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- PDB-8uwa: VH1-18 QxxV class antibody 09-1B12 bound to A/Perth/16/2009 H3N2 ... -

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基本情報

登録情報
データベース: PDB / ID: 8uwa
タイトルVH1-18 QxxV class antibody 09-1B12 bound to A/Perth/16/2009 H3N2 hemagglutinin
要素
  • 09-1B12 heavy chain
  • 09-1B12 light chain
  • Hemagglutinin
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / antibody / stem / influenza / hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
類似検索 - 分子機能
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
類似検索 - ドメイン・相同性
生物種Homo sapiens (ヒト)
Influenza A virus (A型インフルエンザウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.02 Å
データ登録者Maurer, D.P.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 米国
引用ジャーナル: Immunity / 年: 2024
タイトル: Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses.
著者: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca ...著者: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca L Ursin / Mya Vu / Kathrin H Kirsch / Thavaleak Prum / Victoria C Rosado / Thalia Bracamonte-Moreno / Vintus Okonkwo / Julia Bals / Caitlin McCarthy / Usha Nair / Masaru Kanekiyo / Andrew B Ward / Aaron G Schmidt / Facundo D Batista / Daniel Lingwood /
要旨: Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, ...Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
履歴
登録2023年11月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年5月8日Provider: repository / タイプ: Initial release
改定 1.12024年5月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
D: 09-1B12 light chain
E: 09-1B12 light chain
G: 09-1B12 light chain
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
F: 09-1B12 heavy chain
H: 09-1B12 heavy chain
U: 09-1B12 heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)338,42837
ポリマ－321,5649
非ポリマー16,86428
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area50960 Å2
ΔGint131 kcal/mol
Surface area125050 Å2
手法PISA
単位格子
Length a, b, c (Å)158.040, 158.040, 417.206
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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要素

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タンパク質 , 1種, 3分子 ABC

#2: タンパク質 Hemagglutinin


分子量: 57695.562 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (A/Perth/16/2009(H3N2)) (A型インフルエンザウイルス)
株: Influenza A virus (A/Perth/16/2009(H3N2)) / 遺伝子: HA / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: C6KNH7

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抗体 , 2種, 6分子 DEGFHU

#1: 抗体 09-1B12 light chain


分子量: 23881.535 Da / 分子数: 3 / 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 09-1B12 heavy chain


分子量: 25610.791 Da / 分子数: 3 / 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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糖 , 8種, 28分子

#4: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(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: 748.682 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/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)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(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: 1235.105 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]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: 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: 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
#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: 6 / 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: 多糖 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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: 3 / 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
#10: 多糖 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(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: 1072.964 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#11: 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: 9 / 由来タイプ: 合成 / 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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詳細

研究の焦点であるリガンドがあるかN

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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: 4.68 Å3/Da / 溶媒含有率: 73.7 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 15% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% w/v PEG10000

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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: 0.97918 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年6月14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: 0.97918 Å / 相対比: 1
反射解像度: 4.02→50.21 Å / Num. obs: 51070 / % possible obs: 99.69 % / 冗長度: 20.5 % / Biso Wilson estimate: 106.79 Å2 / CC1/2: 0.995 / Net I/σ(I): 7
反射 シェル解像度: 4.021→4.164 Å / Num. unique obs: 4940 / CC1/2: 0.654 / CC star: 0.889

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
XDS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: PDB entries 5KVN & 5K9Q

5kvn

5k9q


解像度: 4.02→50.21 Å / SU ML: 0.4841 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.5167
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2544 2003 3.92 %
Rwork0.2297 49046 -
obs0.2307 51049 99.77 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 113.41 Å2
精密化ステップサイクル: LAST / 解像度: 4.02→50.21 Å
タンパク質核酸リガンド溶媒全体
原子数21861 0 1120 0 22981
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004623454
X-RAY DIFFRACTIONf_angle_d0.721231836
X-RAY DIFFRACTIONf_chiral_restr0.06323797
X-RAY DIFFRACTIONf_plane_restr0.00583991
X-RAY DIFFRACTIONf_dihedral_angle_d13.52583756
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.02-4.120.37291360.30093329X-RAY DIFFRACTION97.33
4.12-4.230.29611420.28063460X-RAY DIFFRACTION99.94
4.23-4.360.2761390.25183472X-RAY DIFFRACTION100
4.36-4.50.26761420.24553481X-RAY DIFFRACTION100
4.5-4.660.22441380.23273458X-RAY DIFFRACTION100
4.66-4.840.27351430.22473469X-RAY DIFFRACTION100
4.84-5.060.30011420.22143478X-RAY DIFFRACTION100
5.06-5.330.21881450.21633469X-RAY DIFFRACTION99.97
5.33-5.670.26521390.22953531X-RAY DIFFRACTION100
5.67-6.10.28081440.2373508X-RAY DIFFRACTION100
6.1-6.710.25061440.25153510X-RAY DIFFRACTION100
6.71-7.680.28311470.2313547X-RAY DIFFRACTION100
7.69-9.670.20021470.1913582X-RAY DIFFRACTION99.97
9.67-50.210.22011550.21033752X-RAY DIFFRACTION99.54
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)
11.420737103860.1551610325380.5983785329610.1358804737610.3122618783220.5004157489180.2496566426920.1121671218390.01092888686730.027593411823-0.6381594063630.3195458176560.689985009559-0.07108752922580.0002134877291031.08542052348-0.0472788279257-0.05563778172930.9005810450140.05941696922650.91350805078451.684-71.486-28.528
20.795055722384-0.618716986060.1670054994980.9044441740880.4686514350010.754497883735-0.002931126845240.06480752379790.362452049323-0.3074496144630.09433577887940.0863320325776-0.485659265255-0.2215054863220.0001612392758080.7370371694310.0387435755911-0.225624476920.9876272183290.1269547648141.0316936066955.501-62.826-24.993
31.4580016495-0.659763583403-0.7974882558870.1055699888560.04063387159071.505770247470.04349112110910.3988463487750.149523961403-0.00518257986694-0.180317616817-0.013809270398-0.290565959734-0.257627175885-0.000161187855880.7705056996870.015102082264-0.03491531669840.696706338543-0.0335878011381.0436711658864.635-73.521-24.819
42.283988476130.454008756255-0.2551576844521.447780592160.8431225704662.48688692478-0.319488047556-0.0571273768569-0.267671360609-0.1502620283230.1442637059570.01335145451110.4295327495740.3076646787656.40210796871E-61.01896546553-0.01222839685880.01866036174530.9346151759-0.02721623455690.88369087774682.588-92.312-24.199
50.7248734795690.988438976799-0.3430230819361.34297549383-0.7023043706370.6695966134710.009947779913510.96189151198-0.115555167065-0.671551917155-0.347655564212-0.0177195575394-0.0629602517663-0.4350597962880.000847810531031.202694302940.022727946067-0.02952942648281.363573761540.07378939255010.997386175951-4.878-90.021-33.176
60.7755718146060.395158981161-0.2042203259380.108397353223-0.06546223504070.9866021106790.2340290163320.706004989544-0.0290170121001-0.6979564999250.1203243045390.235324395124-0.2095292028610.4819823711990.004370013015251.1477590043-0.05241604430130.2325683320121.006858791720.3177051712211.11338662461.146-96.64-31.052
71.143660040310.408451906513-0.3571223332350.37329000914-0.5330840540450.8299027038770.7574537502650.376448815777-0.339220010079-0.264941152055-0.546500316185-1.02191977091-0.278137332335-0.5795473883930.001380883722581.07773183057-0.10008052539-0.04416891851740.971171498603-0.002505255679891.13253721208-4-96.453-30.086
80.5026962656410.5710529127560.1132794591560.467507162470.04775373339110.00704292987425-0.261106679597-0.494812207162-1.4307376881-0.6576651151070.0836374620727-1.14606925408-0.614637507135-0.8239760459320.0005795647480790.975558261916-0.1063081046410.0943700220661.09069656540.02420689314361.15397814924-12.718-97.085-33.539
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271.664806641250.3484727432270.06295677460260.362251033482-0.3967547801710.730704377284-0.1331378790480.3340834786180.1492561176460.00109908668140.1068170043710.0895493395699-0.4405852238080.0664146453652-0.000207337566511.10766774721-0.113328438499-0.03401859352561.204480662770.04742801818841.0645132509529.311-49.904-22.116
280.2131074334830.210723309196-0.09270050575320.4509146043260.2429446710550.302477553571-0.1134399466940.195666109991.208690879440.339246238648-0.6509352896240.563183144208-0.519381992272-0.2432088301760.001468605266491.571148667840.01734914577540.07762089907511.45095051822-0.01500323276351.5311758231730.441-49.1118.624
290.809375951168-0.0181625064614-0.4885404642010.1996381712241.366276530971.74780425617-0.0754513818689-0.3199633094010.1432228887570.1027260289540.02228396890130.07903372159610.3716765519380.04830696040890.000143917836370.933816749537-0.0237910769603-0.03383733054370.938614907813-0.03544663922941.0592959969325.737-58.831-7.766
301.981670330481.428107612790.03732213632191.173188552560.0418603162511.719551521120.0614774712744-0.25485379578-0.1412208694230.558119758698-0.0294363004622-0.120988435303-0.166236821436-0.0312109335114.46726253838E-50.989351628537-0.08565997872550.04147864409081.018151310510.05588049829581.08728818389-7.807-94.098-8.002
311.24052119471-0.0955956467436-0.5772429927161.63280131114-0.7724269466760.7304102078980.06767400695150.1211140222190.135478976244-0.500751450026-0.1357614007830.413359935972-0.00689703539515-0.323586952701-0.7092082505281.032859299370.0473573388465-0.02231566402331.04738076094-0.02624047155730.852873298253-23.135-108.598-21.294
320.1422146810450.261636191848-0.1937498603430.25727647548-0.2983979704380.3573923923830.1333855692940.525597139879-0.5843348258050.3405218716370.4095537470030.8846427515730.720024739801-0.416732112601-0.001400349110981.47918663824-0.212305112342-0.01526627311541.31932632390.1440378113231.0847841832-36.732-121.35-19.803
330.368764095166-0.7698278412860.1165016771141.56632080297-0.2107866838190.449464792615-0.450189507337-0.8348177201890.7972223626050.23299912022-0.2071127622881.367247998670.188242315521-0.384868808895-0.0005393655070840.954802701671-0.02014285469080.1121228344640.850243097612-0.02341222407231.29632969036-2.03-25.627-6.173
340.928787694148-0.3718975709970.6579038295560.61334671112-0.1546776122810.4001248788880.0327747862406-0.211542930114-0.2818152674830.634871082426-0.432625742679-0.2143901946860.3460967391170.5062171771830.0005836168786191.170547519530.02857304470820.04362096357920.889538586719-0.0224940959181.143154297285.561-30.281-4.955
350.593719408865-0.5177450074270.4214845378660.796407549209-0.2306552590980.33544280382-0.2829355817840.2119961355110.3670498556871.031206275630.1754712664660.5372823585640.6391515783741.203758939810.0003824675452861.006770537050.2035504838950.1775624982590.9896253044710.0698814143510.9603223242651.268-30.952-12.607
361.962520054290.787883729586-0.15898968651.285031211750.4014752837180.537399550886-0.2158388727470.8544255098010.447531154153-0.756121444866-0.343181314133-0.377200235225-0.2635620914230.4256681785490.006179595001381.026764112030.0524112185737-0.04231614959180.7869481077080.04603869544081.146538715330.5075.829-18.663
370.247163201125-0.29847723229-0.4223709852690.744560031040.9838779470891.10139962771-0.2301848664780.3838866231780.216630055995-0.01616549822620.2897655165430.000622148927219-0.3468707951520.008090452493070.000218353364471.07864876934-0.0122979061758-0.1956452542430.9102284464390.1203736309191.08683911585-3.1292.97-19.97
380.2946610094440.3785956747050.09309397452370.311949565158-0.002385919588340.0752105839938-0.0306296334508-0.02813079038580.217430339574-0.06942291562580.753962659189-0.2690451178640.710981551107-0.903164132719-0.0005710412061371.3439342501-0.03006760283540.08361544977890.972350572606-0.01194897046471.34480345796-8.67.339-13.446
390.232187218388-0.2065879569160.1020445888670.170713982799-0.03989792544370.0800906844645-0.501602738906-1.4022286829-0.222966637561-0.2934660696370.388777279229-0.100021781179-1.15124821649-0.812922252307-0.002061580669351.517447133980.152621267922-0.2594454139121.35470484672-0.08220004512511.38404224941-3.92928.855-20.647
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430.3665259840050.2372886900850.103862945820.9091982183450.1073286093930.0831274507352-0.1933531466131.01683831359-0.384899287029-1.205430303660.4004270856730.03913572122360.697112371511-0.000894728649465-0.0005486929171.329366722150.120574072936-0.03953644623271.1900586395-0.02165287616970.79262217729793.327-85.694-22.986
441.140625566-1.10852387858-0.2664261634330.9418536102420.09868203646171.48937384746-0.0941265409017-0.271692695895-0.157339292746-0.1377798987590.0210151314984-0.531583281080.1424760721980.191415512614-0.0002338513516380.745412772043-0.05852461626760.02765677955540.8658186566470.1088878283870.88863548329486.412-79.551-13.674
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 1:35 )D1 - 35
2X-RAY DIFFRACTION2( CHAIN D AND RESID 36:76 )D36 - 76
3X-RAY DIFFRACTION3( CHAIN D AND RESID 77:123 )D77 - 123
4X-RAY DIFFRACTION4( CHAIN D AND RESID 124:216 )D124 - 216
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:39 )E1 - 39
6X-RAY DIFFRACTION6( CHAIN E AND RESID 40:76 )E40 - 76
7X-RAY DIFFRACTION7( CHAIN E AND RESID 77:95 )E77 - 95
8X-RAY DIFFRACTION8( CHAIN E AND RESID 96:115 )E96 - 115
9X-RAY DIFFRACTION9( CHAIN E AND RESID 116:216 )E116 - 216
10X-RAY DIFFRACTION10( CHAIN G AND RESID 1:39 )G1 - 39
11X-RAY DIFFRACTION11( CHAIN G AND RESID 40:76 )G40 - 76
12X-RAY DIFFRACTION12( CHAIN G AND RESID 77:99 )G77 - 99
13X-RAY DIFFRACTION13( CHAIN G AND RESID 100:123 )G100 - 123
14X-RAY DIFFRACTION14( CHAIN G AND RESID 124:216 )G124 - 216
15X-RAY DIFFRACTION15( CHAIN A AND RESID 8:57 )A8 - 57
16X-RAY DIFFRACTION16( CHAIN A AND RESID 58:285 )A58 - 285
17X-RAY DIFFRACTION17( CHAIN A AND RESID 286:342 )A286 - 342
18X-RAY DIFFRACTION18( CHAIN A AND RESID 343:366 )A343 - 366
19X-RAY DIFFRACTION19( CHAIN A AND RESID 367:501 )A367 - 501
20X-RAY DIFFRACTION20( CHAIN B AND RESID 8:49 )B8 - 49
21X-RAY DIFFRACTION21( CHAIN B AND RESID 50:317 )B50 - 317
22X-RAY DIFFRACTION22( CHAIN B AND RESID 318:343 )B318 - 343
23X-RAY DIFFRACTION23( CHAIN B AND RESID 344:366 )B344 - 366
24X-RAY DIFFRACTION24( CHAIN B AND RESID 367:499 )B367 - 499
25X-RAY DIFFRACTION25( CHAIN C AND RESID 8:41 )C8 - 41
26X-RAY DIFFRACTION26( CHAIN C AND RESID 42:284 )C42 - 284
27X-RAY DIFFRACTION27( CHAIN C AND RESID 285:336 )C285 - 336
28X-RAY DIFFRACTION28( CHAIN C AND RESID 337:366 )C337 - 366
29X-RAY DIFFRACTION29( CHAIN C AND RESID 367:501 )C367 - 501
30X-RAY DIFFRACTION30( CHAIN F AND RESID 1:83 )F1 - 83
31X-RAY DIFFRACTION31( CHAIN F AND RESID 84:214 )F84 - 214
32X-RAY DIFFRACTION32( CHAIN F AND RESID 215:230 )F215 - 230
33X-RAY DIFFRACTION33( CHAIN H AND RESID 1:40 )H1 - 40
34X-RAY DIFFRACTION34( CHAIN H AND RESID 41:83 )H41 - 83
35X-RAY DIFFRACTION35( CHAIN H AND RESID 84:120 )H84 - 120
36X-RAY DIFFRACTION36( CHAIN H AND RESID 121:157 )H121 - 157
37X-RAY DIFFRACTION37( CHAIN H AND RESID 158:205 )H158 - 205
38X-RAY DIFFRACTION38( CHAIN H AND RESID 206:225 )H206 - 225
39X-RAY DIFFRACTION39( CHAIN H AND RESID 226:239 )H226 - 239
40X-RAY DIFFRACTION40( CHAIN U AND RESID 1:40 )U1 - 40
41X-RAY DIFFRACTION41( CHAIN U AND RESID 41:83 )U41 - 83
42X-RAY DIFFRACTION42( CHAIN U AND RESID 84:138 )U84 - 138
43X-RAY DIFFRACTION43( CHAIN U AND RESID 139:157 )U139 - 157
44X-RAY DIFFRACTION44( CHAIN U AND RESID 158:214 )U158 - 214
45X-RAY DIFFRACTION45( CHAIN U AND RESID 215:230 )U215 - 230

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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

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