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- PDB-6wrw: Crystal structure of computationally designed protein 2DS25.5 in ... -

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基本情報

登録情報
データベース: PDB / ID: 6wrw
タイトルCrystal structure of computationally designed protein 2DS25.5 in complex with the human Transferrin receptor ectodomain
要素
  • Computationally designed protein 2DS25.5
  • Transferrin receptor protein 1
キーワードDE NOVO PROTEIN / Complex / Beta sheet / Receptor
機能・相同性
機能・相同性情報


transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle ...transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle / RND2 GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOB GTPase cycle / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / RAC3 GTPase cycle / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / Hsp70 protein binding / osteoclast differentiation / response to nutrient / cellular response to leukemia inhibitory factor / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / double-stranded RNA binding / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / blood microparticle / early endosome / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / RNA binding / extracellular space / 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: 2.84 Å
データ登録者Abraham, J. / Coscia, A. / Olal, D. / Sahtoe, D.D. / Baker, D. / Clark, L.
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10月16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
C: Computationally designed protein 2DS25.5
D: Computationally designed protein 2DS25.5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)167,24112
ポリマ－163,9664
非ポリマー3,2758
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12990 Å2
ΔGint-33 kcal/mol
Surface area57880 Å2
手法PISA
単位格子
Length a, b, c (Å)138.399, 138.399, 279.847
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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要素

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タンパク質 , 2種, 4分子 ABCD

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


分子量: 71807.258 Da / 分子数: 2 / 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 2DS25.5


分子量: 10175.582 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) / 発現宿主: Escherichia coli (大腸菌)

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糖 , 3種, 6分子

#3: 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: 4 / 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
#4: 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: 1 / 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
#5: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 910.823 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
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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非ポリマー , 1種, 2分子

#6: 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: 2 / 由来タイプ: 合成 / 式: Ca / タイプ: SUBJECT OF INVESTIGATION

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詳細

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: 4.72 Å3/Da / 溶媒含有率: 73.93 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1M BICINE pH 8.5, 12% (w/v) monomethyl ether 550

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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-E / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年10月19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: 2.77→200 Å / Num. obs: 72437 / % possible obs: 97.7 % / 冗長度: 4.03 % / Biso Wilson estimate: 86.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.047 / Net I/σ(I): 11.38
反射 シェル解像度: 2.77→2.94 Å / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 4459 / CC1/2: 0.338 / Rpim(I) all: 0.74 / % possible all: 97.8

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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
XDSJan 26, 2018data 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: 2.84→69.2 Å / SU ML: 0.4952 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.1044
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2353 3632 5.03 %
Rwork0.2109 68612 -
obs0.2121 72244 97.66 %
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: 88.92 Å2
精密化ステップサイクル: LAST / 解像度: 2.84→69.2 Å
タンパク質核酸リガンド溶媒全体
原子数11544 0 213 0 11757
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001812013
X-RAY DIFFRACTIONf_angle_d0.433716287
X-RAY DIFFRACTIONf_chiral_restr0.04141863
X-RAY DIFFRACTIONf_plane_restr0.00272068
X-RAY DIFFRACTIONf_dihedral_angle_d15.98444401
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.880.38271200.39152592X-RAY DIFFRACTION96.24
2.88-2.920.41081620.37612584X-RAY DIFFRACTION98.32
2.92-2.960.41661420.38542624X-RAY DIFFRACTION97.98
2.96-30.38251330.36012638X-RAY DIFFRACTION98.33
3-3.050.35011390.33262600X-RAY DIFFRACTION98.45
3.05-3.10.35871510.33812602X-RAY DIFFRACTION97.83
3.1-3.150.34731350.30162614X-RAY DIFFRACTION96.15
3.15-3.210.30251250.29352496X-RAY DIFFRACTION94.52
3.21-3.270.34331220.29382621X-RAY DIFFRACTION98
3.27-3.340.29691330.27282666X-RAY DIFFRACTION99.47
3.34-3.410.28131500.25292663X-RAY DIFFRACTION99.26
3.41-3.490.30881310.24182659X-RAY DIFFRACTION99.01
3.49-3.580.26091500.23982670X-RAY DIFFRACTION99.12
3.58-3.670.25971560.22782635X-RAY DIFFRACTION99.08
3.67-3.780.25831260.22192642X-RAY DIFFRACTION98.37
3.78-3.90.25281330.21242657X-RAY DIFFRACTION98.31
3.91-4.040.20791590.19792631X-RAY DIFFRACTION98.66
4.04-4.210.22341590.18382668X-RAY DIFFRACTION98.4
4.21-4.40.191410.17682597X-RAY DIFFRACTION97.33
4.4-4.630.21891620.15942544X-RAY DIFFRACTION94.38
4.63-4.920.18891350.15522582X-RAY DIFFRACTION94.67
4.92-5.30.20351530.17962697X-RAY DIFFRACTION99.13
5.3-5.830.23321090.19062722X-RAY DIFFRACTION98.71
5.83-6.680.21241290.20712721X-RAY DIFFRACTION97.9
6.68-8.410.20251200.17642714X-RAY DIFFRACTION96.79
8.41-69.20.18241570.18662773X-RAY DIFFRACTION94.94
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)
12.14963039289-1.11310840770.6131434398582.75985120220.1039533867190.723673195181-0.0242074822331-0.895046643472-0.05198664888550.08578306179250.2598608130360.4161437882010.256299011352-0.301746377955-0.259164018740.968909935621-0.04127237387010.3361612106711.067071537930.2027400242381.0442472722920.8500081992-41.996475494463.7614778688
20.371340564236-0.57487355422-0.154835669710.7986089002310.04327066117921.27857618102-0.08534947015150.130767463999-0.3484908119210.1922596414860.1089562314850.3668939498830.556913092188-0.277604279926-0.03676332352370.949213789342-0.169901663074-0.02202489816320.5371307240320.0884399177720.88365765497134.4290963023-52.318399504251.16725701
31.55603717261-0.8541336864570.03958065547120.925397117668-0.7919881911452.05545380551-0.239768826446-0.119817209949-0.09588392933970.05800763507980.500020170451-0.2208664091240.0265376732890.099680183376-0.2615479245280.8122183496410.0573256431886-0.1101674683590.675428363344-0.04716832587270.78300098667964.2204502791-46.845376274960.6572389079
42.57548332949-0.7472279511391.751902426942.04999647372-0.0665818211241.53149135937-0.0622973995482-0.3187280382373.28552084079E-50.2991263471360.142660829893-0.0272147529740.302124185614-0.106447565704-0.0485928434220.7339573748480.0364555311413-0.005512545141490.5720718006580.0338981617790.62903891029153.8619773119-45.899958192758.1090472113
51.005228351880.2004531548240.2492109516982.768119304280.6923736448932.02230688811-0.121453085349-0.380019191910.01910808780380.3462096692070.1825929101760.2985217576740.0933581807355-0.0362067494013-0.07247197481390.6324328582260.009112485811640.1110373165680.6669230406220.06796785513810.62686033780929.5320458851-33.267474838757.1604799143
63.36929210539-0.735406873722-0.9300675809431.66645510320.2685494230151.6266468525-0.434263148561-0.866453550853-0.2545827634820.8665325127630.21383350867-0.06486916654450.03142147564080.009346204835570.1150497589090.836231604688-0.06712973782450.08963387135890.873432791880.06589828295570.69865618972129.8787194254-37.214141021966.7046903391
71.77909934231.23740458358-1.06094913392.19945038762-0.06908521752861.86071984563-0.0756399617089-0.1210288398040.5415960623490.2607205541550.2127490908560.175966198936-0.276183066959-0.140649435405-0.1603026755880.6251163713120.06293259632370.0006946798343360.513093698429-0.1796881164430.70652715369337.5137627194-9.7512707631949.2311340033
82.252309912930.4971473490970.1494829018133.421569086080.7835751513541.47368694354-0.0440132175922-0.371337023850.01966807743290.2961731812320.0835684128163-0.2280515514350.0406035477060.167202412221-0.04531097592510.7314825372010.018715699314-0.04278563495820.543304073636-0.01215790617280.58922555224249.8516616434-22.173718094646.2881516929
92.479217790011.021247304151.024708662381.202036345040.2016827474221.596827034460.4754805189080.06998295618180.208643604763-0.237089212743-0.2016855727670.232196106893-0.0877603268936-0.0784827285356-0.2710281827960.7168132651380.0531162005670.002759537816690.518642124792-0.06817263322220.52841350768644.3008837693-10.517315964739.8922300137
100.234358005109-0.347859115621-0.2850817235661.500100860450.3446487016492.541175999510.1055713828860.7951269259480.300198466382-0.0228574298026-0.01651004795960.348832161098-0.900643497058-0.149974907223-0.05739862348270.9389542781160.0474183679152-0.2556867255060.5570651157010.1710327629060.96002242113128.6261949961-0.4051416469129.65538747946
111.93513466049-0.104091741973-0.2146886051580.699226532774-0.05408102450740.366305196303-0.05742542622230.1016056937280.624306508454-0.275718389180.1753522834940.139508712672-0.475166846861-0.0108758426258-0.2001271043370.982498627132-0.126383093094-0.02365960102810.4370099719020.01820202840060.84768001293947.7334819688-0.1164951697419.0499232126
122.13617848230.207831850008-1.521119974330.7364288260530.5787122627641.99296019148-0.2129808888960.302273087165-0.0141617754947-0.3415743133240.118685181695-0.109975577248-0.0324884332007-0.01337403436270.09443315554660.891567406161-0.124350450940.06282950781720.449968305325-0.002259408493270.59961145559160.6856541286-17.40438032578.18896506628
132.52779373740.278976595104-0.1972789244212.06732897738-0.1901674775531.34128670094-0.1546613430860.4357802300750.251385965606-0.4387157164390.1230709245630.287063895064-0.123979051733-0.1113933100590.04452098012970.721362556192-0.058788362036-0.1258817917180.4606771897350.06758123842350.65184641274133.4708766596-11.788063707212.8127130746
141.09509465452-0.01255083459180.4528211475213.22991764791-0.8141661986161.2485142979-0.1464761309640.309117923497-0.088067636455-0.3407352970370.1355663685860.3376936186610.183288985921-0.3096192721150.003739825083110.784329665458-0.0873640390122-0.1462475243340.581142936618-0.01189699293470.60012231640828.8063392121-27.294954293914.3605603385
153.84453879637-0.625446658538-0.2640860717823.58750875850.241738771112.16241878383-0.0726712644318-0.168960276313-0.3799565274320.1364023655830.1574202613611.049098656450.314137835707-0.674915375979-0.01437159329460.579368696684-0.0814727203692-0.04470551688620.639092326408-0.0402723620460.67416489001621.6121554166-33.666861149727.0190372684
162.563390864410.3172979557671.458504530052.607533423750.9169689370692.98341669219-0.2176192734920.100331106507-0.0158757359614-0.5564352992770.1783666529740.2154174665-0.08774875215240.27527445892-0.05093348474640.755749383689-0.06988457597580.01511554466250.404345603053-0.01687808206070.50443082270244.3973704862-34.573415516522.8043918536
173.54392511892-1.67438005883-1.254585561112.250417154982.152114850871.944772535820.305291268424-0.474125031453-0.437357470146-0.181554394371-0.1709253984980.65395560281-0.0738555360195-0.316765046068-0.05082721032450.696675780213-0.102676701054-0.05661429398890.5866644085280.1005354808810.60914374797232.8286433236-40.465961176530.8054539983
181.8945276584-2.20425301328-3.410051520752.67213168964.104026359196.304259035960.0271312179051.01490699325-1.43151846605-0.933681519898-0.4798196101020.338921756263-0.292398823351-0.3571008672230.3709113004021.494076449240.154683509736-0.3716971125971.09140905388-0.2980076157521.4116892301168.9685850912-78.293663458856.1952139942
195.082729640440.747519293550.7269208006093.25325696376-0.2973790256665.380239815840.09111340431940.653486165254-0.974710543644-0.602227272335-0.185498623812-0.6005782186180.04938789848490.5244431487480.06028409137141.147601089250.257460867926-0.1352404304760.920240335952-0.07326738202490.86333099049371.4282635818-68.013838840658.811013436
203.67553870974-0.344632322710.4138957258073.770819773671.005901498083.651069345370.17236553336-0.191767946208-1.39862991817-0.2846260897550.2131398983070.2179825079570.9636723219810.496415431615-0.5368570045341.258162000690.276656254666-0.1261578692590.777211692977-0.01864474238191.1121166709272.9516793676-72.879151623371.8652900391
218.79486949531.98833944994-1.987730220576.75324760741-0.5433089512576.85662270415-0.5659046855890.05140933938240.7417786480880.5550428964760.3597371790860.97075878720.555947768023-0.2639982663250.110531911440.9465525444010.0743049592639-0.1832339284210.985017340334-0.05570112405310.95068962984370.030575484-62.702124819974.7461871271
225.91966796410.734843934398-0.3659828881743.37552554581.452754376236.374561884120.183749177572-0.6130921664010.8792774027160.687773366597-0.231279719752-0.781335663431-0.287671827090.3224918586860.05574514677281.03389320077-0.184756478425-0.02414116470240.743714514797-0.04594738123470.79247354000486.8089650561-4.032449703124.15962841851
236.74850578354-0.540654518225-0.5989874762724.404990434110.2774335126642.871488744040.1669662920.5836058274140.7928160701480.296941600499-0.302562519551-0.7922552357650.337507268350.196677187208-0.1038788061240.94065235348-0.1897086985130.03007643546130.6511635914860.1645016850530.82298013077889.9833965139-6.62121814477-13.5093841639
247.70667561579-0.1258664947124.615918535283.459249748860.8473411276217.77910467833-0.1017716540020.1680628938050.895151200421-0.170742653433-0.372398110012-1.07191085113-1.63799738465-0.2219891831960.1262724737351.07498684492-0.182043765469-0.01456910166140.6164571974740.1042388567370.76959483327784.2711463015-0.505362006196-8.96326082242
251.78737156882.26150945794-1.923272530628.324257431912.169912623896.087865084450.1670607968020.1394956503550.935773220479-0.1356343026710.1164895693520.452936643065-0.7232220109050.174977238661-0.4270517448450.734535692652-0.103802058089-0.006533348992070.5110461585990.03846977299670.91736603446882.1169538557-3.05553289915-4.90467982054
263.811634240760.2837573736921.510765056566.59022798153-0.436786176972.13104560827-0.02500818050280.441215237746-0.3315396258070.02589333761930.2285283705450.7579198671810.5782756096910.330381241032-0.2613220960330.996435298843-0.2035581446890.105677795640.659866150992-0.06860773065190.63438388875677.8335540405-10.9169394597-11.2240487525
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 121 through 159 )
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 204 )
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 253 )
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 393 )
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 558 )
6X-RAY DIFFRACTION6chain 'A' and (resid 559 through 610 )
7X-RAY DIFFRACTION7chain 'A' and (resid 611 through 678 )
8X-RAY DIFFRACTION8chain 'A' and (resid 679 through 727 )
9X-RAY DIFFRACTION9chain 'A' and (resid 728 through 759 )
10X-RAY DIFFRACTION10chain 'B' and (resid 121 through 159 )
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 204 )
12X-RAY DIFFRACTION12chain 'B' and (resid 205 through 393 )
13X-RAY DIFFRACTION13chain 'B' and (resid 394 through 582 )
14X-RAY DIFFRACTION14chain 'B' and (resid 583 through 634 )
15X-RAY DIFFRACTION15chain 'B' and (resid 635 through 679 )
16X-RAY DIFFRACTION16chain 'B' and (resid 680 through 728 )
17X-RAY DIFFRACTION17chain 'B' and (resid 729 through 760 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 14 )
19X-RAY DIFFRACTION19chain 'C' and (resid 15 through 40 )
20X-RAY DIFFRACTION20chain 'C' and (resid 41 through 73 )
21X-RAY DIFFRACTION21chain 'C' and (resid 74 through 88 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 40 )
23X-RAY DIFFRACTION23chain 'D' and (resid 41 through 54 )
24X-RAY DIFFRACTION24chain 'D' and (resid 55 through 63 )
25X-RAY DIFFRACTION25chain 'D' and (resid 64 through 73 )
26X-RAY DIFFRACTION26chain 'D' and (resid 74 through 88 )

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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