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Structure paper

タイトルPrinciples of human pre-60 biogenesis.
ジャーナル・号・ページScience, Vol. 381, Issue 6653, Page eadh3892, Year 2023
掲載日2023年7月7日
著者Arnaud Vanden Broeck / Sebastian Klinge /
PubMed 要旨During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an ...During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.
リンクScience / PubMed:37410842
手法EM (単粒子)
解像度2.33 - 3.75 Å
構造データ

EMDB-29104: Human nucleolar pre-60S ribosomal subunit (State A1) - Overall map
手法: EM (単粒子) / 解像度: 3.0 Å

EMDB-29105: Human nucleolar pre-60S ribosomal subunit (State A2) - Overall map
手法: EM (単粒子) / 解像度: 2.85 Å

EMDB-29106: Human nucleolar pre-60S ribosomal subunit (State B1) - Overall map
手法: EM (単粒子) / 解像度: 3.09 Å

EMDB-29107: Human nucleolar pre-60S ribosomal subunit (State B2) - Overall map
手法: EM (単粒子) / 解像度: 3.06 Å

EMDB-29108: Human nucleolar pre-60S ribosomal subunit (State C1) - Overall map
手法: EM (単粒子) / 解像度: 2.98 Å

EMDB-29109: Human nucleolar pre-60S ribosomal subunit (State C2) - Overall map
手法: EM (単粒子) / 解像度: 3.03 Å

EMDB-29110: Human nucleolar pre-60S ribosomal subunit (State D1) - Overall map
手法: EM (単粒子) / 解像度: 2.6 Å

EMDB-29111: Human nucleolar pre-60S ribosomal subunit (State D2) - Overall map
手法: EM (単粒子) / 解像度: 2.63 Å

EMDB-29112: Human nucleolar pre-60S ribosomal subunit (State E) - Overall map
手法: EM (単粒子) / 解像度: 2.75 Å

EMDB-29113: Human nucleolar pre-60S ribosomal subunit (State F) - Overall map
手法: EM (単粒子) / 解像度: 2.84 Å

EMDB-29114: Human nucleolar pre-60S ribosomal subunit (State G) - Overall map
手法: EM (単粒子) / 解像度: 3.19 Å

EMDB-29115: Human nucleolar pre-60S ribosomal subunit (State H) - Overall map
手法: EM (単粒子) / 解像度: 2.96 Å

EMDB-29116: Human nuclear pre-60S ribosomal subunit (State I1) - Overall map
手法: EM (単粒子) / 解像度: 2.71 Å

EMDB-29117: Human nuclear pre-60S ribosomal subunit (State I2) - Overall map
手法: EM (単粒子) / 解像度: 2.53 Å

EMDB-29118: Human nuclear pre-60S ribosomal subunit (State I3) - Overall map
手法: EM (単粒子) / 解像度: 3.05 Å

EMDB-29119: Human nuclear pre-60S ribosomal subunit (State J1) - Overall map
手法: EM (単粒子) / 解像度: 2.76 Å

EMDB-29120: Human nuclear pre-60S ribosomal subunit (State J2) - Overall map
手法: EM (単粒子) / 解像度: 2.66 Å

EMDB-29121: Human nuclear pre-60S ribosomal subunit (State J3) - Overall map
手法: EM (単粒子) / 解像度: 2.99 Å

EMDB-29122: Human nuclear pre-60S ribosomal subunit (State K1) - Overall map
手法: EM (単粒子) / 解像度: 2.84 Å

EMDB-29123: Human nuclear pre-60S ribosomal subunit (State K2) - Overall map
手法: EM (単粒子) / 解像度: 2.64 Å

EMDB-29124: Human nuclear pre-60S ribosomal subunit (State K3) - Overall map
手法: EM (単粒子) / 解像度: 3.05 Å

EMDB-29125: Human nuclear pre-60S ribosomal subunit (State L1) - Overall map
手法: EM (単粒子) / 解像度: 2.72 Å

EMDB-29126: Human nuclear pre-60S ribosomal subunit (State L2) - Overall map
手法: EM (単粒子) / 解像度: 2.49 Å

EMDB-29127: Human nuclear pre-60S ribosomal subunit (State L3) - Overall map
手法: EM (単粒子) / 解像度: 2.83 Å

EMDB-29128: Human nucleolar pre-60S ribosomal subunit (States A1,A2 & B1,B2 combined) - Domain VI root helix focused map
手法: EM (単粒子) / 解像度: 3.46 Å

EMDB-29129: Human nucleolar pre-60S ribosomal subunit (States A1,A2 & B1,B2 combined) - Domain VI helix 96 focused map
手法: EM (単粒子) / 解像度: 3.07 Å

EMDB-29130: Human nucleolar pre-60S ribosomal subunit (State A1) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.87 Å

EMDB-29131: Human nucleolar pre-60S ribosomal subunit (State A1) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.87 Å

EMDB-29132: Human nucleolar pre-60S ribosomal subunit (State A2) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.73 Å

EMDB-29133: Human nucleolar pre-60S ribosomal subunit (State A2) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.73 Å

EMDB-29134: Human nucleolar pre-60S ribosomal subunit (States A1,A2 combined) - Domain VI focused map
手法: EM (単粒子) / 解像度: 3.05 Å

EMDB-29135: Human nucleolar pre-60S ribosomal subunit (States A1,A2 combined) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 2.87 Å

EMDB-29136: Human nucleolar pre-60S ribosomal subunit (State B1) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.93 Å

EMDB-29137: Human nucleolar pre-60S ribosomal subunit (State B1) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.94 Å

EMDB-29138: Human nucleolar pre-60S ribosomal subunit (State B2) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.87 Å

EMDB-29139: Human nucleolar pre-60S ribosomal subunit (State B2) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.89 Å

EMDB-29140: Human nucleolar pre-60S ribosomal subunit (States B1,B2 combined) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 3.08 Å

EMDB-29141: Human nucleolar pre-60S ribosomal subunit (States B1,B2 combined) - Domain VI focused map
手法: EM (単粒子) / 解像度: 3.31 Å

EMDB-29142: Human nucleolar pre-60S ribosomal subunit (States B1,B2 combined) - Domain V & GTPB4 focused map
手法: EM (単粒子) / 解像度: 3.09 Å

EMDB-29143: Human nucleolar pre-60S ribosomal subunit (State C1) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.83 Å

EMDB-29144: Human nucleolar pre-60S ribosomal subunit (State C1) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.85 Å

EMDB-29145: Human nucleolar pre-60S ribosomal subunit (State C2) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.82 Å

EMDB-29146: Human nucleolar pre-60S ribosomal subunit (State C2) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.86 Å

EMDB-29147: Human nucleolar pre-60S ribosomal subunit (States C1,C2 combined) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 3.02 Å

EMDB-29148: Human nucleolar pre-60S ribosomal subunit (States C1,C2 combined) - Domains V-VI focused map
手法: EM (単粒子) / 解像度: 2.77 Å

EMDB-29149: Human nucleolar pre-60S ribosomal subunit (States C1,C2 combined) - DDX54 focused map
手法: EM (単粒子) / 解像度: 2.97 Å

EMDB-29150: Human nucleolar pre-60S ribosomal subunit (States C1,C2 combined) - L1 stalk focused map
手法: EM (単粒子) / 解像度: 3.61 Å

EMDB-29151: Human nucleolar pre-60S ribosomal subunit (States A-F combined) - uL15 focused map
手法: EM (単粒子) / 解像度: 2.78 Å

EMDB-29152: Human nucleolar pre-60S ribosomal subunit (State D1) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.48 Å

EMDB-29153: Human nucleolar pre-60S ribosomal subunit (State D1), Domain II focused map
手法: EM (単粒子) / 解像度: 2.46 Å

EMDB-29154: Human nucleolar pre-60S ribosomal subunit (State D1) - Domains V-VI focused map
手法: EM (単粒子) / 解像度: 2.5 Å

EMDB-29155: Human nucleolar pre-60S ribosomal subunit (State D1) - GNL3 focused map
手法: EM (単粒子) / 解像度: 2.67 Å

EMDB-29156: Human nucleolar pre-60S ribosomal subunit (State D2) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.49 Å

EMDB-29157: Human nucleolar pre-60S ribosomal subunit (State D2) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.5 Å

EMDB-29158: Human nucleolar pre-60S ribosomal subunit (State D2) - Domains V-VI focused map
手法: EM (単粒子) / 解像度: 2.6 Å

EMDB-29159: Human nucleolar pre-60S ribosomal subunit (States D1,D2 combined) - RRS1 focused map
手法: EM (単粒子) / 解像度: 2.33 Å

EMDB-29160: Human nucleolar pre-60S ribosomal subunit (States D1,D2 combined) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 2.62 Å

EMDB-29161: Human nucleolar pre-60S ribosomal subunit (States D1,D2 combined) - Inter-subunit side focused map
手法: EM (単粒子) / 解像度: 2.67 Å

EMDB-29162: Human nucleolar pre-60S ribosomal subunit (States D1,D2 combined) - DDX54 focused map
手法: EM (単粒子) / 解像度: 2.59 Å

EMDB-29163: Human nucleolar pre-60S ribosomal subunit (States D1,D2 combined) - L1 stalk focused map
手法: EM (単粒子) / 解像度: 2.78 Å

EMDB-29164: Human nucleolar pre-60S ribosomal subunit (States D1,D2 combined) - NOC3L & FTSJ3 focused map
手法: EM (単粒子) / 解像度: 3.19 Å

EMDB-29165: Human nucleolar pre-60S ribosomal subunit (States D1,D2 combined) - NOC2L focused map
手法: EM (単粒子) / 解像度: 3.08 Å

EMDB-29166: Human nucleolar pre-60S ribosomal subunit (State E) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.58 Å

EMDB-29167: Human nucleolar pre-60S ribosomal subunit (State E) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.63 Å

EMDB-29168: Human nucleolar pre-60S ribosomal subunit (State E) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 2.97 Å

EMDB-29169: Human nucleolar pre-60S ribosomal subunit (State F) - PeBoW-WDR55 focused map
手法: EM (単粒子) / 解像度: 3.04 Å

EMDB-29170: Human nucleolar pre-60S ribosomal subunit (State F) - PeBoW complex focused map
手法: EM (単粒子) / 解像度: 3.06 Å

EMDB-29171: Human nucleolar pre-60S ribosomal subunit (State F) - WDR55 focused map
手法: EM (単粒子) / 解像度: 3.5 Å

EMDB-29173: Human nucleolar pre-60S ribosomal subunit (State F) - Domain III focused map
手法: EM (単粒子) / 解像度: 2.84 Å

EMDB-29174: Human nucleolar pre-60S ribosomal subunit (State F) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 2.91 Å

EMDB-29175: Human nucleolar pre-60S ribosomal subunit (State F) - Domain I focused map
手法: EM (単粒子) / 解像度: 2.71 Å

EMDB-29176: Human nucleolar pre-60S ribosomal subunit (State F) - Domain II focused map
手法: EM (単粒子) / 解像度: 2.68 Å

EMDB-29177: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - Inter-subunit side focused map
手法: EM (単粒子) / 解像度: 2.86 Å

EMDB-29178: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - DDX54 focused map
手法: EM (単粒子) / 解像度: 2.79 Å

EMDB-29179: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - L1 stalk focused map
手法: EM (単粒子) / 解像度: 2.92 Å

EMDB-29180: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - NOC3L focused map
手法: EM (単粒子) / 解像度: 3.07 Å

EMDB-29181: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - Domain VI focused map
手法: EM (単粒子) / 解像度: 2.58 Å

EMDB-29182: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - DDX18 focused map
手法: EM (単粒子) / 解像度: 2.56 Å

EMDB-29183: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - Domain V focused map
手法: EM (単粒子) / 解像度: 2.58 Å

EMDB-29184: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - RRS1 focused map
手法: EM (単粒子) / 解像度: 2.61 Å

EMDB-29185: Human nucleolar pre-60S ribosomal subunit (States E,F combined) - NOC2L focused map
手法: EM (単粒子) / 解像度: 3.75 Å

EMDB-29186: Human nucleolar pre-60S ribosomal subunit (State G) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 3.35 Å

EMDB-29187: Human nucleolar pre-60S ribosomal subunit (State G) - Domain I focused map
手法: EM (単粒子) / 解像度: 3.06 Å

EMDB-29188: Human nucleolar pre-60S ribosomal subunit (State G) - Domain II focused map
手法: EM (単粒子) / 解像度: 3.07 Å

EMDB-29189: Human nucleolar pre-60S ribosomal subunit (State G) - Domains V-VI focused map
手法: EM (単粒子) / 解像度: 3.13 Å

EMDB-29192: Human nucleolar pre-60S ribosomal subunit (State G) - Domain IV focused map
手法: EM (単粒子) / 解像度: 3.1 Å

EMDB-29193: Human nucleolar pre-60S ribosomal subunit (State H) - 5S RNP focused map
手法: EM (単粒子) / 解像度: 2.88 Å

EMDB-29194: Human nucleolar pre-60S ribosomal subunit (State H) - Domains V-VI focused map
手法: EM (単粒子) / 解像度: 3.0 Å

EMDB-29195: Human nuclear pre-60S ribosomal subunit (States I1,I2,I3 combined) - Central protuberance focused map
手法: EM (単粒子) / 解像度: 2.67 Å

EMDB-29196: Human nuclear pre-60S ribosomal subunit (States I1,I2,I3 combined) - TEX10 focused map
手法: EM (単粒子) / 解像度: 2.99 Å

EMDB-29197: Human nuclear pre-60S ribosomal subunit (States I1,I2,I3 combined) - Rix1 complex focused map
手法: EM (単粒子) / 解像度: 2.87 Å

EMDB-29198: Human nuclear pre-60S ribosomal subunit (States I1,J1,K1,L1 combined) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 2.47 Å

EMDB-29199: Human nuclear pre-60S ribosomal subunit (States I2,J2,K2,L2 combined) - ITS2 module focused map
手法: EM (単粒子) / 解像度: 2.39 Å

EMDB-29200: Human nuclear pre-60S ribosomal subunit (States J1,J2,J3 combined) - Central protuberance focused map
手法: EM (単粒子) / 解像度: 2.52 Å

EMDB-29201: Human nuclear pre-60S ribosomal subunit (States J1,J2,J3 combined) - Domain V focused map
手法: EM (単粒子) / 解像度: 2.59 Å

EMDB-29202: Human nuclear pre-60S ribosomal subunit (States K1,K2,K3 combined) - Central protuberance focused map
手法: EM (単粒子) / 解像度: 2.51 Å

EMDB-29204: Human nuclear pre-60S ribosomal subunit (States K1,K2,K3 combined) - Domain V focused map
手法: EM (単粒子) / 解像度: 2.58 Å

EMDB-29205: Human nuclear pre-60S ribosomal subunit (States L1,L2,L3 combined) - Central protuberance focused map
手法: EM (単粒子) / 解像度: 2.45 Å

EMDB-29206: Human nuclear pre-60S ribosomal subunit (States L1,L2,L3 combined) - Domain V focused map
手法: EM (単粒子) / 解像度: 2.52 Å

EMDB-29252: Human nucleolar pre-60S ribosomal subunit (State A1) - Composite map
PDB-8fkp: Human nucleolar pre-60S ribosomal subunit (State A1)
手法: EM (単粒子) / 解像度: 2.85 Å

EMDB-29253: Human nucleolar pre-60S ribosomal subunit (State A2) - Composite map
PDB-8fkq: Human nucleolar pre-60S ribosomal subunit (State A2)
手法: EM (単粒子) / 解像度: 2.76 Å

EMDB-29254: Human nucleolar pre-60S ribosomal subunit (State B1) - Composite map
PDB-8fkr: Human nucleolar pre-60S ribosomal subunit (State B1)
手法: EM (単粒子) / 解像度: 2.89 Å

EMDB-29255: Human nucleolar pre-60S ribosomal subunit (State B2) - Composite map
PDB-8fks: Human nucleolar pre-60S ribosomal subunit (State B2)
手法: EM (単粒子) / 解像度: 2.88 Å

EMDB-29256: Human nucleolar pre-60S ribosomal subunit (State C1) - Composite map
PDB-8fkt: Human nucleolar pre-60S ribosomal subunit (State C1)
手法: EM (単粒子) / 解像度: 2.81 Å

EMDB-29257: Human nucleolar pre-60S ribosomal subunit (State C2) - Composite map
PDB-8fku: Human nucleolar pre-60S ribosomal subunit (State C2)
手法: EM (単粒子) / 解像度: 2.82 Å

EMDB-29258: Human nucleolar pre-60S ribosomal subunit (State D1) - Composite map
PDB-8fkv: Human nucleolar pre-60S ribosomal subunit (State D1)
手法: EM (単粒子) / 解像度: 2.47 Å

EMDB-29259: Human nucleolar pre-60S ribosomal subunit (State D2) - Composite map
PDB-8fkw: Human nucleolar pre-60S ribosomal subunit (State D2)
手法: EM (単粒子) / 解像度: 2.5 Å

EMDB-29260: Human nucleolar pre-60S ribosomal subunit (State E) - Composite map
PDB-8fkx: Human nucleolar pre-60S ribosomal subunit (State E)
手法: EM (単粒子) / 解像度: 2.59 Å

EMDB-29261: Human nucleolar pre-60S ribosomal subunit (State F) - Composite map
PDB-8fky: Human nucleolar pre-60S ribosomal subunit (State F)
手法: EM (単粒子) / 解像度: 2.67 Å

EMDB-29262: Human nucleolar pre-60S ribosomal subunit (State G) - Composite map
PDB-8fkz: Human nucleolar pre-60S ribosomal subunit (State G)
手法: EM (単粒子) / 解像度: 3.04 Å

EMDB-29263: Human nucleolar pre-60S ribosomal subunit (State H) - Composite map
PDB-8fl0: Human nucleolar pre-60S ribosomal subunit (State H)
手法: EM (単粒子) / 解像度: 2.91 Å

EMDB-29265: Human nuclear pre-60S ribosomal subunit (State I1) - Composite map
PDB-8fl2: Human nuclear pre-60S ribosomal subunit (State I1)
手法: EM (単粒子) / 解像度: 2.67 Å

EMDB-29266: Human nuclear pre-60S ribosomal subunit (State I2) - Composite map
PDB-8fl3: Human nuclear pre-60S ribosomal subunit (State I2)
手法: EM (単粒子) / 解像度: 2.53 Å

EMDB-29267: Human nuclear pre-60S ribosomal subunit (State I3) - Composite map
PDB-8fl4: Human nuclear pre-60S ribosomal subunit (State I3)
手法: EM (単粒子) / 解像度: 2.89 Å

EMDB-29268: Human nuclear pre-60S ribosomal subunit (State J1) - Composite map
PDB-8fl6: Human nuclear pre-60S ribosomal subunit (State J1)
手法: EM (単粒子) / 解像度: 2.62 Å

EMDB-29269: Human nuclear pre-60S ribosomal subunit (State J2) - Composite map
PDB-8fl7: Human nuclear pre-60S ribosomal subunit (State J2)
手法: EM (単粒子) / 解像度: 2.55 Å

EMDB-29271: Human nuclear pre-60S ribosomal subunit (State J3) - Composite map
PDB-8fl9: Human nuclear pre-60S ribosomal subunit (State J3)
手法: EM (単粒子) / 解像度: 2.75 Å

EMDB-29272: Human nuclear pre-60S ribosomal subunit (State K1) - Composite map
PDB-8fla: Human nuclear pre-60S ribosomal subunit (State K1)
手法: EM (単粒子) / 解像度: 2.63 Å

EMDB-29273: Human nuclear pre-60S ribosomal subunit (State K2) - Composite map
PDB-8flb: Human nuclear pre-60S ribosomal subunit (State K2)
手法: EM (単粒子) / 解像度: 2.55 Å

EMDB-29274: Human nuclear pre-60S ribosomal subunit (State K3) - Composite map
PDB-8flc: Human nuclear pre-60S ribosomal subunit (State K3)
手法: EM (単粒子) / 解像度: 2.76 Å

EMDB-29275: Human nuclear pre-60S ribosomal subunit (State L1) - Composite map
PDB-8fld: Human nuclear pre-60S ribosomal subunit (State L1)
手法: EM (単粒子) / 解像度: 2.58 Å

EMDB-29276: Human nuclear pre-60S ribosomal subunit (State L2) - Composite map
PDB-8fle: Human nuclear pre-60S ribosomal subunit (State L2)
手法: EM (単粒子) / 解像度: 2.48 Å

EMDB-29277: Human nuclear pre-60S ribosomal subunit (State L3) - Composite map
PDB-8flf: Human nuclear pre-60S ribosomal subunit (State L3)
手法: EM (単粒子) / 解像度: 2.65 Å

化合物

ChemComp-MG:
Unknown entry / マグネシウムジカチオン

ChemComp-ZN:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP / GDP, エネルギー貯蔵分子*YM

ChemComp-K:
Unknown entry / カリウムカチオン

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP / ADP, エネルギー貯蔵分子*YM

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP / GTP, エネルギー貯蔵分子*YM

由来
  • homo sapiens (ヒト)
  • human (ヒト)
キーワードRIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / Nucleoprotein complex

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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

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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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万見文献

EMDB/PDB/SASBDBから引用されている文献のデータベース

  • EMDB/PDB/SASBDBのエントリから引用されている文献のデータベースです
  • Pubmedのデータを利用しています

関連情報:EMDB / PDB / SASBDB / 万見 (Yorodumi) / EMN文献 / 新しいEM Navigatorと万見の変更点

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