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- PDB-7mfu: Crystal structure of synthetic nanobody (Sb14+Sb68) complexes wit... -

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基本情報

登録情報
データベース: PDB / ID: 7mfu
タイトルCrystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor binding domain
要素
  • Spike protein S1
  • Synthetic Nanobody #14 (Sb14)
  • Synthetic nanobody #68 (Sb68)
キーワードVIRAL PROTEIN / SARS-CoV-2 / Spike Protein / Receptor Binding Domain / RBD / Antibody / Nanobody / Sybody / Complex / Neutralization / Epitope
機能・相同性
機能・相同性情報


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / 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 / 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 / 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, 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 ...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 / 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)
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: 1.7 Å
データ登録者Jiang, J. / Ahmad, J. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
引用ジャーナル: J Biol Chem / 年: 2021
タイトル: Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
著者: Javeed Ahmad / Jiansheng Jiang / Lisa F Boyd / Allison Zeher / Rick Huang / Di Xia / Kannan Natarajan / David H Margulies /
要旨: Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of ...Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures.
履歴
登録2021年4月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年6月2日Provider: repository / タイプ: Initial release
改定 1.12021年9月29日Group: Advisory / Database references / Structure summary
カテゴリ: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
改定 1.22021年10月20日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.title
改定 1.32023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Spike protein S1
B: Synthetic Nanobody #14 (Sb14)
C: Synthetic nanobody #68 (Sb68)
D: Spike protein S1
E: Synthetic Nanobody #14 (Sb14)
F: Synthetic nanobody #68 (Sb68)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,30315
ポリマ－96,7146
非ポリマー5899
水17,330962
1
A: Spike protein S1
B: Synthetic Nanobody #14 (Sb14)
C: Synthetic nanobody #68 (Sb68)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,6357
ポリマ－48,3573
非ポリマー2784
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Spike protein S1
E: Synthetic Nanobody #14 (Sb14)
F: Synthetic nanobody #68 (Sb68)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,6678
ポリマ－48,3573
非ポリマー3105
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)66.820, 83.050, 92.830
Angle α, β, γ (deg.)90.000, 106.711, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

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タンパク質 , 1種, 2分子 AD

#1: タンパク質 Spike protein S1


分子量: 22115.834 Da / 分子数: 2 / 断片: Receptor Binding Domain (RBD) / 由来タイプ: 組換発現 / 詳細: RECEPTOR BINDING DOMAIN
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: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0DTC2

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抗体 , 2種, 4分子 BECF

#2: 抗体 Synthetic Nanobody #14 (Sb14)


分子量: 12550.034 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / プラスミド: pET21b / 発現宿主: Escherichia coli MC1061 (大腸菌)
#3: 抗体 Synthetic nanobody #68 (Sb68)


分子量: 13691.096 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / プラスミド: pET21b / 発現宿主: Escherichia coli MC1061 (大腸菌)

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非ポリマー , 3種, 971分子

#4: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C2H6O2
#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: 1 / 由来タイプ: 合成 / 式: C3H8O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 962 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
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: 2.55 Å3/Da / 溶媒含有率: 51.78 %
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 8000, 0.1M Hepes pH 7.5 / PH範囲: 5.5 -7.5

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年3月26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: 1 Å / 相対比: 1
反射解像度: 1.7→40.27 Å / Num. obs: 105129 / % possible obs: 98.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.1 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.057 / Rrim(I) all: 0.104 / Net I/av σ(I): 8.87 / Net I/σ(I): 8.87
反射 シェル解像度: 1.7→1.76 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 9993 / CC1/2: 0.64 / CC star: 0.88 / Rpim(I) all: 0.51 / Rrim(I) all: 0.925 / % possible all: 93.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
XDSデータ削減
XDS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: 7KLW

7klw


解像度: 1.7→40.27 Å / SU ML: 0.1994 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 24.8564
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2149 5257 5 %
Rwork0.1811 99872 -
obs0.1828 105129 98.45 %
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 mean: 26.88 Å2
精密化ステップサイクル: LAST / 解像度: 1.7→40.27 Å
タンパク質核酸リガンド溶媒全体
原子数6768 0 38 962 7768
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00447008
X-RAY DIFFRACTIONf_angle_d0.73449533
X-RAY DIFFRACTIONf_chiral_restr0.05091017
X-RAY DIFFRACTIONf_plane_restr0.00491231
X-RAY DIFFRACTIONf_dihedral_angle_d17.83322442
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.34531660.29293137X-RAY DIFFRACTION92.26
1.72-1.740.28021660.26973164X-RAY DIFFRACTION94.44
1.74-1.760.3271680.25133192X-RAY DIFFRACTION94.75
1.76-1.780.25251660.22593163X-RAY DIFFRACTION94.07
1.78-1.810.26631710.22713242X-RAY DIFFRACTION94.88
1.81-1.830.27131740.22543308X-RAY DIFFRACTION99.63
1.83-1.860.26051760.22093343X-RAY DIFFRACTION99.07
1.86-1.890.29691760.22333339X-RAY DIFFRACTION99.46
1.89-1.910.27011760.22233340X-RAY DIFFRACTION99.35
1.91-1.950.23861760.20693354X-RAY DIFFRACTION99.46
1.95-1.980.27031750.20043324X-RAY DIFFRACTION98.67
1.98-2.020.24021750.20323316X-RAY DIFFRACTION97.98
2.02-2.050.23591720.18723270X-RAY DIFFRACTION98.46
2.05-2.10.22881780.1813381X-RAY DIFFRACTION99.41
2.1-2.140.2221770.18413368X-RAY DIFFRACTION99.75
2.14-2.190.22621760.18543331X-RAY DIFFRACTION98.9
2.19-2.250.21311760.17483344X-RAY DIFFRACTION99.58
2.25-2.310.22831790.17983401X-RAY DIFFRACTION99.69
2.31-2.380.22711760.18293359X-RAY DIFFRACTION99.75
2.38-2.450.23271770.18713353X-RAY DIFFRACTION99.77
2.45-2.540.24631770.1943372X-RAY DIFFRACTION99.61
2.54-2.640.26071780.19193371X-RAY DIFFRACTION99.61
2.64-2.760.24121760.18533355X-RAY DIFFRACTION99.55
2.76-2.910.21061760.18573345X-RAY DIFFRACTION98.19
2.91-3.090.2131780.17533367X-RAY DIFFRACTION99.83
3.09-3.330.17561790.1733401X-RAY DIFFRACTION99.67
3.33-3.660.16971780.16063398X-RAY DIFFRACTION100
3.66-4.190.19141790.15243387X-RAY DIFFRACTION99.78
4.19-5.280.16161790.14223406X-RAY DIFFRACTION99.61
5.28-40.270.19391810.18343441X-RAY DIFFRACTION98.5
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)
19.289533570182.90521580025-0.3897298291965.238419077541.293308997536.61260351770.215430335982-1.12840881546-0.756172833812-0.191742716821-0.1352807670761.070339069480.102875745238-0.843542487796-0.0775791501250.230923616426-0.0671187703097-0.02041651236960.3471290110560.07921574018650.419912294128-29.4866209334-11.202559557-29.0921287715
26.19644816584-2.25092220975-2.089636643342.67639702270.5723820169615.42319288309-0.0145348533061-0.240067977082-0.6012743108070.0591899088222-0.01649371510610.4173712880370.0152554082803-0.2141277745660.04479993923570.130991383575-0.02805588373050.02573664450680.09815635347830.02827493221840.277334876078-17.9537636608-17.2588580568-35.4591460158
35.808045350774.592174909760.2112252630556.20642863231.430390067561.237374914280.0159418918286-0.3675056983390.4280695342150.22636369617-0.1379790772380.763298780860.0478684767476-0.2840025604130.09982024783550.1601116261350.005313455581040.03813145059040.1677381340290.00892173381960.221798732382-25.3517849845-2.98638042416-29.6979676795
46.1654230668-0.222475645145-0.7009758498482.98976488925-0.05532305413381.669912593080.02599192480360.130161399270.159129145208-0.10520624196-0.006434701655930.394070373698-0.139206198053-0.183914586202-0.01752201833370.1180193260990.00305931407388-0.007696778300850.127208746593-0.003091228436560.141150036787-19.6678724165-4.05986126036-38.4983163553
52.00561692903-0.6791865214660.7131736376231.88770806351-0.01137395715713.50348288206-0.01222060980850.08254719233440.066040679958-0.157908387436-0.01328238219260.0954282427235-0.176361738393-0.1229535380370.01811309081680.0898843601007-0.015375253133-0.001750800350170.08433925798180.00670671418510.173054464323-11.8992489959-8.28204850162-40.9099633532
62.76538247840.5743921107252.967293100891.182616372260.510254804096.964098144530.1548904679720.0260989431229-0.2999647886080.05581272265420.015889086484-0.1479867750580.4387319887720.23316131823-0.2223926897880.1265209371590.0177504463511-0.006885954548840.0964259001240.008918204750860.219863041563-2.44135201437-19.4730286511-37.8256312174
75.4729301749-1.8945853765-1.069645263332.57222811733-0.5556888078180.943235708726-0.05433878283520.583678421983-0.62246963902-0.200488909257-0.0115185063280.1146741086520.2553422737880.05187485630230.04024576767150.209591869846-0.016211730116-0.02880330647910.215948125409-0.1121225663270.238033274048-6.59337867665-22.8410071843-51.1664411624
81.98177478747-0.05208264663540.15088478621.756230844070.3708840021421.14530407433-0.01558822096720.0562946543223-0.235104139402-0.1013646461870.1141868491950.003265107058320.07566924243480.0382783011927-0.09780915508690.0971588248596-0.01976654400440.01658590192590.1164248338280.0140227086860.154354036218-3.33879941538-16.8788362609-38.8139845357
98.919729696730.4527161295250.05372633908037.248050191233.449192751342.027749418570.06894527783310.845557873537-0.412626816168-0.704799852181-0.6706145953441.05187534498-0.519002313688-0.7112330419970.6287223616970.2776471287010.0813137494068-0.1130476673070.30722117432-0.08145468168410.491981734475-36.9234745678-5.75300654776-40.9449605651
109.59083577663-2.793389365644.696112661747.53521066435-2.774454692269.28017432730.4702358874850.9621801410340.109636745713-0.628782902956-0.665682456616-0.4347851022610.289377744750.4837163916150.1714088072650.1840083312790.07127318628160.04420126476740.228966947022-0.001588314485640.17591210894914.237089353-13.1949103103-52.2721335591
113.94372488832.1433428147-1.465647953183.399245977633.258354087327.872002872430.151480297469-0.501202965616-0.05614303315390.4030605936670.226456629537-0.6274625624990.4629717430380.883278349836-0.2325089619470.1622762970250.0635692035041-0.04870820302960.2838405880310.01613419946440.26947820557326.268137215-20.7439196776-34.5114589232
129.80471128276-7.18579842138.717586060018.24954696873-8.504317554579.478587733430.3157584936250.4740253474770.259764793288-0.237978103084-0.39874706331-0.179990987530.1340537204130.5314956112030.09893125499030.1574918724220.004754507067230.03830242856450.1540812257110.001624527636960.20894811740918.8812192154-11.1228024906-44.9536348807
135.90344200078-3.258102187040.02553286122374.99853749517-4.137352650372.044123162220.2450166991750.2367577177380.8777410073750.2076823664040.0732617502663-0.0182314596218-0.449830810524-0.40515771744-0.3051456903130.1948333922970.0122657354216-0.0002661604049240.1562906356370.01744288992870.2378371565927.8576566062-3.3271522938-48.8587383911
145.44077624012-1.219431982381.095142322974.49169875781-0.4109610566375.795939841220.1130635144180.0400021078673-0.5482933572770.226396495006-0.0912914117564-0.04721934750620.223797897621-0.0622167188853-0.0258404808880.1119073492190.02823955234790.00302913828790.1327412336530.02520003657390.1803318694169.09770575165-20.9572549298-39.9556475437
154.37863253864-1.063589464910.4082142004483.99383718215-0.5697188070494.229791821640.0883269038097-0.02821161257260.2399801935110.202406691872-0.0966995761280.151301550776-0.298670199218-0.0787193870844-0.002496782116690.102420820939-0.003733092592130.03715776476140.115744797751-0.005988897440260.1336096549778.63927675047-9.68645979048-33.5580435314
163.896828172890.276441349002-0.4448260418675.49323165866-3.808676392789.456107557710.08436712334730.1745015215810.6310140260330.126097311147-0.22313439188-0.314512879844-0.5696327075110.4376722881020.1211177515390.12728143462-0.02186469392140.02927413837630.1684775830310.01404864538450.22154060224517.4231418384-6.34646054515-41.2976706249
177.195490967376.755181735796.195865057372.025595608567.366442462542.064350052380.23835867885-0.500333849111-0.1182114526630.38986980026-0.331310291642-0.02263124355940.114174833641-0.2518448880460.1338132554480.264587551715-0.01657771867170.007216363081340.2257668286350.03310235616350.19562038697519.611465331-20.8253643473-30.6137709018
187.54241038236-3.558877422932.594486968374.30574142724-1.542542742522.358839621180.07141269263430.18829552485-0.0724599906420.0186970260456-0.0551989664864-0.1189475163390.04231745928680.0574277815177-0.03113955616650.09252866423220.003209173586990.02804461733340.1231084699190.002173196142570.13304605444112.0212272353-18.0911839931-45.0709357626
199.132775721894.993398844966.230900134089.127266110534.13968367658.879301207960.04606411460110.6066876152580.83035300193-0.389598117632-0.1553537317980.0890317271953-0.3043607297520.2763639051950.07847089134020.223100526210.0409747432190.07007315388270.1791930193630.03507684187140.338322951469-12.852890343921.3319836391-41.4162536815
207.856051326261.881771176216.585224034233.10281149005-0.3104231598686.95080074635-0.0143265085446-0.3318689978410.48476870450.363634588628-0.2740370238960.18120563537-0.2404053868980.03521522023840.2654994902540.321960708851-0.0961119797630.008360303505650.296969048469-0.08343621852330.2693285889475.6547476434124.7758975063-25.5882112243
217.644948547692.262126514515.679819423122.778085537061.176880629442.10234311395-0.226634964241-0.5384319920480.7557466020950.0928808536347-0.0332581146490.024214188291-0.37177046646-0.2021173640580.07585193842020.1550309668390.01013589638580.01163594858060.292703562254-0.06444496687040.301757214422-9.322101135323.0994694406-31.8454473901
223.769288457841.64476930264-0.7021585722932.64937565899-1.136390860532.269524074390.0784290281965-0.110245781134-0.0653985242779-0.0845599385473-0.01237592505950.0146641034181-0.05643774134670.112110831469-0.06766879588480.133310650783-0.01729461633430.01690156299440.0809967011002-0.003549416029020.148864628205-6.4853859282312.368699311-35.2602029566
232.02981318416-0.3704866689051.483635058583.57690085714-0.9045528777082.90424677725-0.07776253954-0.542029099206-0.3224294302170.313827879895-0.01869830496160.125754162759-0.02572638465290.02502246632720.05095977756440.178000358246-0.006441050517260.03076483452970.1864539125440.002968967702350.183372334096-9.625032627198.40307456122-25.4880835824
248.64953221255-3.775531680625.497718095035.76191188178-2.759122900749.03196771703-0.206668286213-0.814140615914-0.004728269731010.2982912169190.1512268850630.117518538361-0.352256135226-0.2999658985680.03515598761670.214724698178-0.0355681087130.04331094996190.180681938755-0.02765995646340.129843436898-6.2841393897415.4363821496-23.4919492326
256.9837425963-4.521200494445.432737246028.50124775559-2.601264497589.030080254-0.391137901651-0.7119087287180.0732609557190.4386800711670.301309337810.848580440036-0.6151581958-0.7819676033070.06135673727420.2499085467390.04085175541410.07010101396850.256062794956-0.07862668823830.271765170832-11.755965091121.7058024998-27.6256107063
269.46790229874.26552583048-4.899539173875.84211068771.634333192582.02240659937-0.0421542940566-1.22056307674-0.4885544082840.620064240979-0.0673906082539-0.6983603167620.3309868649760.867824297680.08089784975810.1880630674620.00928953004268-0.06190089945940.3478216624740.05246092511370.2156195999157.1164711006516.9573087116-25.4487607873
274.671600374313.955253621551.402732758884.599666251270.5743522110491.62174835188-0.1875755567460.2185410703660.00762982097695-0.2243513648880.184680996181-0.0904655609324-0.04058794967640.115385707418-0.002694512585780.09605405962870.007870318251510.03250498889110.134148041366-0.0003465107416280.139272433089-7.628861452310.0701755874-36.3174047362
285.940517397573.015120965590.3659981503382.046151352860.9556574267532.78408545048-0.01098750945210.1935920036760.405152333044-0.361373516077-0.08227005045720.196784836304-0.02638677819820.2379957985780.06483873037910.181967551844-0.005575877379670.01730233695020.1599860838020.06595300131440.174468541688-9.0383486031913.0535717268-42.3642085497
292.017046628762.05464653418.971553438296.325371528270.297053398582.05625075464-0.116181936591-0.337213362920.371512365329-0.0962016279378-0.0155574115885-0.275587518738-0.4347398225630.5101428847230.1539035326630.175547270708-0.1048200751080.04563749178670.359519940145-0.05514419124350.2344314211517.2777566764922.4883884723-31.232293843
302.012064227960.426376132287-1.798224461086.244276487161.061280614995.30810974013-0.2747094990460.4008889266761.096065502560.04188498489240.1423141646750.948816900421-0.210205392292-0.9330175671770.1293227352590.2046175676720.06574177995840.008981893495190.322719783850.05488329866440.328846745744-9.20929855301-13.5455742664-14.9474951245
310.5098170490620.8021876472730.7396584026831.71276923550.6092762953262.9368067155-0.02338411754280.1411145278050.4451106257240.005856535558890.004791610345410.268419868683-0.0633939037299-0.2530943861970.02836861468130.1042912719430.02869106006230.00541362008970.1589044952470.01586432331510.2717009171242.16858311118-7.58904675288-8.77531728798
327.61231631839-6.1095864872-1.316737053936.755886369291.97741502661.345719695430.04699340091980.389053805026-0.31105727034-0.0615693004408-0.1806673006750.6980772358090.0176963701874-0.3071265010110.1436677070830.148871988316-0.00991040387253-0.01850741146010.1873246419030.0302517541220.236501316992-5.32886020769-21.8324775214-14.5976055393
331.48710691960.3410116814970.3982629134041.925800603920.4916628138781.805005800250.0728652193748-0.0819921632136-0.0006046139768950.117372959506-0.02942286345820.2309041862340.0740613328527-0.109616100745-0.04520783267970.09018668227750.01206548392990.01128494724670.1141189549940.009430970094480.1635742650954.18838324566-18.8265057865-4.64586969036
342.337060353840.4751697524541.650287917463.610997080761.9415215381.78199983806-0.07708401671130.3227662384570.361332260999-0.3053228633080.131121614174-0.235293397816-0.442710897310.688182827333-0.08684344165950.116990272094-0.03242416134370.01024895901490.2308957918510.006597577233150.3295802978317.8098012764-5.65064304629-6.3952455192
354.250170394463.0681287171.158359811174.653313431270.02662355266621.85785861666-0.0938388136453-0.7104130844830.7412413666830.2747756507890.0133514327072-0.105257425013-0.26851917620.08084660875630.02211020925750.1799211877670.03427564319050.01267663135510.260427235193-0.1474071321780.33978623590213.4499236103-2.133118321446.94316562965
362.85157321037-0.0624325618577-0.2939718545472.862179231480.9024008314091.77355022512-0.0384932807498-0.1267399375980.4057863677740.04393489575950.268887936304-0.269253645899-0.1801959891320.216414699887-0.2231308748260.108545878779-0.00779150176846-0.0006916755095740.183433299101-0.01722692950480.27962577714322.4955382968-4.87602040866-4.38448705846
375.875576232232.48565509103-3.21963620663.38545195849-1.111819982684.110784563580.114816708923-0.04927905959740.7977208147780.1104880123940.1911633008760.414756396694-0.0967765074652-0.115929585914-0.3204679380510.1074508297420.0174601119881-0.01338167487530.1324218243770.02656718813210.1930463334272.43176074996-16.2712460449-8.02957043014
387.65466891637-0.133203332608-0.7368082181583.67216036434-0.04920466555214.602722505070.105594014018-0.8784268421850.3815622452480.384061258343-0.4559392919050.6324374970470.333598422314-0.635517889950.2192732435870.23247300065-0.07163154720810.06508047677620.313093035281-0.04922328232410.415374525994-16.8044275087-19.2614054392-3.88619281149
392.040179317835.33093503112-7.198357672756.76025590586-4.298915546679.610144478370.353311537852-1.00157294746-0.08439554232370.380099717012-0.575260074615-0.17875387097-0.04440059628020.9082873214890.2421722425310.179609354788-0.0206342899522-0.03008724200180.350495551124-0.01762233979070.24718243587233.7782383731-12.27578917438.61975772689
405.213435339292.21016201107-2.424560582382.45937482187-2.585786063825.128032313230.05047921627450.0152458225778-0.2690785633810.0138151364577-0.121607190562-0.354727797325-0.00223423293310.2615661247280.04737554935650.1123492770940.02118594590790.007763814937150.108012228217-0.03851181642670.23941042672637.4382806378-13.5909020984-1.10366627483
417.39037644405-0.8927340025690.1617748641836.051810783633.255712745845.48715721548-0.01084803679560.1742859208810.550515875082-0.178551305927-0.01816142259670.383914963752-0.330389646584-0.07161095069180.01777208633020.0864088147932-0.01495910020220.004350534356030.1546855174510.008781171376090.18341966642829.236500166-4.0275607283-4.30283211169
428.471933666523.54857416022-1.386393011629.06789924834-2.38321372517.363638945230.07715682110070.278779794417-0.0841390260145-0.2400119593560.04749000610410.2629393871960.332655943282-0.123524936249-0.1457868478420.0922088108944-0.0108477497655-0.01115829690510.14591041337-0.0349289733810.1601399904228.8649165485-15.2707439956-10.7071792766
433.98256854559-0.0165684133526-0.590090025126.76050831153-4.113110492152.260298932280.09998820822620.0210871234462-0.621894118139-0.0526833152287-0.182708291228-0.4226799049580.282278508060.453552274780.06852092568830.1647747588640.00553297162781-0.007943097222860.195768742199-0.01100333712450.27199554711737.5497284957-18.6162837195-2.9384048593
447.800788217631.78042259376-3.739339581641.47796462818-0.4044011678483.559530172740.09046295779880.1508812075630.352767050899-0.1567010585630.02157251983830.157560995907-0.1227594536690.00343277696737-0.119377616710.1307916299670.0105646147912-0.01787259798260.1435365583740.01894867929250.20470114428934.1695590267-6.6737127319-5.51037490926
456.777137675923.25195448748-2.606571525434.60693419595-0.8042575518443.648907452750.257748637997-0.09548284199410.8183863955160.1248440047540.02112419458560.0689645653479-0.3164973004460.248492184913-0.3049874553310.100515901450.0190502592341-0.0389958862890.127710936397-0.004365497113170.24805071536833.6765472159-5.6510563010.997696384805
462.05025409147-2.11084598709-6.563285265945.873953427252.99213356429.64556219382-0.0954793005242-0.703738861187-1.012417256170.624986113913-0.2602693500460.1160522529910.6861191373390.3004584979040.3649774372430.270576804973-0.0255404783676-0.0436069477230.2384301030040.06421208345620.4107539555847.22032349215-46.3669243824-3.31257716885
475.77092595633-1.21180337134-0.8321181999582.6190097734-0.3172106618971.606365013380.02366498555640.337312636885-0.589166029006-0.135869097752-0.05820706395250.1124181967160.174924534673-0.01540647789490.02425433727970.1378479658560.0139720047686-0.01619633323030.144159433684-0.01346755611730.1766805429713.452206249-43.9907268791-12.5940183176
482.06495763332-6.068582363177.910758003284.7805909247-3.790977797127.40644256588-0.2048118694710.2031313758860.4995298359010.296225650498-0.0257907396819-0.615698880103-0.2422928733150.4213537223490.3024062085120.1487464048770.00397897755421-0.01102648185150.230657515074-0.003283826309190.28062065934719.3279348843-35.5996680754-9.46635929003
497.198596299060.990191532512-3.021161246665.23417927635-0.002300992784863.22819189769-0.1392948410150.3020751202970.301898394984-0.3561183406130.012592764292-0.0733598780862-0.06665023949660.07774077620660.1255816575640.154211128070.000175822716034-0.01853039729570.1399159638080.04339796706320.13605114067210.5078678985-33.2138174351-19.0672751545
502.141334648134.67032920587-5.238091049377.22473292773-3.004568357989.09881961646-0.1679021251360.636464796826-0.00901941090365-0.3268992091470.1504065603830.4069935316950.470763279326-0.5557257392690.03747650039490.1646350081120.0125109658111-0.04698219716680.217192893702-0.0352354430360.23737524401610.8644107808-43.6136008976-18.8828149043
515.10247285638-3.019254041230.1799924449323.818741336950.04711716036760.6183414912690.05882512195280.243308974650.00357496309073-0.0811497318027-0.0762768256747-0.1684387761180.02631703240370.1815548036880.01750975319870.105512499273-0.00158020037837-0.002640991274550.1657218032630.01378595858090.14090775972116.7578558124-37.0717916276-11.4191956198
526.42694614143-3.0754815282.13193976348.442963115850.9289426916646.856967304260.034783233488-0.44104047627-0.5830135284290.157276971245-0.1590988021520.06037007726360.105155362871-0.04935188807360.1216071372510.126575320972-0.002928379205210.02236687218210.1810977815760.08964351223810.18981870868811.0083337141-37.9648889563-2.2230523636
538.129380372850.402865310565-5.823787123474.78446164683-1.541161740078.08503824278-0.5592099946420.570935541012-0.7785831345140.05705634995640.119530902183-0.4792514903940.6715239892840.5566023846220.485542097330.1558004300330.08504524593310.005006435531520.347665184378-0.0868594700760.33222041328327.3468084174-47.4469045396-13.4604200536
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 332 through 342 )AA332 - 3421 - 11
22chain 'A' and (resid 343 through 358 )AA343 - 35812 - 27
33chain 'A' and (resid 359 through 375 )AA359 - 37528 - 44
44chain 'A' and (resid 376 through 409 )AA376 - 40945 - 78
55chain 'A' and (resid 410 through 442 )AA410 - 44279 - 111
66chain 'A' and (resid 443 through 459 )AA443 - 459112 - 128
77chain 'A' and (resid 460 through 479 )AA460 - 479129 - 148
88chain 'A' and (resid 480 through 516 )AA480 - 516149 - 185
99chain 'A' and (resid 517 through 528 )AA517 - 528186 - 197
1010chain 'B' and (resid 1 through 7 )BB1 - 71 - 7
1111chain 'B' and (resid 8 through 17 )BB8 - 178 - 17
1212chain 'B' and (resid 18 through 25 )BB18 - 2518 - 27
1313chain 'B' and (resid 26 through 33 )BB26 - 3328 - 35
1414chain 'B' and (resid 34 through 45 )BB34 - 4536 - 47
1515chain 'B' and (resid 46 through 67 )BB46 - 6748 - 69
1616chain 'B' and (resid 68 through 83 )BB68 - 8370 - 85
1717chain 'B' and (resid 84 through 91 )BB84 - 9186 - 93
1818chain 'B' and (resid 92 through 115 )BB92 - 11594 - 119
1919chain 'C' and (resid -1 through 7 )CC-1 - 71 - 9
2020chain 'C' and (resid 8 through 17 )CC8 - 1710 - 19
2121chain 'C' and (resid 18 through 26 )CC18 - 2620 - 30
2222chain 'C' and (resid 27 through 52 )CC27 - 5231 - 56
2323chain 'C' and (resid 53 through 64 )CC53 - 6457 - 68
2424chain 'C' and (resid 65 through 73 )CC65 - 7369 - 77
2525chain 'C' and (resid 74 through 83 )CC74 - 8378 - 87
2626chain 'C' and (resid 84 through 91 )CC84 - 9188 - 95
2727chain 'C' and (resid 92 through 109 )CC92 - 10996 - 115
2828chain 'C' and (resid 110 through 118 )CC110 - 118116 - 124
2929chain 'C' and (resid 119 through 125 )CC119 - 125125 - 131
3030chain 'D' and (resid 332 through 342 )DD332 - 3421 - 11
3131chain 'D' and (resid 343 through 358 )DD343 - 35812 - 27
3232chain 'D' and (resid 359 through 375 )DD359 - 37528 - 44
3333chain 'D' and (resid 376 through 442 )DD376 - 44245 - 111
3434chain 'D' and (resid 443 through 459 )DD443 - 459112 - 128
3535chain 'D' and (resid 460 through 479 )DD460 - 479129 - 148
3636chain 'D' and (resid 480 through 506 )DD480 - 506149 - 175
3737chain 'D' and (resid 507 through 516 )DD507 - 516176 - 185
3838chain 'D' and (resid 517 through 528 )DD517 - 528186 - 197
3939chain 'E' and (resid 1 through 7 )EE1 - 71 - 7
4040chain 'E' and (resid 8 through 33 )EE8 - 338 - 35
4141chain 'E' and (resid 34 through 45 )EE34 - 4536 - 47
4242chain 'E' and (resid 46 through 67 )EE46 - 6748 - 69
4343chain 'E' and (resid 68 through 83 )EE68 - 8370 - 85
4444chain 'E' and (resid 84 through 99 )EE84 - 9986 - 103
4545chain 'E' and (resid 100 through 115 )EE100 - 115104 - 119
4646chain 'F' and (resid -1 through 7 )FF-1 - 71 - 9
4747chain 'F' and (resid 8 through 39 )FF8 - 3910 - 42
4848chain 'F' and (resid 40 through 52 )FF40 - 5243 - 55
4949chain 'F' and (resid 53 through 64 )FF53 - 6456 - 67
5050chain 'F' and (resid 65 through 83 )FF65 - 8368 - 86
5151chain 'F' and (resid 84 through 109 )FF84 - 10987 - 113
5252chain 'F' and (resid 110 through 118 )FF110 - 118114 - 122
5353chain 'F' and (resid 119 through 125 )FF119 - 125123 - 129

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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

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