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- PDB-6fyu: Structure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in com... -

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基本情報

登録情報
データベース: PDB / ID: 6fyu
タイトルStructure of H7(A/Shanghai/2/2013) Influenza Hemagglutinin in complex SD36
要素
  • (Hemagglutinin) x 2
  • Single domain antibody SD36
キーワードVIRAL PROTEIN / Influenza / single domain antibody / hemagglutinin
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 / membrane => GO:0016020 / 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
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Hemagglutinin / Hemagglutinin / Hemagglutinin
類似検索 - 構成要素
生物種Influenza A virus (A型インフルエンザウイルス)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.643 Å
データ登録者Laursen, N.S. / Wilson, I.A.
資金援助 米国, 2件
組織認可番号国
National Institutes of HealthR56 AI117675 米国
National Institutes of HealthR56 AI127371 米国
引用ジャーナル: Science / 年: 2018
タイトル: Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin.
著者: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut ...著者: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut Kolfschoten / David Zuijdgeest / Roel Straetemans / Ryan M B Hoffman / Travis Nieusma / Jesper Pallesen / Hannah L Turner / Steffen M Bernard / Andrew B Ward / Jinquan Luo / Leo L M Poon / Anna P Tretiakova / James M Wilson / Maria P Limberis / Ronald Vogels / Boerries Brandenburg / Joost A Kolkman / Ian A Wilson /
要旨: Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza ...Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.
履歴
登録2018年3月12日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年11月7日Provider: repository / タイプ: Initial release
改定 1.12018年11月14日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 2.02020年7月8日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_entity_id / _chem_comp.type ..._atom_site.label_entity_id / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id
改定 3.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_angle / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation

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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
B: Hemagglutinin
C: Single domain antibody SD36
D: Hemagglutinin
E: Hemagglutinin
F: Single domain antibody SD36
G: Hemagglutinin
H: Hemagglutinin
I: Single domain antibody SD36
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)211,63325
ポリマ－208,2779
非ポリマー3,35616
水6,395355
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 area39230 Å2
ΔGint-156 kcal/mol
Surface area75620 Å2
手法PISA
単位格子
Length a, b, c (Å)101.424, 128.159, 192.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 1種, 3分子 BEH

#2: タンパク質 Hemagglutinin


分子量: 21081.207 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)
遺伝子: HA / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: A0A0C4ZTH5, UniProt: A0A097PHH8*PLUS

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抗体 , 2種, 6分子 ADGCFI

#1: 抗体 Hemagglutinin


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)
遺伝子: HA / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: A0A4Y5QYN9, UniProt: A0A097PHH8*PLUS
#3: 抗体 Single domain antibody SD36


分子量: 13350.808 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 細胞株 (発現宿主): HEK293 Expi / 発現宿主: Homo sapiens (ヒト)

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糖 , 2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: 3 / 由来タイプ: 天然 / 参照: UniProt: A0A097PHH8*PLUS
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: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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: 天然 / 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 , 2種, 359分子

#6: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 4 / 由来タイプ: 天然 / 式: Na
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 355 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.99 Å3/Da / 溶媒含有率: 58.88 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M Tri-potassium citrate, 20 % PEG3350

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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-B / 波長: 1.0332 Å
検出器タイプ: MARRESEARCH / 検出器: CCD / 日付: 2013年10月24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: 1.0332 Å / 相対比: 1
反射解像度: 2.64→50 Å / Num. obs: 73520 / % possible obs: 100 % / 冗長度: 7.5 % / Rpim(I) all: 0.05 / Rsym value: 0.14 / Net I/σ(I): 13.2
反射 シェル解像度: 2.64→2.74 Å

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_1839精密化
XDSデータ削減
XSCALE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 / 解像度: 2.643→48.026 Å / SU ML: 0.32 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 21.92
Rfactor反射数%反射
Rfree0.2162 2000 2.72 %
Rwork0.1864 --
obs0.1872 73519 99.4 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.643→48.026 Å
タンパク質核酸リガンド溶媒全体
原子数14227 0 214 355 14796
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00314745
X-RAY DIFFRACTIONf_angle_d0.73119962
X-RAY DIFFRACTIONf_dihedral_angle_d12.8065431
X-RAY DIFFRACTIONf_chiral_restr0.032177
X-RAY DIFFRACTIONf_plane_restr0.0032622
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6434-2.70950.33971310.28474660X-RAY DIFFRACTION92
2.7095-2.78270.28811420.2565074X-RAY DIFFRACTION100
2.7827-2.86460.27211410.23575079X-RAY DIFFRACTION100
2.8646-2.9570.25461420.22885063X-RAY DIFFRACTION100
2.957-3.06270.26291430.235088X-RAY DIFFRACTION100
3.0627-3.18530.27641410.22015094X-RAY DIFFRACTION100
3.1853-3.33020.27021440.21525114X-RAY DIFFRACTION100
3.3302-3.50580.23621420.20265116X-RAY DIFFRACTION100
3.5058-3.72530.18521430.18135103X-RAY DIFFRACTION100
3.7253-4.01280.21731440.16845147X-RAY DIFFRACTION100
4.0128-4.41640.17431450.14865153X-RAY DIFFRACTION100
4.4164-5.05490.14331440.14395163X-RAY DIFFRACTION100
5.0549-6.36630.22031460.1655234X-RAY DIFFRACTION100
6.3663-48.03390.20111520.18145431X-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)
11.7416-1.7428-0.8731.81761.0430.6230.1471-0.21160.488-0.21780.1622-0.432-0.12510.1898-0.30.2717-0.01960.07370.35260.00780.404147.147149.96367.4285
22.3963-0.8789-1.89151.75640.72282.35090.06060.06970.10680.0544-0.00510.0857-0.0801-0.0726-0.06170.18650.0023-0.01730.2096-0.00780.3032-2.6114167.461126.5572
31.5662-0.7547-0.34923.53242.01213.5128-0.1514-0.1856-0.00590.39290.3441-0.06120.24030.2351-0.1830.23650.05750.01180.25070.00750.282-7.2181163.520139.0466
41.3290.6769-0.42771.1891-0.37212.1135-0.02120.1053-0.2504-0.06720.06710.07820.1835-0.1156-0.01080.22480.0491-0.01730.1794-0.00650.3188-6.2167157.310828.1385
52.0525-0.639-0.45420.60640.2180.8833-0.04780.1891-0.0475-0.10830.0025-0.0446-0.0647-0.02610.01760.2473-0.0236-0.00340.25090.01780.275230.4647154.17212.736
66.116-0.0538-1.9021.70960.10853.0669-0.15170.5826-0.0729-0.1370.0258-0.21550.1054-0.12170.13320.3266-0.00920.03630.2239-0.02520.259354.9535140.7754-5.5226
73.9869-0.3364-0.59092.9865-1.31471.9773-0.0731-0.10520.0148-0.23620.2852-0.15250.0758-0.0304-0.22070.29340.001-0.00530.37040.01710.403318.7751154.606723.2821
87.0001-2.6088-6.59431.25662.59767.3976-0.3801-0.3281-0.57420.00820.03860.13250.31730.43120.34980.2513-0.02860.05510.26880.01530.354140.9216140.813715.5169
93.1425-0.4306-0.133.9770.7813.9606-0.34120.583-0.7385-0.2404-0.1797-0.28540.96160.11620.41780.61010.00120.25230.4779-0.11080.582866.3562126.0522-14.2624
102.04819.01614.94448.2768-1.80897.64720.330301.22430.3049-0.22870.4543-0.9620.00050.03340.3232-0.01790.15810.365-0.00890.444231.143153.9622-17.7536
114.44580.1597-0.24422.2682-0.7682.0636-0.11380.45410.1184-0.32260.04110.32040.2363-0.70220.03460.2883-0.0775-0.02970.5221-0.04960.279724.689145.5284-15.1996
122.0746-7.1793-0.41597.76730.8942.37790.0097-0.25990.4216-0.1712-0.13390.1679-0.6287-1.88010.12760.3652-0.00870.04940.7079-0.06910.445322.2585148.5174-4.7354
132.06412.1128-4.20270.9538-0.27382.6367-0.0557-0.365-0.47980.1823-0.13070.15970.3345-0.41130.16290.2656-0.09280.03670.39170.00620.35334.3595136.8802-7.6512
147.85281.4252-3.67763.1107-1.48884.88720.1190.1404-0.48230.1599-0.0090.04690.1464-0.2845-0.12090.2918-0.0866-0.02210.4345-0.02220.354426.9911139.3754-13.7389
153.2787-0.2961.50332.14120.99911.16070.2331-0.8447-0.38680.2403-0.33940.49820.3493-0.52480.05750.3326-0.09590.03910.606-0.01110.434217.6968144.7597-10.6471
160.95570.128-1.88320.3182-0.80954.8173-0.0274-0.08360.4268-0.07160.0882-0.1051-0.6130.297-0.10520.2621-0.04720.01750.3009-0.03850.2638.0998147.3227-3.8438
177.21131.93681.04263.6319-0.38953.4644-0.22290.05830.67840.12560.0920.2647-0.1455-0.31230.17560.25480.01490.02060.3732-0.1220.375724.7382151.6278-10.5766
183.0407-1.4255-1.29831.16990.92813.4952-0.3133-0.9266-0.33940.23870.2312-0.00450.55940.40680.08160.3230.06130.00330.44140.07920.428353.2758127.849231.9073
192.5054-1.5471-0.62474.1870.61621.7359-0.5059-0.45660.09520.37130.73150.22670.12620.0919-0.22260.46780.0274-0.0230.68240.01120.360717.0721166.367859.7871
203.0754-1.0534-0.70253.47171.15931.1614-0.3854-0.32020.039-0.22980.47860.56730.2370.0487-0.07180.4942-0.0153-0.11530.790.07610.379714.0661165.354956.4683
212.9523-1.4262-1.73682.71811.34263.4313-0.1713-0.83980.20250.34050.2646-0.36170.10380.3183-0.09250.27370.0116-0.04520.49610.01910.277743.889139.361940.556
223.9654-1.1415-1.58461.2030.41611.4959-0.0013-0.2325-0.1638-0.08620.0513-0.24280.16580.2468-0.06990.30390.0385-0.0010.27780.03220.314456.9959131.41621.802
232.2205-1.4341.17714.93980.0090.7772-0.42330.3441-0.7134-1.12020.4811-0.73741.20981.26050.29370.93840.10990.35160.7916-0.07160.897881.2938115.9633-2.8475
247.45480.97080.3472.02-3.50748.06740.0145-0.2257-1.360.78670.2793-0.36650.0099-0.4986-0.23070.3159-0.08510.03570.49310.06850.557874.8399150.467337.041
257.67840.23161.79674.14842.40528.78680.4556-0.31630.0374-0.3765-0.2011-1.152-0.86490.5386-0.08010.3489-0.0314-0.01270.4102-0.08330.619966.9209171.439728.8989
269.4791-7.32690.60252.0611-3.76556.87310.16660.0620.48130.38950.176-0.09780.07160.3688-0.34620.3348-0.0901-0.00670.3971-0.08540.450173.4365157.009829.9539
271.8333-0.00060.94494.116-0.3621.5404-0.1477-0.28870.32570.40060.1061-0.53550.2845-0.0992-0.00650.2695-0.0058-0.03210.4437-0.04690.218967.2377149.5331.9952
281.3256-1.053-2.02742.10271.90182.1196-0.1483-1.06920.67571.37250.09141.16660.63740.39190.05670.4343-0.03470.04870.6679-0.0310.370158.9049155.642935.3878
295.0982-4.2545-2.15647.7550.72062.59110.23430.279-0.0186-0.82870.03920.1129-0.1817-0.2553-0.20240.28530.11540.03170.51590.04370.314763.2227147.121421.351
303.6221-3.1756-0.21137.5162-0.31763.5299-0.10190.7527-0.0194-0.2627-0.19030.2991-0.2242-0.30850.26120.27730.0074-0.05030.48150.03280.281762.0421156.965923.6934
312.1888-9.5261-1.85832.09062.80522.51810.6213-0.20490.8023-0.8383-0.0605-0.8338-0.0552-0.1536-0.47570.3718-0.01460.07130.49050.00570.594272.9722154.143525.4322
320.7528-0.31960.12654.5453-1.02492.5223-0.0444-0.30970.2536-0.08260.0394-0.0784-0.332-0.2952-0.03260.32730.05910.04440.4824-0.02310.340262.2834162.606331.915
335.0562-3.1426-2.7992.95252.29421.762-0.3564-0.22-0.12610.67990.01230.38740.6645-0.10790.20370.3206-0.037-0.02520.41050.01610.343562.5202140.85631.2004
346.4958-1.4022-2.05047.2978-4.34334.824-0.1767-1.1708-0.26530.28520.1216-0.13970.6189-0.6770.01410.3919-0.02370.05460.54440.03680.272465.7123147.88638.1875
352.0209-2.27942.37064.5591-0.4142.0438-0.5157-0.47480.83070.6941-0.0643-0.3463-0.6703-0.00680.48190.4138-0.033-0.02840.4789-0.11870.503565.538168.329735.1921
363.6042-0.8033-1.89570.85590.55121.787-0.11690.5506-0.557-0.2719-0.11560.19960.0178-0.28330.20980.4636-0.07950.06170.2979-0.04160.381930.7397120.59368.0892
371.7428-1.53140.22152.02220.01411.1054-0.4713-0.5264-0.59350.690.54440.9437-0.0252-0.4493-0.05010.6550.08940.3180.56210.26160.6963-4.7978133.703950.1218
381.7919-1.17330.20532.475-0.46331.8825-0.3178-0.6684-0.15141.0540.36520.3492-0.4678-0.3519-0.07060.95370.21370.26420.52320.14010.4496-5.943146.665755.3982
391.5748-0.29030.27592.65540.94292.3382-0.229-0.7719-0.41151.16450.43980.0046-0.3621-0.2809-0.19880.94080.1830.25410.6070.29250.53672.6873137.743356.9169
402.39530.2127-1.83712.05150.0672.5433-0.1323-0.272-0.4730.3325-0.04720.02660.31460.12270.16760.3107-0.07160.05610.30710.08970.513515.0193124.833128.3869
414.8188-3.0985-4.10275.55843.30964.96910.23430.7639-0.4579-0.6421-0.3921-0.01280.0936-0.50090.21190.4416-0.0378-0.01490.2879-0.03180.269531.3534123.09356.3462
424.1418-1.29830.58114.10451.90334.5126-0.18340.4195-0.7327-1.0823-0.01190.27020.4731-0.1190.14310.7128-0.11840.14550.3625-0.08610.560145.0376110.0631-1.6278
434.2179-2.7099-3.46034.13083.67767.1418-0.097-0.0389-0.6982-0.53180.11950.11070.12520.2317-0.17690.53710.02740.07260.2329-0.02050.460543.8814110.942910.9607
440.62080.28281.16512.59660.4714.144-0.3197-0.5974-0.55090.65020.5143-0.25280.7280.5606-0.10340.5346-0.04050.00060.43930.06570.630923.6841128.17534.3558
452.05437.26313.06292.0125-0.3124.6156-0.06780.25660.1343-0.87710.52280.753-0.0585-0.4121-0.41110.4256-0.06410.07710.40220.09130.58035.5441140.596433.7287
466.0461-4.9297-4.66614.77823.8614.16190.2679-0.20030.0988-0.46770.0407-0.3058-0.09340.2031-0.30090.3233-0.02010.04680.25630.0050.288235.6727130.408816.3733
475.26-4.53681.02895.3036-2.35131.7838-0.28570.47750.4246-0.2019-0.1081-0.4438-0.1504-0.01160.28850.8108-0.02640.1870.3921-0.08330.797660.8114113.5022-4.2135
483.77070.2306-1.50363.05320.5772.7368-0.5190.003-0.9852-0.51870.3178-0.43460.93240.20750.1280.96330.11740.18340.4544-0.05590.818559.6667102.4203-0.3335
491.0313-0.22671.99141.9887-0.15517.0216-0.1550.6082-0.8296-0.2953-0.1877-0.41050.87621.08070.32170.77220.20490.35140.6277-0.09051.111570.701105.213-4.8173
502.30370.3980.64651.8810.94054.292-0.293-0.3644-0.7107-0.33940.1657-0.07370.8195-0.11220.091.14630.06180.0740.53630.15640.71235.178995.446534.8243
512.84131.35112.05014.3676-1.23612.7981-0.2123-0.042-0.3404-0.13290.0784-0.22080.35470.3490.02990.7447-0.080.15540.4150.08120.43833.9821102.375825.1231
524.4224-0.001-1.30112.8878-0.19195.1104-0.1286-0.5173-0.06420.30790.1250.21180.41840.2523-0.0610.57320.0344-0.00510.27990.04590.300537.052107.987431.0833
533.0429-1.1627-1.80084.41952.6166.9839-0.0473-0.4704-0.9139-0.17870.2455-0.4520.10540.0686-0.11420.87330.0640.17860.5190.13530.659841.632397.319328.6485
542.01074.0737-1.37271.1205-0.96633.3072-0.0203-0.11631.4023-0.0305-0.20370.2252-0.85490.0870.02420.89960.06560.00340.65790.07230.676134.9597105.805444.9093
553.24720.9625-2.06252.641-1.22453.0065-0.32640.0632-0.2302-0.21860.3961-0.01631.1529-0.7072-0.12740.7244-0.04650.0490.37060.10070.432930.3196103.694926.5639
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 163 )
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 237 )
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 268 )
5X-RAY DIFFRACTION5chain 'A' and (resid 269 through 328 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 55 )
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 74 )
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 172 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 7 )
11X-RAY DIFFRACTION11chain 'C' and (resid 8 through 39 )
12X-RAY DIFFRACTION12chain 'C' and (resid 40 through 51 )
13X-RAY DIFFRACTION13chain 'C' and (resid 52 through 59 )
14X-RAY DIFFRACTION14chain 'C' and (resid 60 through 82 )
15X-RAY DIFFRACTION15chain 'C' and (resid 82A through 94 )
16X-RAY DIFFRACTION16chain 'C' and (resid 95 through 100E)
17X-RAY DIFFRACTION17chain 'C' and (resid 100F through 112 )
18X-RAY DIFFRACTION18chain 'D' and (resid 11 through 51 )
19X-RAY DIFFRACTION19chain 'D' and (resid 52 through 213 )
20X-RAY DIFFRACTION20chain 'D' and (resid 214 through 268 )
21X-RAY DIFFRACTION21chain 'D' and (resid 269 through 327 )
22X-RAY DIFFRACTION22chain 'E' and (resid 5 through 162 )
23X-RAY DIFFRACTION23chain 'E' and (resid 163 through 172 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 7 )
25X-RAY DIFFRACTION25chain 'F' and (resid 8 through 17 )
26X-RAY DIFFRACTION26chain 'F' and (resid 18 through 25 )
27X-RAY DIFFRACTION27chain 'F' and (resid 26 through 39 )
28X-RAY DIFFRACTION28chain 'F' and (resid 40 through 51 )
29X-RAY DIFFRACTION29chain 'F' and (resid 52 through 59 )
30X-RAY DIFFRACTION30chain 'F' and (resid 60 through 72 )
31X-RAY DIFFRACTION31chain 'F' and (resid 73 through 82 )
32X-RAY DIFFRACTION32chain 'F' and (resid 82A through 94 )
33X-RAY DIFFRACTION33chain 'F' and (resid 95 through 100E)
34X-RAY DIFFRACTION34chain 'F' and (resid 100F through 106 )
35X-RAY DIFFRACTION35chain 'F' and (resid 107 through 112 )
36X-RAY DIFFRACTION36chain 'G' and (resid 11 through 51 )
37X-RAY DIFFRACTION37chain 'G' and (resid 52 through 163 )
38X-RAY DIFFRACTION38chain 'G' and (resid 164 through 237 )
39X-RAY DIFFRACTION39chain 'G' and (resid 238 through 268 )
40X-RAY DIFFRACTION40chain 'G' and (resid 269 through 308 )
41X-RAY DIFFRACTION41chain 'G' and (resid 309 through 327 )
42X-RAY DIFFRACTION42chain 'H' and (resid 4 through 27 )
43X-RAY DIFFRACTION43chain 'H' and (resid 28 through 55 )
44X-RAY DIFFRACTION44chain 'H' and (resid 56 through 65 )
45X-RAY DIFFRACTION45chain 'H' and (resid 66 through 74 )
46X-RAY DIFFRACTION46chain 'H' and (resid 75 through 126 )
47X-RAY DIFFRACTION47chain 'H' and (resid 127 through 137 )
48X-RAY DIFFRACTION48chain 'H' and (resid 138 through 158 )
49X-RAY DIFFRACTION49chain 'H' and (resid 159 through 171 )
50X-RAY DIFFRACTION50chain 'I' and (resid 2 through 25 )
51X-RAY DIFFRACTION51chain 'I' and (resid 26 through 39 )
52X-RAY DIFFRACTION52chain 'I' and (resid 40 through 72 )
53X-RAY DIFFRACTION53chain 'I' and (resid 73 through 82 )
54X-RAY DIFFRACTION54chain 'I' and (resid 82A through 87 )
55X-RAY DIFFRACTION55chain 'I' and (resid 88 through 112 )

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlc1.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