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- PDB-8cem: Structure of bovine native C3, re-refinement -

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基本情報

登録情報
データベース: PDB / ID: 8cem
タイトルStructure of bovine native C3, re-refinement
要素
  • Complement C3 alpha chain
  • Complement C3 beta chain
キーワードIMMUNE SYSTEM / innate immune system / complement / proteolytic activation / thioester
機能・相同性
機能・相同性情報


Alternative complement activation / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of lipid storage ...Alternative complement activation / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / Neutrophil degranulation / endopeptidase inhibitor activity / G alpha (i) signalling events / complement activation, classical pathway / fatty acid metabolic process / positive regulation of protein phosphorylation / inflammatory response / extracellular space
類似検索 - 分子機能
Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. ...Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
生物種Bos taurus (ウシ)
手法X線回折 / シンクロトロン / 単一同系置換・異常分散 / 解像度: 3 Å
データ登録者Andersen, G.R. / Fredslund, F.
資金援助 デンマーク, 1件
組織認可番号国
LundbeckfondenR155-2015-2666 デンマーク
引用
ジャーナル: J.Mol.Biol. / 年: 2006
タイトル: The structure of bovine complement component 3 reveals the basis for thioester function.
著者: Fredslund, F. / Jenner, L. / Husted, L.B. / Nyborg, J. / Andersen, G.R. / Sottrup-Jensen, L.
#1: ジャーナル: Nat Struct Mol Biol / 年: 2025
タイトル: Cryo-EM analysis of complement C3 reveals a reversible major opening of the macroglobulin ring.
著者: Trine Amalie Fogh Gadeberg / Martin Høgholm Jørgensen / Heidi Gytz Olesen / Josefine Lorentzen / Seandean Lykke Harwood / Ana Viana Almeida / Marlene Uglebjerg Fruergaard / Rasmus Kjeldsen ...著者: Trine Amalie Fogh Gadeberg / Martin Høgholm Jørgensen / Heidi Gytz Olesen / Josefine Lorentzen / Seandean Lykke Harwood / Ana Viana Almeida / Marlene Uglebjerg Fruergaard / Rasmus Kjeldsen Jensen / Philipp Kanis / Henrik Pedersen / Emil Tranchant / Steen Vang Petersen / Ida Buch Thøgersen / Birthe Brandt Kragelund / Joseph Anthony Lyons / Jan Johannes Enghild / Gregers Rom Andersen /
要旨: The C3 protein is the central molecule within the complement system and undergoes proteolytic activation to C3b in the presence of pathogens. Pattern-independent activation of C3 also occurs via ...The C3 protein is the central molecule within the complement system and undergoes proteolytic activation to C3b in the presence of pathogens. Pattern-independent activation of C3 also occurs via hydrolysis, resulting in C3(HO), but the structural details of C3 hydrolysis remain elusive. Here we show that the conformation of the C3(HO) analog, C3MA, is indistinguishable from C3b. In contrast, the reaction intermediate C3* adopts a conformation dramatically different from both C3 and C3MA. In C3*, unlocking of the macroglobulin (MG) 3 domain creates a large opening in the MG ring through which the anaphylatoxin (ANA) domain translocates through a transient opening. C3MA formation is inhibited by an MG3-specific nanobody and prevented by linking the ANA domain to the C3 β-chain. Our study reveals an unexpected dynamic behavior of C3 and forms the basis for elucidation of the in vivo contribution of C3 hydrolysis and for controlling complement upon intravascular hemolysis and surface-contact-induced activation.
#2: ジャーナル: J Mol Biol / 年: 2006
タイトル: The structure of bovine complement component 3 reveals the basis for thioester function.
著者: Fredslund, F. / Jenner, L. / Husted, L.B. / Nyborg, J. / Andersen, G.R. / Sottrup-Jensen, L.
#3: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2012
タイトル: Towards automated crystallographic structure refinement with phenix.refine.
著者: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#4: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2023年2月2日登録サイト: PDBE / 処理サイト: PDBE
置き換え2023年4月5日ID: 2B39
改定 1.02023年4月5日Provider: repository / タイプ: Initial release
改定 1.12024年11月20日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
改定 1.22025年3月5日Group: Database references / カテゴリ: citation / citation_author

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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
E: Complement C3 beta chain
A: Complement C3 alpha chain
F: Complement C3 beta chain
B: Complement C3 alpha chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)370,5166
ポリマ－369,3434
非ポリマー1,1732
水00
1
E: Complement C3 beta chain
A: Complement C3 alpha chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)185,2583
ポリマ－184,6712
非ポリマー5871
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-47 kcal/mol
Surface area72360 Å2
手法PISA
2
F: Complement C3 beta chain
B: Complement C3 alpha chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)185,2583
ポリマ－184,6712
非ポリマー5871
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-43 kcal/mol
Surface area71380 Å2
手法PISA
単位格子
Length a, b, c (Å)254.246, 246.857, 113.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 24 through 662 or resid 672...
d_2ens_1chain "B"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLNA2 - 640
d_12ens_1GLNALAA3 - 72
d_13ens_1ASPASNB81 - 992
d_14ens_1NAGNAGE1
d_15ens_1NAGNAGE2
d_16ens_1BMABMAE3
d_21ens_1PROGLNC2 - 640
d_22ens_1GLNALAC3 - 72
d_23ens_1ASPASND81 - 992
d_24ens_1NAGNAGF1
d_25ens_1NAGNAGF2
d_26ens_1BMABMAF3

NCS oper: (Code: givenMatrix: (-0.999679219701, 0.0253186404984, -0.000651262065037), (-0.0253206413044, -0.999674022288, 0.00327326848974), (-0.000568175059973, 0.00328870886284, 0.99999443077) ...NCS oper: (Code: given
Matrix: (-0.999679219701, 0.0253186404984, -0.000651262065037), (-0.0253206413044, -0.999674022288, 0.00327326848974), (-0.000568175059973, 0.00328870886284, 0.99999443077)
ベクター: 121.837208217, 64.4995503867, -56.7518035685)

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要素

#1: タンパク質 Complement C3 beta chain


分子量: 71474.281 Da / 分子数: 2 / 由来タイプ: 天然
詳細: this is mature C3 with two chains after furin processing, uniprot ID Q2UVX4
由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2UVX4
#2: タンパク質 Complement C3 alpha chain


分子量: 113197.094 Da / 分子数: 2 / 由来タイプ: 天然
詳細: this is mature C3 with two chains after furin processing, uniprot ID Q2UVX4
由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2UVX4
#3: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
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: 4.88 Å3/Da / 溶媒含有率: 74.78 %
結晶化温度: 298 K / 手法: 蒸気拡散法 / pH: 7.7 / 詳細: NaCitrate, Hepes, pH 7.7

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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: BESSY / ビームライン: 14.2 / 波長: 0.9537 Å
検出器タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2004年1月15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: 0.9537 Å / 相対比: 1
反射解像度: 3→40 Å / Num. obs: 138965 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / 冗長度: 4.8 % / Biso Wilson estimate: 68.35 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.8
反射 シェル解像度: 3→3.19 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 21736 / CC1/2: 0.5 / % possible all: 92

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
CNS1.2位相決定
XDSデータ削減
XSCALEデータスケーリング
精密化構造決定の手法: 単一同系置換・異常分散 / 解像度: 3→37.85 Å / SU ML: 0.5462 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 32.846
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2844 1392 1 %
Rwork0.2592 137547 -
obs0.2595 138939 97.2 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 108.43 Å2
精密化ステップサイクル: LAST / 解像度: 3→37.85 Å
タンパク質核酸リガンド溶媒全体
原子数25617 0 78 0 25695
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006226194
X-RAY DIFFRACTIONf_angle_d1.009435471
X-RAY DIFFRACTIONf_chiral_restr0.06394025
X-RAY DIFFRACTIONf_plane_restr0.00884571
X-RAY DIFFRACTIONf_dihedral_angle_d5.50383542
Refine LS restraints NCSタイプ: Torsion NCS / Rms dev position: 1.91618532123 Å
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.110.40761200.40311378X-RAY DIFFRACTION81.52
3.11-3.230.43011480.375813625X-RAY DIFFRACTION97.14
3.23-3.380.35621220.345913927X-RAY DIFFRACTION99.48
3.38-3.560.32271420.312514049X-RAY DIFFRACTION99.99
3.56-3.780.32631420.293614078X-RAY DIFFRACTION100
3.78-4.070.32841310.266314072X-RAY DIFFRACTION99.95
4.07-4.480.28881450.237714112X-RAY DIFFRACTION99.85
4.48-5.130.25321570.217214146X-RAY DIFFRACTION99.79
5.13-6.460.27621390.237214251X-RAY DIFFRACTION99.7
6.46-37.850.19281460.196913909X-RAY DIFFRACTION94.56
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)
10.180394554638-0.2926991672590.3872793894022.30002372740.1279497445431.573784316080.1472833723950.2805337944320.5155170890690.675600772828-0.618317702471-0.679654671719-0.1450747599870.1078794298050.3296301617390.8118923492730.1378279860080.3035137601942.08680099380.3549471112792.15615280736-4.53583.98562.403
24.96560122388-0.5164626692021.195322012694.76234462584-0.6787704567463.731297307080.220772472966-0.3045076361050.686677212970.4653624148230.3936218922060.5677163976170.101422877675-0.944773152469-0.4867179272370.6294429448160.374886424959-0.01053334945441.035690304640.1381274002581.1754565530930.6567.93152.712
31.401847220880.13216493663-0.5151456727467.342123594720.3303130849794.69702630443-0.02436296421531.104110583860.0113292809398-0.042997838562-0.1588610610361.678728908380.05154204298090.6073573628280.1529932023761.174700028520.109488434791-0.2207117300261.661334681170.2153551603781.6172617077733.56759.4615.658
41.230221655530.4269082385470.9961803124442.221869911030.836611361667.034721933730.8114050051150.571154248682-0.131626495327-0.0324927987020.38866793428-0.742651315725-0.1951743383411.78232089764-1.136304517940.900244013767-0.0324638556699-0.01027148328281.630565398830.1054402746722.096381155422.68176.91122.667
52.89830479686-1.440262462380.002365175906841.968368942661.227536701723.10659689823-0.3526977173950.03700087947570.605458838120.00775272844675-0.06765025110490.136916270917-0.335288962383-0.2599977455480.4238049389640.6799705757230.274509384029-0.06163719265441.334441997490.3709959721112.24024099807-4.1591.47340.018
63.9873795626-1.00283914383-2.232745545681.81868891290.9473706888525.447264408830.182025166905-0.2743380530871.28563053527-0.2338135275720.1149119542180.471512572352-0.464714082951-0.149979302881-0.2808918799790.8034962991960.29390554606-0.0009842660208160.8742022290060.1635526831081.7837673621438.7683.40741.83
71.28335660174-0.917923394909-1.376888286760.7142207915071.466854632983.03001385769-0.636297640159-0.787931902347-0.412540607014-0.5023754622320.4676909977330.919307270230.874558557482-0.20133418880.161461457090.7640476571090.261872420653-0.0561205277971.282653046620.4977807648042.457276668864.75775.76244.643
86.236069773030.5289530041770.1670679887843.187721042370.3208635335595.375523231970.1015683174520.9510063845240.151099593372-1.28183938429-0.09040859977171.02384669384-0.246811167438-0.804388304255-0.02191349733330.7705532631070.0464692938784-0.2034525184030.6642729906680.002814339654040.52684891088144.02335.97719.735
96.58009569228-0.7648223212770.09248860920566.53185266826-1.056338376143.962428284550.3011414772520.3865319963291.556796125390.163723397246-0.3431526302540.0504903796281-2.019396203370.3562982139020.1516037183071.31249454397-0.02074014212450.1212373969550.5690154456480.07711266522770.79564568765968.93275.44932.03
107.28631434522-0.342972033513-0.4540051915115.2850911428-1.387137946583.04333851129-0.00436285589057-0.08393606268670.4589987323850.0776080546952-0.0432783990978-0.112388638842-0.6953982691380.38062693671-0.03376404780880.540732834803-0.0312614286953-0.08042341119510.321963811639-0.03092757458260.4465211799273.8849.70670.25
113.656727951912.02355986182-0.1376697126264.64244662125-0.7761194001542.847056486340.0341581335199-0.02919963622240.2040765746560.108136436304-0.05452030185120.00530902357344-0.0940442069588-0.2732643741990.05117961925440.5819314507630.156887810993-0.002840717278310.389693964435-0.0388674358470.22457390286661.90344.35736.335
122.823281544910.3348146421310.8962929623984.00544974009-1.088930473223.239700592070.066450085741-0.102289252520.1401272791020.1840009129590.0250198152880.4620319091860.00920113152352-0.720512350725-0.07517641242670.4777237948050.06433883868230.09591999823160.581001876172-0.02064203482860.29576707964146.75138.24363.703
135.882724603860.4669233953380.9891676723925.589667259730.8694076418223.04435957398-0.266748672908-0.904159486796-0.2600905178050.329009448890.251094770215-1.38928541073-0.2536955737881.407507391570.02697997796410.798124072224-0.1277333723670.004838850843921.744097652750.09484120905721.07392998337100.30356.3641.403
143.218648360273.08209915373-0.5398914204182.93944542937-0.8405095573143.281728352460.691056670275-0.33038171223-0.5706648005030.159838697951-0.852453957854-0.1206603024150.114833760681-0.02430749181650.2077986024611.373115346410.289594790324-0.3496829441561.16769836686-0.1512590254451.34489142583127.989-16.7885.802
157.29476246485-1.64679197457-0.5224872910245.351538497990.7743109449583.961425386430.0924073508083-0.74368027492-0.713818640078-0.02858888066040.438387148672-1.055426718030.4204774594160.675223704333-0.4618203077530.808615221950.291058143272-0.01092146818570.71567720417-0.1409079387190.95374265434692.998-5.061-4.365
167.81275678783-1.766488031230.03956978279351.537182932490.6479757063916.23177446629-0.09817752584090.2631579396281.315800677810.452967957576-0.0253966319525-1.626232036620.1025804389910.7203522733690.1598868365060.9769837405540.0705963015959-0.09856510108320.6170645417-0.07196375040161.751337838889.7683.184-40.056
171.61479783862-2.432211659260.9544306294643.63355870002-1.103610036763.46605109181-0.04645848328080.2423565016840.477399696389-0.05800023873810.03347025725990.358532013983-0.2404980536210.04069647117170.08159091577410.804932459025-0.1937237262130.0764394050561.01052100407-0.2126588019262.22366967434122.218-12.027-33.334
185.103270461060.2176027311430.4292287171891.57116203069-0.7151427092242.86616457456-0.5395514612820.01243295806-0.3460093007580.3155017687020.235717649163-1.000271683510.02389175119540.3883716834590.2575406889110.7863104255130.152930497633-0.03201163449290.809586446762-0.2868060928381.92570268726129.067-25.267-15.914
192.88712653179-1.486111387212.274560997713.42247159449-2.892167279265.403084737250.213525922717-0.235556494539-0.950974181048-0.1693572545580.0566255563068-0.1452044853780.7166673291260.0130926760127-0.2986890044210.8099664697620.09440676857590.1186232520370.597469266719-0.1469762985751.2650598589784.78-20.384-15.592
202.34126266633-1.617849544320.1150931756721.13191524813-0.2742183457760.419620697837-0.913481844691-0.259533396277-0.8621690004830.280616527190.664901051687-0.731339451536-0.593852024950.1033005248480.2212956777020.999283327610.157951008898-0.04908094018490.852550398798-0.2175587863711.55905317207118.394-10.566-12.21
214.2868667965-1.18890613251-1.729400249475.073512352061.578406850515.23930041396-0.6046661865961.04940865424-0.467169871094-1.248049512330.0526607328948-0.77845273718-0.09276578059591.092801146760.529813171820.712948921222-0.03963088517110.2660597258780.8623093527640.02655577298930.58993330030879.28126.72-36.616
223.35459778028-1.373804604150.4532494304363.837740929552.262419992994.070017160380.05019848905550.291559330544-0.755955828620.260224301622-0.237462057454-0.1827221235681.03897614867-0.8442384883050.1722484001270.713984174133-0.2527239506640.09799277855330.516192146148-0.04279197125820.68879513652452.75-12.875-24.732
236.30415314113-0.351697497811.03993717663.971732021840.6929221188692.84591091099-0.01815749907340.109279689973-0.3007273097230.182422282137-0.1662933107620.4340313772180.366474341281-0.4709427342820.1330919724210.50382550022-0.1459710631820.125869330940.456738042167-0.04260417574130.44401960982749.33512.84813.519
245.124865724381.72983119911.371567420145.697465597520.3032720347754.641498963190.0753805307662-0.0057607316004-0.363179412393-0.2024230525880.1103374053910.08276636344140.168357693198-0.10209261673-0.125738730560.4360078949890.00971131195940.07894502016310.3764257388290.002627139026070.23867605994861.22718.231-20.332
252.083851601020.421379747727-0.02556013811233.352809357581.353960493324.318563786330.0294295988021-0.0700981144002-0.103593323881-0.2091223292570.031737014639-0.531172473661-0.1416865485990.404056246015-0.02470546188790.2420215595960.05449350515630.05538091792570.422009530176-0.003479094621280.36481155550276.44424.367.003
265.337979323550.6777989659911.213959327744.31079705223-0.2528979009340.604125315725-0.201828026746-0.9575218356470.03322697174510.214361715054-0.0009999427382061.603049679660.00460540949216-2.145738882080.1898244147960.929420181859-0.03969414160850.0002406603127222.59275848548-0.2464353350771.6272989699922.5237.67-14.846
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 24:127 )E24 - 127
2X-RAY DIFFRACTION2( CHAIN E AND RESID 128:228 )E128 - 228
3X-RAY DIFFRACTION3( CHAIN E AND RESID 229:349 )E229 - 349
4X-RAY DIFFRACTION4( CHAIN E AND RESID 350:449 )E350 - 449
5X-RAY DIFFRACTION5( CHAIN E AND RESID 450:558 )E450 - 558
6X-RAY DIFFRACTION6( CHAIN E AND RESID 559:599 ) OR ( CHAIN A AND RESID 750:827 )E559 - 599
7X-RAY DIFFRACTION6( CHAIN E AND RESID 559:599 ) OR ( CHAIN A AND RESID 750:827 )A750 - 827
8X-RAY DIFFRACTION7( CHAIN E AND RESID 600:663 )E600 - 663
9X-RAY DIFFRACTION8( CHAIN A AND RESID 672:742 )A672 - 742
10X-RAY DIFFRACTION9( CHAIN A AND RESID 828:933 )A828 - 933
11X-RAY DIFFRACTION10( CHAIN A AND ( RESID 934:985 OR RESID 1290:1355 ) )A934 - 985
12X-RAY DIFFRACTION10( CHAIN A AND ( RESID 934:985 OR RESID 1290:1355 ) )A1290 - 1355
13X-RAY DIFFRACTION11( CHAIN A AND RESID 1356:1494 )A1356 - 1494
14X-RAY DIFFRACTION12( CHAIN A AND RESID 986:1289 )A986 - 1289
15X-RAY DIFFRACTION13( CHAIN A AND RESID 1495:1661 )A1495 - 1661
16X-RAY DIFFRACTION14( CHAIN F AND RESID 24:127 )F24 - 127
17X-RAY DIFFRACTION15( CHAIN F AND RESID 128:228 )F128 - 228
18X-RAY DIFFRACTION16( CHAIN F AND RESID 229:349 )F229 - 349
19X-RAY DIFFRACTION17( CHAIN F AND RESID 350:449 )F350 - 449
20X-RAY DIFFRACTION18( CHAIN F AND RESID 450:558 )F450 - 558
21X-RAY DIFFRACTION19( CHAIN F AND RESID 559:599 ) OR ( CHAIN B AND RESID 750:827 )F559 - 599
22X-RAY DIFFRACTION19( CHAIN F AND RESID 559:599 ) OR ( CHAIN B AND RESID 750:827 )B750 - 827
23X-RAY DIFFRACTION20( CHAIN F AND RESID 600:662 )F600 - 662
24X-RAY DIFFRACTION21( CHAIN B AND RESID 672:741 )B672 - 741
25X-RAY DIFFRACTION22( CHAIN B AND RESID 828:933 )B828 - 933
26X-RAY DIFFRACTION23( CHAIN B AND ( RESID 934:985 OR RESID 1290:1355 ) )B934 - 985
27X-RAY DIFFRACTION23( CHAIN B AND ( RESID 934:985 OR RESID 1290:1355 ) )B1290 - 1355
28X-RAY DIFFRACTION24( CHAIN B AND RESID 1356:1494 )B1356 - 1494
29X-RAY DIFFRACTION25( CHAIN B AND RESID 986:1289 )B986 - 1289
30X-RAY DIFFRACTION26( CHAIN B AND RESID 1495:1661 )B1495 - 1661

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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