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- PDB-7bep: Crystal structure of the receptor binding domain of SARS-CoV-2 Sp... -

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基本情報

登録情報
データベース: PDB / ID: 7bep
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs
要素
  • COVOX-384 heavy chain
  • COVOX-384 light chain
  • S309 heavy chain
  • S309 light chain
  • Spike glycoprotein
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / germline / V-gene / receptor-binding-domain / spike / neutralisation / protection / glycosylation / valency / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
GLUTAMIC ACID / GLYCINE / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (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: 2.61 Å
データ登録者Zhou, D. / Zhao, Y. / Ren, J. / Stuart, D.
資金援助 英国, 中国, 2件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 中国
引用ジャーナル: Cell / 年: 2021
タイトル: The antigenic anatomy of SARS-CoV-2 receptor binding domain.
著者: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / ...著者: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / Guido C Paesen / Jose Slon-Campos / César López-Camacho / Natasha M Kafai / Adam L Bailey / Rita E Chen / Baoling Ying / Craig Thompson / Jai Bolton / Alex Fyfe / Sunetra Gupta / Tiong Kit Tan / Javier Gilbert-Jaramillo / William James / Michael Knight / Miles W Carroll / Donal Skelly / Christina Dold / Yanchun Peng / Robert Levin / Tao Dong / Andrew J Pollard / Julian C Knight / Paul Klenerman / Nigel Temperton / David R Hall / Mark A Williams / Neil G Paterson / Felicity K R Bertram / C Alistair Siebert / Daniel K Clare / Andrew Howe / Julika Radecke / Yun Song / Alain R Townsend / Kuan-Ying A Huang / Elizabeth E Fry / Juthathip Mongkolsapaya / Michael S Diamond / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and ...Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.
履歴
登録2020年12月24日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年3月3日Provider: repository / タイプ: Initial release
改定 1.12021年4月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22021年4月28日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.32024年1月31日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
E: Spike glycoprotein
A: COVOX-384 heavy chain
B: COVOX-384 light chain
H: S309 heavy chain
L: S309 light chain
C: Spike glycoprotein
D: COVOX-384 heavy chain
F: COVOX-384 light chain
G: S309 heavy chain
I: S309 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)248,15043
ポリマ－243,57810
非ポリマー4,57233
水32418
1
E: Spike glycoprotein
A: COVOX-384 heavy chain
B: COVOX-384 light chain
H: S309 heavy chain
L: S309 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)124,03921
ポリマ－121,7895
非ポリマー2,25016
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Spike glycoprotein
D: COVOX-384 heavy chain
F: COVOX-384 light chain
G: S309 heavy chain
I: S309 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)124,11122
ポリマ－121,7895
非ポリマー2,32117
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)108.760, 113.221, 302.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

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抗体 , 4種, 8分子 ADBFHGLI

#2: 抗体 COVOX-384 heavy chain


分子量: 26089.506 Da / 分子数: 2 / 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)
#3: 抗体 COVOX-384 light chain


分子量: 24526.352 Da / 分子数: 2 / 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 S309 heavy chain


分子量: 24817.738 Da / 分子数: 2 / 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 S309 light chain


分子量: 23204.697 Da / 分子数: 2 / 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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タンパク質 / 糖 , 2種, 4分子 EC

#1: タンパク質 Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


分子量: 23150.891 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#6: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1056.964 Da / 分子数: 2 / 由来タイプ: 合成
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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非ポリマー , 9種, 49分子

#7: 化合物
ChemComp-IMD / IMIDAZOLE / 1H-イミダゾ-ル-3-カチオン


分子量: 69.085 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C3H5N2
#8: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 10 / 由来タイプ: 合成 / 式: Cl
#9: 化合物 ChemComp-GLU / GLUTAMIC ACID / グルタミン酸


タイプ: L-peptide linking / 分子量: 147.129 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C5H9NO4
#10: 化合物
ChemComp-GLY / GLYCINE / グリシン


タイプ: peptide linking / 分子量: 75.067 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C2H5NO2
#11: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O4
#12: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3H8O3
#13: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 2 / 由来タイプ: 天然 / 式: C8H18O5 / コメント: 沈殿剤*YM
#14: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H10O3
#15: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 18 / 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N
Has protein modificationY

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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: 3.94 Å3/Da / 溶媒含有率: 68.8 %
結晶化温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: containing 0.1 M amino acids (Glu, Ala, Gly, Lys, Ser), 0.1 M MES/imidazole/ pH 6.5, 10% (w/v) PEG 20000 and 20% (w/v) PEG MME 550.

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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: Diamond / ビームライン: I03 / 波長: 0.97625 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2020年9月9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: 0.97625 Å / 相対比: 1
反射解像度: 2.61→63 Å / Num. obs: 114437 / % possible obs: 100 % / 冗長度: 13.1 % / Biso Wilson estimate: 79.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.044 / Net I/σ(I): 13.3
反射 シェル解像度: 2.61→2.65 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5600 / CC1/2: 0.344

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解析

ソフトウェア
名称バージョン分類
GDA1.18.1_3865データ収集
PHENIX1.18.1_3865精密化
xia2データ削減
xia2データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7BEK

7bek


解像度: 2.61→62.93 Å / SU ML: 0.5916 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 33.7863
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2408 5577 4.89 %
Rwork0.2025 108563 -
obs0.2043 114140 99.78 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 99.07 Å2
精密化ステップサイクル: LAST / 解像度: 2.61→62.93 Å
タンパク質核酸リガンド溶媒全体
原子数16614 0 294 18 16926
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003217313
X-RAY DIFFRACTIONf_angle_d0.631823516
X-RAY DIFFRACTIONf_chiral_restr0.04462657
X-RAY DIFFRACTIONf_plane_restr0.00442997
X-RAY DIFFRACTIONf_dihedral_angle_d18.11376241
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.640.47311840.44393449X-RAY DIFFRACTION97.24
2.64-2.670.42852100.433559X-RAY DIFFRACTION99.37
2.67-2.70.3891690.42093596X-RAY DIFFRACTION99.26
2.7-2.740.45671950.41363490X-RAY DIFFRACTION99.49
2.74-2.770.43881860.39663573X-RAY DIFFRACTION99.55
2.77-2.810.45361800.42193595X-RAY DIFFRACTION99.81
2.81-2.850.39911710.40163624X-RAY DIFFRACTION99.82
2.85-2.890.3961720.37263588X-RAY DIFFRACTION100
2.89-2.940.37111910.35013572X-RAY DIFFRACTION99.89
2.94-2.990.40331660.33353604X-RAY DIFFRACTION99.92
2.99-3.040.35432320.30843556X-RAY DIFFRACTION100
3.04-3.090.35431880.29413606X-RAY DIFFRACTION99.97
3.09-3.150.34171760.28683596X-RAY DIFFRACTION99.95
3.15-3.220.30861790.2693599X-RAY DIFFRACTION99.97
3.22-3.290.29861850.26573585X-RAY DIFFRACTION100
3.29-3.360.35411850.26833626X-RAY DIFFRACTION100
3.36-3.450.31121830.25573617X-RAY DIFFRACTION99.97
3.45-3.540.26231880.22813606X-RAY DIFFRACTION99.95
3.54-3.650.25332070.21443611X-RAY DIFFRACTION99.97
3.65-3.760.2671840.20913594X-RAY DIFFRACTION99.95
3.76-3.90.21181690.20173662X-RAY DIFFRACTION100
3.9-4.050.23411790.17993634X-RAY DIFFRACTION100
4.05-4.240.19991450.16423678X-RAY DIFFRACTION100
4.24-4.460.18611690.1443639X-RAY DIFFRACTION100
4.46-4.740.16571840.13193691X-RAY DIFFRACTION99.97
4.74-5.110.16831650.13713664X-RAY DIFFRACTION100
5.11-5.620.17811900.14953672X-RAY DIFFRACTION100
5.62-6.430.20082170.1743684X-RAY DIFFRACTION100
6.43-8.10.22032460.17723696X-RAY DIFFRACTION100
8.1-62.930.19031820.15963897X-RAY DIFFRACTION99.25
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)
18.030506857324.00270235298-1.069571046492.21894010466-0.6057777057180.1608288530620.63710567131-1.348625496020.4890304677231.27356187928-1.118483011280.01470418739070.350071483818-1.086037563440.8515585637381.034866757780.153008526067-0.06646711929541.6677314879-0.2266939124370.9963409596938.51209295027-15.970689687836.1727109995
22.592610684071.3666818272.627986400024.952400286653.124724383915.82648285762-0.0096422041309-0.804866929844-0.08464237283480.9320338936550.0994807072215-0.3253291900060.1862439382740.0687850511032-0.03249767318590.7896125389230.1021820233520.03848605034751.31316487386-0.04449809128650.6524791765411.929029772-22.274428322929.3979318866
31.489820405451.862866534211.014746739115.963533337141.704023098616.715154715730.406136692228-0.554866354290.1626019394070.1290162109430.0922582427678-0.1853591764830.2555461948850.158841858785-0.4237729633120.5464055258540.211377096420.05196209624570.9262412207480.019606751680.5832059668497.71182564236-25.224558665916.5546261242
42.23632210754-0.5511721071551.06981289840.0359738210186-0.8791233941843.06911729514-0.148589053538-0.3172591602270.2118346648390.01901454110080.0220960484278-0.316561318111-0.3900109133320.1335056233270.1075681432760.630640768510.1321309628090.08130485668390.961223472146-0.06103724921110.7300436310917.73058810233-19.26490689469.76178573374
54.59626541667-1.84663281990.7455420159535.53054035871-0.5944875750660.880281126853-0.273240335362-0.8200579232440.04458010602760.392812848010.5461013723860.442487886653-0.0130909794363-0.0649852872185-0.09019643306560.688955324030.1087697528320.2329068055530.7161697332540.03588488143620.719724877908-23.1752145168-12.7729796684-2.6988575999
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542.000005884911.999926444251.999975462282.000071121152.000075803771.99995498323-2.76858629289-0.95917958594-9.06163033223-2.292826692821.71396225534.611118116999.00643641619-4.432812993511.098439513731.618969733740.4159832248040.180761726311.67502608319-0.1795849396961.13158308276-13.0231042142-16.58102603347.01656589175

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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