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- PDB-7nks: Structure of the Hantaan virus Gn glycoprotein ectodomain in comp... -

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基本情報

登録情報
データベース: PDB / ID: 7nks
タイトルStructure of the Hantaan virus Gn glycoprotein ectodomain in complex with Fab HTN-Gn1
要素
  • Envelope polyprotein
  • Fab HTN-Gn1 heavy chain
  • Fab HTN-Gn1 light chain
キーワードVIRAL PROTEIN / Hantaan virus glycoprotein / Gn glycoprotein / Fab / neutralizing antibody / viral glycoprotein in complex with antibody
機能・相同性
機能・相同性情報


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / signal transduction / zinc ion binding / membrane
類似検索 - 分子機能
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Envelopment polyprotein
類似検索 - 構成要素
生物種Hantaan orthohantavirus (ウイルス)
Oryctolagus cuniculus (ウサギ)
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Rissanen, I. / Bowden, T.A. / Huiskonen, J.T. / Stass, R.
資金援助 英国, フィンランド, 米国, 11件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MR/L009528/1 英国
Medical Research Council (MRC, United Kingdom)MR/S007555/1 英国
Medical Research Council (MRC, United Kingdom)MR/N002091/1 英国
Medical Research Council (MRC, United Kingdom)MR/K024426/1 英国
Medical Research Council (MRC, United Kingdom)MC/PC/15068 英国
Academy of Finland309605 フィンランド
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R41AI132047 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R41AI132047-01S1 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R43AI142911 米国
Wellcome Trust203141/Z/16/Z 英国
Wellcome Trust093305/Z/10/Z 英国
引用ジャーナル: mBio / 年: 2021
タイトル: Structural Basis for a Neutralizing Antibody Response Elicited by a Recombinant Hantaan Virus Gn Immunogen.
著者: Ilona Rissanen / Stefanie A Krumm / Robert Stass / Annalis Whitaker / James E Voss / Emily A Bruce / Sylvia Rothenberger / Stefan Kunz / Dennis R Burton / Juha T Huiskonen / Jason W Botten / ...著者: Ilona Rissanen / Stefanie A Krumm / Robert Stass / Annalis Whitaker / James E Voss / Emily A Bruce / Sylvia Rothenberger / Stefan Kunz / Dennis R Burton / Juha T Huiskonen / Jason W Botten / Thomas A Bowden / Katie J Doores /
要旨: Hantaviruses are a group of emerging pathogens capable of causing severe disease upon zoonotic transmission to humans. The mature hantavirus surface presents higher-order tetrameric assemblies of two ...Hantaviruses are a group of emerging pathogens capable of causing severe disease upon zoonotic transmission to humans. The mature hantavirus surface presents higher-order tetrameric assemblies of two glycoproteins, Gn and Gc, which are responsible for negotiating host cell entry and constitute key therapeutic targets. Here, we demonstrate that recombinantly derived Gn from Hantaan virus (HTNV) elicits a neutralizing antibody response (serum dilution that inhibits 50% infection [ID], 1:200 to 1:850) in an animal model. Using antigen-specific B cell sorting, we isolated monoclonal antibodies (mAbs) exhibiting neutralizing and non-neutralizing activity, termed mAb HTN-Gn1 and mAb nnHTN-Gn2, respectively. Crystallographic analysis reveals that these mAbs target spatially distinct epitopes at disparate sites of the N-terminal region of the HTNV Gn ectodomain. Epitope mapping onto a model of the higher order (Gn-Gc) spike supports the immune accessibility of the mAb HTN-Gn1 epitope, a hypothesis confirmed by electron cryo-tomography of the antibody with virus-like particles. These data define natively exposed regions of the hantaviral Gn that can be targeted in immunogen design. The spillover of pathogenic hantaviruses from rodent reservoirs into the human population poses a continued threat to human health. Here, we show that a recombinant form of the Hantaan virus (HTNV) surface-displayed glycoprotein, Gn, elicits a neutralizing antibody response in rabbits. We isolated a neutralizing (HTN-Gn1) and a non-neutralizing (nnHTN-Gn2) monoclonal antibody and provide the first molecular-level insights into how the Gn glycoprotein may be targeted by the antibody-mediated immune response. These findings may guide rational vaccine design approaches focused on targeting the hantavirus glycoprotein envelope.
履歴
登録2021年2月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年6月23日Provider: repository / タイプ: Initial release
改定 1.12021年7月14日Group: Database references / カテゴリ: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22021年9月15日Group: Database references / カテゴリ: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.42024年10月23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

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集合体

登録構造単位
B: Envelope polyprotein
C: Fab HTN-Gn1 heavy chain
D: Fab HTN-Gn1 light chain
H: Fab HTN-Gn1 heavy chain
L: Fab HTN-Gn1 light chain
A: Envelope polyprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)178,12412
ポリマ－175,1576
非ポリマー2,9686
水00
1
B: Envelope polyprotein
C: Fab HTN-Gn1 heavy chain
D: Fab HTN-Gn1 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)89,3118
ポリマ－87,5783
非ポリマー1,7335
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-17 kcal/mol
Surface area33890 Å2
手法PISA
2
H: Fab HTN-Gn1 heavy chain
L: Fab HTN-Gn1 light chain
A: Envelope polyprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)88,8134
ポリマ－87,5783
非ポリマー1,2351
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-18 kcal/mol
Surface area34160 Å2
手法PISA
単位格子
Length a, b, c (Å)228.022, 158.630, 70.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 21 through 34 or resid 37...
21(chain B and (resid 21 through 264 or resid 271 through 371))
12(chain C and resid 3 through 221)
22(chain H and resid 3 through 221)
13(chain D and resid 2 through 216)
23chain L
14chain F
24chain G

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNSERSER(chain A and (resid 21 through 34 or resid 37...AF21 - 346 - 19
121GLUGLUHISHIS(chain A and (resid 21 through 34 or resid 37...AF37 - 19822 - 183
131SERSERASPASP(chain A and (resid 21 through 34 or resid 37...AF205 - 281190 - 266
141SERSERGLUGLU(chain A and (resid 21 through 34 or resid 37...AF291 - 371276 - 356
211ASNASNPHEPHE(chain B and (resid 21 through 264 or resid 271 through 371))BA21 - 2646 - 249
221THRTHRGLUGLU(chain B and (resid 21 through 264 or resid 271 through 371))BA271 - 371256 - 356
112GLNGLNCYSCYS(chain C and resid 3 through 221)CB3 - 2213 - 221
212GLNGLNCYSCYS(chain H and resid 3 through 221)HD3 - 2213 - 221
113GLYGLYASPASP(chain D and resid 2 through 216)DC2 - 2162 - 216
213GLYGLYASPASPchain LLE2 - 2162 - 216
114NAGNAGMANMANchain FFH1 - 7
214NAGNAGMANMANchain GGG1 - 7

NCSアンサンブル:
ID
1
2
3
4

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要素

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抗体 , 2種, 4分子 CHDL

#2: 抗体 Fab HTN-Gn1 heavy chain


分子量: 24284.264 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Oryctolagus cuniculus (ウサギ) / 細胞株 (発現宿主): H293T / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 Fab HTN-Gn1 light chain


分子量: 22943.162 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Oryctolagus cuniculus (ウサギ) / プラスミド: pHLsec / 細胞株 (発現宿主): H293T / 発現宿主: Homo sapiens (ヒト)

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タンパク質 / 非ポリマー , 2種, 5分子 BA

#1: タンパク質 Envelope polyprotein / M polyprotein


分子量: 40350.871 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Hantaan orthohantavirus (ウイルス)
プラスミド: pHLsec / 細胞株 (発現宿主): H293T / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A0A077D153
#6: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 3 / 由来タイプ: 組換発現 / 式: C3H8O3

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糖 , 3種, 3分子

#4: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


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


タイプ: oligosaccharide / 分子量: 1235.105 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 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: 1 / 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: 3.66 Å3/Da / 溶媒含有率: 66.39 %
結晶化温度: 296 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 0.1 M HEPES/MOPS pH 7.5, 0.12 M monosaccharides (glucose, mannose, galactose, fucose, xylose, NAG) and 30% ppt2 (ethylene glycol and polyethylene glycol 8000)

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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: Diamond / ビームライン: I03 / 波長: 0.9762 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2018年7月2日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9762 Å / 相対比: 1
反射解像度: 3.5→62.22 Å / Num. obs: 33293 / % possible obs: 99.66 % / 冗長度: 12.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.042 / Rrim(I) all: 0.151 / Net I/σ(I): 12.1
反射 シェル解像度: 3.5→3.625 Å / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3252 / CC1/2: 0.94 / Rpim(I) all: 0.204 / % possible all: 98.81

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19精密化
PDB_EXTRACT3.27データ抽出
DIALSデータ削減
DIALSデータスケーリング
PHENIX1.19位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5OPG, 5M63

5opg

5m63


解像度: 3.5→57.01 Å / SU ML: 0.46 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 30.58 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2739 1676 5.04 %
Rwork0.2237 31546 -
obs0.2262 33222 99.69 %
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
原子変位パラメータBiso max: 332.73 Å2 / Biso mean: 124.9756 Å2 / Biso min: 48.68 Å2
精密化ステップサイクル: final / 解像度: 3.5→57.01 Å
タンパク質核酸リガンド溶媒全体
原子数11662 0 198 0 11860
Biso mean--150.33 --
残基数----1550
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1948X-RAY DIFFRACTION9.3TORSIONAL
12B1948X-RAY DIFFRACTION9.3TORSIONAL
21C1318X-RAY DIFFRACTION9.3TORSIONAL
22H1318X-RAY DIFFRACTION9.3TORSIONAL
31D1292X-RAY DIFFRACTION9.3TORSIONAL
32L1292X-RAY DIFFRACTION9.3TORSIONAL
41F124X-RAY DIFFRACTION9.3TORSIONAL
42G124X-RAY DIFFRACTION9.3TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.60.3361260.31822574270099
3.6-3.720.34641370.283425932730100
3.72-3.850.34421380.26625702708100
3.85-4.010.3221440.266225792723100
4.01-4.190.34631410.245525982739100
4.19-4.410.27231020.202726552757100
4.41-4.690.26231570.184425712728100
4.69-5.050.23941560.191726132769100
5.05-5.550.23381300.196726452775100
5.55-6.360.2641490.226826552804100
6.36-8.010.30461510.240726772828100
8.01-57.010.22731450.20672816296199
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)
13.42320.4607-4.09243.27861.17895.8289-0.25180.8899-1.0506-0.3116-0.3303-0.38650.37420.58280.41650.77730.06750.07491.39930.10160.67985.5597-26.0145-8.0234
21.95750.813-2.09311.4691-0.91982.4927-0.48690.6249-0.3842-0.31760.1597-1.110.12871.80170.48140.8396-0.05050.28462.29680.00421.4247100.6526-21.9672-12.8492
34.81010.1265-2.41817.5944-3.00762.3573-0.6409-0.11770.59360.41720.2117-1.2994-0.62052.14240.15470.7898-0.3553-0.0981.9310.22661.047100.5613-8.4989-4.4036
45.6275-0.8008-1.66213.18620.74140.57-0.2660.19570.77430.16290.18920.234-0.35740.07850.07680.689-0.13190.00640.98530.13580.563985.65-11.7124-5.3626
58.34230.87391.37153.4560.92966.122-0.07662.00360.8491-0.506-0.56621.0344-0.2956-0.690.68780.51210.2027-0.03111.59940.05230.686149.8776-26.1818-10.5137
66.40763.326-0.4237.99691.29148.4552-0.1431.6611-0.4433-0.34130.1851-0.92590.20690.63530.13810.41560.16030.08431.2195-0.13270.586959.5631-31.9794-9.5639
72.8362-0.48070.28742.3917-0.65563.586-0.02731.161-0.4819-0.3661-0.6043-0.12360.21520.01030.50170.65610.2568-0.04611.8466-0.15880.514349.0019-31.7408-10.249
80.20250.7799-0.55083.5053-1.87756.2629-0.09590.66540.00320.630.60270.5269-0.0711-0.68370.22860.6507-0.00010.03062.0222-0.20720.366719.984-32.05961.9904
90.17250.34840.54380.9261-0.01897.0790.03341.0921-0.5982-0.2730.1615-0.33721.29440.477-0.87580.94480.1536-0.41441.8976-0.73210.565331.4874-43.1573-1.8689
100.76850.4518-1.09522.4598-1.46226.79720.23640.98280.2057-0.140.52380.2501-0.5601-1.23350.30910.750.0411-0.00012.37310.04870.5418.1309-29.2146-2.2408
115.7659-1.4796-4.96652.39512.41666.33350.0979-2.2437-0.25040.4522-0.1459-0.67910.0269-0.01040.06950.49960.0446-0.03531.21170.04660.779653.3895-35.378515.9694
125.6111-0.4672-5.32317.7078-0.63815.87930.0946-0.724-1.3983-0.7938-1.2755-1.0225-1.18170.59161.11650.64170.021-0.05061.24530.06120.597164.2151-32.317311.8725
136.4001-0.4355-1.52446.6322-2.30621.412-0.2373-0.23370.53280.4934-0.0614-0.3096-0.3124-0.89360.28550.70210.1221-0.05871.3168-0.17130.448654.9255-24.493712.065
145.5839-0.286-0.52630.82970.19431.32740.402-0.01930.06510.1101-0.2753-0.0787-0.16510.054-0.01070.71590.0405-0.06831.3787-0.09320.526442.4878-33.61679.2045
151.98493.20373.08257.92293.08916.37090.0870.8498-0.7391-0.9701-0.07891.10850.16290.0216-0.120.67320.1187-0.16211.2184-0.3580.718724.7054-43.10612.6791
163.75654.68821.89046.60121.87584.73680.32880.6644-0.195-0.061-0.242-0.13110.10170.9425-0.14830.65740.2115-0.10541.0397-0.20620.646926.1014-44.0519.015
178.45381.83735.95025.76290.35867.2986-0.08060.6502-1.951-0.3091-0.1920.14210.7233-0.95070.16650.726-0.1074-0.01431.3846-0.23870.837216.0561-47.978914.2421
186.67691.9328-1.44072.272-1.11461.93520.1437-1.0586-0.00630.2184-0.6309-0.46950.3958-0.02410.14740.5385-0.34880.0392.3180.16680.8136-6.2348-31.145-11.4671
198.1382-2.3831-0.41694.219-2.84925.80750.697-1.50481.47730.324-0.5533-0.8930.11020.5689-0.16430.6565-0.34490.17361.5069-0.0950.6878-14.7971-24.2611-16.8765
202.4926-1.2406-1.2253.7184-0.27714.5130.2496-1.6164-0.11660.7668-0.30680.7871-0.7726-0.0297-0.42790.6769-0.62840.17262.3447-0.16770.9156-18.745-28.7916-10.6825
214.6555-4.50691.83388.811-1.17671.85610.9778-0.25790.3487-0.011-1.83230.354-0.12070.22760.86270.6708-0.16570.02382.053-0.08620.6925-14.5378-23.0034-21.2271
222.3789-0.6411-1.63820.96911.87264.8463-0.0928-0.4076-0.85840.0992-0.0263-0.03760.49830.2919-0.00250.7512-0.1126-0.02411.75360.34450.563316.584-37.0639-23.5841
230.953-1.1076-0.9621.23841.46195.72860.4731-0.94380.2228-0.04520.9461-0.3927-0.03760.0493.22010.7234-0.13440.20462.65840.4314-0.21915.5928-31.4086-22.8642
240.70071.3638-1.91476.3968-0.38978.1175-0.14510.94550.3259-0.2838-0.49540.66140.0121-0.73980.35330.63470.0546-0.10881.9540.03650.4086-15.5077-31.651-41.8375
259.91272.0194-0.79377.04612.75763.45240.59920.3081.1160.2727-0.55360.5417-0.23380.5267-0.05980.64180.00790.10781.9952-0.01680.5783-17.2017-23.5887-32.4673
263.82560.5892-1.42411.82560.88171.46330.53820.2521.0538-0.3025-0.39590.235-0.2758-0.3974-0.09840.75110.13050.11462.20460.2770.7326-17.4637-22.0064-37.9636
270.59860.00451.3351.7035-0.10433.00380.63820.3432-0.017-0.0078-0.10470.2866-0.726-1.0936-0.47740.76550.0043-0.05861.55180.03790.3063-8.8274-31.4821-38.1663
286.8451-2.42583.23058.0065-1.76395.34810.1401-0.7582-0.98820.3545-0.0212-0.28930.1378-1.0531-0.30540.7508-0.254-0.10751.64220.12980.587714.0425-42.9543-33.5548
297.29210.91464.19925.29320.19663.403-0.29530.5966-1.2593-0.2995-0.01620.00860.12690.3171-0.01810.5158-0.01110.08590.9465-0.01350.546321.1428-48.2284-38.8216
303.9626-1.0968-3.92375.72020.06034.31250.46050.0805-0.4120.6395-0.33851.2173-0.6553-0.2673-0.34520.73-0.18770.22781.3621-0.17721.4845-65.5682-22.2849-6.5762
315.6534-0.5102-2.64354.6112-1.21944.83470.46550.6889-0.7214-0.24540.14780.47960.3585-0.06010.01620.7009-0.17650.17880.9575-0.05040.7681-52.6813-26.6812-16.887
324.824-2.9571-1.831.8191.29081.05390.09460.2095-0.1617-0.0137-0.09910.3485-0.2635-0.1086-0.0540.7429-0.05670.1421.2181-0.09920.8775-55.3695-16.92-15.2879
334.20210.05241.92060.90440.67381.75530.25121.42460.7052-0.9252-0.3026-0.8805-0.54170.94140.38691.47530.41210.52261.26280.70132.4635-57.6329-0.2983-28.2599
343.58140.101-0.52771.22581.33461.80680.72850.31991.3051-0.2496-0.49410.1446-0.83720.4712-0.33411.0859-0.09380.39980.709-0.02171.3595-49.1804-6.4571-17.5519
353.48732.57960.15183.29333.12827.31270.83680.09981.32050.21350.12770.7394-1.216-0.0593-0.44091.12750.01290.63750.4536-0.2231.776-42.154-10.1069-21.9468
362.348-0.07232.9522.81031.10744.22770.091-0.41290.32990.0574-0.2662-1.1615-0.8604-0.36680.13671.02810.0330.37650.4302-0.20871.4874-55.2889-3.1485-15.0077
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 20 through 106 )B20 - 106
2X-RAY DIFFRACTION2chain 'B' and (resid 107 through 229 )B107 - 229
3X-RAY DIFFRACTION3chain 'B' and (resid 230 through 275 )B230 - 275
4X-RAY DIFFRACTION4chain 'B' and (resid 276 through 372 )B276 - 372
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 41 )C1 - 41
6X-RAY DIFFRACTION6chain 'C' and (resid 42 through 70 )C42 - 70
7X-RAY DIFFRACTION7chain 'C' and (resid 71 through 128 )C71 - 128
8X-RAY DIFFRACTION8chain 'C' and (resid 129 through 173 )C129 - 173
9X-RAY DIFFRACTION9chain 'C' and (resid 174 through 185 )C174 - 185
10X-RAY DIFFRACTION10chain 'C' and (resid 186 through 221 )C186 - 221
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 19 )D1 - 19
12X-RAY DIFFRACTION12chain 'D' and (resid 20 through 34 )D20 - 34
13X-RAY DIFFRACTION13chain 'D' and (resid 35 through 76 )D35 - 76
14X-RAY DIFFRACTION14chain 'D' and (resid 77 through 134 )D77 - 134
15X-RAY DIFFRACTION15chain 'D' and (resid 135 through 155 )D135 - 155
16X-RAY DIFFRACTION16chain 'D' and (resid 156 through 191 )D156 - 191
17X-RAY DIFFRACTION17chain 'D' and (resid 192 through 216 )D192 - 216
18X-RAY DIFFRACTION18chain 'H' and (resid 3 through 18 )H3 - 18
19X-RAY DIFFRACTION19chain 'H' and (resid 19 through 53 )H19 - 53
20X-RAY DIFFRACTION20chain 'H' and (resid 54 through 93 )H54 - 93
21X-RAY DIFFRACTION21chain 'H' and (resid 94 through 114 )H94 - 114
22X-RAY DIFFRACTION22chain 'H' and (resid 115 through 150 )H115 - 150
23X-RAY DIFFRACTION23chain 'H' and (resid 151 through 222 )H151 - 222
24X-RAY DIFFRACTION24chain 'L' and (resid 2 through 26 )L2 - 26
25X-RAY DIFFRACTION25chain 'L' and (resid 27 through 50 )L27 - 50
26X-RAY DIFFRACTION26chain 'L' and (resid 51 through 98 )L51 - 98
27X-RAY DIFFRACTION27chain 'L' and (resid 99 through 119 )L99 - 119
28X-RAY DIFFRACTION28chain 'L' and (resid 120 through 191 )L120 - 191
29X-RAY DIFFRACTION29chain 'L' and (resid 192 through 216 )L192 - 216
30X-RAY DIFFRACTION30chain 'A' and (resid 21 through 38 )A21 - 38
31X-RAY DIFFRACTION31chain 'A' and (resid 39 through 73 )A39 - 73
32X-RAY DIFFRACTION32chain 'A' and (resid 74 through 214 )A74 - 214
33X-RAY DIFFRACTION33chain 'A' and (resid 215 through 248 )A215 - 248
34X-RAY DIFFRACTION34chain 'A' and (resid 249 through 310 )A249 - 310
35X-RAY DIFFRACTION35chain 'A' and (resid 311 through 344 )A311 - 344
36X-RAY DIFFRACTION36chain 'A' and (resid 345 through 371 )A345 - 371

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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