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- PDB-4xak: Crystal structure of potent neutralizing antibody m336 in complex... -

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基本情報

登録情報
データベース: PDB / ID: 4xak
タイトルCrystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD
要素
  • Heavy chain of neutralizing antibody m336
  • Light chain of neutralizing antibody m336
  • Spike glycoprotein
キーワードIMMUNE SYSTEM / MERS-CoV RBD / antibody m336 / neutralization
機能・相同性
機能・相同性情報


membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
類似検索 - 分子機能
ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal ...ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Human coronavirus EMC (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.45 Å
データ登録者Zhou, T. / Dimtrov, D.S. / Ying, T.
引用ジャーナル: Nat Commun / 年: 2015
タイトル: Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody.
著者: Ying, T. / Prabakaran, P. / Du, L. / Shi, W. / Feng, Y. / Wang, Y. / Wang, L. / Li, W. / Jiang, S. / Dimitrov, D.S. / Zhou, T.
履歴
登録2014年12月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年8月26日Provider: repository / タイプ: Initial release
改定 1.12015年9月23日Group: Database references
改定 1.22017年11月22日Group: Derived calculations / Refinement description / カテゴリ: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
改定 1.32020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.42023年9月27日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.52024年10月30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: Spike glycoprotein
H: Heavy chain of neutralizing antibody m336
L: Light chain of neutralizing antibody m336
B: Spike glycoprotein
D: Heavy chain of neutralizing antibody m336
E: Light chain of neutralizing antibody m336
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)155,79412
ポリマ－154,7256
非ポリマー1,0696
水4,252236
1
A: Spike glycoprotein
H: Heavy chain of neutralizing antibody m336
L: Light chain of neutralizing antibody m336
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,9897
ポリマ－77,3623
非ポリマー6274
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-24 kcal/mol
Surface area28660 Å2
手法PISA
2
B: Spike glycoprotein
D: Heavy chain of neutralizing antibody m336
E: Light chain of neutralizing antibody m336
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,8055
ポリマ－77,3623
非ポリマー4422
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-20 kcal/mol
Surface area28570 Å2
手法PISA
単位格子
Length a, b, c (Å)47.795, 146.879, 200.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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要素

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抗体 , 2種, 4分子 HDLE

#2: 抗体 Heavy chain of neutralizing antibody m336


分子量: 26525.562 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK 293F / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 Light chain of neutralizing antibody m336


分子量: 23211.752 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: plasmid / 細胞株 (発現宿主): HEK 293F / 発現宿主: Homo sapiens (ヒト)

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タンパク質 / 糖 , 2種, 6分子 AB

#1: タンパク質 Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


分子量: 27625.014 Da / 分子数: 2 / 断片: Receptor-binding domain (UNP residues 367-601) / 由来タイプ: 組換発現
詳細: MERS-CoV RBD with HRV3C cleavage site and His 6x tag at the C-terminal.
由来: (組換発現) Human coronavirus EMC (ウイルス) / 株: isolate United Kingdom/H123990006/2012 / 遺伝子: S, 3 / プラスミド: pVRC8400 / 細胞株 (発現宿主): GNTI-/- / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: K9N5Q8
#4: 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: 4 / 由来タイプ: 合成 / 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, 238分子

#5: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 236 / 由来タイプ: 天然 / 式: H2O

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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: 2.27 Å3/Da / 溶媒含有率: 45.92 %
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: 7.5 / 詳細: 20% PEG 2000MME, 100 mM HEPES, pH7.5 / PH範囲: 7.5

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データ収集

回折平均測定温度: 100 K / Ambient temp details: Liquid nitrogen stream
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2014年8月23日 / 詳細: MAR300HS
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.45→50 Å / Num. obs: 48854 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / 冗長度: 3.7 % / Biso Wilson estimate: 47.67 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.06 / Rrim(I) all: 0.129 / Χ2: 0.946 / Net I/av σ(I): 10.912 / Net I/σ(I): 6.3 / Num. measured all: 181576
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.492.50.4751.313810.7980.2780.5550.46552.6
2.49-2.542.60.48716960.7760.290.5720.48363.8
2.54-2.592.60.45519390.7960.2740.5360.48875.1
2.59-2.6430.41422260.8230.2380.4820.56884
2.64-2.73.10.39822910.8310.2290.4640.54488.3
2.7-2.763.40.40223890.8220.2280.4670.60791.6
2.76-2.833.60.35825400.8470.2010.4140.64994.4
2.83-2.93.60.33525310.8590.1870.3870.68397.6
2.9-2.993.80.28526440.910.1530.3260.78398.8
2.99-3.093.90.27625880.9140.1470.3160.85198.9
3.09-3.240.23826500.9390.1250.271.02999.4
3.2-3.324.10.20926030.9560.1090.2371.14299.5
3.32-3.484.10.17526330.9630.0910.1991.18199.1
3.48-3.664.10.1426590.9790.0730.1591.24899.1
3.66-3.894.10.1226400.9830.0620.1361.37499.1
3.89-4.194.10.10226420.9870.0530.1161.15798.7
4.19-4.614.10.08426420.9910.0430.0951.22598.2
4.61-5.284.10.07426900.9930.0370.0831.13898.1
5.28-6.6540.06426780.9940.0340.0730.83897.6
6.65-503.80.05427920.9950.0290.0610.94595.2

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: dev_1702)精密化
HKL-2000データスケーリング
PHASER位相決定
PDB_EXTRACT3.15データ抽出
Cootモデル構築
SCALEPACKデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 4KQZ

4kqz


解像度: 2.45→45.449 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 26.71 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2491 2479 5.08 %Random selection
Rwork0.1982 46327 --
obs0.2008 48806 91.51 %-
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: 166.98 Å2 / Biso mean: 67.0747 Å2 / Biso min: 25.67 Å2
精密化ステップサイクル: final / 解像度: 2.45→45.449 Å
タンパク質核酸リガンド溶媒全体
原子数9745 0 68 236 10049
Biso mean--74.74 53 -
残基数----1286
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00210053
X-RAY DIFFRACTIONf_angle_d0.62413656
X-RAY DIFFRACTIONf_chiral_restr0.0241573
X-RAY DIFFRACTIONf_plane_restr0.0031736
X-RAY DIFFRACTIONf_dihedral_angle_d10.3763592
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4463-2.49330.3393760.27831435X-RAY DIFFRACTION51
2.4933-2.54420.3061930.28671807X-RAY DIFFRACTION66
2.5442-2.59950.3341120.27352142X-RAY DIFFRACTION78
2.5995-2.660.32751370.26232386X-RAY DIFFRACTION85
2.66-2.72650.30151460.25812458X-RAY DIFFRACTION90
2.7265-2.80020.29221550.25022621X-RAY DIFFRACTION94
2.8002-2.88260.30571470.25422631X-RAY DIFFRACTION97
2.8826-2.97560.29661480.23792801X-RAY DIFFRACTION99
2.9756-3.0820.29071610.24142729X-RAY DIFFRACTION99
3.082-3.20530.33311430.2282808X-RAY DIFFRACTION99
3.2053-3.35120.25281230.21142765X-RAY DIFFRACTION99
3.3512-3.52780.24761600.20642750X-RAY DIFFRACTION99
3.5278-3.74870.25841320.19192829X-RAY DIFFRACTION99
3.7487-4.0380.23751410.19072816X-RAY DIFFRACTION99
4.038-4.4440.23811520.15962778X-RAY DIFFRACTION98
4.444-5.08640.19671550.15452788X-RAY DIFFRACTION98
5.0864-6.40540.22931400.18132855X-RAY DIFFRACTION98
6.4054-45.45710.20121580.17582928X-RAY DIFFRACTION96
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)
14.3742-1.5417-1.42112.04730.91162.71890.0759-0.17160.09940.0410.1561-0.0589-0.4030.0976-0.20040.3443-0.05780.11140.3861-0.07220.392511.360593.84358.5108
23.7932-2.74611.11614.0719-0.87942.38490.0171-0.3997-0.30160.39960.11090.37130.0926-0.0858-0.10970.3123-0.11460.09850.4985-0.06770.422427.535778.026857.9318
34.1084-2.31330.39561.8696-0.09811.1654-0.0804-0.10270.25230.34580.0722-0.0024-0.10920.0130.020.3406-0.12330.09760.3537-0.06210.382219.206989.611760.6101
44.4019-3.40623.45236.027-3.56613.08850.50950.1014-0.8723-0.42290.31120.83130.2835-0.8334-0.86070.49710.0364-0.0650.5817-0.0030.564554.9952-11.4981118.5089
51.615-2.2848-0.20515.043-3.17596.55470.38410.293-0.2135-0.5275-0.10580.17030.51180.4439-0.28010.38740.0249-0.11040.509-0.08410.422164.7869-16.4298115.9232
69.84352.3618-5.46949.4485-3.67283.7948-0.336-1.1164-0.54570.75710.3739-2.00320.74041.044-0.06950.78690.1711-0.10640.78330.04120.708574.4185-2.8376110.6664
75.6958-4.95282.24776.0623-5.4428.28080.2749-0.706-0.20230.0665-0.355-0.396-0.6682-0.07380.10620.3113-0.0511-0.01650.45670.02620.31468.1952-10.0732116.674
88.50783.6776-1.0885.0952-0.19472.9856-0.1734-0.0179-0.75350.00250.63140.0861-0.2428-0.4396-0.32790.70660.0854-0.33230.8042-0.02660.600752.7392-14.0482102.3274
98.88183.25311.91834.71951.86675.4630.414-0.07550.85130.1112-0.16580.0719-1.04720.4317-0.14130.92870.00070.06130.4542-0.05840.447469.48419.4313111.6984
105.8545-0.4251-2.68258.9803-0.27291.20830.7267-0.10170.3736-1.3285-0.21670.0432-1.9724-0.8661-0.51011.16110.07360.10850.53290.08630.463863.11511.8533106.2483
115.0731-0.8202-0.30124.5016-1.7350.76450.04710.3189-0.2118-1.0335-0.30050.60110.0911-0.36390.23610.56830.0475-0.12180.322-0.03390.313961.6572-12.6662108.9283
124.48624.48395.04834.57175.66519.4420.401-1.4241-0.33170.4712-1.10940.92970.8089-0.30370.82070.51120.0028-0.03880.63480.00720.622358.9162-22.2699132.0814
138.1208-1.99824.78863.88821.36878.6338-0.1037-0.5383-0.16130.3103-0.02030.32780.3696-0.52950.02330.2869-0.06770.09490.36250.04260.462538.526555.714738.4166
144.7507-1.656-4.42653.54920.46933.9101-0.02540.1933-0.39330.10820.00070.3472-0.1637-0.7050.02040.1648-0.03410.01880.4721-0.03350.412836.725667.59540.9502
155.1056-0.57870.89726.5576-1.18484.4123-0.03110.3685-0.32110.37990.03820.71220.0066-1.06130.01580.2396-0.02850.04780.5496-0.09940.530230.34162.128437.855
160.1473-0.9247-0.34433.69142.843.0007-0.0603-0.107-0.0296-0.0473-0.13370.36650.0071-0.15690.23270.2426-0.07210.00110.4831-0.02760.435741.980362.055933.8864
178.045-1.4684-0.52155.4962-0.09116.05670.24460.3157-0.3309-0.4337-0.3172-0.674-0.04310.42560.03730.30030.0110.01940.23950.03460.410660.380447.181517.2007
182.68450.085-3.71557.93970.05566.70850.3037-0.5110.0568-0.0235-0.404-0.8709-0.37090.43610.11290.2352-0.0621-0.04760.3148-0.04720.386861.882252.553321.9429
198.4173-0.8699-0.51445.22870.41055.08150.0536-0.3214-0.6369-0.0147-0.0873-0.30810.32270.44540.00340.27920.05330.04450.30010.01510.36859.369845.917719.1125
203.28360.2941-3.34817.02650.41267.27190.48170.4385-1.1213-0.7452-0.1689-0.14880.3329-0.0769-0.14930.42020.09470.03940.45580.06880.705659.015438.23418.5642
215.1711-3.9061-1.39814.18941.09162.570.2741.5311.0448-0.2992-0.133-0.3696-0.34580.0421-0.07120.387-0.08930.03090.3480.01730.380654.1780.230827.5039
227.8032-4.0932-1.43729.393-1.86123.4926-0.11590.19280.73030.13150.2963-0.2457-0.4629-0.0746-0.16960.2917-0.0468-0.01740.4427-0.05510.329547.87982.500134.8695
232.74112.32950.57512.64711.11015.78970.1058-0.43270.31130.24740.1306-0.0602-0.11230.2511-0.25310.17360.04570.03530.3906-0.02970.372654.158778.14739.2687
247.8756-1.81910.12047.55251.035.3660.12590.3648-0.7638-0.13890.0836-0.1594-0.1150.3239-0.26840.2309-0.05990.03730.31580.00510.339757.474574.538833.3471
252.837-1.0662-3.51833.27093.74645.9391-0.2561-0.3608-0.12950.41480.02-0.40690.56480.49590.23760.27570.04320.00960.33860.07040.300540.274777.96434.6643
269.463-6.2686-0.06092.05225.18564.71670.00130.17931.1832-0.41230.5408-0.87630.2309-0.0064-0.38530.4112-0.09280.13840.5193-0.03430.466566.501270.576519.3208
275.31465.40530.26065.2497-0.3182.6419-0.0628-0.1731-0.7019-0.6827-0.0955-0.36570.9276-0.26020.20320.6644-0.0240.06530.4494-0.10180.446458.982944.17446.8966
288.12944.31095.57986.626.52477.4288-0.09190.47480.2117-0.48920.04750.1482-0.4780.08690.04710.3115-0.00440.01140.33830.03290.391457.648658.57086.2217
295.7712.40111.27818.29363.17994.5301-0.22920.0631-0.0451-0.9080.0811-0.0323-0.0996-0.40670.16070.28840.02380.02460.34870.04860.322558.572254.64847.4335
307.18274.43432.66895.55426.66992.3893-0.27020.7149-0.0302-0.34330.6960.30690.10150.3802-0.46820.6711-0.0592-0.00860.47120.02040.311365.876758.29821.1813
315.79871.2299-2.44636.85331.33478.10550.4992-0.0626-0.07480.2004-0.8731-0.56040.09270.9430.28180.75870.1870.10470.75270.19150.437273.189225.833688.3473
325.2692-0.1653-1.31794.4486-3.38763.10780.18021.1727-0.3191-1.3969-0.8345-0.59081.16180.94370.59670.99470.25340.14620.7136-0.00850.501270.040515.787587.5977
335.6271-1.1393-0.64916.9775-5.69197.72450.63130.1351-0.2357-0.4117-0.49770.14670.27180.65-0.0510.59550.15250.07010.75790.09350.538871.039421.772585.9982
340.32460.6348-1.18373.8693-2.65395.7414-0.3615-0.1763-0.1923-0.2028-0.4876-0.38381.04870.96590.85290.78260.12340.15280.6990.09380.492969.553528.29980.0653
359.2895-6.682-1.35768.78990.15567.32540.2069-0.21960.5384-0.30830.0646-0.39890.23590.5464-0.23580.8675-0.08530.16660.53660.03920.509469.399545.758961.5532
366.0349-1.9996-3.32358.8913.68156.36880.14010.58780.38330.1874-0.42010.0481-0.2721-0.03090.30670.71170.01460.02850.67090.08650.422667.021347.179466.6054
379.893-5.3373.16728.8431-5.92714.27550.0264-0.22810.66730.9713-0.2345-0.0394-1.19950.7640.06571.0858-0.106-0.08820.8890.02270.689875.009652.675265.0059
383.08551.7471-0.63319.5126-2.42562.6836-0.42890.25020.24431.20651.02890.37110.0451-1.3722-0.5240.82120.06440.02091.0105-0.01130.854545.469626.986780.385
394.84580.78622.10856.6837-2.69362.3373-0.30860.1331-0.7615-1.07370.58411.15480.7164-0.6903-0.30740.8758-0.0921-0.00810.89820.08630.937248.527620.620887.7424
409.17320.21480.15234.3596-5.61458.5303-0.1019-1.19930.20740.50530.88311.174-1.0294-1.4694-0.86720.83360.27010.26620.8730.13030.822249.492228.557691.8369
415.5421-7.2519-0.80719.59971.77367.79660.47440.12170.89690.64930.38390.8066-1.9417-1.2721-0.8220.91560.2070.23550.77190.19961.074449.860932.940785.5806
427.014-1.92133.74425.4763-0.16077.6889-0.087-0.87030.8489-0.7773-0.37680.13881.645-0.89360.41910.95140.0059-0.02820.6091-0.11230.770256.300516.612486.3483
432.97992.47472.25372.06491.85621.67430.7539-0.36252.3318-0.66520.30950.59680.2673-0.9561-1.13530.93770.34040.12981.37170.69431.233845.510242.286571.7968
446.88140.2018-3.77215.5628-4.27538.8137-0.44730.45310.6228-0.65921.07970.53690.8653-1.116-0.60330.6763-0.1004-0.11860.98310.21030.549960.354543.520355.897
457.86-2.99980.46768.3578-5.18623.4288-0.6816-0.1880.01390.26850.96370.93510.0222-0.3603-0.3090.6612-0.07990.01640.73070.19120.900356.384640.665265.7702
462.33162.40590.14773.4748-0.34890.2712-0.12721.81050.7113-1.3890.7380.77460.7417-1.6844-0.76521.0335-0.1056-0.10851.46180.41120.766358.524942.196549.1918
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 381 through 496 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 497 through 538 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 539 through 591 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 381 through 410 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 411 through 455 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 456 through 467 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 468 through 484 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 485 through 496 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 497 through 528 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 529 through 561 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 562 through 576 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 577 through 591 )B0
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 25 )H0
14X-RAY DIFFRACTION14chain 'H' and (resid 26 through 60 )H0
15X-RAY DIFFRACTION15chain 'H' and (resid 61 through 83 )H0
16X-RAY DIFFRACTION16chain 'H' and (resid 84 through 123 )H0
17X-RAY DIFFRACTION17chain 'H' and (resid 124 through 157 )H0
18X-RAY DIFFRACTION18chain 'H' and (resid 158 through 169 )H0
19X-RAY DIFFRACTION19chain 'H' and (resid 170 through 202 )H0
20X-RAY DIFFRACTION20chain 'H' and (resid 203 through 227 )H0
21X-RAY DIFFRACTION21chain 'L' and (resid 1 through 18 )L0
22X-RAY DIFFRACTION22chain 'L' and (resid 19 through 38 )L0
23X-RAY DIFFRACTION23chain 'L' and (resid 39 through 75 )L0
24X-RAY DIFFRACTION24chain 'L' and (resid 76 through 90 )L0
25X-RAY DIFFRACTION25chain 'L' and (resid 91 through 102 )L0
26X-RAY DIFFRACTION26chain 'L' and (resid 103 through 113 )L0
27X-RAY DIFFRACTION27chain 'L' and (resid 114 through 128 )L0
28X-RAY DIFFRACTION28chain 'L' and (resid 129 through 163 )L0
29X-RAY DIFFRACTION29chain 'L' and (resid 164 through 197 )L0
30X-RAY DIFFRACTION30chain 'L' and (resid 198 through 213 )L0
31X-RAY DIFFRACTION31chain 'D' and (resid 1 through 40 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 41 through 73 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 74 through 99 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 100 through 123 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 124 through 147 )D0
36X-RAY DIFFRACTION36chain 'D' and (resid 148 through 189 )D0
37X-RAY DIFFRACTION37chain 'D' and (resid 190 through 228 )D0
38X-RAY DIFFRACTION38chain 'E' and (resid 1 through 18 )E0
39X-RAY DIFFRACTION39chain 'E' and (resid 19 through 38 )E0
40X-RAY DIFFRACTION40chain 'E' and (resid 39 through 75 )E0
41X-RAY DIFFRACTION41chain 'E' and (resid 76 through 90 )E0
42X-RAY DIFFRACTION42chain 'E' and (resid 91 through 102 )E0
43X-RAY DIFFRACTION43chain 'E' and (resid 103 through 113 )E0
44X-RAY DIFFRACTION44chain 'E' and (resid 114 through 150 )E0
45X-RAY DIFFRACTION45chain 'E' and (resid 155 through 174 )E0
46X-RAY DIFFRACTION46chain 'E' and (resid 175 through 213 )E0

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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