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- PDB-8uwz: The structure of Raamsizumab in complex with VEGF121 -

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基本情報

登録情報
データベース: PDB / ID: 8uwz
タイトルThe structure of Raamsizumab in complex with VEGF121
要素
  • Isoform VEGF121 of Vascular endothelial growth factor A, long form
  • Raamsizumab heavy chain
  • Raamsizumab light chain S1C variant
キーワードSIGNALING PROTEIN
機能・相同性
機能・相同性情報


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / lymph vessel morphogenesis / primitive erythrocyte differentiation / negative regulation of adherens junction organization / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / regulation of nitric oxide mediated signal transduction / VEGF-activated neuropilin signaling pathway / bone trabecula formation / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lymphangiogenesis / vascular endothelial growth factor receptor-2 signaling pathway / positive regulation of epithelial tube formation / VEGF binds to VEGFR leading to receptor dimerization / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of axon extension involved in axon guidance / lung vasculature development / vascular wound healing / eye photoreceptor cell development / regulation of hematopoietic progenitor cell differentiation / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / camera-type eye morphogenesis / positive regulation of protein autophosphorylation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neuropilin binding / positive regulation of branching involved in ureteric bud morphogenesis / induction of positive chemotaxis / coronary artery morphogenesis / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of cell-cell adhesion mediated by cadherin / commissural neuron axon guidance / positive regulation of vascular permeability / vascular endothelial growth factor receptor 2 binding / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of blood vessel branching / surfactant homeostasis / platelet-derived growth factor receptor binding / retinal ganglion cell axon guidance / sprouting angiogenesis / cell migration involved in sprouting angiogenesis / extracellular matrix binding / endothelial cell proliferation / epithelial cell maturation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / cardiac muscle cell development / positive regulation of endothelial cell chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of cell migration involved in sprouting angiogenesis / artery morphogenesis / vascular endothelial growth factor signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / negative regulation of epithelial to mesenchymal transition / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / outflow tract morphogenesis / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / macrophage differentiation / monocyte differentiation / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / positive regulation of blood vessel endothelial cell migration / neuroblast proliferation / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / heart morphogenesis / ovarian follicle development / cell maturation / lactation / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / extracellular matrix / positive regulation of endothelial cell migration
類似検索 - 分子機能
Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine-knot cytokine
類似検索 - ドメイン・相同性
Vascular endothelial growth factor A, long form
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.5 Å
データ登録者Singer, A.U. / Bruce, H. / Blazer, L. / Sicheri, F. / Adams, J.J. / Sidhu, S.S.
資金援助 インド, 1件
組織認可番号国
Other private インド
引用ジャーナル: to be published
タイトル: Raamsizumab: A Potent Synthetic Human Anti-VEGF Neutralizing Fab for Treatment of Ocular Neovascularization Diseases
著者: Fellouse, F.A. / Harit, R.K. / Arun, S. / Arora, R. / Wagner, N. / Antony, A. / Wong, S. / Yang, N. / Rajakrishnan, S. / Anthony, M. / Gokul, S. / Vinodh, S. / Bhunia, S. / Vinothini, T.M. / ...著者: Fellouse, F.A. / Harit, R.K. / Arun, S. / Arora, R. / Wagner, N. / Antony, A. / Wong, S. / Yang, N. / Rajakrishnan, S. / Anthony, M. / Gokul, S. / Vinodh, S. / Bhunia, S. / Vinothini, T.M. / Choubey, S. / Rajendran, A. / Srivastava, A. / Seshagiri, S. / Gross, M.L. / Leung, D.W. / Amarasinghe, G.K. / Chaudhuri, A. / Sidhu, S.S. / Ramchand, C.N.
履歴
登録2023年11月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年11月13日Provider: repository / タイプ: Initial release

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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
C: Raamsizumab heavy chain
D: Raamsizumab light chain S1C variant
E: Isoform VEGF121 of Vascular endothelial growth factor A, long form
F: Isoform VEGF121 of Vascular endothelial growth factor A, long form
A: Raamsizumab heavy chain
B: Raamsizumab light chain S1C variant
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)125,1308
ポリマ－124,1196
非ポリマー1,0112
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)167.747, 167.747, 42.501
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
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 1 through 2 or (resid 3...
d_2ens_1(chain "C" and (resid 1 through 206 or (resid 207...
d_1ens_2(chain "B" and (resid 5 or (resid 6 and (name...
d_2ens_2(chain "D" and (resid 5 through 17 or (resid 18...
d_1ens_3(chain "E" and ((resid 11 and (name N or name...
d_2ens_3(chain "F" and (resid 11 through 55 or (resid 56...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUSERSERAE1 - 1421 - 134
d_12ens_1LYSLYSSERSERAE144 - 147136 - 139
d_13ens_1THRTHRALAALAAE150 - 151142 - 143
d_14ens_1LEULEUPROPROAE153 - 228145 - 220
d_21ens_1GLUGLUPROPROCA1 - 2281 - 220
d_11ens_2THRTHRSERSERBF5 - 265 - 26
d_12ens_2ALAALATHRTHRBF28 - 12928 - 109
d_13ens_2ALAALACYSCYSBF132 - 234112 - 212
d_21ens_2THRTHRCYSCYSDB5 - 2345 - 212
d_11ens_3HISHISLYSLYSEC11 - 10811 - 108
d_12ens_3NAGNAGNAGNAGGG1
d_21ens_3HISHISLYSLYSFD11 - 10811 - 108
d_22ens_3NAGNAGNAGNAGHH2

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.954351434718, 0.298573908064, 0.00818293805804), (0.298450590061, 0.954328804419, -0.0135564873175), (-0.0118568268916, -0.0104954504293, -0.999874622728)11.5547041973, -2.37546391928, -45.1042859781
2given(-0.960848978196, 0.276761112001, 0.0131349908302), (0.276936042182, 0.960783901768, 0.0141676619053), (-0.00869882987619, 0.0172505358398, -0.999813357268)12.7457837286, -2.18057876966, -46.5452627584
3given(-0.964034585558, 0.265517542993, 0.0117367887998), (0.265579982151, 0.964080118588, 0.00409853925459), (-0.0102269706652, 0.00706818975165, -0.999922721896)12.9833088055, -1.74865459687, -45.9210972023

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要素

#1: 抗体 Raamsizumab heavy chain


分子量: 24602.461 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pSCSTa / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)
#2: 抗体 Raamsizumab light chain S1C variant


分子量: 23379.002 Da / 分子数: 2 / Mutation: HAGLSSP replaced by QGTTS; Q165S, K167Y / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 詳細 (発現宿主): pSCSTa / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)
#3: タンパク質 Isoform VEGF121 of Vascular endothelial growth factor A, long form


分子量: 14078.085 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P15692
#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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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-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: 2.98 Å3/Da / 溶媒含有率: 58.77 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.1 / 詳細: 0.2 M Sodium Phosphate mono basic, 30% PEG600 / Temp details: room temperature

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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: 0.97915 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2023年2月7日 / 詳細: mirrors
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: 0.97915 Å / 相対比: 1
反射解像度: 3.4→83.87 Å / Num. obs: 18391 / % possible obs: 99.8 % / 冗長度: 7.7 % / Biso Wilson estimate: 133.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.046 / Rrim(I) all: 0.13 / Net I/σ(I): 9.2
反射 シェル解像度: 3.4→3.67 Å / 冗長度: 7.8 % / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3833 / CC1/2: 0.769 / Rpim(I) all: 0.458 / Rrim(I) all: 1.297 / % possible all: 99.9

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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
MOSFLMデータ削減
Aimless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 / 解像度: 3.5→83.87 Å / SU ML: 0.5771 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 39.9167
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2981 1696 10.09 %
Rwork0.237 15114 -
obs0.2433 16810 99.63 %
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: 167.82 Å2
精密化ステップサイクル: LAST / 解像度: 3.5→83.87 Å
タンパク質核酸リガンド溶媒全体
原子数7666 0 67 0 7733
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00487933
X-RAY DIFFRACTIONf_angle_d0.947710872
X-RAY DIFFRACTIONf_chiral_restr0.05521247
X-RAY DIFFRACTIONf_plane_restr0.01841394
X-RAY DIFFRACTIONf_dihedral_angle_d17.45592639
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2EAX-RAY DIFFRACTIONTorsion NCS0.984107314105
ens_2d_2FBX-RAY DIFFRACTIONTorsion NCS1.30684378744
ens_3d_2CEX-RAY DIFFRACTIONTorsion NCS1.39378384007
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.60.39351380.40871254X-RAY DIFFRACTION99.57
3.6-3.720.39021370.38911255X-RAY DIFFRACTION99.57
3.72-3.850.33531480.33961296X-RAY DIFFRACTION99.52
3.85-4.010.3521390.35521218X-RAY DIFFRACTION99.49
4.01-4.190.37211420.32631288X-RAY DIFFRACTION99.17
4.19-4.410.28081380.25221230X-RAY DIFFRACTION99.78
4.41-4.680.30011480.23971293X-RAY DIFFRACTION100
4.69-5.050.26861400.2341237X-RAY DIFFRACTION99.85
5.05-5.550.2971420.23161260X-RAY DIFFRACTION99.79
5.56-6.360.31311420.23831256X-RAY DIFFRACTION99.57
6.36-8.010.30871460.21681257X-RAY DIFFRACTION99.93
8.02-83.870.24621360.14891270X-RAY DIFFRACTION99.79
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)
14.349132029880.9075089345922.458629244947.952878620314.743420254633.083874487460.426237173263-0.6190953497271.839997837980.993579216723-1.19661155021-1.41064454716-0.307488093994-0.2506187648850.4559176783961.49708032611-0.351652540319-0.05542539317740.9004585685520.0956089194032.1342628342328.75246.129-17.815
26.15924907012.142370177871.011797781472.17909301721-0.2509911370542.245629352150.111986602544-0.4973881683840.5505909891691.28181038759-0.610514402199-1.60571635965-0.5941229770830.442326133850.4227575240141.49391653922-0.326434878191-0.356273887940.9183127437120.2113139350762.1049945003535.01444.982-12.14
31.64235329477-0.2365578388290.2931933995317.672980762693.001100850756.06150607415-0.09577851148850.172772935317-0.02254579066280.866214064063-0.745270358487-1.02189539721-0.1091086662220.6068843596860.8610668126061.53993635046-0.242302403233-0.6290907939821.205442280880.2367778202672.7765561132754.80359.448-19.456
43.01500378837-2.414727096572.834099999635.320201997380.5063127525245.37871576315-0.312627172035-1.114332240812.05734677182-0.126908439622-0.168742340241-2.003494199920.3670414332330.5481442477710.8500422719632.19045105775-0.060337987803-0.4791917500651.106268025970.3735363880232.9728352634347.98725.707-9.352
55.07928899430.444958378167-1.761569329973.154079822613.536195075014.57199283329-0.908294730581.49537434063-1.134799856191.41646572071.28677931108-0.8744673034680.8678366930220.8919028687230.199388804441.56991561498-0.0572359599296-0.5611427031190.8554386379680.06823848582313.3940954287643.69129.194-19.968
63.754711149391.55427180569-1.345226625554.453847419941.412619674062.0733168671-0.111368532584-0.353928298209-2.867701788461.44752536942-0.456924435505-1.61662782620.7284401823610.7197774529110.2649618106742.13082141612-0.0831555996633-0.7732725273771.291642029250.4877893792933.3991285346244.32126.995-11.515
78.18541922763-3.96926826022-2.828865875572.15070312140.3613504566490.5303504623550.2985247958811.050303926951.66587778842.48992915735-0.477219354858-2.450624361310.3426420481391.280362243090.5113463466621.725147995810.0467414836804-0.7676588148912.259743193830.1644758072753.8037448123864.65556.358-12.664
81.574009351492.814768253211.055100298124.216249577281.528689711778.950123044410.5043756775571.238621334091.065660549461.94329287679-1.05090310554-1.881542469970.125298631483.010593410320.1069906666651.719128102440.20092064746-0.95454761981.98228480007-0.07667326734663.7445864911267.68254.414-6.736
92.851253612462.512260651172.377990040782.392742138721.564976154129.06880262171-1.064722977510.4194980352511.00792689111.247751957220.271616057317-0.480886128033-1.272622638721.750616488690.1772211977391.87869442358-0.360403556567-0.7924092581891.623581471480.3819069945783.3909049932465.42757.036-6.272
104.09926626802-5.40005860576-4.279244060416.228427409273.786229861264.486768255612.81084789615-4.1035299033-2.703837567941.333434621490.355818973004-4.48873715703-1.437790207790.404725737213-1.768875431561.14962101734-0.988348969341-1.920796817692.805835559111.212473168545.792093376375.40258.081-7.276
112.011364062537.212460853579.389341737923.368091455634.252963377845.6231859650.883384969894-2.723263385580.252462600302-0.587609470367-0.0873559988487-3.235407532431.12564154522-1.1060181639-0.3212733426222.055340217050.1230602722430.4534985747932.601714304640.1514537047840.8134686559111.44933.79-5.924
125.86941168959-1.81579780803-0.7021070114138.542944514417.474028949798.076773611830.940991701221-1.30241820434-0.395271780343-0.596054788827-2.020011250231.896661185580.228798211921-0.731862047791.243896737781.21643537556-0.2754630608610.2515843528490.944873899677-0.1052970878811.09400402321-4.44131.594-18.453
133.97042950462-1.18304210423-1.185454967152.811579947260.6838420800391.290880861831.42471478953-0.295925002814-3.25378801650.669382991052-1.158878376511.50496332881-0.205083574492-0.158374986491-0.4852469833581.55934842045-0.1228783246240.3020636747780.881237588424-0.02595249299721.550928293659.80220.703-28.357
149.58901496479-0.339267787555.461768211012.078789144721.846588554242.07969357892-0.140761423141.090704049751.24468482662-2.127632801850.745527673785-1.61601164366-1.91607605883-1.78026808212-0.6439418118721.687107469670.378823340438-0.1609586684731.41690142070.1893525434661.5228054180424.1319.981-36.716
154.465512414491.473369933431.497943073897.40060974441.4618977437.764167825791.82804294666-1.1091066852-0.108463618162-0.839199582256-0.872965880977-0.960335505263-0.0705085706953-0.766904827591-1.075797486360.862821625024-0.06835818281840.2592722514221.10840420009-0.008639736847091.2432718318119.96219.678-29.759
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182.052157810943.91305439697-1.181019351531.993642719797.624430961641.991152121332.957750365460.856665785445-1.92095321998-3.534413181820.3637384585471.25385487467-4.159372707695.29265291519-3.581242402732.48194199371-0.1847947143130.1979751329751.93113552356-0.8042895133482.8824440583236.71813.333-34.381
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246.7172956106-6.621335942482.409163058929.535510328691.107688688875.426066470881.24376242592-1.25724474144-2.6884928318-0.308899927004-0.653607741622.71017583281.38621163904-0.548740408903-0.3191527152641.23040647097-0.299786155306-0.005008113458651.2252428781-0.1567958159041.80067612097-8.11616.996-12.08
254.845571974550.3893092960440.9249284386441.734075258551.166309128754.75640393286-0.21887404419-0.147425528976-0.9105678044531.179170246970.108005972822-0.0133095915196-0.1089129998630.03077503242930.2457880327931.86250143133-0.28180164287-0.01336633394210.894030876149-0.02132247101081.107010857738.82421.339-13.388
264.92302365373.60287372895-2.386086953877.24735706376-2.419355940222.386840017370.13472301363-1.578887427661.792946605230.347868523788-0.4070249010961.517410143-0.839126695110.6073817391750.1934427245651.4129292337-0.1938828817970.3623154049351.10768524149-0.2522662824451.02643175057-7.03722.358-10.373
279.33554178349-5.079348173731.176690778268.284716391571.826204922832.67212756979-1.587053734121.71271042815-0.2725102641661.919128393421.221549307310.5596755546050.62005658693-0.7067952153190.5555113826531.73246503204-0.494742306759-0.2313772774721.364778137160.2811592525461.4366991354522.30317.549-10.717
283.70365818071-4.343950752623.472988510647.70500546405-7.458623760252.50337280772-1.084851337830.6628274584020.3151506057370.457609395473-1.28474325649-2.384062702060.518459210939-0.2005363552282.752757814281.5811568933-0.312126429510.265211372190.917697430338-0.01014509086271.55444953964-4.66157.263-31.852
292.43540892894-8.075196487952.367029794025.94225389797-1.101224893193.588212692970.0688257716124-0.446706092728-0.0836202384813-0.05121219971390.157620052002-1.051587077390.357402678942-0.11738537667-0.07185202759461.25056317846-0.2965372744010.2106571717530.9828705238770.01911507682951.29076780531-0.46445.651-24.54
3010.6325879945-0.7924548912251.842608579216.5077743422-4.897327270594.210872217750.4759927264471.57409083606-0.641609518820.116301233109-0.4601911607750.378103444941-0.06446789094780.066721881135-0.01583649209861.10584147592-0.08599168848670.2170483992560.964054124237-0.2223544941471.11556133993-4.61744.529-37.624
315.92961424219-1.51944439330.3521571994952.53612407513-4.516023781662.216893038190.8825837595410.1151031049971.333930965121.1824957799-0.62592118151-1.53713739021-1.896879477362.56784289141-0.09284811815621.34234182267-0.2314688164870.1588321186241.1436460838-0.1810707226481.858733426942.91549.697-30.394
324.7989909929-2.09976283839-0.9340751804166.83565969124-5.03948568225.35130260148-0.1212853768820.287086671497-0.7963748966751.002654322820.5405735310580.549969150688-0.523414088045-0.31289732622-0.4323971062491.2050360826-0.09605562255640.1787637437940.640690429617-0.2507541949341.30244987406-7.84145.962-34.195
331.89463518161-1.41777690212.477999329221.50452989625-0.7682169347412.05595861299-0.206910174811-0.3706779924241.141366116190.5088315538690.2977109811120.989340870266-1.65819728587-0.0599064417961-0.2413986675391.59799215410.1940776699980.07648611743980.865491696154-0.2309594028341.88853058398-13.2462.818-32.734
344.98929064814-3.957372270852.43737162377.364321602650.6433292834076.2126237891-0.8405292155640.2206714436210.3195271856150.7986764852020.3997840231690.579916171619-1.15013460497-1.399157124610.7844578381481.848409090610.08372617742650.4376360104971.08981524769-0.2177054423022.58577269342-32.22375.457-27.238
353.09380981142-3.857923536810.6662743375825.689482543690.5921306560314.380421559160.696270165279-1.41356310272-0.344867429551.9603524286-0.08215939215050.104878521297-2.529147335110.151763804376-0.6297164180592.10862611075-0.1393689476850.4720783897161.098721647410.171062532341.86687441433-22.10167.454-24.465
363.151845301-1.63393613946-0.2884813615962.71331423122-0.5700564010431.788464086550.09071816627831.767367992390.710123720215-0.182044252917-0.198972007513-0.892820117101-0.304755005816-1.179191413040.6220397437991.784793553320.1427139867190.5075368717141.105438397810.1619558073391.61745041435-25.08869.772-33.839
372.53856071597-0.03057818043216.10736753242.820663650250.6372579679422.99378925934-1.78778060337-4.20406926951-0.4310349332342.487441303590.04493536357910.347708046223-2.293540385720.9232042855611.5948284553.31647396955-0.05255416370150.08085407704011.801535291940.07361824923951.45009129273-26.46874.906-18.627
382.23925871717-4.61267917281-8.380892847212.460152847851.62749739488.25244810796-0.551351785607-2.733297044533.64089188726-0.9327653228921.32828344042-0.623313504221-2.330182673592.04173050178-0.5450607589811.59421074756-0.219265410497-0.0662498349451.68815242219-0.4842650327752.74012773994-18.52476.842-24.359
396.892872341515.3948757874-2.209174868848.56964160351-6.794603203466.873464253111.70918325569-1.107445379784.25632043594-0.0761365161019-0.03846274434252.83754776401-1.61496961383-0.173144879436-1.255900263051.07704252549-0.01711837647350.08229280447191.4772195582-0.2274983941332.84461640281-33.62341.85-37.083
405.540387539640.3062761289123.846437025228.710905083080.7946268784455.107815834950.5030930643340.85881207893-0.196290361465-0.846472485289-1.216867466581.79671222639-0.8509112202570.1076242190680.7789809643841.150041411570.01035918306570.3791570328790.895136794898-0.08466066515522.33599736704-20.35637.533-35.024
415.37799541022-5.002322836251.367913728275.408166886592.559400314933.216363379290.07678006356950.269840419926-1.134482933881.21112588116-0.075343157922.52696590280.341450779881-0.688609015641-0.1249066669191.50797642322-0.2665133282990.5003904683810.984076168959-0.09898983010852.77067485384-26.28235.445-28.543
427.6507990749-2.65033300836-3.877271120032.613228414821.700141601662.938740971721.596402528220.5775587622621.01484000752-0.865390090566-0.659085762446-0.275478970273-0.567890568084-0.523866166139-1.126419101541.13942465693-0.09706448083830.2611451203670.952655927455-0.118951003661.88897409026-15.27839.113-37.977
431.94334235995-0.309348084625-1.194714193171.613924354620.8157313363772.247954485972.89786039760.4686692287771.61940290971-2.05841032399-1.79670268612-0.369593262581-0.799241030023-4.72755796855-0.9574468831720.9894637441081.875815899651.18771787462-0.229714253654-0.2701019347252.94144461634-39.21952.239-33.162
442.688480881591.89368296366-1.404883963914.455548164982.528476179163.697925700542.1554427964-1.093376551360.9180003203593.53847938307-1.07381922561.59706076583-1.3821208630.365216464557-0.7207246304262.499001977070.1286691810710.4468046128151.176573053310.268255587191.61025279118-31.4581.071-32.484
456.694374637133.47977858418-3.70140115555.597212330791.442313850548.019216588150.1068096550460.2867510465261.331882507910.702216635029-0.4609011742712.19876451323-0.54906411538-0.2463006961540.2443487610972.111146273440.2154803592860.4509815029910.9956434283220.3427436377992.06668193046-35.24871.175-33.827
467.02787310988-4.393449729111.77420301756.370055825052.906543857175.294072255370.3901801031573.25303606599-1.581097107550.001336623435930.005994415586343.17040902398-0.360708008642-1.50528561279-0.7897895512561.362707396870.1016793846670.3895480042171.66235453479-0.06261336859522.16798467411-40.24967.858-41.455
477.66480169419-2.69490383784.581849420088.6035642155-9.441804038182.816684151-1.798581700140.0704284071864-1.995131941114.549822841871.922240721232.57978947342-3.34713719933-1.19937736798-0.007747276963382.811672026370.3982873383670.3808648190791.075318333440.08492381093452.15945081159-35.466.186-37.316
487.87245964682-3.26102053013-0.2216145233424.995167309865.260298340047.477868667890.001400421264341.055048934122.13888269884-0.2666577254240.366523998992.11058671363-1.223650634110.412320749839-0.09370878702381.66053554859-0.03476374443480.09187128869541.244716388410.3187966043571.62406855801-32.66177.047-39.095
498.31023391288-3.460503617840.2408344501213.739492523234.072012745847.8305561387-0.4035735883720.9849191702530.8020375593771.313952773470.1024465562761.39908136421-1.44083599685-0.4561441720330.645213838511.729503012270.07702001458390.3586273705461.2773563390.4238820176622.0845372621-41.77976.25-40.688
508.43207230958-4.17402763232-0.8209474073654.511007836742.526514263278.52617211496-1.365379154810.9588941010411.738898375510.8074914315490.4943074003321.63589372513-0.4669147174290.320357137780.7693434600191.945956190340.3705331985760.2293115218321.466195900960.259659505812.13503958285-43.9977.044-35.931
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 1:37 )C1 - 37
2X-RAY DIFFRACTION2( CHAIN C AND RESID 38:153 )C38 - 153
3X-RAY DIFFRACTION3( CHAIN C AND RESID 154:228 )C154 - 228
4X-RAY DIFFRACTION4( CHAIN D AND RESID 5:44 )D5 - 44
5X-RAY DIFFRACTION5( CHAIN D AND RESID 45:75 )D45 - 75
6X-RAY DIFFRACTION6( CHAIN D AND RESID 76:122 )D76 - 122
7X-RAY DIFFRACTION7( CHAIN D AND RESID 123:148 )D123 - 148
8X-RAY DIFFRACTION8( CHAIN D AND RESID 149:170 )D149 - 170
9X-RAY DIFFRACTION9( CHAIN D AND RESID 171:210 )D171 - 210
10X-RAY DIFFRACTION10( CHAIN D AND RESID 211:234 )D211 - 234
11X-RAY DIFFRACTION11( CHAIN E AND RESID 11:16 )E11 - 16
12X-RAY DIFFRACTION12( CHAIN E AND RESID 17:23 )E17 - 23
13X-RAY DIFFRACTION13( CHAIN E AND RESID 24:38 )E24 - 38
14X-RAY DIFFRACTION14( CHAIN E AND RESID 39:45 )E39 - 45
15X-RAY DIFFRACTION15( CHAIN E AND RESID 46:56 )E46 - 56
16X-RAY DIFFRACTION16( CHAIN E AND RESID 57:65 )E57 - 65
17X-RAY DIFFRACTION17( CHAIN E AND RESID 66:83 )E66 - 83
18X-RAY DIFFRACTION18( CHAIN E AND RESID 84:90 )E84 - 90
19X-RAY DIFFRACTION19( CHAIN E AND RESID 91:99 )E91 - 99
20X-RAY DIFFRACTION20( CHAIN E AND RESID 100:108 )E100 - 108
21X-RAY DIFFRACTION21( CHAIN F AND RESID 11:16 )F11 - 16
22X-RAY DIFFRACTION22( CHAIN F AND RESID 17:23 )F17 - 23
23X-RAY DIFFRACTION23( CHAIN F AND RESID 24:38 )F24 - 38
24X-RAY DIFFRACTION24( CHAIN F AND RESID 39:50 )F39 - 50
25X-RAY DIFFRACTION25( CHAIN F AND RESID 51:84 )F51 - 84
26X-RAY DIFFRACTION26( CHAIN F AND RESID 85:99 )F85 - 99
27X-RAY DIFFRACTION27( CHAIN F AND RESID 100:109 )F100 - 109
28X-RAY DIFFRACTION28( CHAIN A AND RESID 1:18 )A1 - 18
29X-RAY DIFFRACTION29( CHAIN A AND RESID 19:38 )A19 - 38
30X-RAY DIFFRACTION30( CHAIN A AND RESID 39:75 )A39 - 75
31X-RAY DIFFRACTION31( CHAIN A AND RESID 76:91 )A76 - 91
32X-RAY DIFFRACTION32( CHAIN A AND RESID 92:114 )A92 - 114
33X-RAY DIFFRACTION33( CHAIN A AND RESID 115:139 )A115 - 139
34X-RAY DIFFRACTION34( CHAIN A AND RESID 140:160 )A140 - 160
35X-RAY DIFFRACTION35( CHAIN A AND RESID 161:180 )A161 - 180
36X-RAY DIFFRACTION36( CHAIN A AND RESID 181:200 )A181 - 200
37X-RAY DIFFRACTION37( CHAIN A AND RESID 201:215 )A201 - 215
38X-RAY DIFFRACTION38( CHAIN A AND RESID 216:229 )A216 - 229
39X-RAY DIFFRACTION39( CHAIN B AND RESID 5:18 )B5 - 18
40X-RAY DIFFRACTION40( CHAIN B AND RESID 19:54 )B19 - 54
41X-RAY DIFFRACTION41( CHAIN B AND RESID 55:99 )B55 - 99
42X-RAY DIFFRACTION42( CHAIN B AND RESID 100:121 )B100 - 121
43X-RAY DIFFRACTION43( CHAIN B AND RESID 122:133 )B122 - 133
44X-RAY DIFFRACTION44( CHAIN B AND RESID 134:148 )B134 - 148
45X-RAY DIFFRACTION45( CHAIN B AND RESID 149:159 )B149 - 159
46X-RAY DIFFRACTION46( CHAIN B AND RESID 160:170 )B160 - 170
47X-RAY DIFFRACTION47( CHAIN B AND RESID 171:192 )B171 - 192
48X-RAY DIFFRACTION48( CHAIN B AND RESID 193:207 )B193 - 207
49X-RAY DIFFRACTION49( CHAIN B AND RESID 208:218 )B208 - 218
50X-RAY DIFFRACTION50( CHAIN B AND RESID 219:234 )B219 - 234

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万見について

-
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