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- PDB-6vw1: Structure of SARS-CoV-2 chimeric receptor-binding domain complexe... -

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基本情報

登録情報
データベース: PDB / ID: 6vw1
タイトルStructure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2
要素
  • Angiotensin-converting enzyme 2
  • SARS-CoV-2 chimeric RBD
キーワードCELL INVASION / coronavirus
機能・相同性
機能・相同性情報


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ / angiotensin-mediated drinking behavior / tryptophan transport / regulation of systemic arterial blood pressure by renin-angiotensin ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ / angiotensin-mediated drinking behavior / tryptophan transport / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / metallocarboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / Attachment and Entry / negative regulation of signaling receptor activity / carboxypeptidase activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / endocytosis involved in viral entry into host cell / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / Maturation of spike protein / viral translation / endopeptidase activity / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
Spike glycoprotein / Spike glycoprotein / Angiotensin-converting enzyme 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Human SARS coronavirus (ウイルス)
Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.68 Å
データ登録者Shang, J. / Ye, G. / Shi, K. / Wan, Y.S. / Aihara, H. / Li, F.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI089728 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI089728 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 米国
引用ジャーナル: Nature / 年: 2020
タイトル: Structural basis of receptor recognition by SARS-CoV-2.
著者: Shang, J. / Ye, G. / Shi, K. / Wan, Y. / Luo, C. / Aihara, H. / Geng, Q. / Auerbach, A. / Li, F.
履歴
登録2020年2月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年3月4日Provider: repository / タイプ: Initial release
改定 1.12020年3月11日Group: Source and taxonomy / カテゴリ: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
改定 1.22020年4月8日Group: Database references / Structure summary / カテゴリ: audit_author / citation
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
改定 1.32020年4月15日Group: Database references / Structure summary
カテゴリ: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
改定 1.42020年5月6日Group: Database references / Source and taxonomy / Structure summary
カテゴリ: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_ec
改定 1.52020年5月27日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.conn_type_id / _struct_conn.id / _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 2.12023年10月11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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Angiotensin-converting enzyme 2
B: Angiotensin-converting enzyme 2
E: SARS-CoV-2 chimeric RBD
F: SARS-CoV-2 chimeric RBD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)192,75124
ポリマ－186,9664
非ポリマー5,78520
水46826
1
A: Angiotensin-converting enzyme 2
E: SARS-CoV-2 chimeric RBD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,47611
ポリマ－93,4832
非ポリマー2,9939
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme 2
F: SARS-CoV-2 chimeric RBD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,27613
ポリマ－93,4832
非ポリマー2,79211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)80.435, 118.034, 112.075
Angle α, β, γ (deg.)90.000, 93.120, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERTYRTYR(chain 'A' and resid 19 through 614)AA19 - 6131 - 595
211SERSERTYRTYR(chain 'B' and resid 19 through 614)BB19 - 6131 - 595
112THRTHRSERSER(chain 'E' and (resid 376 through 384 or resid 386...EC376 - 38358 - 65
122LYSLYSLYSLYS(chain 'E' and (resid 376 through 384 or resid 386...EC38668
132ASPASPILEILE(chain 'E' and (resid 376 through 384 or resid 386...EC389 - 44171 - 123
142THRTHRTHRTHR(chain 'E' and (resid 376 through 384 or resid 386...EC444126
152ASNASNASNASN(chain 'E' and (resid 376 through 384 or resid 386...EC448130
162ASNASNPHEPHE(chain 'E' and (resid 376 through 384 or resid 386...EC450 - 456132 - 138
172ARGARGASPASP(chain 'E' and (resid 376 through 384 or resid 386...EC466 - 467148 - 149
182GLNGLNGLNGLN(chain 'E' and (resid 376 through 384 or resid 386...EC474156
192THRTHRTHRTHR(chain 'E' and (resid 376 through 384 or resid 386...EC478160
1102GLYGLYVALVAL(chain 'E' and (resid 376 through 384 or resid 386...EC482 - 483164 - 165
1112PROPROASNASN(chain 'E' and (resid 376 through 384 or resid 386...EC491 - 501173 - 183
212THRTHRSERSER(chain 'F' and (resid 376 through 384 or resid 386...FD376 - 38358 - 65
222LYSLYSLYSLYS(chain 'F' and (resid 376 through 384 or resid 386...FD38668
232ASPASPILEILE(chain 'F' and (resid 376 through 384 or resid 386...FD389 - 44171 - 123
242THRTHRTHRTHR(chain 'F' and (resid 376 through 384 or resid 386...FD444126
252ASNASNASNASN(chain 'F' and (resid 376 through 384 or resid 386...FD448130
262ASNASNPHEPHE(chain 'F' and (resid 376 through 384 or resid 386...FD450 - 456132 - 138
272ARGARGASPASP(chain 'F' and (resid 376 through 384 or resid 386...FD466 - 467148 - 149
282GLNGLNGLNGLN(chain 'F' and (resid 376 through 384 or resid 386...FD474156
292THRTHRTHRTHR(chain 'F' and (resid 376 through 384 or resid 386...FD478160
2102GLYGLYVALVAL(chain 'F' and (resid 376 through 384 or resid 386...FD482 - 483164 - 165
2112PROPROASNASN(chain 'F' and (resid 376 through 384 or resid 386...FD491 - 501173 - 183

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 2種, 4分子 ABEF

#1: タンパク質 Angiotensin-converting enzyme 2 / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15


分子量: 69153.664 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACE2, UNQ868/PRO1885
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9BYF1, angiotensin-converting enzyme 2, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ
#2: タンパク質 SARS-CoV-2 chimeric RBD / S glycoprotein / E2 / Peplomer protein


分子量: 24329.467 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Human SARS coronavirus (ウイルス), (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P59594, UniProt: P0DTC2

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糖 , 4種, 12分子

#3: 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: 天然
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
#4: 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: 5 / 由来タイプ: 天然
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
#5: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(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: 789.734 Da / 分子数: 1 / 由来タイプ: 天然
記述子タイププログラム
DGlcpNAcb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-1/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)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#9: 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: 天然 / 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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非ポリマー , 4種, 34分子

#6: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 組換発現 / 式: Zn
#7: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 組換発現 / 式: Cl
#8: 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: 4 / 由来タイプ: 組換発現 / 式: C2H6O2
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 26 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.95 Å3/Da / 溶媒含有率: 58.37 %
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: Tris, PEG 6000, and 100 mM NaCl.

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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: APS / ビームライン: 24-ID-E / 波長: 0.979 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年2月11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: 0.979 Å / 相対比: 1
反射解像度: 2.68→118.03 Å / Num. obs: 58219 / % possible obs: 96.7 % / 冗長度: 3.9 % / Biso Wilson estimate: 85.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.08
反射 シェル解像度: 2.68→2.78 Å / 冗長度: 4 % / Rmerge(I) obs: 1.47 / Num. unique obs: 5774 / CC1/2: 0.587 / % possible all: 98.97

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
REFMAC5.8.0258精密化
精密化構造決定の手法: 分子置換
開始モデル: 2AJF

2ajf


解像度: 2.68→59.02 Å / SU ML: 0.4455 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 30.1336
Rfactor反射数%反射
Rfree0.2288 2674 4.6 %
Rwork0.197 --
obs0.1985 58159 98.97 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 108.85 Å2
精密化ステップサイクル: LAST / 解像度: 2.68→59.02 Å
タンパク質核酸リガンド溶媒全体
原子数12782 0 372 26 13180
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002613506
X-RAY DIFFRACTIONf_angle_d0.59718350
X-RAY DIFFRACTIONf_chiral_restr0.04392001
X-RAY DIFFRACTIONf_plane_restr0.0042339
X-RAY DIFFRACTIONf_dihedral_angle_d21.18174914
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.730.40551580.38162849X-RAY DIFFRACTION99.11
2.73-2.780.39821300.35222938X-RAY DIFFRACTION98.84
2.78-2.840.36111640.33552878X-RAY DIFFRACTION99.25
2.84-2.90.35841490.31332901X-RAY DIFFRACTION99.12
2.9-2.970.33681450.30052929X-RAY DIFFRACTION99.1
2.97-3.040.31911400.29632832X-RAY DIFFRACTION96.62
3.04-3.120.34781410.28472893X-RAY DIFFRACTION98.35
3.12-3.220.35041380.27552908X-RAY DIFFRACTION98.99
3.22-3.320.3321360.26912933X-RAY DIFFRACTION99.38
3.32-3.440.29591080.24552944X-RAY DIFFRACTION99.38
3.44-3.580.25581340.22212936X-RAY DIFFRACTION99.22
3.58-3.740.25671290.22452941X-RAY DIFFRACTION99.19
3.74-3.940.22171440.19482917X-RAY DIFFRACTION99.32
3.94-4.180.22591380.17922932X-RAY DIFFRACTION99.16
4.18-4.50.18941280.16232913X-RAY DIFFRACTION97.75
4.5-4.960.17781840.15442899X-RAY DIFFRACTION99.61
4.96-5.670.19771270.16462957X-RAY DIFFRACTION99.71
5.67-7.150.20921410.18432992X-RAY DIFFRACTION99.71
7.15-59.020.18271400.15642993X-RAY DIFFRACTION98.71
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)
15.326795728621.31941146559-0.8631084933574.846094717540.1829330816215.69493657444-0.1346049461840.222295960087-0.2538730681860.301929156454-0.142808577383-0.4448679404510.543275180320.0001902588519330.2717192476370.743662271292-0.181875017609-0.02368548161150.6691052701980.1134056041140.7642793941990.516405952-16.0765706333175.880993265
24.436458281921.89409022778-1.86319593911.89553681299-1.323791938672.29207082879-0.1603072998280.255933361835-0.114950033341-0.1235138530540.0741039290462-0.08819637649430.416007534023-0.2151180999930.1282378574690.7807807438330.08294147744240.09463381095640.5981186004520.0356924286040.700900070338110.12787697-3.84500303203157.093174917
33.372430885811.65172975031-2.27949095655.21186781177-2.146181527534.49057632831.007095311060.2214605557651.740911462850.718952758963-0.1863550155740.350815759827-1.02571803811-0.348788092541-0.7117772022470.860189355873-0.001219271608090.2840045304840.6886642566180.1516893359651.3367533546693.809316578110.5700401803169.216991716
44.043060861892.0298966626-1.661550264251.62321555429-0.6962806122543.147748486810.06470742746290.7172323730780.672780574358-0.3073241184920.2753665364060.1792617086550.175372653853-0.634291615699-0.2539452550980.6676234249890.04013038176930.07497636333090.6208676380370.2407282192320.772820083301104.503541991.71528205753152.360249837
57.568510849112.97571139846-4.199264216162.38487702852-1.65933599992.34448862109-0.1809618721331.869969957841.38279582952-0.3894093036710.7870677987820.6020833465860.137055209552-0.95993294913-0.6112955227220.865267382804-0.03276035835720.01213969055231.188062739170.4204583268480.917198796774102.7393908536.6159986961143.880093958
62.625802172550.386314152748-0.5727152567742.58278301757-1.290460107532.85472984472-0.3425314266350.703811478449-0.163734822151-0.6145286874340.6009818329870.2244840445390.360598020045-0.594297580669-0.2399913543781.10535235154-0.244826640988-0.03636877832261.26589205990.09638840192120.60645574750373.245556587438.447092426895.5594578639
73.278937314950.838664221298-0.490151675414.61345077428-1.79212608152.571253017020.005525524797090.5836321642510.6969320427270.1008602631440.7488782673851.13078979347-0.667490316907-1.35021817294-0.6373441784310.864107615749-0.02638184115340.03041758792391.292257476450.5442153270171.1265286410648.976455010737.5759850018116.490504588
83.040009626840.741321687564-1.073024292773.56398555175-0.6770011194775.09110348811-0.2380357901480.459558985221-0.228908182647-0.3511440403110.5504345821630.240630536622-0.100174342389-0.478056851035-0.2949191150840.685456335685-0.143268353728-0.0001626489351070.6859517687390.09270857033760.67930365371160.322534171220.403118499120.868545144
92.52909456907-0.976521965945-1.719060691424.58127366705-0.3825661370316.50123854237-0.2051881134510.2570272961460.111673451609-0.2827283768870.343704754260.169333628444-0.40161808187-0.522777866965-0.09129096780390.565199399555-0.059546870287-0.07687132614880.8227817210787.16291288097E-50.61397565081177.360925265840.9293255371123.046391634
103.887273469020.475848967388-1.247887760034.158991092120.7952384957977.92720025282-0.288691810538-0.0742833748106-0.158826993315-0.2296669828170.252742122691-0.2024031976670.4237772810330.3421094481790.09396535864090.449661474277-0.00737620405782-0.06781911481540.570277748072-0.0314607309430.63156712966978.81397175428.4576727618124.246093814
115.199875627080.90587668677-0.1663851906723.09335772745-1.232274913072.65267703626-0.3010633383260.780208333847-0.210974211164-0.6409203972460.5800916886340.1842054035050.404274527614-0.534982579778-0.2690049338460.714779707013-0.20420873849-0.03186741246050.7413079848790.01691218450560.50972109284765.982575671921.7754501214117.381504166
128.979096121621.19472956879-0.4095195323764.05771592124-3.427644968215.96645594226-0.380820294998-0.0164967321859-0.767229875263-0.2404349612720.4781883827550.04458727190060.353188740586-0.672934530821-0.1285796788530.806414012399-0.23283888240.09123355266340.678793333611-0.06154777537590.74033860995756.943627639113.2827563184130.988625902
136.30083715914-3.81295086689-0.4018496217978.34785198651-1.234919481923.649908513440.0349137960195-0.541718867315-0.1498627104970.6387865281340.07220884154820.791583276621-1.08848815265-1.102811151270.05184935553951.14872233691-0.1602127714810.1708466082911.34406032764-0.04470819838870.76818200865358.3056598764-3.69792593979194.993680431
142.09204065483-1.891748133543.776409094597.23974803737-2.253561585879.13784286684-0.6148721640780.5862443899552.44143738017-0.941422027602-0.065811533314-0.257564217495-0.243417254206-0.7418547700380.7007773914811.28049419352-0.0668056332508-0.1753757872451.341613631120.2327876924991.2180334919359.42032992325.97477374565184.755107742
158.08110724476-2.23485052574-1.087583249925.34916078064-0.2204298387192.900644332790.08863170501580.612889418538-0.146247078995-0.0940492886340.01336850718480.361231078536-0.132953064784-0.571074051491-0.0863413886220.839591381631-0.26784349994-0.02511749278020.971723394220.02218251991840.46524491917963.8315588115-8.78287962048183.118887646
169.71854270042-6.81611490361-4.179481628594.808041681582.548358536575.29568719452-0.3754487747250.330853232422-1.529068369060.294103979422-0.2259041942710.2367214014431.37792675947-0.4871466536990.5124310713061.21231114197-0.4368455209560.03599094676120.936919130379-0.1259689286180.95988963190474.7839286341-29.6121843415177.401376898
175.127247517-2.03582331462-0.7955500183553.36759738265-0.4631017968771.7896591573-0.1103397502530.835289717509-0.1148150679890.2865097420630.02177027232820.294661600691-0.535747001544-0.419810807960.09629125984050.96454823269-0.2443298837830.08228304616281.04692281419-0.05437344333750.69059853155963.0958551999-3.70621806686187.121884936
188.71189874394-1.392514861793.226739563952.608266716642.559493558825.3987908716-0.7876655736730.7499950033840.416809902037-0.4407282229910.384814242647-1.42763320754-0.6150038595910.9348401050770.3223901790931.09399494894-0.1470451431030.07264404915541.070052013950.2537818625741.59942981506112.53138802262.9388556829102.386907824
199.798213380482.254454366780.6035557158883.396882004612.407175239829.21106891722-0.3864819777010.1424749973310.8153504534720.145015610552-0.0877259040472-0.5667588888410.1693435155851.085911992080.3436961368230.9155360009610.009506549117230.08733221188830.8623003850210.2831292759651.36319607896112.80390016356.8892580386104.02593545
202.173217160642.204591166291.968937878423.289834912134.147344915226.19419907792-1.095999681511.02533346804-0.3020957783340.07083809243340.966595669568-0.8251600090740.1738497604142.34310503844-0.06875321007190.9623532765110.102927492179-0.02914612369871.720159860950.5010458277911.6449179467119.89140003149.4702352116107.830136363
214.39148689502-0.2948635573740.8384730532183.205073779850.6492949768195.76314108006-0.02306902537390.7756096932790.0834081181287-0.239901378713-0.322972796728-0.6555517188860.638316954055-0.03624807710010.2949030706940.8787309332250.04109200024430.2303081207730.7130609286020.1296256909210.872115641004101.35956626946.078223392395.0119461894
220.9243209805610.00969616644232-2.256156087521.83471236651-1.419823967436.383646330810.329827379040.5216964573960.553289136172-0.489621958272-0.162704470322-0.09015681505370.609685531259-1.08604631328-0.02293559743761.00212255961-0.03944760887320.08307468140081.14119848986-0.002047195657110.81242764208588.697406201945.486564657892.3667181071
232.18684089696-2.144971242992.390415798647.311268851132.481169457237.01487346695-0.2698713478971.07380067040.1858842826140.566839457243-0.312433744311-0.979877873684-0.1064634076491.658152992520.5741877521240.841813635570.02794123815970.0339877800671.167892792080.5909298476970.941352245609116.07730072254.201559252102.147282828
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 293 )
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 431 )
4X-RAY DIFFRACTION4chain 'A' and (resid 432 through 560 )
5X-RAY DIFFRACTION5chain 'A' and (resid 561 through 614 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 193 )
8X-RAY DIFFRACTION8chain 'B' and (resid 194 through 293 )
9X-RAY DIFFRACTION9chain 'B' and (resid 294 through 384 )
10X-RAY DIFFRACTION10chain 'B' and (resid 385 through 431 )
11X-RAY DIFFRACTION11chain 'B' and (resid 432 through 581 )
12X-RAY DIFFRACTION12chain 'B' and (resid 582 through 614 )
13X-RAY DIFFRACTION13chain 'E' and (resid 334 through 369 )
14X-RAY DIFFRACTION14chain 'E' and (resid 370 through 385 )
15X-RAY DIFFRACTION15chain 'E' and (resid 386 through 469 )
16X-RAY DIFFRACTION16chain 'E' and (resid 470 through 494 )
17X-RAY DIFFRACTION17chain 'E' and (resid 495 through 527 )
18X-RAY DIFFRACTION18chain 'F' and (resid 331 through 349 )
19X-RAY DIFFRACTION19chain 'F' and (resid 350 through 374 )
20X-RAY DIFFRACTION20chain 'F' and (resid 375 through 394 )
21X-RAY DIFFRACTION21chain 'F' and (resid 395 through 479 )
22X-RAY DIFFRACTION22chain 'F' and (resid 480 through 506 )
23X-RAY DIFFRACTION23chain 'F' and (resid 507 through 527 )

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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://pdbjlvh1.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