732.5341673725
71.738458814750.191481370507-0.1348487359390.5257157307340.156566169352.338148725660.03398077890620.43885165304-0.781045226135-0.617437677590.04332768423930.08450345906870.592850086012-0.103769332352-0.03276856132961.27955585783-0.0653236092123-0.05378693994040.739086103817-0.171263225121.103409098820.413400598689-32.347835877310.9402617403
82.621738403850.7208302186010.465467119215.102003032722.522679124856.042423766160.284229752114-0.98540485157-0.4750358902041.686443126140.03505551838350.5085244058270.937228190202-0.650492169285-0.01551071143962.28696713424-0.4943821447330.4851968642081.540693487660.9493005873622.23772416827-19.9253626639-58.984377149271.1522099929
94.7987881198-0.435090127713-0.005708737756323.25112063990.3948073394633.4978951226-0.444669021303-0.388341349746-0.886134056010.0279785411502-0.27529108820.324337729360.707108042190.2852386371220.6587484012071.74947485856-0.3034313086050.1169959409811.261313872670.6922468010822.10848699844-17.083976972-54.308718178659.1101787985
102.845010050280.4787711023840.2008885226044.225631287472.695218465024.302914510361.3632671926-0.886620635656-0.6503670840850.7033844193310.22355209956-0.5457841176670.199349024224-1.07904310006-1.436479640521.83620621702-0.1832165782810.00417891267681.616278005590.4407362260012.1463343949-14.3265905157-55.186589669768.3908868164
111.966969791140.4768380253030.6701612158811.40457766061-0.5263973034370.5967175755680.269174686031-0.449022843361-0.495397448760.6798210456140.3192308898510.3718976372161.3657371519-1.18035448553-0.4409800913862.02288284954-0.4504970053980.001948982516410.9278672045260.2921820308462.00607207454-22.5218045918-52.808925004358.8456988985
121.857668106020.901063768560.788310180143.285541811410.5379487879190.373394175975-0.569262326045-0.861059738513-1.157362053650.5592866985220.08527127398071.162111113441.39127241012-1.071427360780.499801882333.56388399367-1.312687153961.053389779043.39471616290.05396359510032.56137043553-41.4163050849-59.932876448281.6004095931
135.153743514421.933206031830.6510177013062.6983632920.6173132592380.680769233255-0.926310170409-0.66068483539-0.8015612651180.7373587415160.0339253738880.7571918184560.7734978475860.684085555691.023756690823.5617993136-0.7526373214650.2398135933662.493962508920.2416135041641.85869111306-41.8297557559-69.872199241784.2576332164
145.81724229670.895352091172.421518028881.500739261421.313617661772.33633675331-0.597786761382-0.0375576358410.568132706687-0.176028826495-0.6556041421511.38899425841-0.15235194639-0.198694269511.039620334281.910872368630.09285999638150.2943339253862.036200815270.3391563807632.76697519456-43.123132512-38.936581444353.4480746645
153.37424836354-2.850381125580.9790162506573.597086770270.8155685442926.891436505540.980806524251-0.3459269735430.6807623746270.924027732942-0.2137087911941.320720518630.385335587049-2.03912308474-0.617336160871.31807855207-0.3971968878030.1959519888911.578047185070.570259310912.04635735749-29.7129705434-44.320186701352.6138878915
166.31986054304-1.47787990247-0.4913799707531.588303311211.613171360862.521981657380.5183452035680.04616939007320.430698033480.1803201340830.2579771299811.41814350342-0.203507163474-0.863506989903-0.7271904163191.27662120773-0.293955851545-0.06178462023091.432581325180.4758837759972.68953722043-36.0367934117-46.654213725446.0730442042
171.272542716570.59767853970.7084882478072.18296102244-0.62123995745.785758439571.14979298985-0.50668085633-0.4769502990051.010953352420.2344231029741.148546624540.400044697143-1.02581098462-0.9795953959231.29146504339-0.1191109214110.3686583761470.9729333671740.4812680007332.32162462954-23.4824068493-41.799884780652.4581666836
180.4060265536680.5591051823720.1321171186030.990121115588-0.3979363375151.5035554647-0.0364462042425-3.00428072055-0.6111873319160.834012549363-0.08611559024240.6491882806270.279565075059-0.8980759749960.1823042390612.36985069159-0.04463614726381.06851468264.416621258060.4532146833672.71041831991-48.0548785289-52.820705350580.1900955723
191.90624492722-0.4767385577891.193298870842.97210418008-0.8458740018862.86414300163-0.700525646769-1.58217073538-0.215219133180.5733918146740.9446038266550.4506211359440.081747455698-0.372735828633-0.2715957619774.466923313490.2227332469181.941505217013.022208009140.1731230993173.68893217605-51.2719938458-48.279528750181.4379666911
202.011318487790.345017690140.9632969020962.54636080922-0.6125960607920.704002595832-0.156351365175-1.6419967078-0.302296615620.836842861255-0.2444390730231.251658515720.0361748773499-0.2880349993970.4512012072572.87684744338-0.5195909307351.20873195933.18340815918-0.4012335745462.89334792333-48.113650994-46.737918730181.4344848126
213.529341354750.0718160903646-0.7564746077730.4923851949530.2254488405170.2802697670820.21113183234-1.6073740873-0.2978677045211.534936444370.4487479675720.130631044480.144503728347-0.834229900772-0.468537967944.32159051126-0.6348793632061.274415670263.84186364250.846288991772.34273680368-47.0576447166-51.602246454892.5649844674
221.09832441658-1.256746801151.072937047715.91579903244-4.031473892112.83780237107-0.456983530711-1.21055538642-0.1058607432780.3690029009490.8835722930720.2641177123310.684377721481-0.033770584911-0.4096201042323.75124993569-0.8242418245660.6886081362434.47703299569-0.0324535453313.09916140872-56.7607455254-48.343746313389.8784969473
233.00993561593-1.392900317061.72880014825.41158271895-2.098130199134.46884097754-0.139232689161-0.475776539566-0.1721487063691.189103848910.5400050143340.1661707950020.479549038097-0.375263046396-0.3239967959864.11564850846-0.7178536909120.5132650952554.698485481850.5244791709362.57887628712-59.3520744616-52.449529754787.4952105505
246.008982345820.853717720407-0.4971389716854.37955178833-0.1751887401643.14017177017-0.263558982934-0.706050206356-0.761677034578-0.305892538672-0.0400554002993-0.5001937711950.4882838449220.3739309133210.277192166621.115773882170.2367534962870.1892277933651.02060865727-3.46998502087E-51.0542271340528.4608441738-33.312619561826.2936190973
253.273633376472.523697106071.824253446782.88756421133-0.1603230524463.62025046756-0.799047363948-1.741912002560.253930417224-1.22824023703-0.0106046579462-1.74052337196-0.338436529121-0.4615746655961.149822886632.339125074480.5359210014960.1080419263773.504369207570.1385520021644.08876535559.138850658-41.783139277843.0968023697
262.50542358854-0.1005065532741.717045777260.226083703561-0.9749695189164.873121400350.679915101284-0.335114570904-0.86418914321-0.254395212279-0.455685092085-0.1166848197862.400900195970.319484813689-0.1873391984166.920258194340.179107839443-0.9885389607225.583480313510.822470405132.0885644378370.6690686205-52.150898450349.4945092722
272.386526325810.591759762908-1.006926436474.870696532150.1697071772785.43218748255-0.1808264766860.574007021881-1.41741315966-0.231618028786-0.138617554787-0.6876181787810.582361475371.030659913820.3518878636981.198170905570.4540637066150.4428697530471.32806323178-0.0261517461631.4899592273243.9875955122-35.521173896110.3093557517
280.3648494244840.286205984922-0.3009766691971.28430176023-0.973721998490.994790538111.52827958078-1.23288706545-1.763446951910.0864653082871-1.46995643-0.06721895729471.0473830171.13649429138-0.002375773118482.71809825425-0.320722629513-0.668512767334.005067583450.501792658823.0009121127656.8938220007-54.581331961635.6159996799
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CHAIN 'B' AND (RESID 518 THROUGH 571 )BA518 - 5711 - 33
22CHAIN 'B' AND (RESID 572 THROUGH 610 )BA572 - 61034 - 72
33CHAIN 'B' AND (RESID 611 THROUGH 650 )BA611 - 65073 - 112
44CHAIN 'B' AND (RESID 651 THROUGH 664 )BA651 - 664113 - 126
55CHAIN 'G' AND (RESID 31 THROUGH 98 )GB31 - 981 - 68
66CHAIN 'G' AND (RESID 99 THROUGH 190 )GB99 - 19069 - 148
77CHAIN 'G' AND (RESID 191 THROUGH 505 )GB191 - 505149 - 450
88CHAIN 'H' AND (RESID 1 THROUGH 23 )HE1 - 231 - 23
99CHAIN 'H' AND (RESID 24 THROUGH 63 )HE24 - 6324 - 63
1010CHAIN 'H' AND (RESID 64 THROUGH 90 )HE64 - 9064 - 93
1111CHAIN 'H' AND (RESID 91 THROUGH 124 )HE91 - 12494 - 143
1212CHAIN 'H' AND (RESID 125 THROUGH 184 )HE125 - 184144 - 198
1313CHAIN 'H' AND (RESID 185 THROUGH 216 )HE185 - 216199 - 230
1414CHAIN 'L' AND (RESID 8 THROUGH 22 )LF8 - 221 - 15
1515CHAIN 'L' AND (RESID 23 THROUGH 44 )LF23 - 4416 - 37
1616CHAIN 'L' AND (RESID 45 THROUGH 84 )LF45 - 8438 - 80
1717CHAIN 'L' AND (RESID 85 THROUGH 101 )LF85 - 10181 - 100
1818CHAIN 'L' AND (RESID 102 THROUGH 130 )LF102 - 130101 - 129
1919CHAIN 'L' AND (RESID 131 THROUGH 151 )LF131 - 151130 - 150
2020CHAIN 'L' AND (RESID 152 THROUGH 172 )LF152 - 172151 - 171
2121CHAIN 'L' AND (RESID 173 THROUGH 188 )LF173 - 188172 - 187
2222CHAIN 'L' AND (RESID 189 THROUGH 198 )LF189 - 198188 - 197
2323CHAIN 'L' AND (RESID 199 THROUGH 212 )LF199 - 212198 - 211
2424CHAIN 'D' AND (RESID 1 THROUGH 125 )DG1 - 1251 - 138
2525CHAIN 'D' AND (RESID 126 THROUGH 211 )DG126 - 211139 - 224
2626CHAIN 'D' AND (RESID 212 THROUGH 216 )DG212 - 216225 - 229
2727CHAIN 'E' AND (RESID 2 THROUGH 114 )EH2 - 1141 - 114
2828CHAIN 'E' AND (RESID 115 THROUGH 210 )EH115 - 210115 - 210

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る