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- PDB-6wrv: Crystal structure of computationally designed protein 3DS18 in co... -

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基本情報

登録情報
データベース: PDB / ID: 6wrv
タイトルCrystal structure of computationally designed protein 3DS18 in complex with the human Transferrin receptor ectodomain
要素
  • Computationally designed protein 3DS18
  • Transferrin receptor protein 1
キーワードDE NOVO PROTEIN/METAL TRANSPORT / Complex / Beta sheet / Receptor / DE NOVO PROTEIN / DE NOVO PROTEIN-METAL TRANSPORT complex
機能・相同性
機能・相同性情報


transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / positive regulation of isotype switching / Transferrin endocytosis and recycling / response to manganese ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / RND1 GTPase cycle / RND2 GTPase cycle ...transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / positive regulation of isotype switching / Transferrin endocytosis and recycling / response to manganese ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / RND1 GTPase cycle / RND2 GTPase cycle / response to copper ion / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / response to retinoic acid / regulation of postsynaptic membrane neurotransmitter receptor levels / transport across blood-brain barrier / clathrin-coated pit / positive regulation of B cell proliferation / Hsp70 protein binding / positive regulation of T cell proliferation / response to nutrient / RAC1 GTPase cycle / osteoclast differentiation / cellular response to leukemia inhibitory factor / transferrin transport / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / iron ion transport / HFE-transferrin receptor complex / recycling endosome / receptor internalization / multicellular organismal-level iron ion homeostasis / positive regulation of protein localization to nucleus / cellular response to xenobiotic stimulus / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / melanosome / extracellular vesicle / double-stranded RNA binding / virus receptor activity / cytoplasmic vesicle / blood microparticle / basolateral plasma membrane / intracellular iron ion homeostasis / response to hypoxia / early endosome / endosome membrane / positive regulation of canonical NF-kappaB signal transduction / endosome / intracellular signal transduction / external side of plasma membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
類似検索 - ドメイン・相同性
Transferrin receptor protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 2.47 Å
データ登録者Abraham, J. / Baker, D. / Sahtoe, D.D. / Coscia, A. / Clark, L. / Olal, D.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute on Aging (NIH/NIA)5R01AG063845-02 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2021
タイトル: Transferrin receptor targeting by de novo sheet extension.
著者: Sahtoe, D.D. / Coscia, A. / Mustafaoglu, N. / Miller, L.M. / Olal, D. / Vulovic, I. / Yu, T.Y. / Goreshnik, I. / Lin, Y.R. / Clark, L. / Busch, F. / Stewart, L. / Wysocki, V.H. / Ingber, D.E. ...著者: Sahtoe, D.D. / Coscia, A. / Mustafaoglu, N. / Miller, L.M. / Olal, D. / Vulovic, I. / Yu, T.Y. / Goreshnik, I. / Lin, Y.R. / Clark, L. / Busch, F. / Stewart, L. / Wysocki, V.H. / Ingber, D.E. / Abraham, J. / Baker, D.
履歴
登録2020年4月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年4月28日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22024年11月13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

ダウンロードとリンク

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集合体

登録構造単位
A: Transferrin receptor protein 1
B: Transferrin receptor protein 1
E: Transferrin receptor protein 1
D: Computationally designed protein 3DS18
C: Computationally designed protein 3DS18
F: Computationally designed protein 3DS18
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)253,31418
ポリマ－248,0776
非ポリマー5,23712
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)256.079, 256.079, 128.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
12
22
32

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 121 through 719 or (resid 720...A121 - 720
121(chain 'A' and (resid 121 through 719 or (resid 720...A724 - 758
131(chain 'A' and (resid 121 through 719 or (resid 720...A802 - 803
141(chain 'A' and (resid 121 through 719 or (resid 720...A805
151(chain 'A' and (resid 121 through 719 or (resid 720...A808
211(chain 'B' and (resid 121 through 719 or (resid 720...B121 - 720
221(chain 'B' and (resid 121 through 719 or (resid 720...B724 - 758
231(chain 'B' and (resid 121 through 719 or (resid 720...B802 - 803
241(chain 'B' and (resid 121 through 719 or (resid 720...B806
251(chain 'B' and (resid 121 through 719 or (resid 720...B809
311(chain 'E' and ((resid 121 and (name N or name...E121 - 720
321(chain 'E' and ((resid 121 and (name N or name...E724 - 758
331(chain 'E' and ((resid 121 and (name N or name...E802 - 803
341(chain 'E' and ((resid 121 and (name N or name...E805
351(chain 'E' and ((resid 121 and (name N or name...E808
112chain 'C'C1 - 92
212chain 'D'D1 - 92
312chain 'F'F1 - 92

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 Transferrin receptor protein 1 / Trfr / T9 / p90


分子量: 71660.086 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TFRC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02786
#2: タンパク質 Computationally designed protein 3DS18


分子量: 11032.338 Da / 分子数: 3 / 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)
#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: 8 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Ca / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 4.22 Å3/Da / 溶媒含有率: 70.89 %
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
詳細: 1.1M Sodium Malonate pH 7, 0.1M HEPES pH 7, 0.5% Jeffamine ED-2001 pH 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: APS / ビームライン: 24-ID-C / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年2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: 0.97918 Å / 相対比: 1
反射解像度: 2.47→128.04 Å / Num. obs: 151659 / % possible obs: 100 % / 冗長度: 13.8 % / Biso Wilson estimate: 67.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.037 / Net I/σ(I): 19.8
反射 シェル解像度: 2.47→2.51 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7425 / CC1/2: 0.351 / Rpim(I) all: 0.867 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
XDSVERSION Mar 15, 2019data processing
pointless1.11.7データ削減
Aimless0.5.32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: 3KAS

3kas


解像度: 2.47→128.04 Å / SU ML: 0.4599 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.3632
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2362 7363 4.86 %
Rwork0.221 144163 -
obs0.2218 151526 99.96 %
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: 71.32 Å2
精密化ステップサイクル: LAST / 解像度: 2.47→128.04 Å
タンパク質核酸リガンド溶媒全体
原子数17434 0 340 0 17774
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002318151
X-RAY DIFFRACTIONf_angle_d0.510324593
X-RAY DIFFRACTIONf_chiral_restr0.04242810
X-RAY DIFFRACTIONf_plane_restr0.00323134
X-RAY DIFFRACTIONf_dihedral_angle_d16.32956689
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.50.43162570.42824673X-RAY DIFFRACTION99.56
2.5-2.530.43052430.39914734X-RAY DIFFRACTION99.88
2.53-2.560.47462050.41274812X-RAY DIFFRACTION99.84
2.56-2.590.40082490.38864719X-RAY DIFFRACTION99.98
2.59-2.620.432280.37454806X-RAY DIFFRACTION99.98
2.62-2.660.38722510.35724712X-RAY DIFFRACTION100
2.66-2.70.35022450.34714769X-RAY DIFFRACTION100
2.7-2.740.36622610.30994745X-RAY DIFFRACTION100
2.74-2.780.31272020.30644817X-RAY DIFFRACTION99.98
2.78-2.830.30972670.28684720X-RAY DIFFRACTION99.94
2.83-2.880.30962450.27724778X-RAY DIFFRACTION100
2.88-2.930.29962450.27894754X-RAY DIFFRACTION100
2.93-2.980.31042390.29394802X-RAY DIFFRACTION99.98
2.98-3.050.33722420.28134792X-RAY DIFFRACTION99.98
3.05-3.110.30572200.28484768X-RAY DIFFRACTION100
3.11-3.180.30842470.27944794X-RAY DIFFRACTION100
3.18-3.260.30042390.28174764X-RAY DIFFRACTION100
3.26-3.350.28262380.27064803X-RAY DIFFRACTION100
3.35-3.450.27412520.24654816X-RAY DIFFRACTION100
3.45-3.560.26912460.23164764X-RAY DIFFRACTION100
3.56-3.690.23572460.21574819X-RAY DIFFRACTION100
3.69-3.840.23242500.21084786X-RAY DIFFRACTION100
3.84-4.010.20152320.24840X-RAY DIFFRACTION100
4.01-4.220.19822500.18384840X-RAY DIFFRACTION100
4.22-4.490.19242710.1724798X-RAY DIFFRACTION100
4.49-4.830.16912240.16184870X-RAY DIFFRACTION100
4.83-5.320.19412730.18184876X-RAY DIFFRACTION100
5.32-6.090.20992710.19964894X-RAY DIFFRACTION99.98
6.09-7.670.18972630.19414917X-RAY DIFFRACTION99.98
7.67-128.040.1692620.16115181X-RAY DIFFRACTION99.69
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.30234411370.182236677581.789375999161.367560245660.4437035910422.888669377680.17606803822-0.187706909562-0.5440329479770.368528566995-0.0146783763088-0.1643143834160.6488058960.120262745637-0.1466251393640.7649862260760.05411862799270.05075758182910.5353890774920.0578623254090.61953084029144.0192160013-128.28019022311.8990361958
25.262839651043.541334111550.7660133464087.198140297161.491824376633.71810850855-0.1222381378420.3767303280220.153679605391-0.7336117854490.1010650388570.0199482416283-0.450972620984-0.2457943411890.06066624185050.5523763010830.128198841780.04666217619840.382766033955-0.09958908545730.38852159456629.4166411825-123.870217039-20.8765111058
31.235488483270.5225530552610.5086527156351.469938183380.6663197643681.854981991120.007990598516270.0989117574991-0.249378856993-0.1512709453430.00497605915116-0.1197712522260.2776090510270.115807372937-0.02274791572340.4940249122410.06604821916610.06543548960190.389606570268-0.0363020667260.43257058818638.7824427196-122.53254617-2.77615713418
40.8948770129830.567020364787-0.03280478696120.63125328617-0.2740854238330.8111045368160.01924155784420.0894640826379-0.304440676234-0.166246552077-0.0089572460767-0.2410030520220.2739526976180.288459545208-0.02057026356190.55721824540.1418094673970.03088698912760.610358329756-0.07083131854850.52653410994954.3616905364-115.8829846670.881690469881
55.08202639486-2.172800003643.992399439423.80884258218-3.760224419216.413749933-0.335325973305-0.4137820560440.3640768007340.584692127599-0.107182560877-0.52416457088-0.292895181560.1619026440830.3830941557940.4969160920970.0971493893710.01914148342910.522916269606-0.1543198932110.4776186077560.7161081736-92.56817832926.60443030098
64.390374543540.578990655113-0.1576742586423.22090359338-1.464823086493.32453725328-0.076857551110.564896936659-0.11774286072-0.271446810020.1188871680660.02552837081750.397164465559-0.221700910116-0.01910239686460.4080517916520.08424515813640.03104413042430.5357950285-0.08590498489480.39897329957842.8398526047-98.8955354-7.28428803933
74.523753866340.6310399351253.972213677650.6928309319321.052415653378.01007141511-0.122909399572-0.3465602262380.436632195838-0.165288639666-0.100639806062-0.0330883727435-0.542305335433-0.2030992654850.2069235138860.4140342856840.09469788680570.07402309437350.498035448195-0.06987776128780.45485933822849.6829318419-87.087778429-1.35862145808
82.87694580116-0.781904619621.282873185792.62550642103-0.9927807587423.24458920968-0.159736375379-0.6312757310710.7195167849540.634428601867-0.0963754178286-0.284929604788-0.48808720048-0.04762981538570.2001949292120.569425044945-0.06512087013520.03352650266230.749683871445-0.2322794193120.68726837150345.2041675748-62.776508169924.1234634586
93.10607191351-0.7415546930382.03414241151.36729164447-0.6409946327762.100414618-0.0147781623960.2287386092230.504780212562-0.0511901546057-0.128265581715-0.224383487587-0.2477188735780.3430420971360.1305503163430.503160300766-0.03406959553230.1145362608420.563050695235-0.03407607125610.60977877080641.9864727442-65.24127286983.3810405053
102.92398074157-1.14155432297-0.2624836530074.44556664114-1.229315607943.04797688790.09003133550820.131103917877-0.150933827771-0.09472969746390.02817120506660.4991237565960.0966763972428-0.253730571374-0.1364737384040.4071646947260.0678063236040.0246949885830.491924873805-0.081615036730.57268481798610.8238289985-68.0727269463-2.238601818
111.86104090841-0.5311340290350.3022335631960.781681855275-0.3854950531731.180962182410.000934890478822-0.181195981410.2559480878980.04407775321760.0324144160360.102585066687-0.134544915568-0.0940230193856-0.01903462424740.3872829292450.03642934596630.04328531986550.400079792822-0.08982603119560.49288097487628.8334697034-69.65307822527.37039600182
120.9223346912240.3059915718480.1869366112661.02180249582-0.2195578664940.8240162340950.0164555183463-0.3962918636680.2850711682480.263085918773-0.03925014660680.134084829254-0.150421175156-0.06392755059810.02054785894110.4409288675460.05238537700890.06543378053770.640713272679-0.1570219785540.49266619047732.3178446223-76.481657492822.9282103491
138.329788791553.696966065393.830495754013.429658746531.889229509394.715554187680.507072904218-0.442501964171-0.4760615579220.572722202033-0.249692327793-0.505951783990.4302785484420.266583483475-0.1893021954670.5359982209220.1367647433150.04819843698230.530974724735-0.06116129690640.41731818804838.1038307938-99.832069751829.0717021672
142.970864752451.01059593338-0.6160615190412.591415940470.1451671086352.632556221940.007785907348920.1609888556430.3641672735460.029977795683-0.02122376015860.2506016564780.0148312200706-0.204829962072-0.05121559262260.4461047513970.03799193207260.07057203203410.546653519832-0.09053632440360.45783629841224.1729127721-93.384279102911.454181187
151.360065900950.271060650814-1.036175389931.014082184870.2127933966820.9357630732860.0361399111788-0.13592396468-0.5543349807520.1747428426170.06673219405390.03338887515820.289607272428-6.39685731508E-50.0585994909150.5172586099190.06724530352040.07352486728770.541814103293-0.1047057412860.4879636557130.1135652146-105.01033137517.8931659223
162.67353053588-0.878869596024-0.209177673258.262102220281.968409699494.11011156498-0.0581171201288-0.68312885138-0.4989089799930.7995186241780.148129290598-0.5864289011110.8079338996770.367603356978-0.01323215715010.5222959543790.138111682218-0.06225957356760.6967858718280.1483968358510.580995820749109.611305244-120.103843284-31.0192180939
173.66196080468-1.87788336884-1.263410406691.838886422360.2566430851141.78074918203-0.0791584370833-0.5446585131290.470676753240.3476323664090.0950793695935-0.43363858596-0.0646279144180.486848523615-0.00219966487370.470448767206-0.0647976798236-0.06015304263630.604204488603-0.05959078656950.482115734209105.953267445-99.2186804253-33.0109306626
183.19251448235-0.366208604587-0.7607680366443.427198890070.4788763753164.02341129191-0.1424903286190.04384690621420.009710894341180.02543123964540.004366388646590.430015833552-0.0417033566535-0.4979982005450.1203477035760.4125322078120.03962871191950.04142995457070.450641408689-0.007349383182560.40939638809874.7699059762-94.0259899242-36.0099180575
193.12219342515-0.534959573388-1.018166980731.182230996750.4876065457411.57401273285-0.0621119494401-0.0388220572409-0.09767865319340.136323540967-0.03219263700650.1353827204270.077517194165-0.2034057315430.1099310637270.362369515010.01159509689960.03378633762960.345431918722-0.02903646484110.32288981750184.8160849383-97.982049866-36.7420189344
203.5994691798-1.03651839768-1.075513951613.865104759370.9319940989184.14550202497-0.279114866448-0.415799425985-0.3165116475410.2999385954770.0998339871312-0.3036262826640.633263403210.5654334004390.1470168683450.4001536595120.105484818601-0.008532348462790.4686234458980.09905820972640.451761238257110.835867476-114.660195685-39.3114371833
211.47902004573-0.407516628481-0.1381814370851.869507065070.4390406523091.43860180148-0.143687129607-0.327820175373-0.3130329719080.4059494688260.01610910098030.1250280557560.3930409848590.005252997210790.1211927503730.449976554510.06118631356570.07317338622650.3893934628320.07174787425810.44349812649397.1057935727-117.735558237-40.7172053128
221.61769090151-0.6548438632530.9158486752431.656913627360.1335240031591.74739389149-0.0422126325379-0.0631613361416-0.4147954039490.06360235462850.009451323450280.1709929030960.3122576147610.011366990026-0.05552927315450.466752095839-0.02287073752350.1168854830020.3887553474580.09590865074190.60356149133495.1026080114-122.976908245-53.5511835536
236.89675380538-2.424144197392.757678297864.24749237204-0.860130178933.210134145880.2633709628840.599090866123-0.590716739973-0.208926621372-0.172107587543-0.3210814218890.409512650860.58410373756-0.002484663223190.513786903013-0.02034396390760.1332172184090.4235889823640.03480676722590.471253888143102.31334177-124.784476973-67.7053133305
244.811337784210.3396080718551.16796867142.360978121660.1898210049362.16385246492-0.103723113271-0.276987249880.1875300063610.2055041256950.03080091626490.443655923802-0.0053862165818-0.1784450981810.04008769492140.3793177383360.02348996038940.0753109094280.3157760194750.04484260633670.44622921466589.7898203125-107.280103006-61.2470333835
252.73829555237-3.105349288250.9065420017826.5474179872-0.8342827741882.02980615760.2703838661220.4019329048370.187140604794-0.681375174669-0.253330909598-0.3369584248920.312883702221-0.000814223920746-0.006183171291530.411149261682-0.05418917869340.07201266465830.2779548240640.06380575964210.42246758748994.512781588-113.628551844-72.9320180932
261.59631546862-0.324191699692-0.5141184730263.822703213980.5024413909143.78266270092-0.394491173602-1.710538087750.2013261649461.082375190310.584011084139-0.922927141625-0.6954269925490.833232044061-0.1968310524971.35512186597-0.186152027368-0.3969051395231.344726873170.2175187648620.980446401907-6.91077121639-110.628786876-13.522582548
279.18875628491-7.77784058279-7.140594366022.008612374547.23872469356.78522352664-1.123472496190.545660826259-0.4382075505211.238953055910.1568391654470.9286660655230.389468239182-1.247687789481.005146720160.94143208724-0.007226930961070.1025743942730.962711178255-0.1436366672550.7594232244579.43453341125-132.854379515-20.4470050587
285.7237757967-1.04889490756-1.060481961745.385341099580.2647840350415.377666480810.187602003518-0.1853768199790.2021838335560.1189859118260.03064541513150.2646242145280.238279683559-0.49010037758-0.1621213831150.616534869676-0.1001551077530.01518457967960.548633596684-0.1124444429640.51650787772117.9154550098-146.710472477-26.9272947734
298.192879987073.660860620612.226461901398.373591965042.505632196925.714136273070.004291603143721.14876394161.30276690401-0.9711954507650.772818186016-0.629474876012-0.2692858945931.74162619191-1.013548069380.9156230624970.1952059512660.4286985058441.397847529570.2427345654471.1814069239718.762205694-46.418385544-24.1439121045
308.65838679393-2.05170680663-2.891394655978.253044818913.692823278077.847888156460.05658233146751.01669231679-0.216402751132-0.92733131837-0.182922649728-0.217462707060.1941354284330.01408345629380.1365388245460.574426385760.06233846571840.0417497557730.6396910980810.1055245003170.5104536887016.76650792146-48.2988953517-18.5791591473
315.881755493690.4184146438831.768275624474.884109157671.593350357024.836657534440.0527296489610.348841330568-0.0751181507666-0.04123918129930.267791453142-0.150501234532-0.1066247859780.48287032379-0.35832918030.4497247175720.1118335799150.1184062692640.5769191483020.06576474117860.6377733115936.00877012683-46.8720400179-9.7902374503
327.66882144618-0.4614170229314.152806601412.0431487659-7.437026896342.04198650061-0.39570674864-0.9279742788890.6061628860780.0439141382352-0.64942788341-1.28257285187-1.039332909230.2817896618360.9395053367921.13150170568-0.1491605551320.02756951771920.896656111866-0.2135527675530.95389573319381.2011939173-69.9234876655-15.41051029
336.523901855784.66231148976-4.035107409892.29001968651-4.552244643032.30518556961-0.3243849861250.3323611564770.636887841212-0.6025603140370.3575077760150.271313980953-0.182455136912-0.328000314156-0.0655478529260.8177641563750.0205951423490.01321892540930.626441149353-0.08948320096870.49888903086269.6343151174-77.1810186536-18.157426073
348.888620664141.67165443006-1.527147280441.643562607291.836679979253.626707872010.0239122658505-0.5855287806430.284014292867-0.421800775964-0.00997587788318-0.227851112702-0.2340044858020.359895975307-0.02807155395180.6217661937460.08460674675490.03047187899520.627447901374-0.1408944470840.43802616607772.9879153297-80.3226544594-11.7478989351
352.011489971292.260700489233.413993444194.811445126731.117746279892.28274930730.277357709261-0.824162560980.397859639762-0.0538305167329-0.192924225373-0.1208358785660.397792194562-0.186872596748-0.1422649992920.4917311921560.04333074319180.1397351086480.579501717608-0.04320504438130.43478714191767.7073512095-90.9917844952-15.1950147372
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 121 through 204 )
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 253 )
3X-RAY DIFFRACTION3chain 'A' and (resid 254 through 453 )
4X-RAY DIFFRACTION4chain 'A' and (resid 454 through 634 )
5X-RAY DIFFRACTION5chain 'A' and (resid 635 through 679 )
6X-RAY DIFFRACTION6chain 'A' and (resid 680 through 727 )
7X-RAY DIFFRACTION7chain 'A' and (resid 728 through 759 )
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 159 )
9X-RAY DIFFRACTION9chain 'B' and (resid 160 through 204 )
10X-RAY DIFFRACTION10chain 'B' and (resid 205 through 253 )
11X-RAY DIFFRACTION11chain 'B' and (resid 254 through 453 )
12X-RAY DIFFRACTION12chain 'B' and (resid 454 through 634 )
13X-RAY DIFFRACTION13chain 'B' and (resid 635 through 679 )
14X-RAY DIFFRACTION14chain 'B' and (resid 680 through 727 )
15X-RAY DIFFRACTION15chain 'B' and (resid 728 through 759 )
16X-RAY DIFFRACTION16chain 'E' and (resid 121 through 159 )
17X-RAY DIFFRACTION17chain 'E' and (resid 160 through 204 )
18X-RAY DIFFRACTION18chain 'E' and (resid 205 through 253 )
19X-RAY DIFFRACTION19chain 'E' and (resid 254 through 393 )
20X-RAY DIFFRACTION20chain 'E' and (resid 394 through 460 )
21X-RAY DIFFRACTION21chain 'E' and (resid 461 through 582 )
22X-RAY DIFFRACTION22chain 'E' and (resid 583 through 634 )
23X-RAY DIFFRACTION23chain 'E' and (resid 635 through 679 )
24X-RAY DIFFRACTION24chain 'E' and (resid 680 through 727 )
25X-RAY DIFFRACTION25chain 'E' and (resid 728 through 759 )
26X-RAY DIFFRACTION26chain 'D' and (resid 1 through 20 )
27X-RAY DIFFRACTION27chain 'D' and (resid 21 through 35 )
28X-RAY DIFFRACTION28chain 'D' and (resid 36 through 93 )
29X-RAY DIFFRACTION29chain 'C' and (resid 1 through 20 )
30X-RAY DIFFRACTION30chain 'C' and (resid 21 through 69 )
31X-RAY DIFFRACTION31chain 'C' and (resid 70 through 93 )
32X-RAY DIFFRACTION32chain 'F' and (resid 1 through 20 )
33X-RAY DIFFRACTION33chain 'F' and (resid 21 through 60 )
34X-RAY DIFFRACTION34chain 'F' and (resid 61 through 79 )
35X-RAY DIFFRACTION35chain 'F' and (resid 80 through 93 )

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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