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- PDB-6pxh: Crystal Structure of MERS-CoV S1-NTD bound with G2 Fab -

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基本情報

登録情報
データベース: PDB / ID: 6pxh
タイトルCrystal Structure of MERS-CoV S1-NTD bound with G2 Fab
要素
  • G2 heavy chain
  • G2 light chain
  • MERS-CoV S1-NTD
キーワードIMMUNE SYSTEM/Viral protein / immune system / antibody / fusion glycoprotein / IMMUNE SYSTEM-Viral protein complex
機能・相同性
機能・相同性情報


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / metal ion binding
類似検索 - 分子機能
: / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal ...: / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
DIHYDROFOLIC ACID / Hemin-binding periplasmic protein / Spike glycoprotein
類似検索 - 構成要素
生物種Middle East respiratory syndrome-related coronavirus (ウイルス)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å
データ登録者Wang, N. / McLellan, J.S.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI127521 米国
引用ジャーナル: Cell Rep / 年: 2019
タイトル: Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD.
著者: Nianshuang Wang / Osnat Rosen / Lingshu Wang / Hannah L Turner / Laura J Stevens / Kizzmekia S Corbett / Charles A Bowman / Jesper Pallesen / Wei Shi / Yi Zhang / Kwanyee Leung / Robert N ...著者: Nianshuang Wang / Osnat Rosen / Lingshu Wang / Hannah L Turner / Laura J Stevens / Kizzmekia S Corbett / Charles A Bowman / Jesper Pallesen / Wei Shi / Yi Zhang / Kwanyee Leung / Robert N Kirchdoerfer / Michelle M Becker / Mark R Denison / James D Chappell / Andrew B Ward / Barney S Graham / Jason S McLellan /
要旨: Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the ...Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) protein have been characterized, but much less is known about antibodies targeting non-RBD epitopes. Here, we report the structural and functional characterization of G2, a neutralizing antibody targeting the MERS-CoV S1 N-terminal domain (S1-NTD). Structures of G2 alone and in complex with the MERS-CoV S1-NTD define a site of vulnerability comprising two loops, each of which contain a residue mutated in G2-escape variants. Cell-surface binding studies and in vitro competition experiments demonstrate that G2 strongly disrupts the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4), with the inhibition requiring the native trimeric S conformation. These results advance our understanding of antibody-mediated neutralization of coronaviruses and should facilitate the development of immunotherapeutics and vaccines against MERS-CoV.
履歴
登録2019年7月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年9月25日Provider: repository / タイプ: Initial release
改定 1.12019年10月23日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22019年12月18日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年10月16日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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: MERS-CoV S1-NTD
B: MERS-CoV S1-NTD
C: G2 heavy chain
D: G2 light chain
H: G2 heavy chain
L: G2 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)182,34233
ポリマ－173,0376
非ポリマー9,30527
水12,340685
1
A: MERS-CoV S1-NTD
C: G2 heavy chain
D: G2 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,98618
ポリマ－86,5183
非ポリマー5,46815
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: MERS-CoV S1-NTD
H: G2 heavy chain
L: G2 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)90,35615
ポリマ－86,5183
非ポリマー3,83712
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)85.989, 63.860, 186.778
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 1種, 2分子 AB

#1: タンパク質 MERS-CoV S1-NTD


分子量: 38381.977 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Middle East respiratory syndrome-related coronavirus (ウイルス)
発現宿主: Homo sapiens (ヒト) / 参照: UniProt: V9TWK2, UniProt: K9N5Q8*PLUS

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抗体 , 2種, 4分子 CHDL

#2: 抗体 G2 heavy chain


分子量: 24275.059 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 G2 light chain


分子量: 23861.293 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Homo sapiens (ヒト)

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糖 , 5種, 15分子

#4: 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: 4 / 由来タイプ: 組換発現
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
#5: 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-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
#6: 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)]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: 1397.245 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[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-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]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 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: 1 / 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-Glycam 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
[]{[(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]{}}}}}LINUCSPDB-CARE
#8: 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: 5 / 由来タイプ: 組換発現 / 式: C8H15NO6
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 , 3種, 697分子

#9: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 10 / 由来タイプ: 天然 / 式: SO4
#10: 化合物 ChemComp-DHF / DIHYDROFOLIC ACID / 7,8-ジヒドロ葉酸


分子量: 443.413 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C19H21N7O6
#11: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 685 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.96 Å3/Da / 溶媒含有率: 58.49 %
結晶化温度: 293 K / 手法: 蒸気拡散法
詳細: 0.1 M imidazole pH 6.5, 0.2 M Li2SO4, 19% polyethylene glycol (PEG) 3350, 6% 2-methyl-2,4-pentanediol (MPD)

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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: 19-ID / 波長: 0.9792 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2018年2月22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: 0.9792 Å / 相対比: 1
反射解像度: 2.3→52.713 Å / Num. obs: 88863 / % possible obs: 98.2 % / 冗長度: 3.6 % / Biso Wilson estimate: 35.58 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.067 / Rrim(I) all: 0.132 / Net I/σ(I): 7
反射 シェル解像度: 2.3→2.34 Å / 冗長度: 3.5 % / Rmerge(I) obs: 0.827 / Num. measured all: 15738 / Num. unique obs: 4484 / CC1/2: 0.591 / Rpim(I) all: 0.501 / Rrim(I) all: 0.971 / Net I/σ(I) obs: 1.9 / % possible all: 98

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
Aimless0.6.1データスケーリング
PDB_EXTRACT3.24データ抽出
MOSFLMデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.3→52.71 Å / SU ML: 0.24 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 21.49
Rfactor反射数%反射
Rfree0.2125 4349 4.9 %
Rwork0.1795 --
obs0.1811 88771 97.94 %
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 max: 129.69 Å2 / Biso mean: 44.0596 Å2 / Biso min: 15.43 Å2
精密化ステップサイクル: final / 解像度: 2.3→52.71 Å
タンパク質核酸リガンド溶媒全体
原子数11878 0 607 685 13170
Biso mean--68.52 44.79 -
残基数----1538
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.32610.24611380.2332281598
2.3261-2.35350.30331380.2363273797
2.3535-2.38220.27011230.2396280696
2.3822-2.41240.30461780.2335260094
2.4124-2.44410.25871530.2299279298
2.4441-2.47760.27291480.2237280999
2.4776-2.5130.25951240.227283899
2.513-2.55050.27391630.2308284698
2.5505-2.59030.27221200.2209277398
2.5903-2.63280.28511410.2188282399
2.6328-2.67820.27961500.2156284999
2.6782-2.72690.28111340.2121276599
2.7269-2.77940.25231300.2068290799
2.7794-2.83610.23881610.2042272598
2.8361-2.89770.25651550.1924281596
2.8977-2.96510.2331140.1994273095
2.9651-3.03930.23641270.2023284699
3.0393-3.12150.22551700.1925275899
3.1215-3.21330.22481540.1895287999
3.2133-3.3170.2171440.1894280599
3.317-3.43550.19671490.175285899
3.4355-3.57310.22271380.1605285198
3.5731-3.73560.17081160.1516283297
3.7356-3.93250.19861610.1537273196
3.9325-4.17880.17271750.1487282899
4.1788-4.50130.1471610.1307286199
4.5013-4.9540.15041500.1298286799
4.954-5.67010.18431750.1522280097
5.6701-7.14090.20251290.1842291998
7.1409-52.7130.23411300.2007295797
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)
11.5782-0.4564-0.521.42421.34232.33930.0480.0379-0.058-0.1046-0.01920.00940.03110.02720.01570.2240.0101-0.02640.18510.03990.200784.509-18.32235.021
22.21630.20380.83172.62092.7735.51170.0386-0.23850.46940.03920.1971-0.205-0.31390.4734-0.14320.2497-0.05260.05080.3401-0.13410.347284.3780.41253.702
32.46380.9527-0.5422.44770.32013.54640.0116-0.0027-0.1583-0.10990.1190.0670.2072-0.1069-0.09470.14280.0598-0.03430.1666-0.02440.198780.103-20.46236.955
43.02010.8556-1.30922.09-0.63984.09410.0088-0.30780.0335-0.0321-0.0233-0.26060.04490.3889-0.07550.22420.04230.00460.1962-0.06060.200686.242-16.1738.534
51.5631-0.2792-0.24271.27080.97523.27690.0884-0.0082-0.0242-0.1720.0782-0.0839-0.17380.0741-0.15330.23030.01990.01340.2422-0.05920.249493.001-18.20428.984
63.5872-0.31380.21641.98071.27863.743-0.1016-0.2468-0.45470.13210.1734-0.21860.5688-0.1424-0.23380.32460.0657-0.03440.338-0.07610.363497.197-25.30335.064
72.6290.1243-1.09870.90.52892.77080.0477-0.3973-0.07670.24740.0681-0.288-0.13710.4272-0.25050.2890.008-0.01170.3843-0.09220.271695.105-13.43345.647
82.39140.0401-0.30141.25540.78842.82620.1095-0.2913-0.01360.06310.1406-0.1738-0.01150.3972-0.18610.18940.0136-0.0120.233-0.04880.206890.343-13.35843.728
91.6887-0.03390.12971.70561.13531.95570.1476-0.43120.4940.03020.0312-0.3091-0.2243-0.023-0.10370.2091-0.00310.04160.3509-0.11730.304582.007-0.42650.163
108.2791-4.7494.39165.7853-3.26346.5534-0.0943-0.51150.92560.57950.1393-0.1572-0.8488-0.0015-0.01820.4251-0.04930.16450.4286-0.17450.451978.0165.14659.633
110.4009-0.4897-0.69191.94481.75053.5596-0.02940.1407-0.0052-0.1387-0.11680.1441-0.2044-0.2390.15190.2399-0.0160.01380.4910.03830.2953107.02220.09592.117
121.47730.8623-0.46824.73054.40235.8038-0.07920.0649-0.271-0.13560.2492-0.27950.21530.0242-0.26770.340.0148-0.09150.5666-0.06720.3827109.7081.63673.353
131.4636-0.52550.39352.06030.24053.1505-0.03440.22030.1432-0.05360.02820.1067-0.3356-0.1591-0.00010.2164-0.0032-0.02050.4833-0.01840.2818105.19521.43489.104
141.82870.9095-2.45711.7545-0.18246.54980.07440.25670.13870.13190.17490.0260.2125-0.0105-0.23650.21130.002-0.06360.4747-0.05890.3207112.39714.10499.231
151.1014-0.45620.27961.18611.11612.58480.0170.16080.08840.12360.2004-0.12530.00950.1959-0.23220.2062-0.005-0.02630.4805-0.02460.2493113.84821.674100.889
160.76140.3567-0.32934.0513-1.23293.4067-0.29840.24480.2745-0.13810.2579-0.3134-0.13340.18970.12630.3032-0.0583-0.05490.5654-0.03080.3744120.22525.03195.959
171.5165-1.55970.86182.4702-0.97942.9093-0.0210.21590.0173-0.35160.1188-0.2564-0.05520.5855-0.01260.26980.00260.03630.6557-0.13850.3769119.37513.56684.821
183.335-0.46531.85399.4934-5.99269.67270.19890.7474-0.2892-0.3076-0.0286-0.37530.2310.98340.01570.32820.0327-0.01020.6676-0.16450.4289118.4748.92477.228
190.88110.9607-0.06921.45830.9522.73340.0440.1724-0.31730.11620.114-0.150.48030.4058-0.17140.30090.1147-0.0890.5637-0.09050.289114.9958.45490.82
201.2227-0.38961.0257.08112.2553.6914-0.01780.23680.31080.2137-0.2442-0.1963-0.18550.1380.24060.3129-0.0128-0.0690.5918-0.01310.3878105.91324.83585.489
215.69273.31461.35597.08670.93922.6116-0.19520.9914-0.4669-0.61950.3968-0.53290.18450.0529-0.10030.3994-0.012-0.03240.6638-0.18690.3769107.9680.03668.173
228.7640.45720.37988.53732.09774.91530.19360.1239-0.341-0.04630.1238-0.7769-0.01261.0839-0.20090.4583-0.0632-0.06340.8198-0.18190.4801100.05-7.74960.93
237.46972.03212.2171.85070.7882.5099-0.46570.31080.6022-0.60160.3518-0.0311-0.30530.29090.01310.3181-0.02050.01890.344-0.11350.3794107.736-25.416-4.646
244.0346-1.2372-0.92683.4363-0.12783.3354-0.1036-0.08430.1268-0.00770.249-0.2615-0.17780.1809-0.12440.1764-0.0361-0.01770.1753-0.05720.1956100.925-26.4435.842
253.0205-2.4065.14614.5464-4.213310.0102-0.2406-0.23120.27140.07420.2133-0.3278-0.97750.35050.13780.3386-0.06890.05490.3561-0.06830.3685105.049-20.5155.986
261.3498-1.2171-1.64680.87261.17493.00540.0683-0.29470.1786-0.04230.1446-0.0988-0.11550.4512-0.15410.2368-0.0161-0.04260.228-0.05720.2397112.159-35.335-6.927
271.31050.9548-0.1784.2942.55213.81410.012-0.01960.07590.06240.01810.0887-0.1120.03120.00620.2140.0482-0.04060.1973-0.02170.2943113.872-43.123-19.925
283.04681.94031.62653.92764.45765.32510.0790.2539-0.0806-0.4238-0.1258-0.4481-0.17840.1395-0.03520.40790.04330.00250.29080.07280.2565118.861-42.26-29.76
294.2428-0.5188-0.21576.09721.03864.2822-0.1934-0.3152-0.12940.94590.1909-0.13210.19180.0350.02460.2990.0544-0.02430.28220.01830.252399.269-46.33911.671
302.87051.14280.24986.22562.54752.4396-0.0943-0.0394-0.22740.3204-0.00650.14580.2926-0.1190.07450.23280.02870.01540.19230.01650.200596.042-46.0229.521
313.05070.2967-2.52091.2575-0.2562.6118-0.2177-0.2439-0.24750.0642-0.0576-0.08620.2770.30190.26660.24520.0792-0.02160.27260.02030.2443118.75-55.119-12.198
328.34633.9524-5.02096.7647-2.22675.5981-0.4405-0.1272-0.8424-0.5935-0.1125-0.86740.70160.55270.53840.31580.13630.01310.38770.0650.4318128.945-57.897-18.624
339.6787-1.17823.12781.1712-0.13484.2042-0.16220.1397-0.17320.1930.2778-0.09550.10020.0951-0.13580.30180.01930.02490.20340.02550.2352112.02124.386133.129
345.80482.40612.06315.73111.74766.17360.0680.4825-0.24530.11660.1312-0.61530.23720.5413-0.21080.23410.04610.00160.2755-0.00070.2199119.84926.228123.114
354.3882-0.32545.95642.35121.02058.99310.19790.5532-0.48580.11230.1455-0.05640.7030.698-0.41220.4540.05060.02560.3088-0.00010.3077118.37419.836130.146
361.5204-0.26220.80190.6534-0.07613.58270.02770.0714-0.190.05840.2260.1087-0.26160.0013-0.09250.2408-0.02930.02530.24320.04580.2842113.11532.176126.426
370.93850.82371.23740.94110.50929.548-0.01120.0447-0.12080.2143-0.0163-0.07420.3520.6413-0.16710.26160.0664-0.05440.3247-0.01560.3616126.49325.461145.792
381.9080.45540.84750.4704-0.51683.7508-0.05860.31160.76040.633-0.0778-0.3175-1.42910.01970.12140.7729-0.0804-0.03680.4464-0.08770.6398121.06550.049163.464
391.2138-0.3639-0.49036.60012.66772.97450.07150.11320.463-0.2474-0.0217-0.0873-0.7741-0.1225-0.06810.46630.0123-0.01850.21110.02580.3494118.25141.661151.731
403.2685-0.8382-1.13796.2722.17885.33980.1507-0.08280.29030.2463-0.10960.1346-0.5119-0.0629-0.08210.37740.0075-0.05050.1698-0.0040.2899118.00941.01157.771
414.11390.68281.01698.11880.42854.7684-0.04410.38980.44-0.0660.2553-0.5192-0.86980.1855-0.1390.5209-0.13780.11060.40790.08290.5209123.58950.591120.468
424.34380.29351.49378.5164-0.34864.98960.09990.33270.38430.25490.21270.1206-0.7224-0.2101-0.28370.27350.01120.08170.33410.09280.3544113.5943.544121.397
433.19060.30441.18688.73530.50053.6377-0.07680.31920.4091-0.14020.23080.1402-0.84290.1564-0.21860.379-0.06630.09140.31080.08430.3594118.13445.914120.172
440.64110.0970.48861.8109-0.78653.88840.12330.04290.18280.10490.1079-0.3829-0.94670.6912-0.17620.6103-0.15070.05510.3604-0.08170.5864128.46251.343150.153
452.5567-0.15090.77364.2851-1.11865.83210.2153-0.38770.14490.37390.1635-0.4894-0.79930.6667-0.29190.6569-0.1838-0.04050.5194-0.1880.7175134.15951.962161.179
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:52 )A18 - 52
2X-RAY DIFFRACTION2( CHAIN A AND RESID 53:85 )A53 - 85
3X-RAY DIFFRACTION3( CHAIN A AND RESID 86:136 )A86 - 136
4X-RAY DIFFRACTION4( CHAIN A AND RESID 137:155 )A137 - 155
5X-RAY DIFFRACTION5( CHAIN A AND RESID 156:213 )A156 - 213
6X-RAY DIFFRACTION6( CHAIN A AND RESID 214:235 )A214 - 235
7X-RAY DIFFRACTION7( CHAIN A AND RESID 236:259 )A236 - 259
8X-RAY DIFFRACTION8( CHAIN A AND RESID 260:312 )A260 - 312
9X-RAY DIFFRACTION9( CHAIN A AND RESID 313:327 )A313 - 327
10X-RAY DIFFRACTION10( CHAIN A AND RESID 328:351 )A328 - 351
11X-RAY DIFFRACTION11( CHAIN B AND RESID 18:52 )B18 - 52
12X-RAY DIFFRACTION12( CHAIN B AND RESID 53:85 )B53 - 85
13X-RAY DIFFRACTION13( CHAIN B AND RESID 86:155 )B86 - 155
14X-RAY DIFFRACTION14( CHAIN B AND RESID 156:178 )B156 - 178
15X-RAY DIFFRACTION15( CHAIN B AND RESID 179:213 )B179 - 213
16X-RAY DIFFRACTION16( CHAIN B AND RESID 214:235 )B214 - 235
17X-RAY DIFFRACTION17( CHAIN B AND RESID 236:259 )B236 - 259
18X-RAY DIFFRACTION18( CHAIN B AND RESID 260:278 )B260 - 278
19X-RAY DIFFRACTION19( CHAIN B AND RESID 279:300 )B279 - 300
20X-RAY DIFFRACTION20( CHAIN B AND RESID 301:318 )B301 - 318
21X-RAY DIFFRACTION21( CHAIN B AND RESID 319:342 )B319 - 342
22X-RAY DIFFRACTION22( CHAIN B AND RESID 343:358 )B343 - 358
23X-RAY DIFFRACTION23( CHAIN C AND RESID 1:17 )C1 - 17
24X-RAY DIFFRACTION24( CHAIN C AND RESID 18:59 )C18 - 59
25X-RAY DIFFRACTION25( CHAIN C AND RESID 60:82 )C60 - 82
26X-RAY DIFFRACTION26( CHAIN C AND RESID 83:145 )C83 - 145
27X-RAY DIFFRACTION27( CHAIN C AND RESID 146:202 )C146 - 202
28X-RAY DIFFRACTION28( CHAIN C AND RESID 203:215 )C203 - 215
29X-RAY DIFFRACTION29( CHAIN D AND RESID 1:48 )D1 - 48
30X-RAY DIFFRACTION30( CHAIN D AND RESID 49:101 )D49 - 101
31X-RAY DIFFRACTION31( CHAIN D AND RESID 102:174 )D102 - 174
32X-RAY DIFFRACTION32( CHAIN D AND RESID 175:214 )D175 - 214
33X-RAY DIFFRACTION33( CHAIN H AND RESID 1:32 )H1 - 32
34X-RAY DIFFRACTION34( CHAIN H AND RESID 33:66 )H33 - 66
35X-RAY DIFFRACTION35( CHAIN H AND RESID 67:87 )H67 - 87
36X-RAY DIFFRACTION36( CHAIN H AND RESID 88:106 )H88 - 106
37X-RAY DIFFRACTION37( CHAIN H AND RESID 107:119 )H107 - 119
38X-RAY DIFFRACTION38( CHAIN H AND RESID 120:134 )H120 - 134
39X-RAY DIFFRACTION39( CHAIN H AND RESID 135:168 )H135 - 168
40X-RAY DIFFRACTION40( CHAIN H AND RESID 169:215 )H169 - 215
41X-RAY DIFFRACTION41( CHAIN L AND RESID 1:25 )L1 - 25
42X-RAY DIFFRACTION42( CHAIN L AND RESID 26:61 )L26 - 61
43X-RAY DIFFRACTION43( CHAIN L AND RESID 62:101 )L62 - 101
44X-RAY DIFFRACTION44( CHAIN L AND RESID 102:174 )L102 - 174
45X-RAY DIFFRACTION45( CHAIN L AND RESID 175:214 )L175 - 214

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万見について

-
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