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- PDB-6nk1: EphA2 LBD in complex with bA-WLA-YRPKbio peptide -

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基本情報

登録情報
データベース: PDB / ID: 6nk1
タイトルEphA2 LBD in complex with bA-WLA-YRPKbio peptide
要素
  • Ephrin type-A receptor 2
  • bA-WLA-YRPKbio
キーワードTRANSFERASE / protein-peptide interaction / kinase / ephrin / eph receptor / drug development / SIGNALING PROTEIN
機能・相同性
機能・相同性情報


notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / leading edge membrane ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / response to growth factor / bone remodeling / positive regulation of bicellular tight junction assembly / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / tight junction / RND1 GTPase cycle / RND2 GTPase cycle / neural tube development / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / transmembrane receptor protein tyrosine kinase activity / RAC1 GTPase cycle / osteoclast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / molecular function activator activity / protein localization to plasma membrane / skeletal system development / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / neuron differentiation / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / defense response to Gram-positive bacterium / cell adhesion / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
類似検索 - 分子機能
Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. ...Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
ACETATE ION / Ephrin type-A receptor 2
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 / 分子置換 / 解像度: 1.55 Å
データ登録者Lechtenberg, B.C. / Pasquale, E.B.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS087070 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA030199 米国
引用ジャーナル: J.Biol.Chem. / 年: 2019
タイトル: Engineering nanomolar peptide ligands that differentially modulate EphA2 receptor signaling.
著者: Gomez-Soler, M. / Petersen Gehring, M. / Lechtenberg, B.C. / Zapata-Mercado, E. / Hristova, K. / Pasquale, E.B.
履歴
登録2019年1月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年5月1日Provider: repository / タイプ: Initial release
改定 1.12019年5月8日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22019年6月12日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
改定 1.32019年12月4日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年10月11日Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.52024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Ephrin type-A receptor 2
B: Ephrin type-A receptor 2
C: bA-WLA-YRPKbio
D: bA-WLA-YRPKbio
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,2187
ポリマ－46,0084
非ポリマー2103
水7,404411
1
A: Ephrin type-A receptor 2
C: bA-WLA-YRPKbio


分子量 (理論値)分子数
合計 (水以外)23,0042
ポリマ－23,0042
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area10640 Å2
手法PISA
2
B: Ephrin type-A receptor 2
D: bA-WLA-YRPKbio
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,2145
ポリマ－23,0042
非ポリマー2103
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-14 kcal/mol
Surface area9460 Å2
手法PISA
単位格子
Length a, b, c (Å)44.684, 48.137, 50.211
Angle α, β, γ (deg.)99.391, 96.791, 90.197
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYGLYGLY(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA277
121TRPTRPTRPTRP(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA5232
131GLNGLNGLNGLN(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA5636
141VALVALVALVAL(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA6949
151ILEILEILEILE(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA9474
161CYSCYSCYSCYS(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA11595
171LEULEULEULEU(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA138118
181VALVALVALVAL(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA170150
191ALAALAALAALA(CHAIN A AND (RESID 27 THROUGH 46 OR RESID 52...AA190170
211GLYGLYGLYGLY(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB277
221TRPTRPTRPTRP(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB5232
231GLNGLNGLNGLN(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB5636
241VALVALVALVAL(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB6949
251ILEILEILEILE(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB9474
261CYSCYSCYSCYS(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB11595
271LEULEULEULEU(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB138118
281VALVALVALVAL(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB170150
291ALAALAALAALA(CHAIN B AND (RESID 27 THROUGH 46 OR RESID 52...BB190170
112BALBALBALBAL(CHAIN C AND (RESID 1 THROUGH 8 OR RESID 10 THROUGH 14))CC11
122PROPROPROPRO(CHAIN C AND (RESID 1 THROUGH 8 OR RESID 10 THROUGH 14))CC1010
212BALBALBALBAL(CHAIN D AND (RESID 1 THROUGH 8 OR RESID 10 THROUGH 14))DD11
222PROPROPROPRO(CHAIN D AND (RESID 1 THROUGH 8 OR RESID 10 THROUGH 14))DD1010

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


分子量: 21339.113 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: EPHA2, ECK / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P29317, receptor protein-tyrosine kinase
#2: タンパク質・ペプチド bA-WLA-YRPKbio


分子量: 1664.900 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: Biotin linked to Lys 14 side-chain / 由来: (合成) synthetic construct (人工物)
#3: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H3O2
#4: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H8O3
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 411 / 由来タイプ: 天然 / 式: H2O
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: 2.28 Å3/Da / 溶媒含有率: 45.98 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4.5
詳細: 0.09 M Sodium-Acetate pH 4.5, 22.5% w/v PEG 3,350, 3% w/v 6-aminohexanoic acid

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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: 回転陽極 / タイプ: RIGAKU FR-E SUPERBRIGHT / 波長: 1.5418 Å
検出器タイプ: RIGAKU RAXIS HTC / 検出器: IMAGE PLATE / 日付: 2018年10月1日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.5418 Å / 相対比: 1
反射解像度: 1.55→27.6 Å / Num. obs: 52329 / % possible obs: 87.9 % / 冗長度: 2 % / Biso Wilson estimate: 15.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.021 / Rrim(I) all: 0.03 / Net I/σ(I): 12.3 / Num. measured all: 104127
反射 シェル解像度: 1.55→1.58 Å / 冗長度: 2 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2440 / CC1/2: 0.976 / Rpim(I) all: 0.108 / Rrim(I) all: 0.152 / % possible all: 83.4

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位相決定

位相決定手法: 分子置換
Phasing MRModel details: Phaser MODE: MR_AUTO
最高解像度最低解像度
Rotation3.96 Å32.78 Å
Translation3.96 Å32.78 Å

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解析

ソフトウェア
名称バージョン分類NB
PHENIX精密化
XDSデータ削減
Aimless0.7.3データスケーリング
PHASER2.8.2位相決定
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 6NJZ

6njz


解像度: 1.55→27.6 Å / SU ML: 0.1033 / 交差検証法: FREE R-VALUE / σ(F): 2.03 / 位相誤差: 16.9784
Rfactor反射数%反射
Rfree0.1686 2722 5.2 %
Rwork0.1457 --
obs0.1469 52324 87.96 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 24.67 Å2
精密化ステップサイクル: LAST / 解像度: 1.55→27.6 Å
タンパク質核酸リガンド溶媒全体
原子数3098 0 14 411 3523
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00843376
X-RAY DIFFRACTIONf_angle_d1.03074597
X-RAY DIFFRACTIONf_chiral_restr0.0612470
X-RAY DIFFRACTIONf_plane_restr0.0078601
X-RAY DIFFRACTIONf_dihedral_angle_d10.02531988
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.21381230.19342496X-RAY DIFFRACTION83.83
1.58-1.610.16941390.17452559X-RAY DIFFRACTION85.65
1.61-1.640.19581150.17062578X-RAY DIFFRACTION86.76
1.64-1.680.1851380.17362597X-RAY DIFFRACTION86.94
1.68-1.720.18881290.17022615X-RAY DIFFRACTION87.11
1.72-1.760.18331470.16332584X-RAY DIFFRACTION88.15
1.76-1.810.16761440.15952649X-RAY DIFFRACTION88.08
1.81-1.860.19211250.16182647X-RAY DIFFRACTION88.2
1.86-1.920.17721320.15472620X-RAY DIFFRACTION88.55
1.92-1.990.16241300.15222596X-RAY DIFFRACTION87.65
1.99-2.070.17941530.14522576X-RAY DIFFRACTION87.27
2.07-2.160.15881560.1432606X-RAY DIFFRACTION88.24
2.16-2.280.17561660.14112604X-RAY DIFFRACTION88.19
2.28-2.420.17481700.14792562X-RAY DIFFRACTION87.06
2.42-2.60.17451600.14182587X-RAY DIFFRACTION88.36
2.6-2.870.16461250.13982634X-RAY DIFFRACTION87.78
2.87-3.280.16311760.14182615X-RAY DIFFRACTION89.25
3.28-4.130.14371650.13072679X-RAY DIFFRACTION90.92
4.13-27.610.17731290.14042798X-RAY DIFFRACTION93.34
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.196678160020.0226912877679-0.6982005758154.45554162831-0.5228179239253.541479066950.00319772760567-0.00810366666442-0.215873616051-0.05395782812750.07205923210420.4107400025670.00986230933257-0.423431926788-0.09592683871380.105435823519-0.0117319261821-0.007511170970640.117292015389-0.02566332003320.152848509801-19.5745193755-43.76440225817.94419386777
21.939394776670.697713541136-1.270984715864.222871024920.3945939021554.00511654567-0.0437633754982-0.331741091652-0.3004626290730.481180867531-0.0816039057380.1647087281420.367241825326-0.143296719328-0.1229694252550.187638393764-0.01959993613730.0252910022980.1370160411880.03300233225580.137973428395-17.1933380036-46.403646952721.9779150733
31.89705736741-0.418953097996-0.5359084450542.51414733631-0.4021924081492.411003326870.00380081860048-0.1268859262680.0514037975873-0.0160774949942-0.0571962293131-0.04888602029310.0002458721451040.226326256070.1952627476910.079251488107-0.0316696388424-0.01108697022250.0711405307139-0.003644628244140.101056053486-9.00142076876-37.99632556312.3225618279
41.3623453542-0.153016327796-0.2635318905831.28592509070.366233549421.77614075515-0.0204036898083-0.308477966710.1215172646540.2510309347210.02555645725810.0480966212473-0.2335433261270.07836498056130.02403028536870.210046596613-0.002060705549030.01113667199980.136525416666-0.02064828496980.0989255014036-13.0262159658-32.038569107423.5903732225
51.41010062801-0.2833830799052.0429627690.176160243104-0.1657065944883.417938719020.3283108165540.2137311155010.0222320926568-0.216614787757-0.167827681997-0.299754485402-0.2425297678810.4166502566960.07253997849930.1777947435270.02148066229330.04672067805610.1578623621920.01780667191310.257970406408-0.576916815848-44.87677562586.39500825249
65.57237561693-1.75904920013-1.962776032683.690581910510.8342175208723.078234048950.103367867878-0.1996461802830.263676096284-0.0529302056069-0.00366785748911-0.381426013601-0.4134836705690.253148676174-0.0538048226290.197474150543-0.0627440696677-0.002717117810580.1170200046040.01060048780350.145149849661-4.9273732813-31.755720074313.0290655339
71.96059928135-0.0613950994643-1.205996399421.68898682234-0.001442804551184.76321980895-0.0597564557334-0.1255917148790.03905800747430.253548193298-0.02868489366060.222890134839-0.114077522466-0.276786987937-0.0004371010184610.1893504415660.01604720927160.02852107706140.130813226389-0.02999641463310.152805887408-20.2670345881-32.148558807618.562625083
81.95870617125-0.21262360357-0.6083914422021.427228341380.2906308202833.468612635270.0264809928237-0.2144321110660.07415963406380.08739171783320.0379174559067-0.107508477413-0.3020007095730.3280586169490.01828990593180.148599795874-0.02439772751620.0009698444644550.0995283360390.00422007426920.118772761932-8.92246372435-36.84569593615.8477525667
92.333454546720.096488940329-0.05651981784440.9998512505750.1915686073940.1357716162830.02691804244560.3237203783510.0935156254397-0.106352020260.03389611895590.324514248081-0.288855881029-0.3764705030680.1555163285230.1868080610270.0469531655401-0.008244120278870.183748673262-0.004602184810390.177308141971-25.2176659071-34.59013562194.32812260541
106.012744579780.3024341491710.8430132312443.71074916503-2.550135883667.78866905710.08585693880020.2298244649340.327923301201-0.2764673962880.0364789735174-0.308850882255-0.141109229971-0.187874987237-0.1028212328510.09443473270810.03385569456220.04207895767290.07262154379960.04649736599120.2175138800572.45200523772-52.2536184281-2.05742767999
116.614876537930.580719045071-0.1927664427112.685638953150.5427862252871.498674511280.0342489283439-0.3214192538910.2054943027750.178978359375-0.0677565864575-0.219741423655-0.1369413719110.09061135318530.002484563936780.103572877812-0.00736199044237-0.03768548557030.115100342225-0.01543499104950.1409347216328.27193963168-57.858026961810.9917543194
125.98993478618-2.989949717651.703243556654.27799160386-1.581385055962.8117698409-0.132976667955-0.52050212285-0.3075450915020.2302250327080.155925404130.01566680083450.123002779943-0.05659990576180.06730523663380.10329196296-0.00450245048432-0.008990387044450.1412307411420.0100015591550.1194830696631.92797437703-68.635990405914.1140241565
132.08922146128-0.2871378945030.2576018584442.782660292482.568662861323.89437705619-0.1399779998220.9345989100740.552168689366-0.546970474803-0.1075037013580.215281862505-0.430635856775-0.1049533388870.1006049037650.185335140248-0.0176610187492-0.04691732322660.369530850550.08934715728670.157129742781-9.71314083393-55.2245689297-6.7945339906
142.83406765584-0.6139215780080.1966140370421.12527596201-0.07882343147890.753717397418-0.04263332231330.0407372468949-0.2556272092650.018425530817-0.004244865072990.01117051125540.08689140583930.05999773776160.04138530445730.0928346396237-0.0009974372984940.00824876922830.0892309972644-0.00461377367620.1203458329724.58943561409-70.42664451794.10521841527
153.028754311680.4633762230.803532079351.672825808381.731935024064.02383232432-0.100236711803-0.265859677405-0.03244124902020.1958830789430.1301049472090.298716935909-0.131551514454-0.308040345130.076300854710.106687941014-0.00130633020306-0.01430447927190.117237667748-0.02914114929210.201031759279-13.045005054-55.10071983918.44083252037
164.43120012701-0.238838086519-0.05132105379661.865540170570.1637292292311.047360132820.00280931114420.0846799581493-0.2605572868460.0582689685115-0.09982985399690.2388444151070.00859049396346-0.1378098191880.1529475791480.0864653849831-0.02798533396870.004637780515360.0879012527842-0.001230924386770.15483217147-8.35424863531-68.30512035934.01172943621
173.799338142530.1065208613280.3368348437131.170716916620.216919565621.06484731058-0.06507534974350.1664791857950.1153146793170.01629317439310.00260057957251-0.1233123056730.07141258980390.2996905744890.00664353410280.0986949854834-0.003068176540010.01087513849990.1498891201390.004976551093560.18237841955619.4122113651-69.51772812642.81727892285
184.44392089421-0.8541523278170.2827108121611.161896478340.2222019262371.09357953343-0.2010496542450.715355456599-0.2619943173540.0139303081516-0.03601817084940.232976475364-0.0949094480252-0.237200673771-0.04244274395380.121753540093-0.00741744157547-0.02145320436720.2493710588-0.01821204749090.119005165405-5.90248455186-63.395997661-6.78041160232
193.95431699138-1.138133151850.2736720486771.1952832028-0.4926375347220.943304329973-0.0351720010055-0.0325400615802-0.0241462066506-0.06380527918850.0348173532650.007969053232420.0344659684546-0.07842561929190.05405287660940.0878221917943-0.01360824688140.0004034683674780.0887671546538-0.009119733352760.122688782547-2.07372744506-64.64329717265.37519800967
203.7013444359-1.109886631432.724737741112.29936040043-0.9259458774613.99997497415-0.1153510757670.6149956818110.299088401872-0.2646980287890.030877125169-0.115469676041-0.194375106943-0.06941658167390.117679350610.10461161763-0.005262224043650.005590756724640.2676444577620.05615934468960.1221930477831.89348984216-58.927214584-6.05038086393
211.025237120750.9956238010540.9770365502862.815916127592.752276250782.9014349028-0.0750003004087-0.177137107396-0.4003246485830.569292675015-0.02648740660080.2442605813060.6923408512770.0111275387177-0.2510419974690.398431893969-0.01574135450230.09369556500040.2218218109330.0373950601870.213624614184-19.2333699787-48.384018519226.1083876197
220.5876027113311.233310854560.1382377669317.060187274081.85369048781.338977257540.12628766047-0.3472573174020.3320436842160.297179530712-0.1301277086840.124492280859-0.3716058384570.1451127697180.02073943496660.170004515034-0.0222794985276-0.02304210866830.222897804622-0.03418383183810.24557595634913.6809589764-57.442314634712.1297727281
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 93 )
4X-RAY DIFFRACTION4chain 'A' and (resid 94 through 126 )
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 135 )
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 146 )
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 176 )
8X-RAY DIFFRACTION8chain 'A' and (resid 177 through 188 )
9X-RAY DIFFRACTION9chain 'A' and (resid 189 through 207 )
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 43 )
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 69 )
12X-RAY DIFFRACTION12chain 'B' and (resid 70 through 82 )
13X-RAY DIFFRACTION13chain 'B' and (resid 83 through 93 )
14X-RAY DIFFRACTION14chain 'B' and (resid 94 through 126 )
15X-RAY DIFFRACTION15chain 'B' and (resid 127 through 135 )
16X-RAY DIFFRACTION16chain 'B' and (resid 136 through 146 )
17X-RAY DIFFRACTION17chain 'B' and (resid 147 through 163 )
18X-RAY DIFFRACTION18chain 'B' and (resid 164 through 176 )
19X-RAY DIFFRACTION19chain 'B' and (resid 177 through 188 )
20X-RAY DIFFRACTION20chain 'B' and (resid 189 through 200 )
21X-RAY DIFFRACTION21chain 'C' and (resid 2 through 14 )
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 14 )

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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