登録情報 | データベース: PDB / ID: 5d3g |
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タイトル | Structure of HIV-1 Reverse Transcriptase Bound to a Novel 38-mer Hairpin Template-Primer DNA Aptamer |
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要素 | - (HIV-1 REVERSE TRANSCRIPTASE ...) x 2
- DNA aptamer (38-MER)
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キーワード | TRANSFERASE / reverse transcriptase / HIV / DNA aptamer / 2-O-methylcytidine / p66 / p51 |
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機能・相同性 | 機能・相同性情報
RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / telomerase activity / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / 加水分解酵素; エステル加水分解酵素 / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane類似検索 - 分子機能 HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta類似検索 - ドメイン・相同性 sucrose / DNA / DNA (> 10) / Gag-Pol polyprotein類似検索 - 構成要素 |
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生物種 | Human immunodeficiency virus type 1 group M subtype B (ヒト免疫不全ウイルス) synthetic construct (人工物) |
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手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å |
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データ登録者 | Miller, M.T. / Tuske, S. / Das, K. / Arnold, E. |
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資金援助 | 米国, 3件 組織 | 認可番号 | 国 |
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National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | GM103368 | 米国 | National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | AI027690 | 米国 | National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | GM1033 | 米国 |
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引用 | ジャーナル: Protein Sci. / 年: 2016 タイトル: Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer. 著者: Miller, M.T. / Tuske, S. / Das, K. / DeStefano, J.J. / Arnold, E. |
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履歴 | 登録 | 2015年8月6日 | 登録サイト: RCSB / 処理サイト: RCSB |
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改定 1.0 | 2015年9月30日 | Provider: repository / タイプ: Initial release |
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改定 1.1 | 2016年1月13日 | Group: Database references |
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改定 1.2 | 2017年9月20日 | Group: Author supporting evidence / Database references / Derived calculations カテゴリ: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation |
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改定 2.0 | 2019年7月31日 | Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / computing / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / refine / refine_hist / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _computing.structure_refinement / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.tilt / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_percent_reflns_obs / _refine_hist.d_res_low |
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改定 2.1 | 2019年8月14日 | Group: Data collection / Derived calculations カテゴリ: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop ...pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site / struct_site_gen Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value |
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改定 2.2 | 2019年12月11日 | Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization |
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改定 3.0 | 2020年7月29日 | Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id 解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation |
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改定 3.1 | 2023年9月27日 | Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession |
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