[日本語] English
万見
- PDB-8xk2: A neutralizing nanobody VHH60 against wt SARS-CoV-2 -

+
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: 8xk2
タイトルA neutralizing nanobody VHH60 against wt SARS-CoV-2
要素
  • Spike protein S1
  • VHH60 nanobody
キーワードANTIVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / spike glycoprotein / virus / antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
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)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.4 Å
データ登録者Lu, Y. / Guo, H. / Ji, X. / Yang, H.
資金援助2件
組織認可番号国
Other government92169109
Other governmentZD2021CY001
引用ジャーナル: Cell Death Dis / 年: 2024
タイトル: A broad neutralizing nanobody against SARS-CoV-2 engineered from an approved drug.
著者: Qianyun Liu / Yuchi Lu / Chenguang Cai / Yanyan Huang / Li Zhou / Yanbin Guan / Shiying Fu / Youyou Lin / Huan Yan / Zhen Zhang / Xiang Li / Xiuna Yang / Haitao Yang / Hangtian Guo / Ke Lan / ...著者: Qianyun Liu / Yuchi Lu / Chenguang Cai / Yanyan Huang / Li Zhou / Yanbin Guan / Shiying Fu / Youyou Lin / Huan Yan / Zhen Zhang / Xiang Li / Xiuna Yang / Haitao Yang / Hangtian Guo / Ke Lan / Yu Chen / Shin-Chen Hou / Yi Xiong /
要旨: SARS-CoV-2 infection is initiated by Spike glycoprotein binding to the human angiotensin-converting enzyme 2 (ACE2) receptor via its receptor binding domain. Blocking this interaction has been proven ...SARS-CoV-2 infection is initiated by Spike glycoprotein binding to the human angiotensin-converting enzyme 2 (ACE2) receptor via its receptor binding domain. Blocking this interaction has been proven to be an effective approach to inhibit virus infection. Here we report the discovery of a neutralizing nanobody named VHH60, which was directly produced from an engineering nanobody library based on a commercialized nanobody within a very short period. VHH60 competes with human ACE2 to bind the receptor binding domain of the Spike protein at S, Sand S as determined by structural analysis, with an affinity of 2.56 nM. It inhibits infections of both ancestral SARS-CoV-2 strain and pseudotyped viruses harboring SARS-CoV-2 wildtype, key mutations or variants at the nanomolar level. Furthermore, VHH60 suppressed SARS-CoV-2 infection and propagation 50-fold better and protected mice from death for twice as long as the control group after SARS-CoV-2 nasal infections in vivo. Therefore, VHH60 is not only a powerful nanobody with a promising profile for disease control but also provides evidence for a highly effective and rapid approach to generating therapeutic nanobodies.
履歴
登録2023年12月22日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年7月10日Provider: repository / タイプ: Initial release

-
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 protein S1
B: VHH60 nanobody
C: Spike protein S1
D: VHH60 nanobody
E: Spike protein S1
F: VHH60 nanobody
G: Spike protein S1
H: VHH60 nanobody


分子量 (理論値)分子数
合計 (水以外)152,4038
ポリマ－152,4038
非ポリマー00
水00
1
A: Spike protein S1
B: VHH60 nanobody


分子量 (理論値)分子数
合計 (水以外)38,1012
ポリマ－38,1012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Spike protein S1
D: VHH60 nanobody


分子量 (理論値)分子数
合計 (水以外)38,1012
ポリマ－38,1012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Spike protein S1
F: VHH60 nanobody


分子量 (理論値)分子数
合計 (水以外)38,1012
ポリマ－38,1012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Spike protein S1
H: VHH60 nanobody


分子量 (理論値)分子数
合計 (水以外)38,1012
ポリマ－38,1012
非ポリマー00
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)80.850, 100.610, 227.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

-
要素

#1: タンパク質
Spike protein S1


分子量: 24689.797 Da / 分子数: 4 / 断片: receptor binding domain / 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: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P0DTC2
#2: 抗体
VHH60 nanobody


分子量: 13410.872 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)

-
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: 3.03 Å3/Da / 溶媒含有率: 59.47 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 1.0 M Sodium acetate trihydrate, 0.1 M Sodium HEPES 7.5

-
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: SSRF / ビームライン: BL19U1 / 波長: 0.97853 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2022年12月3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: 0.97853 Å / 相対比: 1
反射解像度: 3.4→31.21 Å / Num. obs: 26210 / % possible obs: 99.84 % / 冗長度: 12.66 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.09947 / Rpim(I) all: 0.09947 / Rrim(I) all: 0.1407 / Net I/σ(I): 6.56
反射 シェル
解像度 (Å)Rmerge(I) obsNum. unique obsCC1/2Diffraction-IDRrim(I) all
3.4-3.61.39541640.8311
3.6-3.850.94539470.91710.983
3.85-4.150.58236790.96810.606
4.15-4.550.37533930.98610.391
4.55-5.080.32831070.98810.342
5.08-5.850.34727530.9810.362
5.85-7.140.32123590.98610.335
7.14-100.18418830.99310.192

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1-4487精密化
autoPXデータ削減
XDSデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7VNB/tFold model

7vnb


解像度: 3.4→31.21 Å / SU ML: 0.52 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.05 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3 1998 7.62 %
Rwork0.2557 --
obs0.2592 26210 99.84 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.4→31.21 Å
タンパク質核酸リガンド溶媒全体
原子数9406 0 0 0 9406
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0039643
X-RAY DIFFRACTIONf_angle_d0.5613085
X-RAY DIFFRACTIONf_dihedral_angle_d4.0871350
X-RAY DIFFRACTIONf_chiral_restr0.0441368
X-RAY DIFFRACTIONf_plane_restr0.0061723
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.480.37011390.34771684X-RAY DIFFRACTION100
3.48-3.580.3571410.30581712X-RAY DIFFRACTION100
3.58-3.680.3241390.29661696X-RAY DIFFRACTION100
3.68-3.80.3331400.28751694X-RAY DIFFRACTION100
3.8-3.940.3331400.28161700X-RAY DIFFRACTION100
3.94-4.10.29171410.25711713X-RAY DIFFRACTION100
4.1-4.280.28111430.23431719X-RAY DIFFRACTION100
4.28-4.510.25451420.21221724X-RAY DIFFRACTION100
4.51-4.790.25731430.22291724X-RAY DIFFRACTION100
4.79-5.160.27211420.21751723X-RAY DIFFRACTION100
5.16-5.670.30231430.24181730X-RAY DIFFRACTION100
5.67-6.490.3071440.25261754X-RAY DIFFRACTION100
6.49-8.150.33721470.2661783X-RAY DIFFRACTION100
8.15-31.210.27721540.25331856X-RAY DIFFRACTION99
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)
14.44042.5147-0.09228.1327-0.1637-0.0217-0.13220.52640.69591.00310.3723-0.10080.56070.2148-0.32980.7403-0.0080.1430.5614-0.00640.5108-19.1494-23.3736-20.9777
25.88515.8082-0.15286.4821-1.06256.04210.93560.38231.67011.6235-0.74060.90940.19150.1174-0.34970.94430.07790.2220.7106-0.13780.7756-21.8824-28.2238-7.8357
37.1215-2.1198-4.57063.4472-0.60976.76870.76030.19121.59930.61391.4742-0.0557-1.20481.18430.08510.5184-0.10370.02471.0431-0.12780.7759-7.7185-25.545-9.4356
43.5045-1.18480.83462.72090.69621.2001-0.1148-0.3304-0.1492-0.4828-0.0120.0286-0.12870.03280.06890.6442-0.03640.04560.56350.00840.4426-23.9572-39.3026-21.8159
50.92730.29340.55373.92370.77972.47430.08880.0969-0.16840.2591-0.02780.0230.57360.05790.04980.47660.0991-0.00910.5914-0.01370.5504-26.6373-41.4554-26.9387
65.0366-1.05950.47921.90870.6383.47810.0884-0.30650.238-0.0737-0.1346-0.2868-0.71590.07110.07070.7543-0.0786-0.03310.5580.07180.4462-33.0435-35.256-47.5052
70.05070.1004-0.04760.1268-0.05170.08010.31121.03070.83250.06330.66-1.39250.86731.4977-0.79360.61930.1506-0.16950.9227-0.10310.8983-18.7411-36.1375-47.8534
86.6312.2889-3.05095.3678-1.24099.07751.4414-0.2831-0.0061-0.1984-1.56460.442-1.1346-0.6570.0280.70190.0219-0.04010.8146-0.18080.4922-32.6309-27.7389-46.2983
93.08581.835-0.78274.2504-2.07835.7899-0.0613-0.65-0.0757-0.0276-0.0859-0.2524-0.06730.53390.27210.43540.1185-0.12670.4775-0.04710.5429-32.8467-39.4162-49.535
106.39255.8659-1.00166.6653-0.02331.1281-0.60760.5757-0.5769-0.24250.4862-0.55640.2745-0.33550.00370.518-0.0327-0.00940.61970.00120.5329-67.1494-78.4643-23.483
112.36321.77362.71581.37711.16416.16460.6572-0.3922-0.96812.06250.2635-0.5320.3396-1.2069-0.78121.0040.0269-0.29670.72860.14920.9328-70.7497-74.3119-11.1557
121.9579-0.3377-1.25581.8568-0.62330.4856-0.0855-0.0983-0.15330.14770.078-0.1395-0.0811-0.1319-0.01720.5158-0.0132-0.03010.60180.00510.4848-60.1585-61.1759-27.3472
132.71450.43033.70353.41940.30274.93640.96330.935-0.32550.23-0.43290.55342.55540.851-0.18980.9910.14850.07720.91340.04110.477-52.373-69.3902-58.7889
146.5001-4.63443.28395.3408-3.62866.036-0.18840.4251.1554-0.5341-0.6338-1.03480.69240.62680.49810.9216-0.0035-0.01380.7832-0.01840.5695-50.6868-61.8098-48.6716
153.9094-1.121-4.60547.30451.33235.38230.0676-0.46890.0330.36240.3492-0.09090.3702-0.3336-0.28760.67520.0016-0.07150.80210.09190.6444-60.5426-68.1021-46.4041
161.47030.03692.69495.356-1.78078.70550.3210.0588-0.2827-0.5281-0.0159-0.15990.07220.2863-0.20580.7310.01360.10660.72240.08960.5394-52.8644-64.5023-51.9494
171.6861-0.2421.80673.19841.0243.9129-0.26310.3953-0.7212-0.83220.4691-0.3747-0.23910.4089-0.42150.68370.0520.17320.51090.14850.8907-61.3758-6.7148-16.3398
182.6916-2.57542.64636.67911.11555.6244-0.2284-0.4458-0.2768-0.0871.13130.6848-1.1457-1.18720.0770.98750.21920.17960.66940.130.9587-70.7595-0.3024-17.2259
196.0522.2611-1.68272.76771.59083.3457-0.07250.65440.5416-1.83270.2422-0.2426-0.36850.4343-0.30940.53460.05840.11140.86320.38361.3869-62.45432.0666-28.3699
205.1436-0.65250.01334.1219-0.3683.91080.71691.02680.6758-0.8946-0.4332-0.0265-0.86040.1131-0.28690.55630.04160.1110.80320.20160.7795-62.5356-12.1656-29.2259
213.5382-0.27890.87763.2295-0.81851.50810.50020.465-0.4102-0.3424-0.1794-0.0975-0.2837-0.3195-0.29090.75030.078-0.09420.7765-0.10470.6099-58.8339-23.5257-22.3349
227.4516-1.4891-2.51652.8195-0.5737.2404-0.87980.0377-0.7347-1.35-0.11410.67781.52360.41590.84590.75360.26670.02810.9753-0.0390.6162-56.7581-35.9398-21.8664
237.5199-1.976-0.30543.655-0.88762.91960.68520.54470.7987-0.2893-0.462-0.6373-0.40760.6697-0.29860.7232-0.11710.04950.70460.13660.5907-52.0402-11.1796-25.0797
249.36630.6029-3.02525.9721-1.81275.6279-0.44820.4905-1.02150.48190.3971-0.56760.11210.4565-0.10420.90410.0774-0.13350.7931-0.01390.4185-59.2576-35.55423.3816
253.7918-0.0366-0.88955.556-0.31444.89050.35070.21010.04060.1436-0.2609-0.01511.16040.2681-0.10850.36930.06030.01070.52520.01350.369-59.1497-30.9177-9.0719
261.9963-2.6634-1.15994.9906-1.6858.68530.7908-0.4739-1.67210.33190.3419-0.4156-0.0092-2.0194-1.06640.74130.0570.09120.68760.19990.7732-68.8393-29.4364-5.3966
276.80096.24914.6167.65610.81459.03832.2816-0.1943-1.02261.071-1.0818-0.588-0.21730.6179-0.93031.20510.22540.15320.6443-0.01340.7491-57.8662-26.79921.2747
284.45854.2147-4.36255.9688-2.02958.830.2413-0.3283-0.5155-0.0775-0.50720.07260.3337-0.15050.19330.69210.1105-0.12230.61160.0750.7674-59.1335-36.6635-6.3415
295.4356-1.1201-1.06043.6196-0.13322.3416-0.7793-0.1490.0121-0.15480.2344-0.99420.17640.22490.25780.6094-0.1132-0.09930.5080.01710.7045-21.9436-97.5259-17.4218
304.3227-0.32252.30930.0278-0.2161.21530.65851.57850.2451-0.4879-1.10780.20470.08610.2355-0.7580.43680.1713-0.17470.8714-0.16621.0331-17.8967-102.1891-29.9778
313.3061-1.83660.79586.12030.31884.35210.30760.7173-0.6126-0.9696-0.34030.10020.647-0.17350.00640.8297-0.0601-0.05440.5864-0.15810.7717-23.6738-90.3951-30.4758
325.5084-6.3957-3.14117.49114.30649.25330.17271.64610.01522.18380.0950.18991.0215-0.87040.04670.6201-0.0495-0.04880.73960.11460.7314-39.5006-87.978-18.9308
336.4082-1.0681-1.13575.3070.17546.73770.39280.84510.781-0.8670.0351-0.42190.06310.446-0.51110.7050.07660.17270.691-0.04510.6047-20.4608-78.8492-26.9675
341.95490.150.99486.9734-3.20044.8486-0.2844-0.03020.1909-1.3217-0.6224-0.12970.4112-0.13250.7470.60670.0802-0.0540.72560.17210.5257-26.9479-65.3954-25.7273
353.1076-3.05810.44483.34350.79064.7081-0.39620.4092-0.034-0.350.54380.27620.0226-0.47620.11311.0381-0.1866-0.2560.7015-0.05850.7834-34.0341-91.1612-26.1465
362.57133.62881.70795.08552.76865.0696-0.17320.042-0.027-0.51090.1390.1501-0.05520.34350.07290.92260.02550.00540.6504-0.10330.6351-25.1121-62.37740.9851
376.89136.67793.45787.65031.57054.2323-0.751-0.0741.5910.3033-0.01610.45430.6248-0.23930.49530.9088-0.096-0.06150.692-0.09450.3648-27.0872-68.26160.2678
382.01452.666-5.02894.75761.17763.92040.29790.10360.55570.7543-0.2844-0.37172.0175-2.02850.20971.07-0.2867-0.15020.7864-0.25280.6702-39.9656-75.459-11.4987
391.60611.8071-0.59032.35290.36993.2166-0.4778-0.22-0.2636-0.3960.67760.1012-0.0801-0.0855-0.06830.6087-0.1578-0.04310.6967-0.04360.5939-25.4161-65.8863-10.1339
401.83961.71991.13182.77513.0974.6693-0.80530.22360.4311-0.20170.99020.1033-1.27440.40530.07080.30530.233-0.09130.70420.13980.4281-21.9878-63.2626-12.4507
414.91113.01842.55551.86361.46981.6654-0.33230.46840.4879-0.9889-0.26220.10370.4665-0.8392-0.3290.4109-0.07490.03040.43260.11710.9678-24.5367-80.3554-12.6781
424.21364.8962-1.49158.3585-2.51820.7575-0.80060.54250.5735-0.74961.1123-0.88590.22240.72270.57580.0135-0.06140.29820.9601-0.14641.2681-13.3073-69.7803-10.9092
433.0045-2.4708-0.13435.17150.58464.68240.2052-0.1759-2.3393-1.2115-0.59170.17070.7931-0.8536-1.1281.092-0.1554-0.21120.6495-0.04640.6419-27.8418-75.6852-3.0921
443.11271.46243.22036.8873-0.58764.07462.172-0.2963-0.8274-0.6227-1.53030.9891.16930.3645-0.01840.7568-0.0594-0.08410.53240.08310.7671-22.5281-70.6641-1.0702
458.4801-5.3924.9618.6579-1.14393.66880.07521.36420.87560.5048-0.9899-1.446-0.32322.11310.74570.9495-0.12070.09940.85550.27210.8599-12.169-60.2144-3.6934
462.5931.22673.06611.28390.74894.3104-0.30520.54390.40860.67380.10710.8253-0.9309-0.07060.12660.72360.13870.05240.6937-0.16860.6466-26.7515-62.0545-7.4727
475.54545.89742.68766.89634.72454.68510.2002-0.3260.211-0.0699-0.08620.0151-0.508-0.3644-0.12710.58760.07190.01160.6205-0.06360.7404-31.5349-65.5965-11.6955
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 332 through 365 )
2X-RAY DIFFRACTION2chain 'A' and (resid 366 through 380 )
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 394 )
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 469 )
5X-RAY DIFFRACTION5chain 'A' and (resid 470 through 526 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 59 )
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 83 )
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 121 )
10X-RAY DIFFRACTION10chain 'C' and (resid 332 through 365 )
11X-RAY DIFFRACTION11chain 'C' and (resid 366 through 394 )
12X-RAY DIFFRACTION12chain 'C' and (resid 395 through 525 )
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 24 )
14X-RAY DIFFRACTION14chain 'D' and (resid 25 through 45 )
15X-RAY DIFFRACTION15chain 'D' and (resid 46 through 73 )
16X-RAY DIFFRACTION16chain 'D' and (resid 74 through 121 )
17X-RAY DIFFRACTION17chain 'E' and (resid 335 through 353 )
18X-RAY DIFFRACTION18chain 'E' and (resid 354 through 365 )
19X-RAY DIFFRACTION19chain 'E' and (resid 366 through 394 )
20X-RAY DIFFRACTION20chain 'E' and (resid 395 through 437 )
21X-RAY DIFFRACTION21chain 'E' and (resid 438 through 479 )
22X-RAY DIFFRACTION22chain 'E' and (resid 480 through 494 )
23X-RAY DIFFRACTION23chain 'E' and (resid 495 through 515 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 25 )
25X-RAY DIFFRACTION25chain 'F' and (resid 26 through 59 )
26X-RAY DIFFRACTION26chain 'F' and (resid 60 through 73 )
27X-RAY DIFFRACTION27chain 'F' and (resid 74 through 83 )
28X-RAY DIFFRACTION28chain 'F' and (resid 84 through 121 )
29X-RAY DIFFRACTION29chain 'G' and (resid 334 through 375 )
30X-RAY DIFFRACTION30chain 'G' and (resid 376 through 395 )
31X-RAY DIFFRACTION31chain 'G' and (resid 396 through 437 )
32X-RAY DIFFRACTION32chain 'G' and (resid 438 through 451 )
33X-RAY DIFFRACTION33chain 'G' and (resid 452 through 469 )
34X-RAY DIFFRACTION34chain 'G' and (resid 470 through 494 )
35X-RAY DIFFRACTION35chain 'G' and (resid 495 through 515 )
36X-RAY DIFFRACTION36chain 'H' and (resid 2 through 16 )
37X-RAY DIFFRACTION37chain 'H' and (resid 17 through 25 )
38X-RAY DIFFRACTION38chain 'H' and (resid 26 through 32 )
39X-RAY DIFFRACTION39chain 'H' and (resid 33 through 39 )
40X-RAY DIFFRACTION40chain 'H' and (resid 40 through 52 )
41X-RAY DIFFRACTION41chain 'H' and (resid 53 through 59 )
42X-RAY DIFFRACTION42chain 'H' and (resid 60 through 67 )
43X-RAY DIFFRACTION43chain 'H' and (resid 68 through 77 )
44X-RAY DIFFRACTION44chain 'H' and (resid 78 through 84 )
45X-RAY DIFFRACTION45chain 'H' and (resid 85 through 91 )
46X-RAY DIFFRACTION46chain 'H' and (resid 92 through 98 )
47X-RAY DIFFRACTION47chain 'H' and (resid 99 through 121 )

+
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://pdbjlvh1.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