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- PDB-7lmv: SPECIFIC INHIBITOR OF INTEGRIN ALPHA-V BETA-6 -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 7lmv
タイトルSPECIFIC INHIBITOR OF INTEGRIN ALPHA-V BETA-6
要素Integrin inhibitor
キーワードDE NOVO PROTEIN / de novo design / inhibitor / integrin / fibrosis
生物種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: 1.9 Å
データ登録者Dong, X. / Bera, A.K. / Roy, A. / Shi, L. / Springer, T.A. / Baker, D.
資金援助 米国, 1件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
引用ジャーナル: Nat Commun / 年: 2023
タイトル: De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8.
著者: Anindya Roy / Lei Shi / Ashley Chang / Xianchi Dong / Andres Fernandez / John C Kraft / Jing Li / Viet Q Le / Rebecca Viazzo Winegar / Gerald Maxwell Cherf / Dean Slocum / P Daniel Poulson / ...著者: Anindya Roy / Lei Shi / Ashley Chang / Xianchi Dong / Andres Fernandez / John C Kraft / Jing Li / Viet Q Le / Rebecca Viazzo Winegar / Gerald Maxwell Cherf / Dean Slocum / P Daniel Poulson / Garrett E Casper / Mary L Vallecillo-Zúniga / Jonard Corpuz Valdoz / Marcos C Miranda / Hua Bai / Yakov Kipnis / Audrey Olshefsky / Tanu Priya / Lauren Carter / Rashmi Ravichandran / Cameron M Chow / Max R Johnson / Suna Cheng / McKaela Smith / Catherine Overed-Sayer / Donna K Finch / David Lowe / Asim K Bera / Gustavo Matute-Bello / Timothy P Birkland / Frank DiMaio / Ganesh Raghu / Jennifer R Cochran / Lance J Stewart / Melody G Campbell / Pam M Van Ry / Timothy Springer / David Baker /
要旨: The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between ...The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integrins, stabilize specific conformational states, and have high thermal stability could have considerable therapeutic utility. Existing small molecule and antibody inhibitors do not have all these properties, and hence new approaches are needed. Here we describe a generalized method for computationally designing RGD-containing miniproteins selective for a single RGD integrin heterodimer and conformational state. We design hyperstable, selective αvβ6 and αvβ8 inhibitors that bind with picomolar affinity. CryoEM structures of the designed inhibitor-integrin complexes are very close to the computational design models, and show that the inhibitors stabilize specific conformational states of the αvβ6 and the αvβ8 integrins. In a lung fibrosis mouse model, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.
履歴
登録2021年2月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年8月10日Provider: repository / タイプ: Initial release
改定 1.12024年2月21日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
改定 1.22024年4月3日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Integrin inhibitor
B: Integrin inhibitor
C: Integrin inhibitor
D: Integrin inhibitor
E: Integrin inhibitor
F: Integrin inhibitor
G: Integrin inhibitor
H: Integrin inhibitor
I: Integrin inhibitor
J: Integrin inhibitor
K: Integrin inhibitor
L: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)93,35912
ポリマ－93,35912
非ポリマー00
水5,963331
1
A: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
9
I: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
10
J: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
11
K: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
12
L: Integrin inhibitor


分子量 (理論値)分子数
合計 (水以外)7,7801
ポリマ－7,7801
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)92.270, 92.270, 82.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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要素

#1: タンパク質
Integrin inhibitor


分子量: 7779.935 Da / 分子数: 12 / 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)
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 331 / 由来タイプ: 天然 / 式: H2O

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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: 2.17 Å3/Da / 溶媒含有率: 43.31 %
結晶化温度: 297 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.2 M KNO3, 20% PEG3350

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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: 23-ID-B / 波長: 1.0322 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2014年8月14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: 1.0322 Å / 相対比: 1
反射解像度: 1.9→40.26 Å / Num. obs: 61653 / % possible obs: 99.99 % / 冗長度: 5.6 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.4
反射 シェル解像度: 1.9→1.97 Å / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3570 / CC1/2: 0.114 / % possible all: 99.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18rc2_3793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: Designed Model

解像度: 1.9→40.26 Å / SU ML: 0.2423 / 交差検証法: FREE R-VALUE / σ(F): 1.99 / 位相誤差: 34.9264
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2678 1475 2.39 %
Rwork0.221 60178 -
obs0.2222 61653 99.68 %
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: 38.02 Å2
精密化ステップサイクル: LAST / 解像度: 1.9→40.26 Å
タンパク質核酸リガンド溶媒全体
原子数6374 0 0 334 6708
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00576491
X-RAY DIFFRACTIONf_angle_d0.68438724
X-RAY DIFFRACTIONf_chiral_restr0.0499971
X-RAY DIFFRACTIONf_plane_restr0.00411128
X-RAY DIFFRACTIONf_dihedral_angle_d11.63662450
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.34621360.28285498X-RAY DIFFRACTION99.77
1.96-2.030.31381340.25875462X-RAY DIFFRACTION99.66
2.03-2.110.35341340.22225472X-RAY DIFFRACTION99.8
2.11-2.210.2591340.23715448X-RAY DIFFRACTION99.73
2.21-2.330.3161340.26265479X-RAY DIFFRACTION99.73
2.33-2.470.31731400.27835467X-RAY DIFFRACTION99.82
2.47-2.660.24271400.25515481X-RAY DIFFRACTION99.77
2.66-2.930.28041310.25245485X-RAY DIFFRACTION99.93
2.93-3.350.29771280.23095494X-RAY DIFFRACTION99.98
3.35-4.220.29511320.17745494X-RAY DIFFRACTION99.82
4.22-40.260.18011320.18135398X-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)
13.550415110861.56164353517-0.356046229685.415646777252.029758699527.77908281725-0.106206001445-0.117367567683-0.0374631448454-0.21647286543-0.0185429511277-0.133827074174-0.25890141695-0.05517787869750.1003036780080.12011837476-0.01285524051870.02831644170260.1652625679860.0411997898240.15605147002930.545-17.319-0.726
24.293359900571.03759462751-0.0848806049996.33069496750.3916981260222.853796888-0.7701533384690.585968572878-0.519276974923-0.7808016655050.471928866744-0.3031439759820.737067711264-0.07873941457230.2717989990420.396924566829-0.0900309376040.1692860994540.248780123978-0.01659201643320.29116606292133.23-20.43-9.084
36.23605319113-0.333705070838-0.4920669970675.755077006264.003079277638.77736096584-0.4203335650510.669828647873-1.21601303633-0.833139192330.04327055099920.252312235303-0.00743276242862-0.1563866604440.2930937057170.722118673243-0.202492600362-0.002402655461350.314081319738-0.001954518571860.52715700810223.118-27.589-7.217
41.2396246578-0.6331484129831.224125082242.98874248978-0.04265120417477.98481882392-0.5010920013460.595654038933-0.418991358425-0.2764237914440.2468414113090.307448461177-0.307932161603-0.6503215948980.159516025770.22922662418-0.1882626730910.004170378524020.2783631008130.03077497468550.2266384841522.315-19.441-7.456
54.16064590120.274116172873-0.8278661784863.86794564223-1.952152577568.873175742860.0542722399974-0.2771680729640.162680121989-0.1153954859840.02925361164420.02746416239480.5029612234250.00598232207285-0.06461210377080.376816640249-0.03893119270540.005154989588090.222501969456-0.03421393152790.245288241363-28.3417.31141.794
64.86754615031.689825957-0.9743422126852.70233195895-0.3080252146495.80989652362-0.01099193796870.1640046638320.955147235423-0.438264231337-0.1782048869960.4453350808370.0583047688132-0.2709337430160.2235469615190.352161063156-0.00178263928463-0.02572627905650.2224040592250.01640469233610.437864600588-32.18120.35233.546
75.10011931930.5491176499360.2066101177394.216969136670.1646011245535.439183987870.248357524141-0.04773561494730.813412463840.5634722917660.05350468901850.346825946691-0.1423687597240.186488521589-0.2989800940260.463004483457-0.04447390959070.07971172146410.174961966934-0.002786189096990.28346257357-21.85223.43533.744
85.11340040035-0.07228739414821.885173500343.153798602741.52845588536.75616158913-0.03823313547230.182407888322-0.1678762928140.1188628292170.02984906163740.00487695259099-0.1551979288920.09874855312960.01103743529440.1130395726060.03185573456760.0471433508490.184970523119-0.005707275013280.18283035461346.415-8.495-14.425
94.85303995019-2.06011194553-0.2270084607144.666319358090.7624447327332.991382641090.2045707562981.08893018691-0.514276384398-0.391248802442-0.3878098284740.7050422284810.181874890739-0.6728067692010.1223608163120.253687744805-0.0329849933907-0.003671474342520.477410338582-0.08937568009340.30012892491541.032-10.491-22.146
103.19670664019-0.368279629967-0.3175084746844.959554408990.04407089537886.848511485510.2385158164330.603661207553-0.317933658735-0.285308241324-0.2751081880150.58759248388-0.678784756119-0.306009850373-0.06142976599880.1283975192190.05425278084480.02778959928670.3716297754740.003710097296860.21164728872640.506-2.78-22.053
113.418479264181.16328871884-2.338336397894.53619257988-2.16642264197.74585635533-0.123366063845-0.03449928863180.1262312910750.5349051452530.0801969850707-0.0447430631921-0.273925557213-0.6836562930090.004073267200150.250936111892-0.0112268424967-0.02935294208970.342551087235-0.04205505933940.216999005568-45.3296.63928.08
124.86959141012-0.3656044931090.8228340736794.97440623222-0.1587978998975.38310066211-0.3085422889740.08028052758530.5096203487490.05284014623660.0154365476084-0.327417915428-0.8111853643340.3832389495830.2913737815110.380370471445-0.0675299115118-0.08931790633860.286121689195-0.0001379949100180.322920590226-44.86214.37821.121
135.18176090239-1.529417238870.4454027028125.50714334649-1.338466555374.956907138740.2258582758730.28234309340.693736083310.257536414126-0.477975931634-0.533350538305-0.01302741166150.6842828955260.2310439785260.289516901705-0.09501463549340.02053222552540.524219288384-0.06504471920760.285014942185-38.5767.33820.382
143.302944874910.7300275533320.220843827956.7830092088-2.211336829958.46243724524-0.0994828117935-0.0872290055255-0.4957299050650.332947522259-0.454851850659-0.8311954582270.6140075250560.03912179003920.3587228887560.1416972117260.000349982606279-0.02973689075070.445887574154-0.08580629354420.220210646145-40.151.26719.112
152.43336698294-0.687085665072-1.234307962824.81727313559-1.695145482657.428544397760.378649822479-0.0985943789226-0.102705491909-0.339582929191-0.4456862467750.0608634824748-0.07472933927710.04803782755770.03817829541990.255357236567-0.0701877754311-0.03802968869660.369948255191-0.0234900869640.23557139024915.934-8.88-25.457
161.78784620797-2.252764462961.611704583267.050027256171.635688658797.430714375720.291878931209-0.4269132507280.1397765225810.664202167479-0.7352537402461.07496100778-0.0979013062958-1.225055849840.4415490256560.35570262105-0.04650294352690.09342231335950.463894385557-0.1248529106510.3498537379669.383-6.465-17.622
170.799797777199-0.48823249124-0.3965529092433.857549575420.5640438703280.855148867005-0.3789338791210.310117978707-0.0769323303865-0.03396555596910.1942507976650.836073119390.226077983971-0.3666276715960.2558239450640.344346927652-0.316307315634-0.06531548829740.6824399334970.1035177197050.42853713072912.634-15.54-17.685
180.60266638608-1.251069456850.7519196715833.69810609020.3507450076923.93451528708-0.1162302288080.743368005427-0.254772090771-0.4057792383360.1149028283860.3177706172360.00897728301826-0.256251063433-0.1274761378660.407130542061-0.332567862869-0.1142394994840.6592533039320.1783540288210.015911966585618.11-16.958-17.893
191.804862426740.2980094787860.4316674447354.76203023227-1.028277223496.451307888890.0752426999248-0.1355932074510.0233709606064-0.0149490526538-0.120258656897-0.341844012530.1874638628680.08228156813960.02070670883740.213292860619-0.04052006505010.02701322652380.224824244314-0.009847182569810.288522704245-14.1168.12717.699
200.542127360486-1.4257763070.7581296868883.97084053399-1.939888207192.16044192216-0.6231021519560.650810433501-0.185028240390.1237594250090.653878266777-1.43571107433-0.8138822925090.4714221750330.1130253041760.492217991925-0.2350269469960.08723334400620.508000978184-0.1324666071210.493329094081-12.37515.4423.343
214.237775240930.0237419872986-1.064607880634.532158980650.5738423311437.2070980253-0.3613539007360.6220321004270.1546608635140.1521519190810.674379080239-0.655552731243-0.1849888257260.0770484181531-0.2695551280250.440035706943-0.0928209932032-0.02097439148150.301331438246-0.07631806353860.241392464877-17.34616.60524.212
224.07189125610.7302531646291.806388666872.84266256458-0.8924814457648.18103643071-0.05054270362620.05030460104760.0800476658421-0.2319699484530.0917654587075-0.166571763814-0.0218230907784-0.223398785516-0.04436904824960.1671474090160.02501410743520.01652702775980.265093524833-0.01672146764410.245535837765-0.302-35.1651.967
237.186749593882.99065592069-4.039050058435.875721048181.263320894629.05384965106-0.142961756994-1.25238217351-1.351531834230.2896631399920.141534190858-1.018279622451.257238955360.7357874945960.07928295972120.361925569880.0496068020179-0.0256593818240.5214891966090.1033484918180.5888744986280.777-42.1549.683
241.24424305331.39263703572-0.2368757477423.42891265312-2.196805354313.494906481360.3600870483720.645150246803-0.9172293221390.0510975624856-0.737533526308-0.497165806552-0.1471605917940.8002140782660.3865093298050.2624765152570.106835216244-0.0610369076990.661052210575-0.09503859152170.5113249313977.159-34.9119.556
254.099089037842.2548805333-0.7019668242285.310144907791.994346214023.781123470660.5495305812360.384967221345-0.498931001377-0.163883101725-0.173166141355-0.645291030195-0.400499818921-0.124905055639-0.2340978595170.2763348192710.0532986389901-0.01296112929390.473840564924-0.01501361957710.2152544381965.786-29.1958.728
263.6151945836-0.876126353739-2.857399816523.042952989061.323067171842.7280102617-0.166708660456-0.192818681007-0.446485015140.155952086219-0.0008465067642750.0679976421940.7962484026180.1978843941620.1292390943480.1485512248890.0326268017758-0.02114019539080.2069790138640.01251979393490.220894470340.07628.256-37.149
273.32547045734-1.014176152890.6119238668984.086907592961.212654973524.41860529582-0.0240581909623-0.2684600453480.350628345272-0.217220170063-0.07307440997930.110743886204-0.586149244496-0.1216792948860.08000632514350.184397650015-0.00232270429947-0.030622857140.145437302061-0.0174058266480.184299395757-1.62338.837-39.179
285.784157980161.41566255549-0.9714825359344.12323540671.314592025875.275621268270.0510874397299-0.3101076206920.6807919506650.249275111860.0437391250720.485917210640.0270660879835-0.253661461614-0.08424765854020.1649871668880.0332036916522-0.0253986550690.2376313811480.01795302308830.244288568679-7.64733.788-32.75
295.026823150030.2393990917550.9089971712125.605413461571.799512571912.19488312068-0.0605240426229-0.909892104486-0.0405669906080.222188085505-0.208573990660.5086484791270.0831758522205-0.05004215508790.2395109614890.136005487096-0.0281956526156-0.007647963658290.2777863141170.04315667899770.230106250203-5.76928.781-29.813
302.449302544380.5145470222362.002387219824.819482830081.990212152418.12483470650.22344206543-0.05681094497470.16733272787-0.0840954361591-0.327280124094-0.07688718284320.403289174466-0.1597893012220.09347473161220.228671203166-0.05931995968660.040895363950.3128730589810.01637746287070.244077174634-15.932-44.41515.726
312.69321044284-0.3429468611780.2540580627887.837824963581.401034617796.524691589330.642247018428-0.1546742484390.2092687245771.01863200496-0.486239992843-0.7762435752310.5253967664550.596647658217-0.01019732725030.384860409639-0.0950346502056-0.01926842553530.4534378000090.0140253267740.367637081458-11.885-45.13924.234
322.563264730410.7962917053090.5871068265593.033512802220.3321328388281.50193682149-0.2311664615560.2009926602280.507054474878-0.3075774774780.369695794263-0.764300341127-0.03719390135010.2255337246510.06029882316520.368423801151-0.7080129569740.07010620292160.789517435372-0.1170628470740.392965638995-10.998-32.56222.357
332.25880392192-0.699168270244-1.427781136584.64961683972-1.352722914882.05671079643-0.1156803714480.229210866272-0.09244499036570.07299100997750.00226318657783-0.140901836077-0.123496027516-0.02612983649340.1082016185550.298329005935-0.1516398498550.03624603998750.428280257591-0.07154959410220.215319205204-18.011-36.45723.432
344.621628782290.781271701479-3.509559345263.24598008551-1.470617592912.98564865735-0.227472111032-0.0742557127537-0.1059410864550.02734061896410.0980795237458-0.3332418342160.5640951457130.3522590622450.06479341432870.200679283374-0.0571066452777-0.03340030259070.189023332247-0.01392411709250.19522565959821.69840.828-23.43
355.09034903305-0.34414016629-1.111452785533.333979655862.180789410925.772491849140.1334761394930.228905282660.04026863555640.0701355419545-0.3024554403250.370997582548-0.164111302891-0.7980810616210.1647608345790.1698917885810.0185692757006-0.003547143525780.180494197695-0.02219316121110.18175943358212.16344.601-25.723
364.310141215990.0801651220574-1.996953635215.569577693820.3574499423044.576711779250.14365118531-0.208646460063-0.1224960142360.412906042239-0.1826447244510.7653781215840.275996854229-0.2100299343340.04977192503260.217863495783-0.0787618482012-0.01294907353960.211773318437-0.004473637008760.22237611339613.00936.951-19.036
374.24802600191-0.229960690648-2.276519363654.427510178312.006137113262.86233780593-0.13608691291-0.295307387878-0.6641316759660.443128005478-0.5782774886850.1253406449-0.07844899917670.3810385435750.6336961766860.192556582561-0.0322141350514-0.05044079580440.1408031503280.0003158878943480.24899715083419.15335.382-17.871
384.03179961240.694535013029-4.122190087313.96808571137-2.751106693499.62239519411-0.137163840501-0.2370902743250.03384528744690.1005948267540.101001307495-0.02218217289360.903677749236-0.5766196054150.02037033204320.332628403925-0.2000636507820.004916699984370.449920726313-0.06091860081780.23483486712-0.122-25.06824.672
399.561760249365.75698865509-3.599156375869.76976527002-3.544042091486.96766618860.398583624411-0.9162002086470.4895244290710.202181221305-0.3445153182670.0677720693781-0.1795092303710.252871679029-0.05117267203620.3253607849470.0392975815445-0.04089779630840.403057283451-0.01953586597940.2749253882731.496-16.46730.502
405.54083179021-0.518613971972-0.5611219376373.716758708160.7792189375994.70481506173-0.2635398568090.3575936747540.507180454184-0.370714035395-0.008641544559-0.746821274179-0.216359942573-0.02833424356110.25733813010.259952686973-0.04530527783280.00560284866580.4338356233020.06479851066970.4100798991551.52-15.22819.826
415.48274183642-0.884930629408-0.2294006472115.247920653490.02265202931046.89448373640.32176581968-0.5244010574050.8142056657750.3056793980620.119792017994-0.664677926168-0.07978704197030.180407368703-0.3842635013850.203641940571-0.07814315630070.03263585662490.42649883093-0.09001381971860.3236734721169.562-22.82220.5
424.255168294081.18749551242.946601783084.124255919142.869318083413.8024309399-0.206803512135-0.5605357921450.264705812355-0.01690791658110.104340585756-0.0739154410477-1.132578842020.336051839575-0.02989672130130.320580692867-0.1504219709-0.03004993803270.4116822489970.1082674956350.1909689385090.14724.908-16.613
435.013300334275.045784532791.499366211285.371679163062.908931181028.122916514090.344704549141-0.672671504367-0.1379494864070.737882973154-0.3061486073190.2197754101110.6557795357140.2913612543340.01390233427360.3088607328520.04210571364840.01313108394510.3078374008210.02940209959490.326550491282-1.50716.435-10.652
449.76750351326-0.625630810727-2.80759367474.93298789454-0.8247392028947.85427351712-0.313999296577-0.0923900059374-1.33239961038-0.1603345464080.2056977513430.127261871331.40198083334-0.4708623524110.04447966275420.513131643932-0.0158899541440.0733588709280.28634053748-0.002177525290540.395793883706-1.27512.251-20.075
454.6980430691-1.01333781737-0.877413637464.688304399521.992815514935.310893559750.2860658406940.156318360591-0.5263657157550.112708842485-0.5482358810850.3774022575920.141171370019-0.9659619291860.2394228558950.303113280463-0.079849968837-0.02009085314320.485213319230.05410017236760.251239366953-7.61219.391-20.897
464.94612535422-0.390236233056-0.303108963346.362864387291.834415762667.5687656233-0.200340866378-0.3029935828140.1238235439960.256807666401-0.3407525242260.73329821514-0.345569596627-0.1053665961440.3808886041570.118840684894-0.01881842295050.0274201761590.2818686674320.07905889410460.187238363151-5.85924.279-23.822
47-0.02813822840490.02717474131670.00474021433579-0.0607499587548-0.05389678931260.02315218882680.003245492591160.0117186416490.004459898122990.003790812399620.002826004068070.01867805047330.0306633751895-0.0118052222141-0.01330423605750.251073398149-0.04072187774110.01351339985620.251689438679-0.003601870768070.2155119020941.1662.761-0.173
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:25 )A0 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:44 )A26 - 44
3X-RAY DIFFRACTION3( CHAIN A AND RESID 45:54 )A45 - 54
4X-RAY DIFFRACTION4( CHAIN A AND RESID 55:65 )A55 - 65
5X-RAY DIFFRACTION5( CHAIN B AND RESID 0:25 )B0 - 25
6X-RAY DIFFRACTION6( CHAIN B AND RESID 26:44 )B26 - 44
7X-RAY DIFFRACTION7( CHAIN B AND RESID 45:66 )B45 - 66
8X-RAY DIFFRACTION8( CHAIN C AND RESID 0:25 )C0 - 25
9X-RAY DIFFRACTION9( CHAIN C AND RESID 26:54 )C26 - 54
10X-RAY DIFFRACTION10( CHAIN C AND RESID 55:66 )C55 - 66
11X-RAY DIFFRACTION11( CHAIN D AND RESID 0:25 )D0 - 25
12X-RAY DIFFRACTION12( CHAIN D AND RESID 26:34 )D26 - 34
13X-RAY DIFFRACTION13( CHAIN D AND RESID 35:55 )D35 - 55
14X-RAY DIFFRACTION14( CHAIN D AND RESID 56:65 )D56 - 65
15X-RAY DIFFRACTION15( CHAIN E AND RESID 0:25 )E0 - 25
16X-RAY DIFFRACTION16( CHAIN E AND RESID 26:34 )E26 - 34
17X-RAY DIFFRACTION17( CHAIN E AND RESID 35:54 )E35 - 54
18X-RAY DIFFRACTION18( CHAIN E AND RESID 55:66 )E55 - 66
19X-RAY DIFFRACTION19( CHAIN F AND RESID 0:34 )F0 - 34
20X-RAY DIFFRACTION20( CHAIN F AND RESID 35:54 )F35 - 54
21X-RAY DIFFRACTION21( CHAIN F AND RESID 55:67 )F55 - 67
22X-RAY DIFFRACTION22( CHAIN G AND RESID 0:25 )G0 - 25
23X-RAY DIFFRACTION23( CHAIN G AND RESID 26:34 )G26 - 34
24X-RAY DIFFRACTION24( CHAIN G AND RESID 35:54 )G35 - 54
25X-RAY DIFFRACTION25( CHAIN G AND RESID 55:65 )G55 - 65
26X-RAY DIFFRACTION26( CHAIN H AND RESID 0:10 )H0 - 10
27X-RAY DIFFRACTION27( CHAIN H AND RESID 11:34 )H11 - 34
28X-RAY DIFFRACTION28( CHAIN H AND RESID 35:55 )H35 - 55
29X-RAY DIFFRACTION29( CHAIN H AND RESID 56:67 )H56 - 67
30X-RAY DIFFRACTION30( CHAIN I AND RESID 0:25 )I0 - 25
31X-RAY DIFFRACTION31( CHAIN I AND RESID 26:44 )I26 - 44
32X-RAY DIFFRACTION32( CHAIN I AND RESID 45:54 )I45 - 54
33X-RAY DIFFRACTION33( CHAIN I AND RESID 55:66 )I55 - 66
34X-RAY DIFFRACTION34( CHAIN J AND RESID 0:10 )J0 - 10
35X-RAY DIFFRACTION35( CHAIN J AND RESID 11:34 )J11 - 34
36X-RAY DIFFRACTION36( CHAIN J AND RESID 35:55 )J35 - 55
37X-RAY DIFFRACTION37( CHAIN J AND RESID 56:65 )J56 - 65
38X-RAY DIFFRACTION38( CHAIN K AND RESID 0:10 )K0 - 10
39X-RAY DIFFRACTION39( CHAIN K AND RESID 11:25 )K11 - 25
40X-RAY DIFFRACTION40( CHAIN K AND RESID 26:44 )K26 - 44
41X-RAY DIFFRACTION41( CHAIN K AND RESID 45:65 )K45 - 65
42X-RAY DIFFRACTION42( CHAIN L AND RESID 0:10 )L0 - 10
43X-RAY DIFFRACTION43( CHAIN L AND RESID 11:25 )L11 - 25
44X-RAY DIFFRACTION44( CHAIN L AND RESID 26:34 )L26 - 34
45X-RAY DIFFRACTION45( CHAIN L AND RESID 35:55 )L35 - 55
46X-RAY DIFFRACTION46( CHAIN L AND RESID 56:67 )L56 - 67
47X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )A101 - 127
48X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )B101 - 125
49X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )C101 - 131
50X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )D101 - 135
51X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )E101 - 127
52X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )F101 - 121
53X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )G101 - 120
54X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )H101 - 137
55X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )I101 - 123
56X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )J101 - 132
57X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )K101 - 132
58X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )L101 - 121

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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

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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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