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- PDB-6pcu: VP8* of a G2P[4] human rotavirus in complex with scFv antibody 9 -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6pcu
タイトルVP8* of a G2P[4] human rotavirus in complex with scFv antibody 9
要素
  • Outer capsid protein VP4
  • Variable domain of antibody scFv9
キーワードviral protein/immune system / rotavirus / VIRAL PROTEIN / antibody / scFv / viral protein-immune system complex
機能・相同性
機能・相同性情報


viral capsid / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane
類似検索 - 分子機能
Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Outer capsid protein VP4
類似検索 - 構成要素
生物種Rotavirus A (ロタウイルス A)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Hu, L. / Venkataram Prasad, B.V.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36040 米国
Robert A. Welch FoundationQ1279 米国
引用ジャーナル: J.Clin.Invest. / 年: 2019
タイトル: Human VP8* mAbs neutralize rotavirus selectively in human intestinal epithelial cells.
著者: Feng, N. / Hu, L. / Ding, S. / Sanyal, M. / Zhao, B. / Sankaran, B. / Ramani, S. / McNeal, M. / Yasukawa, L.L. / Song, Y. / Prasad, B.V.V. / Greenberg, H.B.
履歴
登録2019年6月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年9月4日Provider: repository / タイプ: Initial release
改定 1.12019年9月11日Group: Data collection / Database references / カテゴリ: citation / Item: _citation.page_first / _citation.page_last
改定 1.22019年12月18日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02019年12月25日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / 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.label_seq_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_ref_seq_dif.align_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
改定 2.12023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Outer capsid protein VP4
B: Variable domain of antibody scFv9
D: Outer capsid protein VP4
E: Variable domain of antibody scFv9
G: Outer capsid protein VP4
H: Variable domain of antibody scFv9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)134,55916
ポリマ－133,6146
非ポリマー94510
水9,476526
1
A: Outer capsid protein VP4
B: Variable domain of antibody scFv9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,8225
ポリマ－44,5382
非ポリマー2843
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-21 kcal/mol
Surface area17150 Å2
手法PISA
2
D: Outer capsid protein VP4
E: Variable domain of antibody scFv9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1068
ポリマ－44,5382
非ポリマー5686
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-41 kcal/mol
Surface area16910 Å2
手法PISA
3
G: Outer capsid protein VP4
H: Variable domain of antibody scFv9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)44,6303
ポリマ－44,5382
非ポリマー921
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area16860 Å2
手法PISA
単位格子
Length a, b, c (Å)182.428, 182.428, 193.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDモデル要素
11D-435-

HOH

21D-449-

HOH

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要素

#1: タンパク質 Outer capsid protein VP4 / Indian G2P[4] rotavirus VP8*


分子量: 18498.297 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Rotavirus A (ロタウイルス A) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q2VE61
#2: 抗体 Variable domain of antibody scFv9


分子量: 26039.730 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#3: 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: 4 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 6 / 由来タイプ: 合成 / 式: SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 526 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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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: 3.08 Å3/Da / 溶媒含有率: 60.07 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: 100 mM HEPES (pH 7.0) 20% w/v PEG8000

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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: ALS / ビームライン: 5.0.1 / 波長: 0.97741 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2018年4月15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: 0.97741 Å / 相対比: 1
反射解像度: 2.4→35 Å / Num. obs: 63500 / % possible obs: 100 % / 冗長度: 13 % / Net I/σ(I): 10.83
反射 シェル解像度: 2.4→2.44 Å / 冗長度: 12.6 % / Num. unique obs: 3131 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(DEV_3374: ???)精密化
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: 5VX4

5vx4


解像度: 2.4→35 Å / SU ML: 0.31 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 23.42
Rfactor反射数%反射
Rfree0.237 3157 5 %
Rwork0.186 --
obs0.189 63183 99.5 %
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: 2.4→35 Å
タンパク質核酸リガンド溶媒全体
原子数9184 0 54 526 9764
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0039441
X-RAY DIFFRACTIONf_angle_d0.71312827
X-RAY DIFFRACTIONf_dihedral_angle_d3.145504
X-RAY DIFFRACTIONf_chiral_restr0.0491397
X-RAY DIFFRACTIONf_plane_restr0.0051656
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4023-2.43810.33781270.27312497X-RAY DIFFRACTION96
2.4381-2.47620.38581400.26392492X-RAY DIFFRACTION97
2.4762-2.51680.2761380.26312551X-RAY DIFFRACTION98
2.5168-2.56020.31291510.25712548X-RAY DIFFRACTION99
2.5602-2.60680.31191410.24972566X-RAY DIFFRACTION99
2.6068-2.65690.27941470.24062554X-RAY DIFFRACTION100
2.6569-2.71110.3551580.25322575X-RAY DIFFRACTION100
2.7111-2.770.34031530.25442598X-RAY DIFFRACTION100
2.77-2.83440.31741200.24682611X-RAY DIFFRACTION100
2.8344-2.90530.33661570.24052565X-RAY DIFFRACTION100
2.9053-2.98380.30711270.23182638X-RAY DIFFRACTION100
2.9838-3.07150.31191460.21412575X-RAY DIFFRACTION100
3.0715-3.17060.24291550.20542614X-RAY DIFFRACTION100
3.1706-3.28380.23691500.19342575X-RAY DIFFRACTION100
3.2838-3.41520.25511130.18792647X-RAY DIFFRACTION100
3.4152-3.57050.21961120.17182638X-RAY DIFFRACTION100
3.5705-3.75850.19531230.16062649X-RAY DIFFRACTION100
3.7585-3.99370.20181260.15782631X-RAY DIFFRACTION100
3.9937-4.30160.1831470.14212640X-RAY DIFFRACTION100
4.3016-4.73350.14491060.12682682X-RAY DIFFRACTION100
4.7335-5.41630.15921410.13862667X-RAY DIFFRACTION100
5.4163-6.81570.21441280.17392706X-RAY DIFFRACTION100
6.8157-35.00660.22271510.18042807X-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)
13.19074.0589-1.87576.1035-1.34142.28640.5369-0.855-0.3959-0.117-0.8391-0.54390.64251.3250.46330.43870.0274-0.05360.63970.14180.3263-42.79512.260854.7414
26.72345.14074.12864.19383.6993.42441.40470.9495-2.14390.5579-1.20950.20660.7335-0.4384-0.36310.52390.02580.00320.5533-0.16180.5451-42.49737.213227.466
37.51237.18172.54719.55526.00266.1656-0.7081.29461.1963-0.47020.4090.6822-0.86262.22630.15790.401-0.0784-0.01440.81980.19940.4708-22.295217.376431.4741
45.84456.38362.79576.96782.91272.1180.60280.6521-1.04460.1795-0.4252-1.3857-0.13140.6522-0.1240.29140.013-0.03590.69220.05480.4288-35.060614.393626.0534
51.9708-3.27092.95864.077-3.38817.2777-0.15660.09190.18370.0878-0.2682-0.2464-0.4632-0.41370.470.203-0.0327-0.00890.43450.02060.3245-43.068217.640832.2089
65.53632.38245.77017.32343.74816.1741-0.5721-0.530.23520.10640.4281-0.6553-1.4119-0.35010.21810.35910.0028-0.09040.42410.09570.5879-41.235427.288131.2395
78.90321.69365.13095.6991-1.27414.4481-0.42160.73520.3826-0.1827-0.3126-0.4788-0.27160.69020.59140.319-0.039-0.00310.55010.20830.4636-36.567621.239325.0066
87.49961.34592.0795.5357-0.21851.005-0.04540.66740.08650.2242-0.2518-0.8724-0.42940.4080.27710.3247-0.0589-0.05960.43820.08470.3613-35.707417.232435.06
93.18882.23152.23112.0454-0.0417.5448-0.4523-0.698-0.09840.25460.4502-0.32060.0035-1.0352-0.12130.4037-0.0482-0.08920.3433-0.03240.287-50.314612.693932.693
102.2818-0.4385-2.36333.4727-2.17688.24870.132-0.2337-1.2828-0.3034-0.5244-1.8802-1.6310.33440.4750.45380.0395-0.02530.38360.14010.5396-24.976713.251836.342
114.62591.90872.57211.66771.50883.4125-0.1526-0.07590.02920.2774-0.092-0.0325-0.35170.17510.24380.3570.07020.0010.2460.01660.2063-39.4374-22.90490.7895
120.9568-1.503-0.7343.18461.0652.3855-0.02690.1975-0.2394-0.0418-0.14340.77430.167-0.1130.20470.3111-0.0128-0.02020.3854-0.08230.3626-57.3384-27.03261.4244
131.6524-0.43820.7051.7262-0.11691.45990.08710.29260.0289-0.303-0.1339-0.12410.04270.02470.04630.27770.01690.02230.3239-0.00010.2292-46.3815-24.7756-6.7451
140.9132-1.12790.26212.17550.24798.6012-0.1553-0.3134-0.14970.0906-0.34040.2124-0.12050.19850.58880.18010.01340.00460.364-0.01640.3611-77.84411.459810.9831
153.4739-0.5902-1.39133.92062.93073.45020.0530.74060.04260.1308-0.304-0.38720.4443-0.8263-0.00060.23960.03040.0010.33410.05140.3156-78.4393-3.15739.7639
163.73280.1225-1.33553.72790.95382.47740.02630.03270.2309-0.1415-0.25290.1402-0.1242-0.3685-0.10240.2260.0475-0.03460.2839-0.01140.2354-69.4996-2.18278.0044
176.38563.10061.83124.19291.31373.3582-0.1171-0.0147-0.2793-0.09050.1840.4197-0.16130.2618-0.04720.32380.1067-0.00420.29870.00570.2463-67.4551-8.323311.3205
188.55664.02442.17695.32084.71299.33440.2245-1.0078-0.6281.0019-0.2897-0.04170.75350.819-0.08450.530.0464-0.00380.37170.07240.2958-65.7262-8.927420.5365
191.80152.54891.84944.13093.35552.7137-0.3882-0.15590.52880.2479-0.67490.53880.2617-0.42720.98250.38160.00690.02930.2908-0.01390.3921-76.3556-8.487711.3716
208.3423-2.3034-2.76673.7211-0.98187.7057-0.0198-1.3114-0.06632.23910.39990.2214-0.57540.3705-0.32490.7278-0.00310.0420.4969-0.06610.3391-74.7135-1.03926.6384
218.1209-3.64890.88148.06214.47653.9762-0.31420.1072-0.38340.0116-0.79780.6325-0.4876-0.21050.88910.268-0.04330.03830.2503-0.0020.2338-69.31090.52828.1216
228.3342-4.8232-6.24572.80143.61114.68170.31450.6698-0.1746-0.53110.0539-0.2140.24320.0783-0.08270.5059-0.0003-0.10450.4757-0.07390.3659-59.8475-3.3969-7.9507
231.58960.1251-2.4051.1281-0.01782.7879-0.4223-0.3155-0.3548-0.0482-0.05680.47070.12970.21680.15160.2390.0693-0.00750.38430.01630.3138-72.7383.914211.3817
245.24770.1380.8290.3184-0.62962.11310.3236-1.3226-0.44251.52670.0298-1.23260.07680.3823-0.34520.40660.0534-0.08910.6566-0.05230.7399-50.20964.256414.9919
253.7787-2.92484.58992.9627-5.0518.6263-0.41910.04491.4104-0.4216-0.2201-0.8803-0.73840.05460.69780.5432-0.11180.08990.27450.01750.756-53.764924.01483.3387
263.356-3.655-0.98246.25690.14842.8121-0.3625-0.3940.53930.35480.5106-0.8281-0.32940.1552-0.12140.2886-0.0208-0.03270.3659-0.06530.3454-50.67653.57456.8881
277.4139-5.3641-4.62215.78615.14584.8848-0.27280.29-0.20790.09780.0780.11240.3516-0.27360.090.28710.04670.00880.22690.09160.3024-61.35926.36092.5627
287.2354-2.5988-3.37814.51314.87565.98080.46580.13530.0351-1.29450.05630.0097-0.2004-0.1879-0.21930.323-0.03170.03610.24210.02950.2127-54.6344.3734-4.8838
294.9589-6.46352.39739.2039-3.28345.9140.2686-0.02660.16070.0081-0.11690.00860.5878-0.206-0.15050.4811-0.05390.07790.28110.01090.5008-51.37539.871-2.9894
307.1533-4.12223.18272.7704-3.19278.27251.01160.61630.7773-0.2669-0.8445-1.07560.09091.9056-0.00610.40320.1016-0.05520.47990.05580.7231-45.14888.23024.0189
312.7094-2.8390.31924.6221.19531.47240.42530.09950.2987-0.7541-0.2559-0.24270.17090.0708-0.05150.29730.0304-0.01140.31830.02770.3102-58.040210.71744.8228
322.2552-2.1321-0.20915.5893-0.52690.79860.12160.0689-0.22310.7144-0.08880.30690.34280.1603-0.20070.2606-0.0361-0.13530.3592-0.01080.3079-56.2426-3.572910.2698
333.62912.7001-1.51723.26351.51426.2063-0.5367-0.09850.48560.81810.9747-0.8637-1.2127-1.0609-0.14440.38450.1430.07740.3405-0.09250.4665-58.712321.877.7059
343.87321.743-0.70130.75660.05490.3648-0.18190.3221-0.0926-0.11230.0769-0.05860.0429-0.24550.12150.30310.0073-0.0110.3334-0.04910.2696-92.5466-24.4783-3.7422
353.366-2.421.32785.05062.69057.7409-0.1053-0.37530.0570.59311.0021-0.6059-0.01481.7063-0.85570.36520.0517-0.01210.5374-0.13170.3826-76.4497-30.86924.6436
363.939-1.3025-5.76650.92011.11578.5821-0.2528-0.46190.07760.13980.1062-0.15330.32280.40620.12960.3242-0.0252-0.02480.3741-0.06520.3305-79.9493-21.27283.0073
374.02631.9381-1.07284.2889-0.68472.6301-0.0971-0.0770.4230.08760.18520.08270.04490.3805-0.120.26270.03760.0230.2804-0.04350.349-90.3443-14.50981.7605
382.56710.1378-2.85572.81820.26024.4343-0.0640.04360.19380.13950.09240.203-0.1109-0.2542-0.02180.1920.0378-0.06670.2619-0.02820.2594-96.5154-19.1704-1.2939
398.5604-4.6289-3.94551.98894.75658.1707-0.52510.4342-0.39250.24110.72170.3054-0.22410.1134-0.10790.2447-0.0604-0.01550.2902-0.02550.1894-61.8683-26.1781-26.8045
403.7387-0.8229-0.49534.68260.88442.94640.0288-0.17910.06980.2187-0.0005-0.23230.12890.0705-0.0320.24430.0059-0.03030.24230.00270.1958-65.2042-36.0662-21.0882
412.22472.2542.97465.26956.47658.63190.51030.0409-0.87741.6157-0.1965-0.30621.07430.1083-0.20450.47910.00110.02150.36850.06420.328-71.7821-45.0932-15.8223
420.51351.52761.8613.48894.66486.2471-0.28240.2177-0.098-0.29920.914-0.27160.27460.4439-0.5610.30280.02880.02820.40560.00330.2586-60.9047-36.1208-16.0854
437.7831-2.75943.34573.72820.33512.27040.1859-0.0118-0.3578-0.72870.67170.89411.2580.2949-0.7140.50460.0274-0.1030.40550.01260.3383-62.8284-51.3254-23.3537
447.6957-8.4496-6.4469.86557.11956.2834-0.4258-0.28560.1320.16890.868-0.1971-0.1918-0.1063-0.42150.2503-0.0172-0.06020.3942-0.02140.2753-67.7236-32.7603-25.2377
452.2477-0.09881.43333.7313-5.07297.6432-0.4319-0.95512.0987-0.8257-0.27341.0072-2.4742-0.86170.96570.56930.0531-0.07560.5016-0.27250.8113-76.9192-16.3629-21.7512
465.5558-5.0293-1.2334.21271.55991.96330.27460.0657-0.3795-0.8343-0.2670.4159-0.0033-0.0829-0.11760.367-0.0501-0.00110.2687-0.02090.3071-64.2808-36.131-28.5581
476.03541.8571-2.47259.1521-5.2793.34720.3459-0.0665-0.7932-0.5157-0.02660.30681.0659-0.9732-0.36680.4473-0.0636-0.06380.5165-0.0910.4763-86.7279-39.5591-29.315
485.9236-0.4925-3.17011.72080.68785.38090.29791.08940.0715-0.317-0.3341-0.0466-0.1313-0.6685-0.02160.34730.1167-0.05520.4932-0.05620.328-84.7751-29.9654-43.6734
492.6089-1.9573-1.62531.6090.77682.2126-0.04930.23780.03430.00810.00080.1102-0.1649-0.2320.08560.30.0001-0.0250.358-0.03430.2268-81.2295-29.2628-28.2562
507.2261-0.0213-2.31713.61940.28083.26590.22390.17610.2771-0.042-0.2491-0.0382-0.7481-0.1365-0.1130.33910.0108-0.0430.3242-0.00210.2954-81.897-19.5093-29.5485
515.4822-3.6692-0.82732.59020.91338.1710.6545-0.71841.19660.37770.06030.0746-0.7147-0.1678-0.68740.49080.19240.00880.4287-0.0350.2622-85.4315-21.3618-35.269
523.22334.2104-4.01155.8767-5.40376.96781.33830.95960.53450.1776-0.07222.0359-0.5097-1.3893-1.05960.49710.1064-0.05980.66440.04180.6101-91.6882-28.4153-33.7107
531.94810.2553-4.16051.9712-0.81557.1520.25880.13730.38-0.3656-0.14320.40840.2545-0.1643-0.11280.28950.0747-0.04740.4038-0.03490.2962-78.6549-29.4605-35.7722
542.9650.1453-1.90950.1792-1.31847.8657-0.30360.0792-0.1559-0.07780.03580.02680.91380.34570.17780.2210.03820.0110.24060.00990.2928-80.7256-34.6237-21.3377
557.9406-2.37185.31397.0731-1.49823.5552-0.44951.3935-1.0027-0.9237-0.3615-0.27130.3242-1.02270.54260.34140.0976-0.04460.4397-0.15670.3325-78.3137-33.1748-45.5066
566.356-0.8470.51235.52191.59714.6173-0.03160.37940.2476-0.11620.05620.0251-0.2463-0.004-0.01370.30560.0162-0.00080.2531-0.00440.2548-68.029722.936314.6894
577.579-0.06231.26642.30470.67071.3398-0.1344-0.6259-0.00360.1865-0.01460.2536-0.0087-0.20150.16490.32210.0511-0.00130.4694-0.01860.241-73.058423.117932.4571
589.4417-0.45498.8313-0.0448-0.39677.9134-0.1511-0.75990.27460.2446-0.05930.2445-0.0571-0.64750.26590.41870.0384-0.00710.5141-0.15990.3699-68.22329.346433.9892
595.4954-0.10192.27672.24920.92092.1439-0.23310.08930.5332-0.1298-0.00510.0001-0.3707-0.07410.26280.38580.046-0.04620.35830.03290.268-70.1531.113318.3978
607.9298-1.29471.59880.70270.90223.2289-0.4668-0.75960.2641-0.12120.83880.0359-0.3303-0.3155-0.14780.55810.1084-0.18980.6038-0.20770.4651-45.028621.619351.3313
615.4357-3.41562.0046.9175-4.59126.7268-0.4834-1.3861-0.28550.60850.5749-0.3430.2255-0.8003-0.23340.540.08870.00030.71110.07790.3003-49.55596.773856.35
623.22490.5183-4.16056.6292-1.38038.3598-0.6085-0.77471.25271.40890.99140.4926-1.1845-0.8885-0.13750.73750.28570.0110.5037-0.0580.486-54.564226.392649.3153
636.8409-7.4668-2.20348.65852.41387.7547-0.6928-0.3916-0.36310.77660.45880.13030.430.01220.2290.26850.01660.02350.3834-0.02180.3247-47.89459.590344.0115
646.0469-4.00550.48873.00130.53657.4072-0.19850.6127-0.27090.3490.08490.02590.424-0.49760.10060.3504-0.01720.03080.37240.09130.3844-48.88127.818941.6149
654.88271.09414.08379.5951-1.43455.9280.029-0.77370.09930.63690.36581.3708-0.307-1.1429-0.22930.39380.16420.06430.57410.11540.505-60.421112.213743.569
668.2947-6.6284-6.69517.24386.91649.4291-0.47750.2201-1.34980.9786-0.68561.14370.1725-0.46420.93030.5638-0.14850.05690.54120.13970.5866-56.7955.007246.863
676.4415-0.86830.00988.67924.62613.1123-0.1669-0.8807-0.30761.14420.6979-0.0861-0.6298-0.7153-0.49890.58760.21150.05540.79470.14110.3614-54.995213.815653.3284
684.17855.7197-3.63749.3958-2.71956.7999-0.0405-0.5008-1.74730.14350.5463-0.25411.1132-0.377-0.44430.45080.0927-0.06050.73810.1750.6815-49.8436-3.402751.0072
693.1571-3.83330.21299.564-0.68930.19550.0925-0.37730.0810.3063-0.1981-0.2445-0.21490.16120.00790.40080.05050.02530.4530.01960.2943-46.742414.864445.7269
709.7202-5.57225.41234.3533-5.49918.54430.02510.20430.66330.4896-0.49810.0495-1.0949-0.30050.35210.46280.0962-0.09380.3922-0.08140.4533-46.630625.308540.4431
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 113:118 )H113 - 118
2X-RAY DIFFRACTION2( CHAIN H AND RESID 119:125 )H119 - 125
3X-RAY DIFFRACTION3( CHAIN H AND RESID 126:135 )H126 - 135
4X-RAY DIFFRACTION4( CHAIN H AND RESID 136:142 )H136 - 142
5X-RAY DIFFRACTION5( CHAIN H AND RESID 143:172 )H143 - 172
6X-RAY DIFFRACTION6( CHAIN H AND RESID 173:183 )H173 - 183
7X-RAY DIFFRACTION7( CHAIN H AND RESID 184:202 )H184 - 202
8X-RAY DIFFRACTION8( CHAIN H AND RESID 203:219 )H203 - 219
9X-RAY DIFFRACTION9( CHAIN H AND RESID 220:230 )H220 - 230
10X-RAY DIFFRACTION10( CHAIN H AND RESID 231:237 )H231 - 237
11X-RAY DIFFRACTION11( CHAIN A AND RESID 63:89 )A63 - 89
12X-RAY DIFFRACTION12( CHAIN A AND RESID 90:144 )A90 - 144
13X-RAY DIFFRACTION13( CHAIN A AND RESID 145:223 )A145 - 223
14X-RAY DIFFRACTION14( CHAIN B AND RESID 2:19 )B2 - 19
15X-RAY DIFFRACTION15( CHAIN B AND RESID 20:26 )B20 - 26
16X-RAY DIFFRACTION16( CHAIN B AND RESID 27:45 )B27 - 45
17X-RAY DIFFRACTION17( CHAIN B AND RESID 46:58 )B46 - 58
18X-RAY DIFFRACTION18( CHAIN B AND RESID 59:68 )B59 - 68
19X-RAY DIFFRACTION19( CHAIN B AND RESID 69:82 )B69 - 82
20X-RAY DIFFRACTION20( CHAIN B AND RESID 83:90 )B83 - 90
21X-RAY DIFFRACTION21( CHAIN B AND RESID 91:99 )B91 - 99
22X-RAY DIFFRACTION22( CHAIN B AND RESID 100:105 )B100 - 105
23X-RAY DIFFRACTION23( CHAIN B AND RESID 106:118 )B106 - 118
24X-RAY DIFFRACTION24( CHAIN B AND RESID 119:125 )B119 - 125
25X-RAY DIFFRACTION25( CHAIN B AND RESID 126:135 )B126 - 135
26X-RAY DIFFRACTION26( CHAIN B AND RESID 136:159 )B136 - 159
27X-RAY DIFFRACTION27( CHAIN B AND RESID 160:172 )B160 - 172
28X-RAY DIFFRACTION28( CHAIN B AND RESID 173:183 )B173 - 183
29X-RAY DIFFRACTION29( CHAIN B AND RESID 184:192 )B184 - 192
30X-RAY DIFFRACTION30( CHAIN B AND RESID 193:202 )B193 - 202
31X-RAY DIFFRACTION31( CHAIN B AND RESID 203:219 )B203 - 219
32X-RAY DIFFRACTION32( CHAIN B AND RESID 220:230 )B220 - 230
33X-RAY DIFFRACTION33( CHAIN B AND RESID 231:236 )B231 - 236
34X-RAY DIFFRACTION34( CHAIN D AND RESID 63:108 )D63 - 108
35X-RAY DIFFRACTION35( CHAIN D AND RESID 109:130 )D109 - 130
36X-RAY DIFFRACTION36( CHAIN D AND RESID 131:159 )D131 - 159
37X-RAY DIFFRACTION37( CHAIN D AND RESID 160:189 )D160 - 189
38X-RAY DIFFRACTION38( CHAIN D AND RESID 190:223 )D190 - 223
39X-RAY DIFFRACTION39( CHAIN E AND RESID 2:10 )E2 - 10
40X-RAY DIFFRACTION40( CHAIN E AND RESID 11:58 )E11 - 58
41X-RAY DIFFRACTION41( CHAIN E AND RESID 59:68 )E59 - 68
42X-RAY DIFFRACTION42( CHAIN E AND RESID 69:82 )E69 - 82
43X-RAY DIFFRACTION43( CHAIN E AND RESID 83:90 )E83 - 90
44X-RAY DIFFRACTION44( CHAIN E AND RESID 91:99 )E91 - 99
45X-RAY DIFFRACTION45( CHAIN E AND RESID 100:105 )E100 - 105
46X-RAY DIFFRACTION46( CHAIN E AND RESID 106:118 )E106 - 118
47X-RAY DIFFRACTION47( CHAIN E AND RESID 119:125 )E119 - 125
48X-RAY DIFFRACTION48( CHAIN E AND RESID 126:142 )E126 - 142
49X-RAY DIFFRACTION49( CHAIN E AND RESID 143:172 )E143 - 172
50X-RAY DIFFRACTION50( CHAIN E AND RESID 173:183 )E173 - 183
51X-RAY DIFFRACTION51( CHAIN E AND RESID 184:192 )E184 - 192
52X-RAY DIFFRACTION52( CHAIN E AND RESID 193:202 )E193 - 202
53X-RAY DIFFRACTION53( CHAIN E AND RESID 203:219 )E203 - 219
54X-RAY DIFFRACTION54( CHAIN E AND RESID 220:230 )E220 - 230
55X-RAY DIFFRACTION55( CHAIN E AND RESID 231:236 )E231 - 236
56X-RAY DIFFRACTION56( CHAIN G AND RESID 63:89 )G63 - 89
57X-RAY DIFFRACTION57( CHAIN G AND RESID 90:144 )G90 - 144
58X-RAY DIFFRACTION58( CHAIN G AND RESID 145:159 )G145 - 159
59X-RAY DIFFRACTION59( CHAIN G AND RESID 160:223 )G160 - 223
60X-RAY DIFFRACTION60( CHAIN H AND RESID 2:10 )H2 - 10
61X-RAY DIFFRACTION61( CHAIN H AND RESID 11:26 )H11 - 26
62X-RAY DIFFRACTION62( CHAIN H AND RESID 27:34 )H27 - 34
63X-RAY DIFFRACTION63( CHAIN H AND RESID 35:41 )H35 - 41
64X-RAY DIFFRACTION64( CHAIN H AND RESID 42:52 )H42 - 52
65X-RAY DIFFRACTION65( CHAIN H AND RESID 53:62 )H53 - 62
66X-RAY DIFFRACTION66( CHAIN H AND RESID 63:74 )H63 - 74
67X-RAY DIFFRACTION67( CHAIN H AND RESID 75:82 )H75 - 82
68X-RAY DIFFRACTION68( CHAIN H AND RESID 83:90 )H83 - 90
69X-RAY DIFFRACTION69( CHAIN H AND RESID 91:99 )H91 - 99
70X-RAY DIFFRACTION70( CHAIN H AND RESID 100:112 )H100 - 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