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- PDB-5kuy: Influenza hemagglutinin H3 A/Hong Kong/1/1968 in complex with des... -

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基本情報

登録情報
データベース: PDB / ID: 5kuy
タイトルInfluenza hemagglutinin H3 A/Hong Kong/1/1968 in complex with designed inhibitor protein HSB.2A
要素
  • (Hemagglutinin ...) x 2
  • Designed influenza inhibitor HSB.2A
キーワードPROTEIN BINDING / Influenza / inhibitor / complex / design
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 / membrane
類似検索 - 分子機能
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 / Alpha-Beta Complex / Alpha Beta
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)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.598 Å
データ登録者Bernard, S.M. / Wilson, I.A.
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)R56 AI117675 米国
引用ジャーナル: Nat. Biotechnol. / 年: 2017
タイトル: Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site.
著者: Strauch, E.M. / Bernard, S.M. / La, D. / Bohn, A.J. / Lee, P.S. / Anderson, C.E. / Nieusma, T. / Holstein, C.A. / Garcia, N.K. / Hooper, K.A. / Ravichandran, R. / Nelson, J.W. / Sheffler, W. ...著者: Strauch, E.M. / Bernard, S.M. / La, D. / Bohn, A.J. / Lee, P.S. / Anderson, C.E. / Nieusma, T. / Holstein, C.A. / Garcia, N.K. / Hooper, K.A. / Ravichandran, R. / Nelson, J.W. / Sheffler, W. / Bloom, J.D. / Lee, K.K. / Ward, A.B. / Yager, P. / Fuller, D.H. / Wilson, I.A. / Baker, D.
履歴
登録2016年7月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年6月14日Provider: repository / タイプ: Initial release
改定 1.12017年6月28日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22017年7月26日Group: Author supporting evidence / Database references / カテゴリ: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
改定 1.32019年12月11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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _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10月4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11月13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: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Designed influenza inhibitor HSB.2A
H: Designed influenza inhibitor HSB.2A
I: Designed influenza inhibitor HSB.2A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)203,99321
ポリマ－199,9579
非ポリマー4,03612
水8,467470
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)154.259, 219.322, 104.524
Angle α, β, γ (deg.)90.00, 117.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11G-102-

HOH

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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: 35506.949 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (strain A/Hong Kong/1/1968 H3N2) (A型インフルエンザウイルス)
株: A/Hong Kong/1/1968 H3N2 / 遺伝子: HA / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q91MA7
#2: タンパク質 Hemagglutinin HA2


分子量: 20284.391 Da / 分子数: 3 / Mutation: R452G / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (strain A/Hong Kong/1/1968 H3N2) (A型インフルエンザウイルス)
株: A/Hong Kong/1/1968 H3N2 / 遺伝子: HA / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q91MA7

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タンパク質 / 非ポリマー , 2種, 473分子 GHI

#3: タンパク質 Designed influenza inhibitor HSB.2A


分子量: 10861.091 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 470 / 由来タイプ: 天然 / 式: H2O

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糖 , 3種, 12分子

#4: 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: 5 / 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
#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: 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
#6: 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


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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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: 3.91 Å3/Da / 溶媒含有率: 68.56 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 10% PEG 6000, 100 mM MES pH 6.0

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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: 23-ID-D / 波長: 1.033 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2015年10月18日
放射モノクロメーター: double crystal / 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: 1.033 Å / 相対比: 1
反射解像度: 2.598→48.134 Å / Num. obs: 95012 / % possible obs: 100 % / 冗長度: 6.4 % / Net I/σ(I): 13.3
反射 シェル解像度: 2.6→2.69 Å / 冗長度: 5.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2 / CC1/2: 0.831 / % possible all: 99.9

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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
HKL-2000データ削減
SCALA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: 4FNK

4fnk


解像度: 2.598→48.134 Å / SU ML: 0.27 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 20.61 / 立体化学のターゲット値: ML
詳細: Density for the third HSB copy was clearly observable at the third RBS and a copy was manually placed by superimposing an HA-HSB complex from within the model. The position of the manually ...詳細: Density for the third HSB copy was clearly observable at the third RBS and a copy was manually placed by superimposing an HA-HSB complex from within the model. The position of the manually placed copy was further optimized by rigid body fitting within the FO-FC map in COOT and rigid body refinement in Phenix. The model was refined through iterative rounds of model building in COOT and refinement in Phenix. Several regions of the third copy of HSB are poorly ordered. The final model contains regions of the protein with 2FO-FC density for backbone atoms at 1.0 sigma.
Rfactor反射数%反射
Rfree0.2042 4710 5.01 %
Rwork0.1728 --
obs0.1744 94061 99.77 %
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: 2.598→48.134 Å
タンパク質核酸リガンド溶媒全体
原子数13234 0 263 470 13967
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00313811
X-RAY DIFFRACTIONf_angle_d0.56618782
X-RAY DIFFRACTIONf_dihedral_angle_d12.3248178
X-RAY DIFFRACTIONf_chiral_restr0.0442114
X-RAY DIFFRACTIONf_plane_restr0.0032428
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.598-2.62760.29461500.24022818X-RAY DIFFRACTION94
2.6276-2.65850.281720.22722964X-RAY DIFFRACTION100
2.6585-2.69090.25861640.22312998X-RAY DIFFRACTION100
2.6909-2.7250.23351530.2192964X-RAY DIFFRACTION100
2.725-2.76080.24791470.21752999X-RAY DIFFRACTION100
2.7608-2.79860.27111430.20892973X-RAY DIFFRACTION100
2.7986-2.83860.25031750.21442925X-RAY DIFFRACTION100
2.8386-2.8810.26541530.20952993X-RAY DIFFRACTION100
2.881-2.9260.25431530.20233007X-RAY DIFFRACTION100
2.926-2.97390.25651680.1992968X-RAY DIFFRACTION100
2.9739-3.02520.20481460.19532954X-RAY DIFFRACTION100
3.0252-3.08020.24691640.19082990X-RAY DIFFRACTION100
3.0802-3.13950.21441540.18892959X-RAY DIFFRACTION100
3.1395-3.20350.23491620.18592981X-RAY DIFFRACTION100
3.2035-3.27320.2371590.19623013X-RAY DIFFRACTION100
3.2732-3.34930.22321630.19722951X-RAY DIFFRACTION100
3.3493-3.4330.20421420.1932994X-RAY DIFFRACTION100
3.433-3.52580.22951540.20563000X-RAY DIFFRACTION100
3.5258-3.62950.23631610.1842945X-RAY DIFFRACTION100
3.6295-3.74660.22881610.18013005X-RAY DIFFRACTION100
3.7466-3.88050.21271500.16952979X-RAY DIFFRACTION100
3.8805-4.03580.19491640.15292978X-RAY DIFFRACTION100
4.0358-4.21940.17891530.14342981X-RAY DIFFRACTION100
4.2194-4.44170.14931550.13162993X-RAY DIFFRACTION100
4.4417-4.71970.16171590.1262990X-RAY DIFFRACTION100
4.7197-5.08380.17641570.13262971X-RAY DIFFRACTION100
5.0838-5.59470.16351490.14953022X-RAY DIFFRACTION100
5.5947-6.40260.17941630.16933011X-RAY DIFFRACTION100
6.4026-8.06050.18841570.17232996X-RAY DIFFRACTION100
8.0605-48.14240.16271590.16433029X-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)
10.35460.34790.3589.38793.33012.390.1230.05350.2183-0.7307-0.04880.1606-0.2743-0.0757-0.080.3830.06440.03420.46410.06670.451326.17925.368313.1908
23.238-3.6177-1.49054.17631.28791.27350.22330.14260.269-0.535-0.121-0.4216-0.25220.0987-0.14540.3960.01680.05320.38980.01020.550553.1093-33.8002-4.099
31.1639-0.77690.97173.43721.93124.84340.07520.1267-0.1052-0.0973-0.18060.073-0.0228-0.05010.15770.24770.01260.00980.37080.00240.439248.2726-46.34-5.1018
41.42040.4101-0.12461.59930.44911.4124-0.12310.0071-0.15930.02280.0647-0.01220.24750.14920.03560.35090.02920.07780.36-0.00850.567959.6742-60.3025-4.8108
51.6961-0.1751-0.20942.20751.34863.8113-0.1268-0.0835-0.25170.2270.01810.24850.1381-0.25560.08360.383-0.0220.12920.3734-0.00870.621650.9024-62.2823-0.5221
62.5785-2.9323-1.54144.6871.12751.2781-0.1438-0.25820.1138-0.17850.1183-0.31140.01280.09490.00080.2773-0.0240.05070.39760.00620.395455.9159-46.61852.7235
72.8595-2.5616-2.95522.92393.47953.54120.3172-0.06980.4969-0.37980.1561-0.543-0.42660.0498-0.43430.46070.04130.04610.33380.02510.527544.4263-22.28020.5042
82.8902-3.5615-1.9018.08242.93092.25790.18060.13210.1426-0.9812-0.17270.0024-0.207-0.07740.00810.40040.0106-0.04420.3754-0.00250.285232.6855-11.658.4912
98.15323.0932-3.63291.9977-1.65046.05940.0631-0.24530.7553-0.25470.008-0.04520.0683-0.0429-0.12340.45110.0857-0.00680.38120.01670.513426.751910.024316.9308
101.446-0.40920.32249.46211.38121.1045-0.07970.05340.31820.34580.3067-1.0070.01890.0332-0.22760.32640.01780.04310.4089-0.00570.619335.615510.286720.0248
113.90930.33271.40812.3295-0.6070.483-0.19840.23170.1244-0.31430.3077-0.4334-0.14020.517-0.18010.4390.02460.06230.47030.0260.523640.3905-32.83146.4456
120.3845-0.9237-0.21017.88342.40760.69910.0205-0.02240.0260.1315-0.00160.0781-0.0301-0.0395-0.02610.37120.0391-0.020.39720.0220.401628.0567-9.268519.684
130.89231.0937-0.61169.28063.64094.4442-0.1193-0.34230.2707-0.13030.1769-0.637-0.27540.00460.00820.48140.0782-0.0110.38420.04750.529728.636825.665626.33
147.9247-2.70120.07562.8168-2.01451.99270.1023-0.14790.2470.40640.0622-0.5901-0.0171-0.0302-0.18310.63040.0441-0.12010.458-0.16830.692323.836730.415435.9762
152.9629-3.2539-1.29344.72484.07315.3341-0.178-0.37120.18910.3410.6524-0.6363-0.17850.6852-0.55330.58170.0042-0.1420.43490.00930.525336.2145-2.329840.375
160.3858-0.6663-0.00934.13540.12210.2412-0.1022-0.1056-0.11760.5590.0708-0.09740.1326-0.00260.00340.48020.0664-0.04240.44360.08670.501140.3972-52.988332.992
172.09250.44010.37212.84480.17072.37870.01820.2529-0.4008-0.12520.0760.12020.2769-0.2003-0.11810.4982-0.003-0.01090.40690.01240.522538.9144-77.908721.3044
185.65562.1475-0.51155.96661.6044.55180.09421.0949-0.3673-0.4216-0.0855-0.0607-0.0046-0.17810.00580.51570.0555-0.00730.440.08290.406941.9026-72.26312.2088
190.43260.801-0.18632.95380.98721.3001-0.01310.30430.0314-0.01810.14210.42240.1887-0.2468-0.08440.43220.0594-0.03560.5550.0860.634531.517-68.448621.1338
200.6155-1.2449-0.2584.54140.1193-0.565-0.1963-0.1828-0.00150.67510.1763-0.0771-0.0245-0.04910.03810.51370.0813-0.1020.43930.02880.442239.0173-32.730435.586
213.38160.4704-1.22332.53552.16393.597-0.1375-0.42260.08190.71220.2132-0.451-0.44090.2907-0.07910.75340.1634-0.23530.4955-0.07140.532731.52393.637547.0763
221.4874-0.9039-0.64898.93256.33974.8963-0.5664-0.12770.01640.9434-0.05270.88750.15880.06230.62440.68270.1464-0.05570.55470.02280.380625.2261-9.18345.6282
231.32480.3047-1.39242.00621.01754.0386-0.297-0.2626-0.18040.52690.111-0.00640.38360.07830.2890.50770.0664-0.05950.45320.0650.454336.3475-41.76925.767
240.6629-1.1957-0.52354.5751.91531.2833-0.1496-0.17920.03840.36640.2618-0.2028-0.0530.0947-0.11680.41540.0551-0.06220.40520.02730.339329.5551-13.175830.0817
253.8032-0.2539-1.43453.2486-0.75263.9137-0.4641-0.23380.47051.35960.5403-0.3934-0.2298-0.1538-0.07270.98340.2215-0.10170.5599-0.10120.521919.283116.803751.7388
26-0.11980.006-0.16984.49272.69481.9932-0.00670.0743-0.13210.3312-0.12950.50880.1489-0.13790.20940.31390.03340.00960.5407-0.00560.52486.8273-23.264622.039
271.8547-0.182-0.68342.16150.14951.6675-0.07520.4276-0.4177-0.4969-0.04330.09980.4042-0.28070.12640.5351-0.0363-0.06160.5726-0.15660.659218.4177-61.0571-6.8067
282.4402-0.73890.56343.1921-1.32292.6189-0.06960.1509-0.4494-0.4941-0.259-0.46230.67620.19740.34820.58910.04060.06370.5264-0.17140.776429.4433-67.4027-4.8256
290.6317-0.3646-0.60432.29841.29591.7185-0.030.1518-0.2012-0.0627-0.09170.3627-0.0645-0.17720.15710.30080.0126-0.04150.4197-0.01520.435812.7332-36.544711.2158
306.4826-3.5331-0.34435.48520.71781.7161-0.2637-0.21790.010.6222-0.03040.2853-0.0737-0.20460.26760.42010.07140.09160.45960.04980.40513.25862.011833.0654
318.1398-7.0409-5.55876.69875.7046.70030.46630.2491-0.4007-0.4033-0.55130.6947-0.3848-0.0457-0.06570.33030.0502-0.02050.44140.03680.42297.3386-3.715620.4669
322.3194-1.0961-0.38970.8346-0.59263.5042-0.01630.1824-0.0174-0.38280.0094-0.0963-0.0075-0.31880.01550.34280.001-0.09690.4948-0.07870.597520.3929-39.958911.1691
331.382-2.5611-0.73896.32571.47850.6645-0.1234-0.13210.03770.27350.2028-0.040.03460.086-0.08710.3310.0632-0.02180.41550.01330.333919.4947-13.814425.2935
343.3348-1.72791.65217.74820.47056.8052-0.0295-0.3326-0.28840.71360.29910.8176-0.2221-0.4319-0.24660.43860.10860.16980.44950.10.55023.545916.13736.9092
353.84451.89791.61714.1037-0.75652.6754-0.11930.04920.25760.0735-0.0780.3169-0.2039-0.12550.21650.48960.16250.07180.40950.02690.43734.427722.304730.1805
367.5286-4.9201-3.98876.13595.53894.88950.27731.2264-0.32510.3439-0.67380.30920.5967-0.01620.11650.40430.10960.07580.6490.17430.848163.8192-97.864333.3802
374.98832.95040.88414.1986-0.62414.69180.03020.35070.51690.0138-0.03550.23510.1031-0.253-0.01220.46210.07390.10280.35240.00690.515447.401-87.054535.0292
385.36040.8442-0.50144.9388-1.29455.65830.21730.1484-0.2776-0.2543-0.1114-0.063-0.1050.1132-0.07830.4808-0.00080.03330.298-0.03920.569450.2906-93.370434.8806
396.72241.0919-5.35624.9608-3.03756.60810.2649-0.1602-0.18590.1224-0.53150.354-0.6425-0.41320.24270.53050.0290.1080.3561-0.06090.742147.1989-94.678536.8888
401.5371.5307-2.04994.5418-6.42089.62940.04140.198-0.29650.0775-0.2615-0.52820.07430.02220.51540.43980.03990.14660.444-0.04840.629449.6658-91.462529.1345
415.4475.6703-5.82865.8579-6.31736.77470.00210.42640.0159-0.48160.15580.42060.3481-0.291-0.10470.4570.06680.0040.4357-0.03210.618545.4002-91.682228.0896
423.25980.1948-0.03012.69623.30745.6164-0.04450.09510.1731-0.29920.0175-0.02060.0135-0.0519-0.09340.5176-0.07010.07830.34820.03580.559268.7303-61.1717-25.9707
435.73384.04560.85465.23181.0473.0345-0.28620.11880.3106-0.22880.1403-0.0474-0.09030.26640.16810.4656-0.00580.11180.430.00890.571873.8869-62.1324-24.5273
442.76370.8491-3.60424.81340.50525.1373-0.1290.887-0.4193-0.4389-0.0552-0.04040.25230.04940.14760.43970.02210.07010.3606-0.04890.488568.2278-65.1808-22.0811
452.7442-0.8722-3.96875.71421.06855.694-0.2839-0.6495-0.97210.0299-0.0161-0.19010.55310.47380.19010.4807-0.0220.0680.396-0.01980.502570.8477-65.8704-18.4621
462.68590.7083-0.60372.8772-0.81385.2794-0.59861.0371-0.1029-0.32370.187-0.8856-0.5091-1.09940.37741.0892-0.1418-0.12181.2226-0.68091.9217.1026-77.5216-15.716
470.09610.05050.00260.02640.0001-0.00220.33210.2063-2.046-0.4299-0.0445-0.54170.7228-0.33770.00541.3125-0.4034-0.15821.8330.20321.2418.4381-70.3406-24.847
483.4901-2.85031.9133.0412-2.70737.1281-0.0161-0.15720.24710.1038-0.35011.42340.8435-0.91810.39121.6243-0.3862-0.10091.0676-0.6441.62888.2702-84.8336-16.4107
491.68240.1352-0.39182.48322.01824.2038-0.55240.66-0.14-0.4918-0.04030.82761.14410.57320.02371.272-0.2547-0.07610.9176-0.29171.27514.9159-80.7772-12.2679
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 269 )
7X-RAY DIFFRACTION7chain 'A' and (resid 270 through 300 )
8X-RAY DIFFRACTION8chain 'A' and (resid 301 through 325 )
9X-RAY DIFFRACTION9chain 'B' and (resid 330 through 351 )
10X-RAY DIFFRACTION10chain 'B' and (resid 352 through 384 )
11X-RAY DIFFRACTION11chain 'B' and (resid 385 through 404 )
12X-RAY DIFFRACTION12chain 'B' and (resid 405 through 461 )
13X-RAY DIFFRACTION13chain 'B' and (resid 462 through 482 )
14X-RAY DIFFRACTION14chain 'B' and (resid 483 through 505 )
15X-RAY DIFFRACTION15chain 'C' and (resid 9 through 33 )
16X-RAY DIFFRACTION16chain 'C' and (resid 34 through 122 )
17X-RAY DIFFRACTION17chain 'C' and (resid 123 through 195 )
18X-RAY DIFFRACTION18chain 'C' and (resid 196 through 228 )
19X-RAY DIFFRACTION19chain 'C' and (resid 229 through 265 )
20X-RAY DIFFRACTION20chain 'C' and (resid 266 through 324 )
21X-RAY DIFFRACTION21chain 'D' and (resid 330 through 359 )
22X-RAY DIFFRACTION22chain 'D' and (resid 360 through 384 )
23X-RAY DIFFRACTION23chain 'D' and (resid 385 through 404 )
24X-RAY DIFFRACTION24chain 'D' and (resid 405 through 461 )
25X-RAY DIFFRACTION25chain 'D' and (resid 462 through 501 )
26X-RAY DIFFRACTION26chain 'E' and (resid 9 through 65 )
27X-RAY DIFFRACTION27chain 'E' and (resid 66 through 175 )
28X-RAY DIFFRACTION28chain 'E' and (resid 176 through 249 )
29X-RAY DIFFRACTION29chain 'E' and (resid 250 through 325 )
30X-RAY DIFFRACTION30chain 'F' and (resid 330 through 359 )
31X-RAY DIFFRACTION31chain 'F' and (resid 360 through 384 )
32X-RAY DIFFRACTION32chain 'F' and (resid 385 through 404 )
33X-RAY DIFFRACTION33chain 'F' and (resid 405 through 461 )
34X-RAY DIFFRACTION34chain 'F' and (resid 462 through 474 )
35X-RAY DIFFRACTION35chain 'F' and (resid 475 through 500 )
36X-RAY DIFFRACTION36chain 'G' and (resid 5 through 13 )
37X-RAY DIFFRACTION37chain 'G' and (resid 14 through 31 )
38X-RAY DIFFRACTION38chain 'G' and (resid 32 through 48 )
39X-RAY DIFFRACTION39chain 'G' and (resid 49 through 62 )
40X-RAY DIFFRACTION40chain 'G' and (resid 63 through 76 )
41X-RAY DIFFRACTION41chain 'G' and (resid 77 through 88 )
42X-RAY DIFFRACTION42chain 'H' and (resid 5 through 31 )
43X-RAY DIFFRACTION43chain 'H' and (resid 32 through 62 )
44X-RAY DIFFRACTION44chain 'H' and (resid 63 through 76 )
45X-RAY DIFFRACTION45chain 'H' and (resid 77 through 89 )
46X-RAY DIFFRACTION46chain 'I' and (resid 11 through 30 )
47X-RAY DIFFRACTION47chain 'I' and (resid 31 through 35 )
48X-RAY DIFFRACTION48chain 'I' and (resid 36 through 53 )
49X-RAY DIFFRACTION49chain 'I' and (resid 54 through 84 )

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る