[日本語] English
万見
- PDB-6z2m: H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6z2m
タイトルH11-D4, SARS-CoV-2 RBD, CR3022 ternary complex
要素
  • (CR3022 antibody) x 2
  • Spike glycoprotein
  • nanobody D4
キーワードVIRAL PROTEIN / Antibody / nanobody complex / rbd
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly 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Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.71 Å
データ登録者Naismith, J.H. / Ren, J. / Zhou, D. / Zhao, Y. / Stuart, D.I.
資金援助 英国, 2件
組織認可番号国
Wellcome Trust100209/Z/12/Z 英国
Engineering and Physical Sciences Research CouncilEP/S025243/1. 英国
引用ジャーナル: To Be Published
タイトル: Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2
著者: Naismith, J.H.
履歴
登録2020年5月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年6月3日Provider: repository / タイプ: Initial release
改定 1.12020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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.22024年1月24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 1.32024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
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

-
集合体

登録構造単位
A: Spike glycoprotein
B: CR3022 antibody
C: CR3022 antibody
E: Spike glycoprotein
H: CR3022 antibody
L: CR3022 antibody
F: nanobody D4
D: nanobody D4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,90210
ポリマ－166,4608
非ポリマー4422
水00
1
A: Spike glycoprotein
B: CR3022 antibody
C: CR3022 antibody
D: nanobody D4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)83,4515
ポリマ－83,2304
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: Spike glycoprotein
H: CR3022 antibody
L: CR3022 antibody
F: nanobody D4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)83,4515
ポリマ－83,2304
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)149.717, 150.395, 119.537
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
要素

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


分子量: 22115.834 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#2: タンパク質 CR3022 antibody


分子量: 22874.785 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 CR3022 antibody


分子量: 24186.740 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 nanobody D4


分子量: 14052.671 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli (大腸菌)
#5: 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: 2 / 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
研究の焦点であるリガンドがあるかN
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 4.05 Å3/Da / 溶媒含有率: 69.62 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: Purified RBD, Fab CR3022 and nanobody H11-D4 were mixed together at a molar ratio of 1:1:1 to a final concentration of approximately 7 mg/ml and incubated at room temperature for one hour. ...詳細: Purified RBD, Fab CR3022 and nanobody H11-D4 were mixed together at a molar ratio of 1:1:1 to a final concentration of approximately 7 mg/ml and incubated at room temperature for one hour. Initial screening was performed in 96-well plates using the nanolitre sitting-drop vapour diffusion method. The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.

-
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: 0.97625 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2020年5月10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: 0.97625 Å / 相対比: 1
反射解像度: 2.71→106.1 Å / Num. obs: 73071 / % possible obs: 99 % / 冗長度: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.065 / Net I/σ(I): 7.4
反射 シェル解像度: 2.71→2.76 Å / 冗長度: 9 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 3426 / CC1/2: 0.087 / Rpim(I) all: 3.953 / % possible all: 94

-
位相決定

位相決定手法: 分子置換

-
解析

ソフトウェア
名称バージョン分類
XDSデータ削減
PHASER位相決定
PHENIX1.17.1_3660精密化
PDB_EXTRACT3.25データ抽出
XSCALE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: 6YZ7

6yz7


解像度: 2.71→74.86 Å / SU ML: 0.26 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 26.16 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.241 2365 4.99 %
Rwork0.1983 45047 -
obs0.2004 47412 64.33 %
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: 213.92 Å2 / Biso mean: 53.5819 Å2 / Biso min: 11.46 Å2
精密化ステップサイクル: final / 解像度: 2.71→74.86 Å
タンパク質核酸リガンド溶媒全体
原子数11699 0 28 0 11727
Biso mean--70.23 --
残基数----1516
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.71-2.770.289350.2988951002
2.77-2.830.4119360.379747150712
2.83-2.890.3867410.336276180219
2.89-2.970.3558470.3204997104424
2.97-3.050.3781420.30771264130630
3.05-3.140.3256950.29161544163938
3.14-3.240.29891170.27541985210249
3.24-3.350.29771260.26192480260661
3.35-3.490.32561590.25052953311272
3.49-3.650.26622000.22183376357683
3.65-3.840.29121720.20764015418797
3.84-4.080.25472140.190841194333100
4.08-4.390.22032100.164141104320100
4.39-4.840.16872380.147341354373100
4.84-5.530.19131860.165941984384100
5.54-6.970.23342460.200741854431100
6.97-74.860.22292310.19054359459099
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)
13.83970.8253-0.66432.35760.92284.4238-0.09270.38780.7183-0.44720.086-0.6446-0.90610.0734-0.24430.40110.04080.13670.65560.15720.491712.709748.040649.9923
23.14841.0326-2.42826.5753-2.40584.85790.0805-0.17111.206-0.26740.0385-0.14320.0440.1141-0.11640.12460.080.14190.48310.04180.504123.167139.156645.3228
35.8064-1.6961-1.63450.82350.77380.72590.9291.62291.0128-0.7020.03180.8049-0.7377-0.9859-0.15870.57730.32-0.02761.03380.33250.476514.799339.587435.1974
42.76740.5962-1.32442.44590.18923.6668-0.16650.8275-0.4068-0.16290.1942-0.21770.5458-0.1973-0.0560.2561-0.01980.06910.3491-0.05990.340513.186231.841256.6216
53.6950.0429-1.00691.9984-0.28993.9439-0.0308-0.0677-0.15220.08650.1147-0.06620.07160.0703-0.07250.1545-0.02780.03950.2966-0.02150.263910.847134.302864.5598
61.4141-3.26470.51777.6473-0.20968.84110.41471.9086-0.3169-1.3042-0.01370.5983-0.14470.1023-0.01430.6725-0.2246-0.00641.19130.14050.82767.425443.595634.2127
71.4611-0.43850.08061.53710.56791.37130.2186-0.4182-0.2954-0.001-0.0513-0.22570.2996-0.3478-0.09530.2064-0.04930.02070.16780.05820.263436.152724.044737.6237
81.4667-0.14180.22440.6552-1.02411.5752-0.0711-0.1403-0.49250.2633-0.03310.25830.9238-0.5176-0.05940.3846-0.0685-0.00760.23710.030.293827.889817.012433.1507
92.23850.35780.47111.7470.22190.14260.0591-0.4407-0.7970.43580.03140.39940.6234-0.3546-0.04930.3928-0.4510.0770.25490.5830.238727.434317.0244.2507
102.01990.2170.14071.60540.98671.5029-0.0415-0.4701-0.41660.04910.18970.32250.4393-0.21790.00580.4046-0.0152-0.03990.13480.06560.267535.506518.032938.5573
111.2872-0.6513-0.29761.59180.68612.0005-0.067-0.01820.0678-0.23930.5021-0.26720.4283-0.0618-0.21730.3473-0.21280.01860.1485-0.03240.323143.825515.712618.3452
123.13541.1752-1.64534.7179-4.00223.5471-0.2033-0.28850.50230.01150.2589-0.2863-1.30060.41690.19060.7219-0.1564-0.01270.2622-0.19110.568550.668915.570116.5341
133.08510.4378-0.21460.1682-0.34072.0091-0.1032-0.15580.01790.01950.12010.1416-0.77110.1464-0.11980.6099-0.0019-0.1280.3588-0.06990.433545.277412.283212.5509
141.7662-0.4605-0.66361.668-1.18621.4296-0.0574-0.21041.1345-0.03720.2365-0.6898-0.67690.9171-0.00710.8883-0.3264-0.07140.5297-0.04640.619254.834718.64694.1383
152.1593-0.1366-0.53982.0881-0.68320.3793-0.4283-0.22410.2417-0.38460.5553-0.6924-0.62650.909-0.14720.6595-0.3164-0.06260.7275-0.24080.64459.082713.690811.9532
162.65610.1841-1.47452.49380.28015.00830.0861-0.084-0.0014-0.3035-0.03980.74760.5596-0.7491-0.09250.289-0.0149-0.23720.4211-0.02020.636413.384822.30821.766
171.3913-1.3564-1.33582.16551.77472.47490.33350.0172-0.1766-0.4145-0.15820.1839-0.2152-0.4092-0.11570.2946-0.0524-0.14310.28350.03570.282824.485923.91217.2897
181.7878-0.8647-0.58373.17781.19192.2266-0.2551-0.1563-0.0863-0.34530.16560.0133-0.3325-0.00590.0230.576-0.0719-0.04640.2393-0.12580.339242.77833.92080.9943
195.26050.5910.52973.1085-0.77263.746-0.0256-0.5386-0.3747-0.3830.19471.10430.2335-0.7394-0.01030.4005-0.0869-0.09620.35980.11880.580923.048551.14363.8263
203.922-0.3828-2.65482.5299-0.17453.14430.14-0.1273-0.31310.20810.17410.9499-0.3421-0.3905-0.47990.5345-0.03820.34010.1530.47150.173427.09957.85355.6529
211.13350.2976-0.7780.32420.28141.5067-0.0114-0.0364-0.20320.0380.34320.82710.1624-0.31940.67870.49390.0559-0.15530.20320.29040.65129.0742.463412.1205
222.0919-0.83731.98295.4804-1.23311.9116-0.6326-0.67490.00750.75130.3310.8706-0.6112-0.3177-0.18120.6240.12440.10980.29010.00720.444233.196751.497118.1742
232.97710.33980.07294.67940.80734.28220.04910.2421-0.40680.43770.0186-0.2828-0.34490.3982-0.17250.2785-0.01520.00550.06580.04950.17937.892651.89331.6912
242.66030.0313-0.8373.8497-0.65613.333-0.04970.1066-0.1639-0.03470.3291-0.10370.03980.0379-0.13670.2233-0.0656-0.00370.11370.03520.25739.114550.7598-1.1796
253.0506-0.10180.25212.4129-0.15493.33160.20070.32390.1434-0.5945-0.0908-0.3283-0.65750.4151-0.12840.5289-0.02560.08410.2348-0.050.199644.132659.0329-12.3592
263.076-1.6364-1.55345.69532.83265.7818-0.0886-0.31070.58960.70810.29410.2706-0.7577-0.0812-0.03350.6782-0.09020.01310.00360.06580.4430.041256.648312.1121
272.44970.30760.92191.9983-0.18711.48170.1217-0.0071-0.3097-0.20940.24020.05160.20190.047-0.1370.20240.02870.00410.1041-0.03610.148445.762830.942222.9209
282.5283-1.63310.13642.1789-0.06222.06910.09140.19460.2576-0.17180.013-0.3109-0.0540.2755-0.16050.18140.01140.04540.1003-0.00950.172553.453638.256421.7916
291.5378-0.23460.34741.0767-0.78731.73280.147-0.0571-0.05790.4785-0.12460.0557-0.27930.2146-0.03770.2974-0.010.03540.0362-0.00250.250551.244231.289438.2845
302.0584-1.06370.45832.01920.28093.51560.1298-0.1641-0.3185-0.0006-0.04330.47390.5811-0.3188-0.02910.2538-0.0289-0.00380.31720.12970.487952.761520.835755.0345
311.7765-0.13430.03731.2692-0.58014.0934-0.3361-0.36910.7133-0.17790.07880.1971-0.78010.0796-0.44620.55030.0187-0.09030.021-0.15110.473945.713757.309636.458
322.87170.02140.13253.5491-0.97623.8979-0.08210.03580.02670.33650.1070.2816-0.4606-0.423-0.05440.24590.08260.03010.2072-0.03370.123938.262447.45236.0181
331.7786-0.23441.05180.7041-0.84672.4375-0.0436-0.24510.18850.0548-0.0388-0.0824-0.417-0.10470.10920.35410.05170.01940.2117-0.09640.231244.504750.820841.7827
346.3274-3.1117-0.02083.41471.31271.85130.5977-0.1367-0.3162-0.188-0.3878-0.21050.1670.1267-0.1550.3193-0.0595-0.02750.25590.020.281259.772728.569561.665
353.2741-0.86593.72040.4012-1.00354.22740.1784-0.21410.4811-0.0377-0.298-0.5301-0.39230.6867-0.06920.22930.0037-0.07160.47150.0380.399269.447536.784265.205
361.8725-2.0277-0.19052.2827-0.25342.51741.13770.3012-0.2674-0.2587-0.77050.1301-0.056-0.1067-0.27630.348-0.0478-0.00270.3146-0.01580.421352.837936.786255.8665
374.0997-2.14630.34833.0851-0.19192.411-0.2267-0.7276-0.1980.63420.2121-0.2703-0.0580.281-0.14210.30570.0382-0.05550.41330.0180.338765.650931.501665.9058
383.31380.09410.87282.64931.05555.0222-0.0806-0.17790.4114-0.2287-0.0010.409-0.3516-2.3753-0.08450.59310.3126-0.0781.01910.01210.44528.401954.5267-36.027
392.35420.9813-0.32324.75443.82493.682-0.33540.1496-0.90570.3142-0.12910.22820.18710.03080.21920.48930.21230.03670.8208-0.13520.230639.584650.3061-36.9406
401.41920.8781.231.4259-0.56053.0471-0.02980.4480.0279-0.1269-0.0050.113-1.2633-0.9304-0.03820.75260.33980.02390.81150.00170.233936.446658.0494-37.2396
412.64870.4554-0.40231.34990.11386.87180.20270.0808-0.3159-0.13620.1643-0.1980.4524-0.8955-0.14250.38450.15570.01580.5535-0.05760.247137.993350.4158-31.6518
425.4668-0.337-3.71793.4890.71666.9115-0.6979-0.40390.55540.36510.2408-0.3892-0.5073-0.36760.4640.5491-0.0178-0.05270.8333-0.4070.7626.283652.987294.4418
434.60530.30481.97615.66923.13772.7834-0.48770.05540.9732-0.6113-0.5395-0.7721-1.40870.73080.7370.35940.0032-0.06380.62890.00990.510210.697846.631284.4724
444.9526-0.08031.14464.6705-0.16454.2825-0.3285-0.77820.11740.5912-0.0027-0.3103-0.21580.13170.37330.24910.0356-0.01070.6267-0.0360.36274.893842.707493.2615
450.351-0.5874-0.29511.0340.93683.0345-0.0232-0.54070.18550.28410.3543-0.3247-0.50460.9746-0.23910.249-0.08760.0520.9169-0.13450.386612.538943.351388.9513
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 332 through 364 )A332 - 364
2X-RAY DIFFRACTION2chain 'A' and (resid 365 through 380 )A365 - 380
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 393 )A381 - 393
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 421 )A394 - 421
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 516 )A422 - 516
6X-RAY DIFFRACTION6chain 'A' and (resid 517 through 528 )A517 - 528
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 39 )B0 - 39
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 52 )B40 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 73 )B53 - 73
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 100 )B74 - 100
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 147 )B101 - 147
12X-RAY DIFFRACTION12chain 'B' and (resid 148 through 161 )B148 - 161
13X-RAY DIFFRACTION13chain 'B' and (resid 162 through 181 )B162 - 181
14X-RAY DIFFRACTION14chain 'B' and (resid 182 through 204 )B182 - 204
15X-RAY DIFFRACTION15chain 'B' and (resid 205 through 219 )B205 - 219
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 38 )C1 - 38
17X-RAY DIFFRACTION17chain 'C' and (resid 39 through 128 )C39 - 128
18X-RAY DIFFRACTION18chain 'C' and (resid 129 through 219 )C129 - 219
19X-RAY DIFFRACTION19chain 'E' and (resid 333 through 349 )E333 - 349
20X-RAY DIFFRACTION20chain 'E' and (resid 350 through 364 )E350 - 364
21X-RAY DIFFRACTION21chain 'E' and (resid 365 through 375 )E365 - 375
22X-RAY DIFFRACTION22chain 'E' and (resid 376 through 393 )E376 - 393
23X-RAY DIFFRACTION23chain 'E' and (resid 394 through 409 )E394 - 409
24X-RAY DIFFRACTION24chain 'E' and (resid 410 through 451 )E410 - 451
25X-RAY DIFFRACTION25chain 'E' and (resid 452 through 506 )E452 - 506
26X-RAY DIFFRACTION26chain 'E' and (resid 507 through 527 )E507 - 527
27X-RAY DIFFRACTION27chain 'H' and (resid 0 through 32 )H0 - 32
28X-RAY DIFFRACTION28chain 'H' and (resid 33 through 91 )H33 - 91
29X-RAY DIFFRACTION29chain 'H' and (resid 92 through 138 )H92 - 138
30X-RAY DIFFRACTION30chain 'H' and (resid 139 through 219 )H139 - 219
31X-RAY DIFFRACTION31chain 'L' and (resid 1 through 38 )L1 - 38
32X-RAY DIFFRACTION32chain 'L' and (resid 39 through 67 )L39 - 67
33X-RAY DIFFRACTION33chain 'L' and (resid 68 through 119 )L68 - 119
34X-RAY DIFFRACTION34chain 'L' and (resid 120 through 149 )L120 - 149
35X-RAY DIFFRACTION35chain 'L' and (resid 150 through 161 )L150 - 161
36X-RAY DIFFRACTION36chain 'L' and (resid 162 through 178 )L162 - 178
37X-RAY DIFFRACTION37chain 'L' and (resid 179 through 219 )L179 - 219
38X-RAY DIFFRACTION38chain 'F' and (resid 1 through 32 )F1 - 32
39X-RAY DIFFRACTION39chain 'F' and (resid 33 through 52 )F33 - 52
40X-RAY DIFFRACTION40chain 'F' and (resid 53 through 99 )F53 - 99
41X-RAY DIFFRACTION41chain 'F' and (resid 100 through 127 )F100 - 127
42X-RAY DIFFRACTION42chain 'D' and (resid 1 through 25 )D1 - 25
43X-RAY DIFFRACTION43chain 'D' and (resid 26 through 39 )D26 - 39
44X-RAY DIFFRACTION44chain 'D' and (resid 40 through 91 )D40 - 91
45X-RAY DIFFRACTION45chain 'D' and (resid 92 through 127 )D92 - 127

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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