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- PDB-5k9o: Crystal structure of multidonor HV1-18+HD3-9 class broadly neutra... -

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基本情報

登録情報
データベース: PDB / ID: 5k9o
タイトルCrystal structure of multidonor HV1-18+HD3-9 class broadly neutralizing Influenza A antibody 31.b.09 in complex with Hemagglutinin H1 A/California/04/2009
要素
  • 31.b.09 Heavy Fv
  • 31.b.09 Light Fv
  • Hemagglutinin
キーワードIMMUNE SYSTEM / HV1-18 / multidonor / H5 / universal influenza vaccine
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 / 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 / metal ion binding / membrane
類似検索 - 分子機能
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
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: 3.387 Å
データ登録者Joyce, M.G. / Thomas, P.V. / Wheatley, A.K. / McDermott, A.B. / Mascola, J.R. / Kwong, P.D.
引用ジャーナル: Cell / 年: 2016
タイトル: Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.
著者: Joyce, M.G. / Wheatley, A.K. / Thomas, P.V. / Chuang, G.Y. / Soto, C. / Bailer, R.T. / Druz, A. / Georgiev, I.S. / Gillespie, R.A. / Kanekiyo, M. / Kong, W.P. / Leung, K. / Narpala, S.N. / ...著者: Joyce, M.G. / Wheatley, A.K. / Thomas, P.V. / Chuang, G.Y. / Soto, C. / Bailer, R.T. / Druz, A. / Georgiev, I.S. / Gillespie, R.A. / Kanekiyo, M. / Kong, W.P. / Leung, K. / Narpala, S.N. / Prabhakaran, M.S. / Yang, E.S. / Zhang, B. / Zhang, Y. / Asokan, M. / Boyington, J.C. / Bylund, T. / Darko, S. / Lees, C.R. / Ransier, A. / Shen, C.H. / Wang, L. / Whittle, J.R. / Wu, X. / Yassine, H.M. / Santos, C. / Matsuoka, Y. / Tsybovsky, Y. / Baxa, U. / Mullikin, J.C. / Subbarao, K. / Douek, D.C. / Graham, B.S. / Koup, R.A. / Ledgerwood, J.E. / Roederer, M. / Shapiro, L. / Kwong, P.D. / Mascola, J.R. / McDermott, A.B.
履歴
登録2016年6月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年12月28日Provider: repository / タイプ: Initial release
改定 1.12017年5月24日Group: Structure summary
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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 2.12023年9月27日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: 31.b.09 Heavy Fv
B: 31.b.09 Light Fv
F: Hemagglutinin
H: 31.b.09 Heavy Fv
I: Hemagglutinin
L: 31.b.09 Light Fv
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)210,8137
ポリマ－210,2276
非ポリマー5871
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 area13090 Å2
ΔGint-80 kcal/mol
Surface area85130 Å2
手法PISA
単位格子
Length a, b, c (Å)208.648, 208.648, 252.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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要素

#1: 抗体 31.b.09 Heavy Fv


分子量: 24235.127 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)
#2: 抗体 31.b.09 Light Fv


分子量: 24229.977 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: タンパク質 Hemagglutinin


分子量: 56648.316 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (strain swl A/California/04/2009 H1N1) (A型インフルエンザウイルス)
株: swl A/California/04/2009 H1N1 / 遺伝子: HA / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: C3W5S1
#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: 1 / 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
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: 3.97 Å3/Da / 溶媒含有率: 69.05 %
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: 6.5
詳細: 0.1M imidazole, pH 6.5, 0.1M MgCl2, 1.75M NaCl, and 15% PEG-3350

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データ収集

回折平均測定温度: 100 K
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: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2015年5月23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: 3.38→50 Å / Num. obs: 29074 / % possible obs: 71 % / 冗長度: 6.6 % / Net I/σ(I): 11.76

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10_2155: ???)精密化
PDB_EXTRACT3.2データ抽出
HKL-2000データ削減
HKL-2000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: 1wt5, 3al4, 3lzg, 3ube, 3ubj, 3ubn, 3ubq, 3ztn, 4jtv, 4jtx, 4juo, 4lss

1wt5

3al4

3lzg

3ube

3ubj

3ubn

3ubq

3ztn

4jtv

4jtx

4juo

4lss


解像度: 3.387→38.965 Å / SU ML: 0.54 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 41.41 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3456 1431 4.92 %
Rwork0.2913 --
obs0.294 29074 63.8 %
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: 3.387→38.965 Å
タンパク質核酸リガンド溶媒全体
原子数14019 0 39 0 14058
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00414412
X-RAY DIFFRACTIONf_angle_d0.84119590
X-RAY DIFFRACTIONf_dihedral_angle_d15.1938584
X-RAY DIFFRACTIONf_chiral_restr0.0482159
X-RAY DIFFRACTIONf_plane_restr0.0062509
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.387-3.5080.2697120.3498253X-RAY DIFFRACTION6
3.508-3.64830.4487280.3362653X-RAY DIFFRACTION15
3.6483-3.81420.309580.32711092X-RAY DIFFRACTION26
3.8142-4.01510.39870.32611870X-RAY DIFFRACTION44
4.0151-4.26640.33341460.30542775X-RAY DIFFRACTION65
4.2664-4.59530.33512030.28963576X-RAY DIFFRACTION84
4.5953-5.05690.28542170.26854063X-RAY DIFFRACTION94
5.0569-5.78660.33672090.30134326X-RAY DIFFRACTION99
5.7866-7.28270.38142340.33994395X-RAY DIFFRACTION100
7.2827-38.96780.35762370.2644640X-RAY DIFFRACTION100
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)
13.78840.4979-1.39853.06890.91514.0566-0.34680.9194-0.6048-1.48110.879-0.31331.46050.57070.07323.49990.2040.06532.89240.0556-0.2477172.819251.9749.769
20.78821.1242-0.80172.5911-0.64193.27731.3350.12870.6114-0.3068-0.59830.0261-0.6476-0.2135-0.06542.29191.04040.49492.35240.35931.345180.032251.10114.254
31.2744-0.3217-0.8451.91780.32731.731-0.94151.0856-1.1701-0.2841-0.3187-0.17740.6008-0.3221-0.06011.4595-0.50952.15671.9476-1.03391.2752174.752238.36417.954
42.02640.2184-1.46162.241-0.88112.4890.74740.457-0.4593-1.50280.3937-0.74311.0625-2.2914-0.07762.0361-0.55250.62242.23750.14291.4799181.239248.20927.206
51.4312-1.5701-1.03435.7127-1.00881.9919-0.7208-0.0799-0.6730.84310.8983-0.3806-0.32950.8194-0.02972.1346-0.62840.77052.9137-0.0061.992185.077248.01520.005
68.24556.92419.38695.98757.4512.02073.29181.9217-1.99861.17691.7396-1.7357-1.34061.03053.62471.94430.12950.50261.60660.61360.7294180.673238.74314.982
70.69140.234-0.16840.86970.4771.15150.2707-0.9094-0.3374-0.3896-0.18881.42720.2365-0.1039-0.00852.787-0.2480.13672.04650.05171.3415171.723248.86322.141
80.10740.17770.4790.16430.56511.6708-0.62450.61720.0754-0.88-0.2238-1.01560.06830.3175-0.05282.8828-0.2526-0.06651.636-0.09441.6689157.032229.77524.724
91.0783-0.2721-0.23420.6763-0.21622.3892-0.54471.2348-1.0544-1.0682-1.57090.95980.3497-0.30620.01481.4674-0.52350.2711.6259-0.34071.8243165.47244.51736.925
101.4928-0.2709-2.25751.9125-0.25773.70240.1198-1.31710.96990.0736-1.0214-1.8549-0.0680.0708-0.1322.7272-1.080.29732.6382-0.67571.1501162.215240.49116.021
111.4628-0.5657-2.65791.67811.19254.7732-0.0795-1.20471.10741.45-0.8552-0.79110.2445-0.7242-0.04682.9765-0.12650.12472.2601-0.2071.24158.637246.15125.375
123.6724-2.32843.67645.20870.87068.26370.14230.1346-0.2799-0.24570.3640.2293-0.04650.3120.07072.2959-1.1904-1.17684.14450.89333.6319154.409249.57722.188
133.0919-1.06990.20285.1797-2.80611.57310.67930.81991.1548-1.3199-0.02140.2526-0.3524-0.5437-0.07362.2451-0.0820.45932.28910.01621.606150.065242.8322.889
141.5744-0.82813.18540.9357-2.05547.43160.37160.4559-0.431.01010.1998-0.5187-0.1741-0.3416-0.07372.2633-0.72740.49882.4466-1.07521.5598155.853235.43431.675
150.05340.15760.39210.6081.07272.94530.29220.6451-0.3242-0.59810.6872-0.0350.5857-0.64832.10113.7028-2.2257-1.07453.4354-0.7381-0.1677154.111236.82115.637
162.8731.00042.24390.73860.91832.60490.40271.32760.18050.33620.4742-0.66310.1915-0.07580.32831.6536-1.7323-0.25312.1314-0.821.9128171.02237.99428.698
173.52861.12183.34837.73432.00853.29330.08970.12410.2126-1.1750.9670.3307-0.14580.0336-0.07412.36910.33510.2552.7084-0.0572.1623156.592229.74914.183
181.8883-0.29160.53175.02631.12367.00370.289-0.0117-0.44260.5466-0.01810.04670.2983-0.0430.02283.5411-0.65541.12210.9538-1.08762.6782160.134256.27133.648
192.7457-0.36760.80171.8204-2.51434.3834-0.3268-0.26360.10310.0504-0.1787-0.1894-0.25970.3564-0.09144.04361.0141-0.53762.20090.44961.4595157.886243.224141.503
203.3533-2.56-0.49974.52152.6162.0299-0.29560.52090.3047-0.1497-0.3052-0.1201-0.15180.06550.04553.0324-0.7497-0.02064.4060.83373.5802154.743225.528145.107
213.0323-0.85683.48630.7093-0.16585.4877-1.9801-1.39722.08560.2559-1.40720.5113-0.5118-0.2492-0.2691.77230.81770.25064.1057-2.21064.0507157.183240.302137.072
222.7888-1.3857-1.13633.00840.40323.7046-0.53730.17740.2108-0.6314-0.40620.2853-0.6701-0.2078-0.74191.82210.8971-0.47663.843-0.52020.2643159.573251.959127.425
231.1689-0.2421-0.41430.57490.54392.20920.1072-1.6105-0.75230.2691-1.3109-1.1738-0.79390.90140.00462.6791-0.215-0.25363.5715-0.12692.2693159.475239.144131.975
240.01710.2222-0.22874.4189-2.2641.3960.3191-2.0903-0.45270.31790.1737-0.23690.19740.10910.12721.52240.152-0.59964.55070.11892.1532166.448237.609138.814
254.48443.9637-0.16284.36040.6886.4073-0.0579-0.03420.65210.0479-0.4189-0.17580.32090.0550.00752.0732-0.224-1.12924.037-0.20932.4702167.8246.355139.038
265.55133.0457-3.8384.5609-4.30174.3243-0.0386-0.12760.05680.1623-0.10810.5338-0.2734-0.2995-0.46443.8556-0.40741.06623.45562.1473.2225159.272233.065150.477
274.8079-0.2711-0.54042.64750.57754.0457-0.4156-0.80990.59770.5956-0.4805-0.1366-0.09310.2471-0.16344.8077-1.521-0.33491.9995-0.79841.2978149.915228.994135.94
285.4558-3.5669-0.60068.0408-1.26261.4076-0.435-0.1722-0.642-0.0199-0.794-0.24820.40020.3611-0.0123.28810.30180.41394.2495-0.9821.795153.377247.219148.191
293.31820.4941-1.12987.50980.06164.20190.9806-0.31840.024-0.1571-0.3494-0.12930.48711.1214-0.01342.5087-0.06731.18580.7263-0.5732.7153149.202236.849137.543
304.34890.3972-1.86735.2358-0.79714.6689-0.7148-1.3389-1.0289-0.17431.7011-0.8459-0.5804-0.1564-0.00143.561-0.3828-0.05642.2043-0.03511.8737143.33230.78129.304
310.4830.4316-1.19090.363-0.97953.07340.8698-0.8645-0.97890.37151.46730.3414-0.00290.1513-0.00032.7771-0.0342-0.23484.04270.50443.3629135.242239.61139.623
323.9746-1.9323-2.06776.56510.28213.8286-2.64480.3839-0.3521-1.1932-0.7553-0.5923-0.5078-0.4165-0.00523.45650.19890.22363.0513-0.19763.4856153.125231.872124.187
332.0559-0.4936-1.06282.83071.44943.2422-1.70330.1368-0.4034-0.26890.0173-0.8507-0.5297-0.2211-0.02093.3947-0.09590.36373.35180.05382.5432143.801243.729142.761
342.5420.534-0.59166.2321-1.16794.61370.1932-0.30430.1058-0.3734-0.7229-0.6921-0.19070.5343-0.04234.3249-0.76340.90862.0215-0.07461.585140.168228.393136.908
352.25112.24753.01542.60752.00666.8152-0.7793-0.2119-0.1134-0.5654-0.4283-0.81560.62980.5429-0.10094.93230.07330.89852.43270.06031.9938144.463232.075147.666
362.1173-0.84141.27381.1939-1.30186.3969-0.09610.3925-0.0928-0.20110.0135-0.04310.0781-0.3784-0.03374.2981-1.74612.06965.387-0.31752.2618180.71237.514-7.63
370.7677-0.656-0.38272.7412-0.55643.66250.4561-0.2379-0.2613-0.56880.76090.89882.06170.49410.43526.0283-1.0602-0.90023.82180.10691.32156.545234.251-17.456
388.1229-0.9131.38142.25290.38572.7852-1.2797-0.07670.21690.1816-1.6642-1.12370.65380.8821-0.01035.8248-0.28840.51044.1534-0.19432.991164.619235.022-10.895
394.0978-1.22930.92941.3218-1.4151.5669-0.4278-0.1478-0.16630.2132-0.29110.00540.869-0.1935-0.16316.01531.62680.37982.344-0.1741.1816176.462236.769-1.359
401.90760.2341-0.06591.76230.73542.7083-1.68770.82111.4646-1.45691.24741.21130.96650.15410.02164.32810.27340.1482.5292-0.34292.984164.544237.622-4.904
416.1713-1.51270.52483.71520.0421.92110.2510.3451-0.2521-0.43260.3825-0.1684-0.9844-2.55030.01264.18081.28330.0712.914-0.17033.8811161.247235.877-7.629
424.5236-0.1322.14780.0661-0.25051.3997-0.8828-0.17990.0605-0.4541-0.00062.21731.58181.05330.10864.29940.3093-0.50322.60990.0572.6261162.07244.405-12.21
432.28572.60712.1133.0411.63489.3462-0.25520.12390.00140.26180.6256-0.1530.6711-0.39220.08993.68330.47620.91792.39510.48843.6532170.84245.635-12.524
441.79031.18361.20032.27351.5481.21140.0427-0.01540.0624-0.0405-0.03960.12010.019-0.0778-0.00252.3162-0.727-2.04784.24410.61052.8007157.23237.844-24.072
454.32442.0889-0.38471.9259-0.20380.1102-0.31031.06111.49710.08030.25770.4481-0.40330.31870.00840.9264-0.38250.25851.08420.06521.0177140.657243.95646.02
465.4761.7708-0.99294.9566-1.07746.1775-0.15480.889-0.9583-0.56910.0240.3368-0.09480.1622-0.11010.51310.0227-0.03330.6185-0.17730.9137114.894222.89346.535
471.5231.59620.19961.4302-0.46193.6842-0.34320.6105-0.1044-0.39510.3568-0.721-0.32030.03020.07781.111-0.36620.31831.3452-0.10061.775168.414249.26346.774
483.2557-0.90721.973.4902-2.16214.0294-0.08431.71330.15990.35420.0477-0.82811.50731.3250.0698-0.8497-1.57790.83871.2810.26390.9466182.935252.53750.98
492.24810.7333-0.68163.63550.13628.5915-0.66090.72730.2483-0.7746-0.0656-0.7483-0.68230.7364-0.1373.545-1.25110.44625.73090.03780.7638153.204228.108-9.89
508.8829-2.824-1.66293.14960.60760.3168-0.4484-0.14210.6529-0.4142-0.08990.73120.2553-0.045-0.35812.9554-1.55751.36764.6195-0.61643.5223171.292231.811-22.304
518.65670.7839-0.27135.18260.92355.6692-0.6035-0.4050.0833-0.43640.01070.3156-0.644-0.52020.16443.22771.4763-0.5935.1471-0.86582.4231161.03227.315-11.658
525.0370.29191.10585.45380.96055.26561.2157-0.20620.1828-1.11110.6905-0.2546-0.162-0.3718-0.02922.72060.8184-0.50264.7547-0.79731.9693154.956221.214-3.604
530.31390.21480.96540.65120.62453.07190.25460.6045-0.0061-0.67580.31420.53780.1734-0.28110.00626.4105-0.3785-0.95313.23470.64222.0705163.479213.439-14.415
546.4292-5.6627-4.66189.39096.22294.4144-0.16970.5067-0.1971-0.4513-0.1589-0.12610.25110.0435-0.01526.05580.4064-0.04253.24280.98442.4184164.341224.283-3.616
556.2296-0.4113-0.28383.97852.00483.55280.3520.1532-0.74050.3455-0.0961-0.0426-0.18950.33610.03512.10470.6620.20383.95560.20612.2623152.929233.4974.173
563.338-0.7362-0.72571.91350.41353.6152-1.3847-0.51741.0489-0.2972-1.0396-1.2921-0.5177-0.1401-0.01493.4270.0199-0.37273.11060.35482.2247167.731222.067-17.25
576.2432-0.55131.44573.51321.18638.05990.50790.5870.1661-0.3005-0.0643-0.3101-0.03850.38320.00272.54660.08030.04253.8812-0.81771.3489157.964218.156-16.613
587.86130.64814.41056.8033.87437.04020.0834-1.88270.37220.52530.18280.3594-0.1042-1.15180.08753.6284-0.7644-0.57133.2435-0.53212.7795145.041218.81-4.215
591.50991.6104-2.64011.7172-3.09329.03140.5240.35280.88490.2726-0.4803-1.0063-0.1125-0.67630.2143.27561.62190.18874.49211.25542.2994156.007223.112-21.925
606.6093-4.4056-4.235.184.85424.8902-1.1463-0.20480.3448-0.14920.59810.613-0.08870.2716-0.03112.309-0.20990.1752.0641-0.4841.6089175.014248.116116.368
610.15940.286-0.45171.6043-0.82771.2027-0.4123-0.0869-0.0350.02390.10410.11110.0348-0.29410.09752.99661.472-0.59951.9422-1.02722.0785160.466265.065118.894
623.2971-1.5965-0.60170.9280.15310.2009-0.0854-0.79-0.01340.2622-1.5482-0.54030.6454-1.06030.02221.32110.4830.34361.9061-0.06361.9822179.225251.142109.187
639.41952.7-3.43481.6716-0.53582.1042-0.1225-1.0835-0.10630.1403-0.0658-0.27860.7209-0.50570.12452.2846-0.01350.67282.1778-0.68362.7921161.772250.282108.438
640.41160.57-0.01340.94750.47411.4186-0.52390.24080.3485-0.5175-0.16060.7805-1.32010.0209-0.03491.744-0.12-2.71471.5774-2.14562.2302166.056253.126102.131
654.567-0.8243-0.3963.85210.98370.60740.04721.1673-0.103-0.4679-0.18640.96530.6142-0.1678-0.27792.3205-0.68120.89241.9087-0.61451.1401175.223257.47397.228
666.4097-1.68151.37711.90481.42362.473-1.22970.2741-0.087-0.742-2.38670.963-1.3584-1.3922-0.05461.49130.09540.03631.7882-0.41732.2996167.125261.472103.14
676.4156-1.34670.18150.65970.36380.53240.2271-0.60770.27710.832-0.12221.6753-0.8433-0.053-0.01442.48910.30520.05141.6772-0.10371.5237176.684258.732110.072
683.42270.52130.04832.48792.03842.5629-0.4265-0.73510.636-0.14210.24390.1871-0.3245-0.5955-0.76391.1128-0.44671.34861.9837-0.59872.4677156.799261.015111.761
691.219-0.2439-0.73711.86441.11452.6675-0.0428-0.52430.44020.9613-0.33220.4989-0.4162-0.06160.21382.4811-0.7173-0.50741.888-1.75771.3867168.639248.692109.801
701.18241.4964-0.82251.9638-1.41443.87311.81410.09540.2706-0.59520.8078-0.2589-0.8803-0.8594-0.03472.091-0.92420.15771.4197-0.63351.6385175.56247.29694.645
711.6363-0.8917-0.89033.12021.69992.6473-0.2597-0.5286-0.5774-0.3962-0.4719-0.30831.35640.47790.01111.30440.14590.1392.0788-0.32772.0987169.083246.683112.278
720.76050.04130.34330.5679-0.83642.31880.9362.02050.7094-0.83980.1563-0.5631.12020.06230.09110.2453-0.9746-0.06731.2677-0.50740.8978182.784246.77675.155
731.19992.67570.49955.88330.86620.97780.7406-1.1371-0.21320.8758-0.9132-0.518-0.68570.8449-0.06680.3847-0.06240.25180.6735-0.18250.9971161.619204.61881.969
743.97920.86690.05925.63821.15744.87470.1284-0.2885-0.31060.3284-0.00580.480.05460.031-0.10520.26560.06280.10770.41690.06490.9035146.065190.59478.916
751.09560.4123-0.97322.1767-0.52791.88960.38561.01680.34131.37680.2246-0.34740.3660.87180.09151.3615-0.34270.15780.771-0.17471.4035178.692241.96479.717
760.91390.11560.38065.8338-1.13810.2166-0.55830.09051.15490.24640.17421.708-0.333-0.1541-0.0051.3613-0.47270.12680.9978-0.1611.0453176.088258.1176.581
773.09352.907-0.99115.3948-3.01394.12520.4806-0.39260.2458-0.282-0.2746-0.11820.5096-0.18080.8212.039-0.86191.29942.4185-0.75620.8256154.074243.40395.828
782.3809-1.2888-2.39081.08371.04622.5866-0.8477-2.23520.65560.7695-0.68231.26270.75910.6726-0.23551.6854-1.4014-0.30452.60210.1951.682152.386228.866104.171
795.89930.7404-0.80461.12750.00161.8445-0.617-0.04420.76461.33171.24221.05240.6557-0.280.01061.8443-0.1481-0.11470.916-0.25491.1214165.135242.72786.983
800.6187-0.1157-1.5901-0.01530.28935.237-1.1359-0.62760.85180.45960.17490.03680.1029-1.55170.02941.8141-0.22170.59142.38440.39921.923164.492237.958105.002
815.1615-1.8847-0.92513.93853.34877.787-0.51260.4310.0560.02950.0493-0.08730.3146-0.4845-0.9492.2562-0.6037-0.99782.64150.821.9155168.484235.389105.799
823.05430.3871.07962.44412.13612.56230.33570.5571-0.08120.535-0.0015-0.9006-0.0448-0.6095-0.00553.3071-0.6237-0.78992.39780.86152.2582170.206232.43595.431
835.7421-2.498-1.30622.2121-2.07628.44320.411-0.4241-0.06990.60110.4090.4639-0.4342-0.05360.02251.60420.00920.2112.24210.9263.3334172.694229.644103.861
844.3237-2.45791.61142.703-0.57452.0983-0.9295-1.6485-0.75441.4630.8312-0.39530.8851.00690.00632.0769-0.37050.73672.0625-0.39672.4492165.689225.719102.095
850.2291-0.13910.42430.4787-1.35173.7565-0.11140.24841.3265-0.32671.11810.73250.1316-0.0696-0.07141.4055-0.3050.20392.1345-0.84752.1354158.184230.67694.576
860.03650.0824-0.13720.2255-0.3480.55510.0333-0.3959-0.0580.2725-0.02690.33940.267-0.39190.26673.2346-2.52522.3844.59710.43921.9307159.792229.325110.182
870.29710.76630.29774.0347-1.3482.51630.3326-0.83030.04871.72752.4799-0.65210.5788-0.1881-0.09041.8152-0.37790.40783.0991-0.53621.8864161.42246.34597.246
886.0319-0.0241-3.6352.31-0.99866.09780.1116-1.1422-0.110.37270.12760.12180.3722-0.16630.5462.47120.14141.25532.3555-0.31271.2976152.705231.856111.482
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:10 )A1 - 10
2X-RAY DIFFRACTION2( CHAIN A AND RESID 11:33 )A11 - 33
3X-RAY DIFFRACTION3( CHAIN A AND RESID 34:45 )A34 - 45
4X-RAY DIFFRACTION4( CHAIN A AND RESID 46:61 )A46 - 61
5X-RAY DIFFRACTION5( CHAIN A AND RESID 62:83 )A62 - 83
6X-RAY DIFFRACTION6( CHAIN A AND RESID 84:98 )A84 - 98
7X-RAY DIFFRACTION7( CHAIN A AND RESID 99:119 )A99 - 119
8X-RAY DIFFRACTION8( CHAIN B AND RESID 5:28 )B5 - 28
9X-RAY DIFFRACTION9( CHAIN B AND RESID 29:36 )B29 - 36
10X-RAY DIFFRACTION10( CHAIN B AND RESID 41:48 )B41 - 48
11X-RAY DIFFRACTION11( CHAIN B AND RESID 49:58 )B49 - 58
12X-RAY DIFFRACTION12( CHAIN B AND RESID 59:63 )B59 - 63
13X-RAY DIFFRACTION13( CHAIN B AND RESID 64:70 )B64 - 70
14X-RAY DIFFRACTION14( CHAIN B AND RESID 71:80 )B71 - 80
15X-RAY DIFFRACTION15( CHAIN B AND RESID 81:92 )B81 - 92
16X-RAY DIFFRACTION16( CHAIN B AND RESID 93:104 )B93 - 104
17X-RAY DIFFRACTION17( CHAIN B AND RESID 108:111 )B108 - 111
18X-RAY DIFFRACTION18( CHAIN H AND RESID 127:128 )H127 - 128
19X-RAY DIFFRACTION19( CHAIN H AND RESID 129:133 )H129 - 133
20X-RAY DIFFRACTION20( CHAIN H AND RESID 134:134 )H134
21X-RAY DIFFRACTION21( CHAIN H AND RESID 144:154 )H144 - 154
22X-RAY DIFFRACTION22( CHAIN H AND RESID 155:159 )H155 - 159
23X-RAY DIFFRACTION23( CHAIN H AND RESID 160:194 )H160 - 194
24X-RAY DIFFRACTION24( CHAIN H AND RESID 195:212 )H195 - 212
25X-RAY DIFFRACTION25( CHAIN H AND RESID 213:219 )H213 - 219
26X-RAY DIFFRACTION26( CHAIN H AND RESID 220:225 )H220 - 225
27X-RAY DIFFRACTION27( CHAIN L AND RESID 114:126 )L114 - 126
28X-RAY DIFFRACTION28( CHAIN L AND RESID 127:133 )L127 - 133
29X-RAY DIFFRACTION29( CHAIN L AND RESID 134:142 )L134 - 142
30X-RAY DIFFRACTION30( CHAIN L AND RESID 143:155 )L143 - 155
31X-RAY DIFFRACTION31( CHAIN L AND RESID 156:163 )L156 - 163
32X-RAY DIFFRACTION32( CHAIN L AND RESID 164:179 )L164 - 179
33X-RAY DIFFRACTION33( CHAIN L AND RESID 180:193 )L180 - 193
34X-RAY DIFFRACTION34( CHAIN L AND RESID 194:209 )L194 - 209
35X-RAY DIFFRACTION35( CHAIN L AND RESID 210:219 )L210 - 219
36X-RAY DIFFRACTION36( CHAIN A AND RESID 124:128 )A124 - 128
37X-RAY DIFFRACTION37( CHAIN A AND RESID 129:140 )A129 - 140
38X-RAY DIFFRACTION38( CHAIN A AND RESID 144:154 )A144 - 154
39X-RAY DIFFRACTION39( CHAIN A AND RESID 155:159 )A155 - 159
40X-RAY DIFFRACTION40( CHAIN A AND RESID 160:184 )A160 - 184
41X-RAY DIFFRACTION41( CHAIN A AND RESID 185:194 )A185 - 194
42X-RAY DIFFRACTION42( CHAIN A AND RESID 195:212 )A195 - 212
43X-RAY DIFFRACTION43( CHAIN A AND RESID 213:219 )A213 - 219
44X-RAY DIFFRACTION44( CHAIN A AND RESID 220:225 )A220 - 225
45X-RAY DIFFRACTION45( CHAIN F AND RESID 11:104 )F11 - 104
46X-RAY DIFFRACTION46( CHAIN F AND RESID 105:284 )F105 - 284
47X-RAY DIFFRACTION47( CHAIN F AND RESID 285:410 )F285 - 410
48X-RAY DIFFRACTION48( CHAIN F AND RESID 411:491 )F411 - 491
49X-RAY DIFFRACTION49( CHAIN B AND RESID 114:126 )B114 - 126
50X-RAY DIFFRACTION50( CHAIN B AND RESID 127:133 )B127 - 133
51X-RAY DIFFRACTION51( CHAIN B AND RESID 134:142 )B134 - 142
52X-RAY DIFFRACTION52( CHAIN B AND RESID 143:155 )B143 - 155
53X-RAY DIFFRACTION53( CHAIN B AND RESID 156:163 )B156 - 163
54X-RAY DIFFRACTION54( CHAIN B AND RESID 164:168 )B164 - 168
55X-RAY DIFFRACTION55( CHAIN B AND RESID 169:179 )B169 - 179
56X-RAY DIFFRACTION56( CHAIN B AND RESID 180:193 )B180 - 193
57X-RAY DIFFRACTION57( CHAIN B AND RESID 194:202 )B194 - 202
58X-RAY DIFFRACTION58( CHAIN B AND RESID 203:209 )B203 - 209
59X-RAY DIFFRACTION59( CHAIN B AND RESID 210:219 )B210 - 219
60X-RAY DIFFRACTION60( CHAIN H AND RESID 1:10 )H1 - 10
61X-RAY DIFFRACTION61( CHAIN H AND RESID 11:17 )H11 - 17
62X-RAY DIFFRACTION62( CHAIN H AND RESID 18:31 )H18 - 31
63X-RAY DIFFRACTION63( CHAIN H AND RESID 35:44 )H35 - 44
64X-RAY DIFFRACTION64( CHAIN H AND RESID 45:51 )H45 - 51
65X-RAY DIFFRACTION65( CHAIN H AND RESID 52:61 )H52 - 61
66X-RAY DIFFRACTION66( CHAIN H AND RESID 62:73 )H62 - 73
67X-RAY DIFFRACTION67( CHAIN H AND RESID 74:83 )H74 - 83
68X-RAY DIFFRACTION68( CHAIN H AND RESID 84:92 )H84 - 92
69X-RAY DIFFRACTION69( CHAIN H AND RESID 93:98 )H93 - 98
70X-RAY DIFFRACTION70( CHAIN H AND RESID 99:108 )H99 - 108
71X-RAY DIFFRACTION71( CHAIN H AND RESID 109:119 )H109 - 119
72X-RAY DIFFRACTION72( CHAIN I AND RESID 11:37 )I11 - 37
73X-RAY DIFFRACTION73( CHAIN I AND RESID 38:104 )I38 - 104
74X-RAY DIFFRACTION74( CHAIN I AND RESID 105:284 )I105 - 284
75X-RAY DIFFRACTION75( CHAIN I AND RESID 285:366 )I285 - 366
76X-RAY DIFFRACTION76( CHAIN I AND RESID 367:493 )I367 - 493
77X-RAY DIFFRACTION77( CHAIN L AND RESID 1:7 )L1 - 7
78X-RAY DIFFRACTION78( CHAIN L AND RESID 8:23 )L8 - 23
79X-RAY DIFFRACTION79( CHAIN L AND RESID 25:31 )L25 - 31
80X-RAY DIFFRACTION80( CHAIN L AND RESID 37:48 )L37 - 48
81X-RAY DIFFRACTION81( CHAIN L AND RESID 49:53 )L49 - 53
82X-RAY DIFFRACTION82( CHAIN L AND RESID 54:58 )L54 - 58
83X-RAY DIFFRACTION83( CHAIN L AND RESID 59:63 )L59 - 63
84X-RAY DIFFRACTION84( CHAIN L AND RESID 64:71 )L64 - 71
85X-RAY DIFFRACTION85( CHAIN L AND RESID 72:80 )L72 - 80
86X-RAY DIFFRACTION86( CHAIN L AND RESID 81:92 )L81 - 92
87X-RAY DIFFRACTION87( CHAIN L AND RESID 96:104 )L96 - 104
88X-RAY DIFFRACTION88( CHAIN L AND RESID 108:111 )L108 - 111

+
万見について

-
お知らせ

-
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

+
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

+
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。

-
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