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- PDB-6jpv: Structural analysis of AIMP2-DX2 and HSP70 interaction -

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基本情報

登録情報
データベース: PDB / ID: 6jpv
タイトルStructural analysis of AIMP2-DX2 and HSP70 interaction
要素Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
キーワードCHAPERONE / HSP70 / AIMP2-DX2 / substrate binding domain
機能・相同性
機能・相同性情報


type II pneumocyte differentiation / positive regulation of endoribonuclease activity / denatured protein binding / Selenoamino acid metabolism / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding ...type II pneumocyte differentiation / positive regulation of endoribonuclease activity / denatured protein binding / Selenoamino acid metabolism / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / Cytosolic tRNA aminoacylation / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / aminoacyl-tRNA synthetase multienzyme complex / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / positive regulation of protein ubiquitination / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / protein-containing complex assembly / vesicle / ficolin-1-rich granule lumen / molecular adaptor activity / receptor ligand activity / blood microparticle / protein stabilization / protein ubiquitination / nuclear speck / ribonucleoprotein complex / cadherin binding / translation / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / centrosome / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily ...AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal domain superfamily / ATPase, nucleotide binding domain
類似検索 - ドメイン・相同性
Heat shock 70 kDa protein 1A / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
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: 2.15000649024 Å
データ登録者Cho, H.Y. / Son, S.Y. / Jeon, Y.H.
資金援助 韓国, 1件
組織認可番号国
National Research Foundation (Korea)NRF-2013M3A6A4045160 韓国
引用ジャーナル: Nat.Chem.Biol. / 年: 2020
タイトル: Targeting the interaction of AIMP2-DX2 with HSP70 suppresses cancer development.
著者: Lim, S. / Cho, H.Y. / Kim, D.G. / Roh, Y. / Son, S.Y. / Mushtaq, A.U. / Kim, M. / Bhattarai, D. / Sivaraman, A. / Lee, Y. / Lee, J. / Yang, W.S. / Kim, H.K. / Kim, M.H. / Lee, K. / Jeon, Y.H. / Kim, S.
履歴
登録2019年3月28日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02019年10月2日Provider: repository / タイプ: Initial release
改定 1.12019年11月20日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
改定 1.22019年12月18日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
改定 1.32020年1月1日Group: 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.year / _citation_author.identifier_ORCID
改定 1.42023年11月22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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
B: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2


分子量 (理論値)分子数
合計 (水以外)33,7382
ポリマ－33,7382
非ポリマー00
水5,963331
1
A: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

B: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2


分子量 (理論値)分子数
合計 (水以外)33,7382
ポリマ－33,7382
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area16040 Å2
手法PISA
単位格子
Length a, b, c (Å)41.111, 77.054, 88.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLU(chain 'A' and (resid 394 through 534 or resid 536 through 545))AA394 - 5341 - 141
12VALVALHISHIS(chain 'A' and (resid 394 through 534 or resid 536 through 545))AA536 - 545143 - 152
21SERSERGLUGLU(chain 'B' and (resid 394 through 534 or resid 536 through 545))BB394 - 5341 - 141
22VALVALHISHIS(chain 'B' and (resid 394 through 534 or resid 536 through 545))BB536 - 545143 - 152

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要素

#1: タンパク質 Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Heat shock 70 kDa protein 1 / HSP70.1 / Multisynthase complex auxiliary component p38 / Protein JTV-1


分子量: 16869.021 Da / 分子数: 2
断片: HSP70 substrate binding domain/peptide sequences of DX2
由来タイプ: 組換発現
詳細: SF file contains Friedel pairs.,SF file contains Friedel pairs.
由来: (組換発現) Homo sapiens (ヒト)
遺伝子: HSPA1A, HSP72, HSPA1, HSX70, AIMP2, JTV1, PRO0992
発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-CodonPlus(DE3)-RIPL / 参照: UniProt: P0DMV8, UniProt: Q13155
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 331 / 由来タイプ: 天然 / 式: H2O
配列の詳細Substrate binding domain of HSP70: S394-S537 Peptide from AIMP2-DX2: M538-G546

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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: 2.09 Å3/Da / 溶媒含有率: 41.03 %
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: 5.5
詳細: PEG1500, Succinic Acid, Sodium Dihydrogen Phosphate, Glycine

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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: PAL/PLS / ビームライン: 5C (4A) / 波長: 0.9795 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2018年9月18日
放射モノクロメーター: DCM Si (111) Crystal / 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: 0.9795 Å / 相対比: 1
反射解像度: 2.15→28.08 Å / Num. obs: 15918 / % possible obs: 99.72 % / 冗長度: 7.7 % / Biso Wilson estimate: 18.93 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1036 / Rpim(I) all: 0.04137 / Rrim(I) all: 0.1118 / Net I/σ(I): 14.26
反射 シェル解像度: 2.15→2.227 Å / 冗長度: 8 % / Rmerge(I) obs: 0.2348 / Mean I/σ(I) obs: 8.73 / Num. unique obs: 1551 / CC1/2: 0.97 / Rpim(I) all: 0.08955 / Rrim(I) all: 0.2517 / % possible all: 99.87

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX1.12_2829位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4WV5

4wv5


解像度: 2.15000649024→28.0785408959 Å / SU ML: 0.257560777566 / 交差検証法: FREE R-VALUE / σ(F): 1.35779936231 / 位相誤差: 22.9145895941
Rfactor反射数%反射Selection details
Rfree0.23478720108 2154 7.69203299646 %Random selection
Rwork0.173762231727 ---
obs0.17847200903 15894 94.6239102521 %-
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: 25.3642749192 Å2
精密化ステップサイクル: LAST / 解像度: 2.15000649024→28.0785408959 Å
タンパク質核酸リガンド溶媒全体
原子数2359 0 0 331 2690
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006880919159852398
X-RAY DIFFRACTIONf_angle_d0.9575778231763244
X-RAY DIFFRACTIONf_chiral_restr0.0559951226453377
X-RAY DIFFRACTIONf_plane_restr0.00582881842173430
X-RAY DIFFRACTIONf_dihedral_angle_d18.19063440421501
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.2638592076221120.1822787155151323X-RAY DIFFRACTION73.4390992835
2.2-2.2550.2330753598281190.1936072986461457X-RAY DIFFRACTION79.5557799091
2.255-2.31590.2572158287831270.1889482890321584X-RAY DIFFRACTION86.7647058824
2.3159-2.38410.269949248481460.1784277243471675X-RAY DIFFRACTION91.5075376884
2.3841-2.4610.2992541412351410.1913281428491745X-RAY DIFFRACTION96.0774325013
2.461-2.54890.3111983364151520.1904684523571797X-RAY DIFFRACTION98.6835443038
2.5489-2.65080.2937042448871510.1860061541931813X-RAY DIFFRACTION99.8982706002
2.6508-2.77140.2810013494941520.1844138668521820X-RAY DIFFRACTION99.8481012658
2.7714-2.91740.2314381537151520.1890999160771828X-RAY DIFFRACTION99.8487140696
2.9174-3.09990.25534646581530.1831940920211814X-RAY DIFFRACTION99.6958945768
3.0999-3.33890.2144666234521520.1685701991271799X-RAY DIFFRACTION99.2370295015
3.3389-3.67430.2183056406821450.1540161847741822X-RAY DIFFRACTION99.2431886983
3.6743-4.20440.1854949306331490.1502899391121802X-RAY DIFFRACTION99.3380855397
4.2044-5.29130.1892164266871520.1476471215971792X-RAY DIFFRACTION98.9816700611
5.2913-28.08090.2225312818481510.1940991122191778X-RAY DIFFRACTION97.5227502528
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)
11.77884450176-0.814271882398-1.490756458856.292562516384.080035419714.67381333651-0.0987149500286-0.00683156194868-0.0896445824362-0.0347879359709-0.3025509909320.7295034321970.133280704096-0.3206402846370.302533628610.0977832294423-0.0294161600288-0.0001530643225580.14901121680.01849735246230.165118260552-9.47613986407-9.21916932182110.289183073
21.17345392268-0.305918440722-2.253720429021.034395613421.685401939615.599530809890.07241228911680.0266598111335-0.0745040798497-0.342033903966-0.2880746083110.670578568938-0.660957912907-1.488961457460.2793251324430.1949265590840.128177404506-0.06311492887530.6383256599130.05753026240410.472455623529-14.3421544748-6.73347803518106.838925159
33.561505535231.06778420168-3.517954830195.199063643520.8492654030234.21329068817-0.6754623017921.697514456210.166110689918-0.6097150755820.42834827365-0.08320254854460.486205878661-0.45414135640.4933694722390.8644399520410.295812686151-0.04667470051830.899263913653-0.04003958401760.383029070793-0.734238492554-16.099231069190.2586945679
48.369080204195.305474114585.932947874874.063807717883.999303872554.280797126640.283634163781.23336142320.299482666944-0.239393665811.04137497018-0.469513973481-0.04341257127121.0286526108-0.9542607062630.5678879700360.1376184658130.1645476867270.7275811610510.05680205739960.51020421789413.4762757764-18.829503005196.9927160983
58.75390201988-5.97351033716-5.929871674818.868962006155.727417927584.819913255470.00906354250828-0.4104204147850.3715938968690.2344610403810.0908829210534-0.5946504997790.5875376362890.181936761256-0.05744725401850.255669551156-0.0484430199625-0.02716305829250.31968671754-0.03085149304160.17038036578115.5675129127-11.2004919429112.851964662
68.710468159112.54283610811-1.278486460415.701230332844.997613998728.22375864613-0.598122673266-0.1851466186730.594461823774-0.7370933313960.01750312017080.815634078019-0.9893820304310.3989389096120.4108485345390.366272220730.0189392897379-0.09839864212190.292354360042-0.05241079698530.16543687664110.78228899361.96211975939127.547342205
73.4100109347-3.56240701289-2.44669710624.537660531383.99888601755.64189643967-0.01488511076710.08351384129120.4164626693360.01863388528570.0606289508288-0.189160628909-0.04947195645950.181263060802-0.03851727577330.133239304771-0.0153684641899-0.01234042819060.1232766634320.002318452701520.10523316369311.566804680911.613861821896.0099593298
81.631559387450.137740066932-0.09464477862694.423950991172.636671102884.01276115093-0.05229407237230.211464841984-0.107571833362-0.06247060035470.01736728880540.276573172852-0.1055820823080.06511069721950.06719114731090.06142944729170.0121633336935-0.006068716193810.1178518850440.0002088469572360.0935777883785.865408172582.3656202133883.0539226477
94.675019449913.007332487622.556876238142.850792445421.158698046983.040713816260.104849429188-0.105033928004-0.229005056706-0.0836357970373-0.0767180596296-0.234393692394-0.1433406054630.239869124610.03030983725920.0901217030703-0.002814117466060.02105258000610.1325998000270.01663055572330.11332948166615.95442525092.5001666305993.8569495101
102.891678218972.798042070982.078327566694.357188850832.815806024992.19892350602-0.1118457313260.0594788019499-0.5096937398730.2694650023660.284461388701-0.1708705461640.1164953132140.260859699925-0.3809391855390.108000767085-0.0304159877245-0.01461677211740.193401496653-0.02466840717920.1221330874597.54173131829-3.0460050512594.9518724133
111.81251207232-0.12699012935-0.5803296104031.645676742010.306420026343.514770473170.01625327006250.1070906083580.003706881777550.0369631903003-0.1599472653290.0508954442538-0.193896434124-0.5467328307040.02539620968590.0590618479517-0.02223974739920.0053789971330.09254336229070.004012965497560.1351830834711.735051813353.4516307575688.3962439564
125.745329401511.563903584032.857743568043.016855441540.7242179789096.72592192530.141177307252-0.2216026262240.1924417474280.551101286884-0.17871520333-0.0945253612680.01361418001340.303026225911-0.0532920624460.154457120571-0.0209792559497-0.002600291324430.114652592147-0.01288757187970.1448604523752.956682880372.3431699746898.5268498779
135.60074340953-2.93702121982-4.807538970125.053018415931.36658539267.5961784850.266980974996-1.274183570850.4179679510091.371319228060.083979538469-0.5982808434160.9060789584840.762574534553-0.2735142759610.499189425933-0.123371942-0.1403916071630.493666487733-0.0359823355280.29565312225923.701946343311.4508592633104.489663099
148.63240079007-0.211039031641.646061313769.329629940953.406721536566.655342494830.03476800388150.5513018728780.347710355023-0.530003005218-0.175246298232-0.8792814372350.1067338557770.8064387478810.0672037618680.255009338947-0.05053370063030.02229321862070.4342215623150.0417904341490.21493367930426.69662889939.5075000405587.2030962864
153.157101231941.71385326709-0.118919330935.041340643692.055890299943.203935616730.369360004177-0.5345871012140.1559256280440.8511533370450.275591175155-0.008604977081440.5011528211080.293453717330.2854172185760.1188175000210.0675629450278-0.1693135500450.157393894830.08663794297970.11863087092422.52624715441.1152643465468.8849722161
162.603883941190.1071076299470.7002526196196.22398348744.134239939514.790483334390.07374070930250.04968255559160.0211203312025-0.538946275458-0.1145844669030.107502346232-0.192786030336-0.04361352665290.02174444005060.07589084243430.01421839971050.001048554330230.07514206004880.001992812400540.08340105881511.79462589867-15.8559167453104.766431821
170.233805609147-0.09010812043340.8534066077335.154039054160.3912627421323.358433214420.242730426338-0.20593157520.035484977542-0.260030178769-0.251900289660.03058929127540.4998970745790.1246415912640.002886140697240.09139044976370.008547058577930.00983361063920.153059023758-0.01736830256330.155271704711.54096774952-19.7526573897106.833054591
181.79768756089-1.07785501539-0.704694916342.822542472541.107592600573.431013985730.0648593315286-0.03162338085280.05204356819390.03315652553470.0377507663244-0.0178466394589-0.09907995280240.143220790861-0.1034868700720.0459484391155-0.03258354501390.02741715578170.106781056602-0.01196553210360.134743065596-4.23003737175-5.64022423462111.495639434
193.1406899662-1.37428096051-1.266837301842.278122257231.008563498273.389401842320.09955570473670.1396780613090.200375684187-0.2030890569080.0304791519998-0.261440660149-0.347898930317-0.16329267417-0.06995231615950.1190755209820.00431262264490.03682925551350.1469362802690.02877079051880.08135988457842.5454626425-6.8094734179102.988823351
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 463 through 492 )
2X-RAY DIFFRACTION2chain 'B' and (resid 493 through 503 )
3X-RAY DIFFRACTION3chain 'B' and (resid 504 through 511 )
4X-RAY DIFFRACTION4chain 'B' and (resid 512 through 524 )
5X-RAY DIFFRACTION5chain 'B' and (resid 525 through 537 )
6X-RAY DIFFRACTION6chain 'B' and (resid 538 through 545 )
7X-RAY DIFFRACTION7chain 'A' and (resid 394 through 421 )
8X-RAY DIFFRACTION8chain 'A' and (resid 422 through 436 )
9X-RAY DIFFRACTION9chain 'A' and (resid 437 through 453 )
10X-RAY DIFFRACTION10chain 'A' and (resid 454 through 462 )
11X-RAY DIFFRACTION11chain 'A' and (resid 463 through 492 )
12X-RAY DIFFRACTION12chain 'A' and (resid 493 through 511 )
13X-RAY DIFFRACTION13chain 'A' and (resid 512 through 524 )
14X-RAY DIFFRACTION14chain 'A' and (resid 525 through 536 )
15X-RAY DIFFRACTION15chain 'A' and (resid 537 through 546 )
16X-RAY DIFFRACTION16chain 'B' and (resid 394 through 408 )
17X-RAY DIFFRACTION17chain 'B' and (resid 409 through 421 )
18X-RAY DIFFRACTION18chain 'B' and (resid 422 through 444 )
19X-RAY DIFFRACTION19chain 'B' and (resid 445 through 462 )

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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://pdbjlvh1.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