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- PDB-8t1g: The crystal structure of hemagglutinin form a h7n9 influenza viru... -

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基本情報

登録情報
データベース: PDB / ID: 8t1g
タイトルThe crystal structure of hemagglutinin form a h7n9 influenza virus (a/shanghai/1/2013) in complex with antibody 1E11
要素
  • (Hemagglutinin ...) x 2
  • 1E11 Fab Heavy chain
  • 1E11 Fab Light chain
キーワードIMMUNE SYSTEM/VIRAL PROTEIN / hemagglutinin / influenza / virus / antibody / H7N9 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN 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Influenza A virus (A型インフルエンザウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.5 Å
データ登録者Zhou, T. / Kwong, P.D.
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: Structure / 年: 2025
タイトル: Distinct binding modes drive the broad neutralization profile of two persistent influenza hemagglutinin stem-specific antibody lineages.
著者: Grace E Mantus / Gabriele Cerutti / Michael Chambers / Rebecca A Gillespie / Geoffrey D Shimberg / Abby Spangler / Jason Gorman / Tongqing Zhou / Chen-Hsiang Shen / Masaru Kanekiyo / Peter D ...著者: Grace E Mantus / Gabriele Cerutti / Michael Chambers / Rebecca A Gillespie / Geoffrey D Shimberg / Abby Spangler / Jason Gorman / Tongqing Zhou / Chen-Hsiang Shen / Masaru Kanekiyo / Peter D Kwong / Lawrence Shapiro / Sarah F Andrews /
要旨: Elicitation of antibodies to the influenza hemagglutinin stem is a critical part of universal influenza vaccine strategies. While numerous broadly reactive stem antibodies have been isolated, our ...Elicitation of antibodies to the influenza hemagglutinin stem is a critical part of universal influenza vaccine strategies. While numerous broadly reactive stem antibodies have been isolated, our understanding of how these antibodies mature within the human B cell repertoire is limited. Here, we isolated and tracked two stem-specific antibody lineages over a decade in a single participant that received multiple seasonal and pandemic influenza vaccinations. Despite similar binding and neutralization profiles, antibodies from these lineages utilized fundamentally different interactions to engage the central epitope on the influenza stem. Structural analysis of an unmutated common ancestor from one lineage identified critical residues that were the main drivers of increased affinity and breadth to group 1 influenza subtypes. These observations demonstrate the heterogeneous pathways by which stem-specific antibodies can mature within the human B cell repertoire.
履歴
登録2023年6月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年5月29日Provider: repository / タイプ: Initial release
改定 1.12024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
改定 1.22025年3月26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_DOI / _citation.title / _citation.year
改定 1.32025年4月2日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.42025年5月14日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first

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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: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: 1E11 Fab Heavy chain
H: 1E11 Fab Heavy chain
I: 1E11 Fab Light chain
J: 1E11 Fab Heavy chain
K: 1E11 Fab Light chain
L: 1E11 Fab Light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)328,82227
ポリマ－323,36912
非ポリマー5,45315
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 area58080 Å2
ΔGint-182 kcal/mol
Surface area121410 Å2
手法PISA
単位格子
Length a, b, c (Å)303.277, 303.277, 153.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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要素

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Hemagglutinin ... , 2種, 6分子 ACEBDF

#1: タンパク質 Hemagglutinin HA1


分子量: 34993.559 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (A型インフルエンザウイルス)
株: H7N9 (A/shanghai/1/2013) / 遺伝子: HA / Cell (発現宿主): HEK 293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A0A8E4VRS4
#2: タンパク質 Hemagglutinin HA2


分子量: 24095.545 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (A型インフルエンザウイルス)
株: H7N9 (A/shanghai/1/2013) / 遺伝子: HA / Cell (発現宿主): HEK 293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A0A8E4VRS4

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抗体 , 2種, 6分子 GHJIKL

#3: 抗体 1E11 Fab Heavy chain


分子量: 24538.465 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / Cell (発現宿主): HEK 293F / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 1E11 Fab Light chain


分子量: 24162.018 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / Cell (発現宿主): HEK 293F / 発現宿主: Homo sapiens (ヒト)

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糖 , 4種, 12分子

#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#9: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 6 / 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 , 1種, 3分子

#8: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Ca

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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: 5.46 Å3/Da / 溶媒含有率: 77.46 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 0.1 M HEPES (pH 7.5), 1.08 M sodium citrate

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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: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年3月5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: 1 Å / 相対比: 1
反射解像度: 3.5→50 Å / Num. obs: 89938 / % possible obs: 99.9 % / 冗長度: 9.7 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.062 / Rrim(I) all: 0.194 / Χ2: 0.596 / Net I/σ(I): 3.3 / Num. measured all: 868574
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.5-3.569.61.64144570.6140.8720.5561.7350.405100
3.56-3.639.41.3544090.7150.9130.4631.4290.412100
3.63-3.698.51.14144550.730.9190.4091.2150.508100
3.69-3.778.70.95544260.7960.9420.3381.0160.41799.9
3.77-3.8510.20.83644480.8670.9640.2740.880.425100
3.85-3.94100.76244640.8640.9630.2530.8040.517100
3.94-4.0410.30.59144540.9310.9820.1930.6220.44100
4.04-4.1510.30.47344430.9470.9860.1540.4980.467100
4.15-4.2710.20.37244610.9620.990.1220.3920.495100
4.27-4.4110.10.29844540.9740.9930.0980.3140.536100
4.41-4.57100.24544580.9810.9950.0810.2580.581100
4.57-4.759.90.21944840.9850.9960.0730.2320.588100
4.75-4.979.70.20644920.9850.9960.0690.2180.62100
4.97-5.239.40.17645010.9890.9970.060.1860.644100
5.23-5.558.30.16244780.9870.9970.0590.1730.64899.8
5.55-5.9810.10.15645240.9920.9980.0520.1650.62100
5.98-6.5810.30.13145360.9930.9980.0430.1380.647100
6.58-7.5310.10.145680.9950.9990.0330.1050.71399.9
7.53-9.489.60.06346210.9980.9990.0210.0670.9599.9
9.48-508.60.05148050.9980.9990.0180.0541.31599.4

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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
SCALEPACKデータスケーリング
HKL-2000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: 3.5→45.77 Å / SU ML: 0.4 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 19.89 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2152 1978 2.23 %
Rwork0.1817 --
obs0.1824 88663 98.59 %
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
精密化ステップサイクル: LAST / 解像度: 3.5→45.77 Å
タンパク質核酸リガンド溶媒全体
原子数22458 0 354 0 22812
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00423281
X-RAY DIFFRACTIONf_angle_d0.65731565
X-RAY DIFFRACTIONf_dihedral_angle_d18.4983349
X-RAY DIFFRACTIONf_chiral_restr0.0443564
X-RAY DIFFRACTIONf_plane_restr0.0064074
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.28121380.28955956X-RAY DIFFRACTION96
3.59-3.690.27961400.26816025X-RAY DIFFRACTION97
3.69-3.80.27831380.25886033X-RAY DIFFRACTION97
3.8-3.920.30911390.25386070X-RAY DIFFRACTION98
3.92-4.060.27761390.23056134X-RAY DIFFRACTION98
4.06-4.220.23971410.19876126X-RAY DIFFRACTION99
4.22-4.410.19941380.17556177X-RAY DIFFRACTION99
4.41-4.650.23271420.1686205X-RAY DIFFRACTION99
4.65-4.940.161410.15716204X-RAY DIFFRACTION99
4.94-5.320.18851420.1546259X-RAY DIFFRACTION99
5.32-5.850.19551440.16736256X-RAY DIFFRACTION99
5.85-6.690.23021400.17926284X-RAY DIFFRACTION99
6.69-8.430.19571460.17266358X-RAY DIFFRACTION99
8.43-45.770.19131500.14936598X-RAY DIFFRACTION99
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)
10.27150.7723-0.56570.71210.0070.8478-0.2139-0.1314-0.09440.51710.1468-0.10870.29060.34220.00021.13640.0654-0.05320.9718-0.09940.9229-102.5942-14.2992-9.0895
20.3783-0.19080.27250.0708-0.16730.16361.3256-0.7064-0.38430.5333-0.8141-0.4424-0.1694-0.4385-01.308-0.00190.01141.1407-0.09931.1718-137.8061-24.851212.0486
30.56160.24320.76080.65260.86241.36210.2454-0.2475-0.0460.05710.0205-0.0957-0.24390.3297-0.00011.1457-0.00780.14280.9168-0.1181.0923-126.7036-21.21967.2004
40.5305-0.58060.33920.5033-0.37140.2397-0.61950.0676-1.02240.71950.6413-1.4199-0.07630.01720.0021.4772-0.08370.03671.2325-0.19931.2266-122.8487-19.284514.9897
50.8343-0.42571.15511.9065-1.10382.35840.05830.1471-0.1425-0.05150.14090.03190.13940.1296-00.93050.0033-0.00231.092-0.03471.0314-101.304215.7329-75.6728
61.5469-0.21191.37511.3572-0.48181.4348-0.08760.3676-0.1041-0.2011-0.1543-0.40380.20010.4514-0.00011.0209-0.06580.17251.28990.01981.0806-94.138939.1547-104.2179
71.043-1.0374-0.09820.7628-0.62051.1257-0.009-0.07290.24880.08440.0744-0.2802-0.11460.351200.96920.1426-0.0341.2528-0.18611.0799-45.1245-25.076-52.2493
80.94090.96760.65141.35310.26480.7456-0.2703-0.25660.2233-0.24980.2119-0.5636-0.1459-0.063601.02590.2310.01281.2283-0.06431.0994-29.4034-52.5017-60.4271
90.4480.3112-0.19140.1972-0.1880.42780.82180.72040.31650.0062-1.6666-0.8034-0.1003-0.97310.00031.32110.19020.11081.4827-0.04441.4254-19.9964-52.9666-59.9723
101.0164-0.8514-0.44780.8139-0.19050.4758-0.0430.1035-0.1249-0.0234-0.1830.34590.1204-0.0598-0.00021.07350.0557-0.00751.1412-0.17191.0738-65.2442-35.5398-60.576
110.46780.73090.12521.16120.05390.7409-0.2464-0.02790.0777-0.20870.0619-0.2624-0.0982-0.0808-00.95750.16730.00181.0909-0.2281.0803-58.0642-33.4694-67.4987
121.68270.18640.47590.8755-0.8511.1683-0.07950.1223-0.2522-0.0023-0.12650.33020.0924-0.2331-0.00050.93290.06550.05661.095-0.17770.9252-58.2166-41.0844-63.6645
130.2618-0.49760.15421.25840.1861.1568-0.1612-0.41370.19190.5094-0.115-0.04670.6681-0.0636-0.00011.10750.17560.09571.18130.08141.1065-34.9752-63.4167-57.3423
141.24250.1495-0.91090.17660.27661.0381-0.4685-0.72220.10880.48130.2979-0.14430.159-0.1686-0.00011.30150.26310.14711.06170.02461.0283-37.3346-64.5962-55.134
150.42130.2518-0.61430.3213-0.50720.921-0.14611.00990.1473-0.07770.25890.17150.52860.5303-0.00031.38670.3020.23251.3114-0.04511.5005-35.0912-72.4752-62.2289
163.26560.7646-1.37420.4842-0.57641.4214-0.0430.1986-0.1704-0.16130.0810.01510.161-0.02030.00011.0531-0.00150.00590.9808-0.09130.9529-112.72-25.0227-22.5421
171.32180.8811-0.62370.5913-0.42031.10850.26570.00230.5063-0.08360.06720.3287-0.3381-0.12140.00011.06130.02560.07890.96780.00441.1188-140.439-17.74711.7854
181.0619-0.04350.7361-0.09470.85831.2641-0.11210.26490.1565-0.25520.06620.0516-0.09260.2551-0.00011.09830.01880.01731.2845-0.06591.0815-76.3886-15.6066-68.4996
190.52240.19690.41620.69520.78420.6985-0.06750.45360.10140.01990.3883-0.12830.06210.341301.08880.095-0.03891.1957-0.18931.0643-95.5879-44.2347-86.6279
200.7006-0.5021.0112.6071-1.4181.11230.020.2621-0.64470.06290.25730.26990.22510.13630.00021.1741-0.0019-0.01351.2735-0.24791.2582-103.958-58.6858-90.9448
210.1644-0.01380.11140.1737-0.06390.0389-0.6691-0.0109-0.9515-0.2246-0.43370.08690.53941.173-0.00111.36420.1161-0.26221.6637-0.1931.4713-118.0539-54.7559-100.7588
220.7490.5041-0.30771.12990.4830.5514-0.08030.2362-0.08510.52910.23570.4952-0.19550.38280.00041.24580.1311-0.111.249-0.05951.2245-111.254-51.9543-86.3839
230.62030.35160.4135-0.11590.1955-0.18180.1450.3666-0.02340.55620.06250.06360.3220.38380.00011.20430.2129-0.15181.2156-0.21191.2985-91.2231-45.8507-82.5593
240.5353-0.6589-0.12950.67830.1357-0.07720.05880.45920.0553-0.08390.02830.2565-0.071-0.0795-00.87580.0412-0.01451.0756-0.13150.8438-82.1787-18.5668-69.2755
250.16840.13940.06960.1180.0640.1133-0.7070.1874-0.5659-0.4343-0.78630.19090.01360.42770.00862.8831-0.00910.41191.4729-0.39951.8701-61.895915.3822-58.1151
260.8368-0.93660.42241.0827-0.36610.06570.2460.02540.09060.2792-0.1677-0.1754-0.0641-0.0257-00.96010.02880.04051.1832-0.17011.075-62.0102-3.2454-51.2704
270.12950.0145-0.00570.1932-0.30020.3443-0.146-0.4536-0.27141.19611.0338-0.07420.1304-0.3177-0.00081.17060.0807-0.04931.3433-0.12211.4101-86.5911-31.2568-65.468
280.1399-0.0537-0.03730.16470.23580.28480.41771.20150.929-0.78290.05870.77690.2139-1.19060.00361.04790.1494-0.07561.2928-0.34410.9443-100.5607-31.544-82.1049
290.99290.64570.03590.7830.1772-0.29950.1409-0.04030.1202-0.16610.1353-0.2911-0.1318-0.2047-0.00010.87130.0645-0.01980.9659-0.23020.9717-84.7889-12.0561-56.8029
301.03620.9121-0.05320.83410.03150.11440.04230.0725-0.16680.03-0.0153-0.3585-0.29540.7985-01.1842-0.069-0.08021.3905-0.26161.3664-53.94298.6992-33.0404
31-0.0067-0.1520.11630.3488-0.29370.09340.7761-0.76050.24810.5052-0.9811-0.26880.9282-0.1737-01.5491-0.1324-0.15021.9941-0.42031.7277-42.140624.534-8.1893
320.5560.47230.69621.35310.68210.29060.08-0.0082-0.05460.22310.02950.25470.05250.0035-01.0064-0.02560.1011.1728-0.13211.078-103.59231.4358-51.3972
331.45320.1587-1.06230.7538-0.81340.9625-0.13450.21540.1512-0.26650.11060.3163-0.1613-0.146700.9980.101-0.1681.23440.02181.1271-124.5285-20.2678-87.2084
340.81981.0421-0.34460.9773-0.65191.8162-0.26530.56270.0813-0.60260.1750.28330.2877-0.24970.00011.19590.0323-0.18151.2037-0.10361.1086-128.5602-28.9332-96.6857
350.12560.1864-0.00870.14820.14740.42290.4289-0.67540.2571-0.7441-0.0153-0.00920.458-0.06210.00071.467-0.094-0.13941.28660.01451.2749-127.861-40.4474-93.3435
360.40260.00340.40391.6910.12540.2411-0.2093-0.01890.4326-0.80570.17270.73060.70270.1979-0.00011.21810.0287-0.03831.229-0.09221.1552-125.8851-33.1786-90.7949
370.1633-0.4707-0.22790.43770.51920.25860.09180.47780.4252-0.20450.15580.1469-0.08480.2619-01.1209-0.0314-0.06961.1557-0.05671.1973-116.4792-8.462-77.0334
38-0.4867-0.09940.39480.48160.32811.2690.10540.25160.13780.21050.11160.3290.43170.14530.00010.80690.06530.05450.9405-0.13260.9812-104.1546-4.1594-52.5391
390.0747-0.01920.09180.0422-0.01830.09790.65440.22320.25910.9303-0.1373-0.90360.4812-0.2507-0.00141.8121-0.11930.14711.434-0.21731.1975-88.0414.8279-26.7494
400.45481.3032-0.99541.2861-1.0840.9364-0.1649-0.18210.0922-0.01080.3147-0.1728-0.36260.1080.00020.87820.1003-0.01141.0669-0.12861.0577-88.59914.2808-43.7548
410.25480.0658-0.34250.1123-0.09530.3340.5058-0.2682-0.9086-0.4732-1.137-1.2203-0.3191-0.2627-0.00061.21980.02390.07171.1664-0.01171.2155-102.884-10.3013-69.8627
420.114-0.092-0.11140.39830.0630.20290.04380.1181-0.50330.7486-0.28241.96920.7178-0.6487-0.00081.12890.0518-0.30811.2084-0.02621.3144-119.7092-24.1156-70.043
43-0.09820.2911-0.43960.69220.64360.84460.1597-0.3112-0.19640.3948-0.1451-0.1549-0.0795-0.1889-0.00010.92080.0874-0.13830.9793-0.09460.882-93.7284-8.2042-50.4946
441.35620.17410.8260.0420.38491.07510.0665-0.07630.58330.1954-0.0924-0.0831-0.2337-0.1566-01.2899-0.0781-0.00931.3244-0.28261.2502-70.039822.1354-30.174
450.0091-0.0782-0.0159-0.03290.026-0.01420.03250.61420.131-0.13570.3954-0.2985-0.32160.17840.00011.4633-0.1991-0.23851.4399-0.05011.6184-45.503234.1359-13.9684
460.06480.85790.24761.00970.12380.4930.14230.08690.03240.2217-0.0219-0.03150.27030.1299-0.00011.12630.1021-0.02691.1556-0.18771.2238-91.0459-29.3908-38.564
471.0454-1.1067-0.48021.30230.69041.42270.2913-0.2128-0.12040.0285-0.25410.02610.4193-0.4598-01.1323-0.0965-0.0621.1561-0.04141.1571-126.2137-50.1698-59.6944
480.8547-0.0665-1.02810.1415-0.07440.90530.61590.0567-0.1505-0.0652-0.6577-0.77640.1717-1.1975-0.00041.13010.0297-0.21151.6097-0.30121.5687-139.3045-48.1585-71.216
490.4126-0.20720.29630.1361-0.26990.35870.22360.3557-0.09380.2726-0.57990.85190.0439-0.5802-0.00021.0888-0.1164-0.06051.3544-0.27021.3074-129.0663-55.8787-74.9125
500.32990.21420.00840.0933-0.03090.03920.26660.89890.26960.0417-0.08350.12810.0358-0.2405-01.15190.0901-0.02791.5682-0.08871.3313-128.8872-47.5111-79.2328
510.26470.3056-0.82760.0575-0.48722.15130.1010.46450.06510.25710.2199-0.170.3719-0.9709-0.00021.1310.0161-0.07151.3359-0.13981.3388-129.2204-48.1623-70.3477
520.35930.04880.3624-0.0931-0.11680.8716-0.1234-0.18530.05240.36280.25830.04380.0903-0.125401.0298-0.01730.02141.0478-0.17071.0548-115.7756-40.1942-47.4355
530.22750.3359-0.10580.4067-0.26830.1168-0.0930.69430.15760.3583-0.07880.45570.06320.52430.00041.08920.041-0.09530.8096-0.14111.0649-101.0331-33.9427-47.0213
540.62220.1436-0.7338-0.1591-0.28141.36750.16760.545-0.24580.2196-0.0464-0.07520.94570.23540.00010.87840.0777-0.07860.9851-0.15110.8438-85.9364-25.6792-42.1774
550.0990.0440.29030.02060.11450.8399-0.39740.2714-0.0384-0.3521-0.1794-0.13490.381-0.4577-0.00131.83320.05450.02551.72420.19221.8794-62.0697-19.7432-23.2262
560.5339-0.0947-0.1393-0.06690.00540.0047-0.0588-0.27330.09470.0521-0.1692-0.26330.16950.0387-0.00011.06930.0441-0.08831.1098-0.0911.0558-78.7764-12.3682-24.8446
570.7006-0.38160.11670.4542-0.53960.7692-0.10750.3198-0.315-0.10950.23690.1783-0.18210.12530.00011.16970.05190.02381.2603-0.13651.111-107.5635-34.6718-55.4797
580.9167-0.00221.474-0.38120.12121.07170.2609-0.1962-0.08890.0603-0.1711-0.07930.3220.13820.00040.8522-0.09360.041.1346-0.15670.9649-87.7811-17.6434-46.9629
590.93420.21380.62281.5214-0.58790.63190.0296-0.31220.02880.97960.055-0.3408-0.1294-0.38150.00021.18970.001-0.16341.384-0.27251.1866-67.01556.3342-16.7662
600.0385-0.11850.10750.296-0.0769-0.0322-0.1135-0.80220.3913-0.0996-0.36930.7719-0.0083-0.9119-0.00021.7486-0.1289-0.0461.485-0.2541.4699-51.277130.4442-4.3394
610.2236-0.1749-0.29760.39390.04840.3396-0.60070.58920.85430.39710.2589-0.4453-0.282-0.08670.00011.2777-0.1079-0.02261.10360.04871.5022-89.908338.1045-66.0682
620.1913-0.57880.26870.9945-0.41990.4237-0.1168-0.00280.00540.27110.1477-0.10910.10630.4372-0.00010.97360.02370.01461.1807-0.06521.0779-87.81426.6271-62.0778
630.4015-0.6396-0.17440.6579-1.28620.2867-0.065-0.05330.41970.3786-0.06960.3621-0.41670.028-0.00011.0193-0.08140.05911.0978-0.09181.179-90.19930.8871-64.6326
640.1373-0.4159-0.27790.6010.73640.4994-0.6979-0.39761.9597-0.0568-0.38760.322-1.6297-0.2568-01.059-0.0922-0.03811.22060.1221.3378-100.421949.8922-101.8179
650.69620.38340.55360.74790.05750.69370.16420.21480.09650.1515-0.3342-0.1379-0.32050.014701.0398-0.12450.10761.2110.05351.2709-96.881345.6182-89.6056
660.311-0.3641-0.24590.36540.24540.16841.2715-0.40580.60140.41250.7174-0.06450.2745-0.5864-0.00461.38920.03530.12661.31440.13651.4155-96.743655.5582-90.9801
670.68430.2468-0.01760.1592-0.09880.2123-0.1944-0.4342-0.15990.86710.26840.1678-0.28330.16140.00041.2945-0.03520.09741.1703-0.17361.1977-104.5528-11.853-0.0136
681.2635-0.2168-1.64021.62040.68641.93680.1103-0.27080.23740.4353-0.1105-0.2666-0.010.1293-01.0445-0.0702-0.02970.9222-0.09530.9249-97.7672-13.1569-8.5141
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 82A through 119 )
2X-RAY DIFFRACTION2chain 'H' and (resid 120 through 135 )
3X-RAY DIFFRACTION3chain 'H' and (resid 136 through 194 )
4X-RAY DIFFRACTION4chain 'H' and (resid 195 through 215 )
5X-RAY DIFFRACTION5chain 'I' and (resid 1 through 113 )
6X-RAY DIFFRACTION6chain 'I' and (resid 114 through 212 )
7X-RAY DIFFRACTION7chain 'J' and (resid 1 through 119 )
8X-RAY DIFFRACTION8chain 'J' and (resid 120 through 203 )
9X-RAY DIFFRACTION9chain 'J' and (resid 204 through 216 )
10X-RAY DIFFRACTION10chain 'K' and (resid 1 through 32 )
11X-RAY DIFFRACTION11chain 'K' and (resid 33 through 69 )
12X-RAY DIFFRACTION12chain 'K' and (resid 70 through 113 )
13X-RAY DIFFRACTION13chain 'K' and (resid 114 through 150 )
14X-RAY DIFFRACTION14chain 'K' and (resid 151 through 198 )
15X-RAY DIFFRACTION15chain 'K' and (resid 199 through 214 )
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 113 )
17X-RAY DIFFRACTION17chain 'L' and (resid 114 through 212 )
18X-RAY DIFFRACTION18chain 'A' and (resid 11 through 66 )
19X-RAY DIFFRACTION19chain 'A' and (resid 67 through 113 )
20X-RAY DIFFRACTION20chain 'A' and (resid 114 through 184 )
21X-RAY DIFFRACTION21chain 'A' and (resid 185 through 201 )
22X-RAY DIFFRACTION22chain 'A' and (resid 202 through 247 )
23X-RAY DIFFRACTION23chain 'A' and (resid 248 through 279 )
24X-RAY DIFFRACTION24chain 'A' and (resid 280 through 325 )
25X-RAY DIFFRACTION25chain 'A' and (resid 326 through 328 )
26X-RAY DIFFRACTION26chain 'B' and (resid 5 through 55 )
27X-RAY DIFFRACTION27chain 'B' and (resid 56 through 65 )
28X-RAY DIFFRACTION28chain 'B' and (resid 66 through 74 )
29X-RAY DIFFRACTION29chain 'B' and (resid 75 through 125 )
30X-RAY DIFFRACTION30chain 'B' and (resid 126 through 180 )
31X-RAY DIFFRACTION31chain 'B' and (resid 181 through 208 )
32X-RAY DIFFRACTION32chain 'C' and (resid 11 through 60 )
33X-RAY DIFFRACTION33chain 'C' and (resid 61 through 135 )
34X-RAY DIFFRACTION34chain 'C' and (resid 136 through 184 )
35X-RAY DIFFRACTION35chain 'C' and (resid 185 through 213 )
36X-RAY DIFFRACTION36chain 'C' and (resid 214 through 255 )
37X-RAY DIFFRACTION37chain 'C' and (resid 256 through 288 )
38X-RAY DIFFRACTION38chain 'C' and (resid 289 through 328 )
39X-RAY DIFFRACTION39chain 'D' and (resid 2 through 11 )
40X-RAY DIFFRACTION40chain 'D' and (resid 12 through 55 )
41X-RAY DIFFRACTION41chain 'D' and (resid 56 through 65 )
42X-RAY DIFFRACTION42chain 'D' and (resid 66 through 74 )
43X-RAY DIFFRACTION43chain 'D' and (resid 75 through 126 )
44X-RAY DIFFRACTION44chain 'D' and (resid 127 through 180 )
45X-RAY DIFFRACTION45chain 'D' and (resid 181 through 208 )
46X-RAY DIFFRACTION46chain 'E' and (resid 11 through 65 )
47X-RAY DIFFRACTION47chain 'E' and (resid 66 through 153 )
48X-RAY DIFFRACTION48chain 'E' and (resid 154 through 175 )
49X-RAY DIFFRACTION49chain 'E' and (resid 176 through 195 )
50X-RAY DIFFRACTION50chain 'E' and (resid 196 through 220 )
51X-RAY DIFFRACTION51chain 'E' and (resid 221 through 255 )
52X-RAY DIFFRACTION52chain 'E' and (resid 256 through 284 )
53X-RAY DIFFRACTION53chain 'E' and (resid 285 through 304 )
54X-RAY DIFFRACTION54chain 'E' and (resid 305 through 325 )
55X-RAY DIFFRACTION55chain 'E' and (resid 326 through 328 )
56X-RAY DIFFRACTION56chain 'F' and (resid 4 through 55 )
57X-RAY DIFFRACTION57chain 'F' and (resid 56 through 74 )
58X-RAY DIFFRACTION58chain 'F' and (resid 75 through 126 )
59X-RAY DIFFRACTION59chain 'F' and (resid 127 through 181 )
60X-RAY DIFFRACTION60chain 'F' and (resid 182 through 208 )
61X-RAY DIFFRACTION61chain 'G' and (resid 1 through 28 )
62X-RAY DIFFRACTION62chain 'G' and (resid 29 through 71 )
63X-RAY DIFFRACTION63chain 'G' and (resid 72 through 119 )
64X-RAY DIFFRACTION64chain 'G' and (resid 120 through 134 )
65X-RAY DIFFRACTION65chain 'G' and (resid 135 through 203 )
66X-RAY DIFFRACTION66chain 'G' and (resid 204 through 215 )
67X-RAY DIFFRACTION67chain 'H' and (resid 1 through 17 )
68X-RAY DIFFRACTION68chain 'H' and (resid 18 through 82 )

+
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

-
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