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- PDB-8z9l: Crystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2 -

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基本情報

登録情報
データベース: PDB / ID: 8z9l
タイトルCrystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2
要素
  • Angiotensin-converting enzyme
  • Spike protein S1
キーワードVIRAL PROTEIN/HYDROLASE / SARS-CoV-2 RBD / Rhinolophus affinis ACE2 / VIRAL PROTEIN-HYDROLASE complex
機能・相同性
機能・相同性情報


加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space ...加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / 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 / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / 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 / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / proteolysis / extracellular space / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
類似検索 - 分子機能
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
類似検索 - ドメイン・相同性
Angiotensin-converting enzyme / Spike glycoprotein
類似検索 - 構成要素
生物種Rhinolophus affinis (ナカキクガシラコウモリ)
Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.598 Å
データ登録者Lan, J. / Wang, C.H.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Protein Sci. / 年: 2025
タイトル: Molecular mechanisms of RaTG13 and SARS-CoV-2 RBD bound to Rhinolophus affinis bat ACE2.
著者: Wang, C. / Li, M. / Nan, X. / Deng, Y. / Fan, S. / Lan, J.
履歴
登録2024年4月23日登録サイト: PDBJ / 処理サイト: PDBC
改定 1.02025年4月30日Provider: repository / タイプ: Initial release
改定 1.12025年5月14日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
B: Angiotensin-converting enzyme
F: Spike protein S1
I: Angiotensin-converting enzyme
L: Spike protein S1
O: Angiotensin-converting enzyme
R: Spike protein S1
U: Angiotensin-converting enzyme
X: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)369,81120
ポリマ－366,8648
非ポリマー2,94712
水00
1
B: Angiotensin-converting enzyme
F: Spike protein S1
O: Angiotensin-converting enzyme
R: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)184,75910
ポリマ－183,4324
非ポリマー1,3276
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
I: Angiotensin-converting enzyme
L: Spike protein S1
U: Angiotensin-converting enzyme
X: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)185,05210
ポリマ－183,4324
非ポリマー1,6206
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)63.736, 129.479, 563.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
Angiotensin-converting enzyme


分子量: 69607.344 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Rhinolophus affinis (ナカキクガシラコウモリ)
発現宿主: Trichoplusia ni (イラクサキンウワバ)
参照: UniProt: A0A7D7JS29, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素
#2: タンパク質
Spike protein S1


分子量: 22108.758 Da / 分子数: 4 / Fragment: RBD 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: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P0DTC2
#3: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 367.349 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 10 / 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
研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.18 Å3/Da / 溶媒含有率: 61.31 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1M HEPES pH7.5, 10% w/v Polyethylene 8000, 8% v/v Ethylene glycol

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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: SSRF / ビームライン: BL19U1 / 波長: 0.99 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2021年7月21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: 0.99 Å / 相対比: 1
反射解像度: 3.598→50 Å / Num. obs: 55023 / % possible obs: 99.9 % / 冗長度: 11 % / CC1/2: 0.965 / Net I/σ(I): 4.67
反射 シェル解像度: 3.598→3.727 Å / Num. unique obs: 5181 / CC1/2: 0.699

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2精密化
HKL-3000データ削減
HKL-3000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 / 解像度: 3.598→38.013 Å / SU ML: 0.5 / 交差検証法: NONE / σ(F): 1.36 / 位相誤差: 26.27 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2767 2657 4.83 %
Rwork0.2419 --
obs0.2436 55002 98.69 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.598→38.013 Å
タンパク質核酸リガンド溶媒全体
原子数25754 0 192 0 25946
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01426749
X-RAY DIFFRACTIONf_angle_d1.22236360
X-RAY DIFFRACTIONf_dihedral_angle_d17.15415742
X-RAY DIFFRACTIONf_chiral_restr0.0643805
X-RAY DIFFRACTIONf_plane_restr0.0084684
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.598-3.6630.36521220.33422427X-RAY DIFFRACTION89
3.663-3.73340.3251330.3222749X-RAY DIFFRACTION99
3.7334-3.80950.36461430.30592724X-RAY DIFFRACTION100
3.8095-3.89230.33361240.28842709X-RAY DIFFRACTION100
3.8923-3.98270.28411500.28412803X-RAY DIFFRACTION100
3.9827-4.08220.29851420.27512669X-RAY DIFFRACTION100
4.0822-4.19250.29211410.26932775X-RAY DIFFRACTION100
4.1925-4.31570.26311190.24762758X-RAY DIFFRACTION100
4.3157-4.45480.25971440.23732757X-RAY DIFFRACTION100
4.4548-4.61370.27431470.23192757X-RAY DIFFRACTION100
4.6137-4.79810.26531290.22712770X-RAY DIFFRACTION100
4.7981-5.0160.28421460.23012738X-RAY DIFFRACTION99
5.016-5.27980.25261280.23152801X-RAY DIFFRACTION100
5.2798-5.60970.27991490.23642735X-RAY DIFFRACTION99
5.6097-6.04120.30561410.25022788X-RAY DIFFRACTION99
6.0412-6.64620.30931500.2382771X-RAY DIFFRACTION99
6.6462-7.60130.25881780.2292800X-RAY DIFFRACTION99
7.6013-9.55160.23341390.18492872X-RAY DIFFRACTION99
9.5516-38.0130.22421320.20362942X-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)
12.7575-0.5584-1.14971.1909-0.371.4485-0.3304-0.0549-0.57510.07630.05190.6404-0.1444-0.29680.14610.65010.0995-0.10980.9224-0.10871.00660.9015-2.8079111.5113
21.2185-0.87910.24991.44510.5880.8784-0.1259-0.05230.1981-0.3890.02151.21-0.1057-0.38750.2050.63020.0961-0.10940.98350.12081.0577-7.1188-7.8998100.1421
33.0931-0.80750.3632.6923-0.34672.0177-0.3674-0.7602-0.65010.17640.3523-0.12490.43650.00570.03590.76250.08810.1130.840.14760.64778.4364-33.199391.6745
42.92140.4792-0.37532.19150.97452.3681-0.0542-0.1199-0.0803-0.2544-0.23260.02040.0143-0.1910.11690.74340.19810.04110.78070.19170.545710.1169-17.069478.9379
51.8102-0.352-0.38260.98620.29971.8202-0.3726-0.4788-0.10860.062-0.060.31230.34921.05350.02790.59840.08450.03861.01220.15130.92930.8864-9.3868100.2011
61.44150.49150.10531.87870.37781.3426-0.0729-0.08740.1224-0.22780.0052-0.1084-0.13640.02820.05090.5140.117-0.00260.74730.11930.614816.106-9.447487.4986
71.1901-0.5966-0.99273.63991.00242.04960.21350.533-0.1926-0.9634-0.5144-0.1421-0.2178-0.2420.18930.8830.1280.04570.9260.09650.636218.07-16.534469.6927
82.58680.9861.46732.79151.22842.22430.0412-0.60181.11511.5367-0.09140.0416-0.5870.74360.64891.3164-0.2738-0.07321.4601-0.38911.149518.517523.8851133.7677
94.18642.1304-1.04822.541-0.36062.1608-0.47040.09150.1-0.2623-0.3552-0.0229-0.93230.07720.37391.34510.1748-0.04591.65720.41851.095726.040429.8229124.7881
104.469-2.2243-0.73633.4777-2.60525.0037-0.70060.38710.8574-0.2340.4734-0.4938-0.7441-0.62360.5960.87840.266-0.24911.0886-0.04270.948910.900123.1273117.1984
110.5813-0.2996-0.0043.0297-0.25721.14770.0410.10730.13460.2308-0.13860.2647-0.5581-0.03820.08620.8740.2037-0.06111.197-0.06470.82945.780616.7681122.1202
120.97710.5879-1.05051.66620.13742.58870.75230.37420.1766-1.1109-0.82590.37640.14460.0690.07580.86330.0879-0.06890.792-0.04850.6135-3.798645.18330.6215
132.9350.0135-0.48830.4251-0.0780.03130.14230.1901-0.1009-0.0105-0.0358-0.13370.4432-0.1716-0.04831.08660.1067-0.07921.0321-0.08770.8576-16.410138.866433.5574
142.51680.2170.29760.9598-0.04352.42610.1324-0.1193-0.0973-0.34080.05170.21030.122-0.236-0.11250.8097-0.0145-0.12850.58580.10940.771-35.047949.728554.3723
153.5372-2.3289-1.38725.2480.40922.94790.82881.0710.3771-1.0566-0.8633-0.1239-0.9963-0.30110.05330.93820.15210.03310.79180.10410.8664-18.630670.582437.4314
161.4658-0.1461-0.40270.302-0.10432.21970.2123-0.07760.0836-0.1178-0.14420.23150.0686-0.07160.02630.8020.0385-0.09890.66140.04690.6016-25.826855.252751.8395
173.1117-0.2908-1.27560.7465-0.52293.48580.1501-0.60020.08140.00630.12970.0071-0.07030.4169-0.23670.6245-0.05910.01020.80360.050.6528-18.451658.215162.2198
182.7405-0.67761.80223.0111.36092.3037-0.60950.37230.80240.79910.21030.1624-1.41340.12620.61841.2713-0.04420.10931.07960.22550.737513.688165.188311.2095
192.2688-1.1442-0.78925.3112-0.99270.69790.36561.17060.111-0.4316-0.77950.2539-1.2511.04060.51141.70190.11710.07341.28680.27820.567722.227267.317710.1531
202.00654.8462-6.11352.8689-4.05225.87660.82690.22422.9842-0.22490.28320.5108-1.63520.5663-0.5322.163-0.17430.08150.7355-0.01761.282913.895677.163120.1019
214.92520.3186-3.65520.6012-0.34153.33970.04280.04960.24490.133-1.11260.314-0.89360.94610.81411.2664-0.0112-0.05781.64110.25321.201524.682873.222422.1375
223.11521.33730.20864.4439-0.09363.50660.4602-0.2277-0.22740.0926-1.0939-0.2089-0.14590.73430.69190.80750.25580.02481.04030.15530.639913.166357.63825.6061
232.078-0.8453-0.95.8915-1.32063.02190.85420.56890.62220.3658-0.9079-0.5103-0.47711.1486-0.42211.1248-0.0034-0.00160.92910.12230.693713.403662.85622.5293
242.65441.46720.79770.88830.19272.57450.35950.40630.9776-0.6819-0.2888-0.58710.3015-0.0824-0.03190.8426-0.09230.02520.71050.03120.84663.721150.427920.0655
251.870.618-1.57932.6174-1.55092.92270.2433-0.0268-0.48280.1174-0.5774-0.3585-0.01220.37770.16050.8144-0.0119-0.17830.8639-0.02410.61137.374544.508622.5548
261.68710.94740.38713.8033-0.49161.9358-0.1219-0.01450.99190.0733-0.076-0.1049-0.13632.080.13871.13630.1109-0.11772.09970.20070.54224.423167.933815.8811
271.43150.64321.22541.12940.30421.9639-0.22780.54540.50570.21220.21610.0822-0.60360.04420.11310.67160.04040.08070.99850.23580.9484-26.5894-50.1116103.6959
284.8773-1.10542.52732.0389-0.93024.2721-0.48130.88710.0642-0.61530.8208-0.3686-0.3519-0.5038-0.39280.80120.05350.06951.96970.10431.29912.7323-40.379121.586
292.19780.88430.43132.0911-1.10531.96430.29470.60640.3492-0.0759-0.4897-0.0091-0.18330.57290.2420.82280.0276-0.00361.07340.14720.7815-16.6812-45.6241127.8696
301.14770.46670.20450.79610.73911.28240.0052-0.05980.00820.2555-0.0055-0.262-0.08140.3449-0.0370.78540.0611-0.0911.24730.21250.8244-11.9172-60.4894123.3352
310.33620.240.02822.65741.35541.3963-0.2186-0.1415-0.4494-0.21540.05530.78461.9382-0.4330.08991.0956-0.0326-0.08380.66610.1041.0425-33.3464-86.305378.0848
321.66841.2185-1.12295.40822.00163.2984-0.0899-0.1228-1.2999-0.4657-0.3695-1.24610.1195-0.39520.71611.22830.07450.05620.89370.08741.3448-30.8556-98.738385.7656
332.0618-0.20370.44152.7444-0.0683.60780.0468-0.03710.0197-0.17640.12450.53880.8059-0.2954-0.22260.5858-0.1839-0.04690.72560.16920.8117-39.223-77.748990.0739
342.09690.01180.12964.14790.41033.0440.0199-0.1481-0.029-0.70680.38890.33070.03020.0499-0.29220.55090.00560.01930.58660.2050.6946-36.1412-71.449990.2176
351.6778-1.49761.2551.8242-0.91751.1287-0.2029-0.02660.1481-0.0711-0.46160.459-0.71590.24830.54271.44320.0969-0.12781.4241-0.13251.4174-42.1422-104.19877.6539
361.6238-0.2828-0.79793.88350.63691.5417-0.11780.1065-0.32631.3444-0.0747-0.72670.96520.20880.31181.12660.02990.11560.99250.15521.0387-25.7452-16.307737.5354
373.25130.05680.84691.9422-0.87482.6636-0.2299-0.06280.01140.2999-0.1601-0.4795-0.27830.3350.30551.0987-0.04480.04590.63410.02090.6733-14.98014.48415.3628
382.6179-0.20240.56542.4891-0.75810.8372-0.1233-0.27030.12590.05320.0614-0.0119-0.2945-0.27990.15361.18560.08730.1060.82830.03260.6837-40.3158.228726.5344
392.08480.1980.27461.9769-0.57822.1696-0.120.2982-0.1146-0.03650.03210.0136-0.04740.24730.06090.9548-0.06590.0430.716-0.03450.5436-26.47851.75588.9983
401.7179-0.2319-0.78230.41470.04910.4640.2101-0.0728-0.24760.2066-0.50110.0997-0.6602-0.642-0.00840.76610.09770.06631.1358-0.02480.6772-53.9896-18.908159.0722
415.39530.7868-1.07530.2660.75075.7560.1218-1.30921.19410.7458-0.15151.5291-0.6753-1.3348-0.56790.78270.07740.21291.1542-0.19871.8528-67.6295-15.855857.8514
422.04761.3901-1.11071.4147-0.60690.7597-0.20021.01380.2934-0.15030.3360.19280.932-0.55870.05971.8543-0.3246-0.55211.28630.24731.3864-63.4571-17.052145.3305
438.1178-0.4728-0.40383.5106-0.52062.99330.16630.1946-0.4622-0.4416-0.03711.9206-0.3604-0.65630.00961.040.01440.05080.55260.06851.2201-64.4893-22.744754.495
447.23923.92931.2354.71872.85542.07030.14171.8426-0.26660.21990.26760.2925-0.1895-0.6135-0.27451.25940.11270.01320.96450.13860.7247-50.436-21.560640.9577
452.6506-0.92670.05822.84821.15041.51730.0908-0.1358-0.3707-0.2504-0.16830.42160.04060.09770.01841.07180.18590.04240.85070.05080.9172-49.3734-18.1449.7192
462.10940.49370.19561.94440.2052.20630.08520.5465-0.0965-0.81790.3823-0.3330.82380.1387-0.14841.46820.04720.24260.8918-0.13610.9259-39.4248-32.302548.972
472.0233-1.28590.08370.7859-0.0421-0.007-0.12230.1739-0.054-0.60680.0474-1.84530.96580.34210.46411.59250.532-0.15421.50830.01761.4385-28.6005-29.270148.9078
481.82620.13590.43622.0841-0.82040.92670.6896-0.02071.1286-0.3754-0.07970.61890.5859-0.4127-0.34021.17680.02050.03970.87250.13140.6697-48.1284-13.003248.5858
490.1687-0.2297-0.07670.33310.13650.0627-0.1504-0.2084-0.3309-0.4017-1.3981.0349-0.5419-0.19270.78921.2810.12530.08622.0185-0.69882.2561-75.9672-28.217755.5578
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 18 through 81 )
2X-RAY DIFFRACTION2chain 'B' and (resid 82 through 128 )
3X-RAY DIFFRACTION3chain 'B' and (resid 129 through 193 )
4X-RAY DIFFRACTION4chain 'B' and (resid 194 through 282 )
5X-RAY DIFFRACTION5chain 'B' and (resid 283 through 346 )
6X-RAY DIFFRACTION6chain 'B' and (resid 347 through 574 )
7X-RAY DIFFRACTION7chain 'B' and (resid 575 through 615 )
8X-RAY DIFFRACTION8chain 'F' and (resid 332 through 365 )
9X-RAY DIFFRACTION9chain 'F' and (resid 366 through 396 )
10X-RAY DIFFRACTION10chain 'F' and (resid 397 through 431 )
11X-RAY DIFFRACTION11chain 'F' and (resid 432 through 525 )
12X-RAY DIFFRACTION12chain 'I' and (resid 18 through 50 )
13X-RAY DIFFRACTION13chain 'I' and (resid 51 through 128 )
14X-RAY DIFFRACTION14chain 'I' and (resid 129 through 293 )
15X-RAY DIFFRACTION15chain 'I' and (resid 294 through 352 )
16X-RAY DIFFRACTION16chain 'I' and (resid 353 through 512 )
17X-RAY DIFFRACTION17chain 'I' and (resid 513 through 615 )
18X-RAY DIFFRACTION18chain 'L' and (resid 333 through 353 )
19X-RAY DIFFRACTION19chain 'L' and (resid 354 through 364 )
20X-RAY DIFFRACTION20chain 'L' and (resid 365 through 375 )
21X-RAY DIFFRACTION21chain 'L' and (resid 376 through 394 )
22X-RAY DIFFRACTION22chain 'L' and (resid 395 through 421 )
23X-RAY DIFFRACTION23chain 'L' and (resid 422 through 442 )
24X-RAY DIFFRACTION24chain 'L' and (resid 443 through 459 )
25X-RAY DIFFRACTION25chain 'L' and (resid 460 through 506 )
26X-RAY DIFFRACTION26chain 'L' and (resid 507 through 528 )
27X-RAY DIFFRACTION27chain 'O' and (resid 18 through 143 )
28X-RAY DIFFRACTION28chain 'O' and (resid 144 through 172 )
29X-RAY DIFFRACTION29chain 'O' and (resid 173 through 278 )
30X-RAY DIFFRACTION30chain 'O' and (resid 279 through 615 )
31X-RAY DIFFRACTION31chain 'R' and (resid 333 through 358 )
32X-RAY DIFFRACTION32chain 'R' and (resid 359 through 393 )
33X-RAY DIFFRACTION33chain 'R' and (resid 394 through 479 )
34X-RAY DIFFRACTION34chain 'R' and (resid 480 through 516 )
35X-RAY DIFFRACTION35chain 'R' and (resid 517 through 528 )
36X-RAY DIFFRACTION36chain 'U' and (resid 18 through 109 )
37X-RAY DIFFRACTION37chain 'U' and (resid 110 through 282 )
38X-RAY DIFFRACTION38chain 'U' and (resid 283 through 431 )
39X-RAY DIFFRACTION39chain 'U' and (resid 432 through 615 )
40X-RAY DIFFRACTION40chain 'X' and (resid 336 through 355 )
41X-RAY DIFFRACTION41chain 'X' and (resid 356 through 373 )
42X-RAY DIFFRACTION42chain 'X' and (resid 374 through 383 )
43X-RAY DIFFRACTION43chain 'X' and (resid 384 through 403 )
44X-RAY DIFFRACTION44chain 'X' and (resid 404 through 417 )
45X-RAY DIFFRACTION45chain 'X' and (resid 418 through 451 )
46X-RAY DIFFRACTION46chain 'X' and (resid 452 through 479 )
47X-RAY DIFFRACTION47chain 'X' and (resid 480 through 494 )
48X-RAY DIFFRACTION48chain 'X' and (resid 495 through 515 )
49X-RAY DIFFRACTION49chain 'X' and (resid 516 through 525 )

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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