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- PDB-9nyz: Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist bi... -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 9nyz
タイトルCrystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with UCM-101
要素(Glutamate receptor ionotropic, NMDA ...) x 2
キーワードMEMBRANE PROTEIN / ligand-gated ion channel allosteric modulation NMDA receptor synaptic protein neurotransmitter receptor
機能・相同性
機能・相同性情報


regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication ...regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / auditory behavior / positive regulation of Schwann cell migration / olfactory learning / response to other organism / response to hydrogen sulfide / cellular response to magnesium ion / dendritic branch / conditioned taste aversion / response to methylmercury / protein localization to postsynaptic membrane / serotonin metabolic process / regulation of ARF protein signal transduction / regulation of respiratory gaseous exchange / response to manganese ion / transmitter-gated monoatomic ion channel activity / suckling behavior / sleep / positive regulation of inhibitory postsynaptic potential / response to carbohydrate / cellular response to lipid / propylene metabolic process / response to glycine / regulation of NMDA receptor activity / cellular response to dsRNA / dendritic spine organization / RAF/MAP kinase cascade / locomotion / response to amine / neurotransmitter receptor complex / response to glycoside / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / glutamate receptor signaling pathway / neuromuscular process / regulation of axonogenesis / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / male mating behavior / regulation of synapse assembly / protein heterotetramerization / response to morphine / spinal cord development / glycine binding / startle response / positive regulation of reactive oxygen species biosynthetic process / dopamine metabolic process / cellular response to zinc ion / parallel fiber to Purkinje cell synapse / response to lithium ion / monoatomic ion channel complex / regulation of postsynaptic membrane potential / monoatomic cation transmembrane transport / action potential / positive regulation of calcium ion transport into cytosol / cellular response to glycine / associative learning / positive regulation of dendritic spine maintenance / modulation of excitatory postsynaptic potential / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / regulation of neuronal synaptic plasticity / positive regulation of protein targeting to membrane / monoatomic cation transport / prepulse inhibition / glutamate receptor binding / conditioned place preference / social behavior / ligand-gated monoatomic ion channel activity / multicellular organismal response to stress / neuron development / phosphatase binding / long-term memory / postsynaptic density, intracellular component / monoatomic cation channel activity / synaptic cleft / response to fungicide / calcium ion homeostasis / positive regulation of synaptic transmission, glutamatergic / cellular response to manganese ion / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule binding / sensory perception of pain / excitatory synapse
類似検索 - 分子機能
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
類似検索 - ドメイン・相同性
: / 5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID / GLUTAMIC ACID / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
類似検索 - 構成要素
生物種Rattus norvegicus (ドブネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.71 Å
データ登録者Lotti, J.S. / Syrenne, J.T. / Yates-Hansen, C.K. / McClelland, L.J. / Hansen, K.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)R01NS097536 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM140963 米国
引用ジャーナル: J.Gen.Physiol. / 年: 2026
タイトル: Novel binding mode for negative allosteric NMDA receptor modulators.
著者: Lotti, J.S. / Syrenne, J.T. / Benton, A.J. / Al-Mousawi, A. / Cornelison, L.E. / Trolinder, C.J. / Yi, F. / Zhang, Z. / Yates-Hansen, C.K. / McClelland, L.J. / Bosco, J. / Rau, A.R. / Clausen, R.P. / Hansen, K.B.
履歴
登録2025年3月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年10月29日Provider: repository / タイプ: Initial release
改定 1.12026年2月4日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,9355
ポリマ－65,1252
非ポリマー8103
水8,953497
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)54.474, 88.329, 137.273
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

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要素

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Glutamate receptor ionotropic, NMDA ... , 2種, 2分子 AB

#1: タンパク質 Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


分子量: 33340.031 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Grin1, Nmdar1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P35439
#2: タンパク質 Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / ...GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NMDAR2A / NR2A


分子量: 31785.299 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Grin2a / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q00959

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非ポリマー , 4種, 500分子

#3: 化合物 ChemComp-DK1 / 5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID / DCKA / 5,7-DICHLOROKYNURENIC ACID


分子量: 258.058 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H5Cl2NO3 / タイプ: SUBJECT OF INVESTIGATION / コメント: アンタゴニスト*YM
#4: 化合物 ChemComp-A1B7E / N-(cyclohexylmethyl)-2-[(5-{[(1R)-1-phenylpropyl]amino}-1,3,4-thiadiazol-2-yl)sulfanyl]acetamide


分子量: 404.593 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C20H28N4OS2 / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物 ChemComp-GLU / GLUTAMIC ACID


タイプ: L-peptide linking / 分子量: 147.129 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C5H9NO4 / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 497 / 由来タイプ: 天然 / 式: H2O

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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: 2.54 Å3/Da / 溶媒含有率: 51.49 %
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: ammonium acetate, PEG 4000

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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: NSLS-II / ビームライン: 17-ID-2 / 波長: 0.979338 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2023年12月11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: 0.979338 Å / 相対比: 1
反射解像度: 1.71→33.28 Å / Num. obs: 71610 / % possible obs: 99.37 % / 冗長度: 6.4 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.14
反射 シェル解像度: 1.71→1.77 Å / 冗長度: 6.6 % / Mean I/σ(I) obs: 0.93 / Num. unique obs: 7030 / CC1/2: 0.376

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解析

ソフトウェア
名称バージョン分類
autoPROCdata processing
PHASER位相決定
PHENIX1.20.1_4487精密化
Cootモデル構築
autoPROCデータ削減
autoPROCデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 1.71→33.28 Å / SU ML: 0.2221 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.414
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2019 1999 2.79 %
Rwork0.1683 69571 -
obs0.1692 71570 99.39 %
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: 38.96 Å2
精密化ステップサイクル: LAST / 解像度: 1.71→33.28 Å
タンパク質核酸リガンド溶媒全体
原子数4502 0 53 497 5052
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0124763
X-RAY DIFFRACTIONf_angle_d1.12756457
X-RAY DIFFRACTIONf_chiral_restr0.0656705
X-RAY DIFFRACTIONf_plane_restr0.012835
X-RAY DIFFRACTIONf_dihedral_angle_d6.9578656
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.760.32511410.30424907X-RAY DIFFRACTION98.65
1.76-1.80.31741400.28814885X-RAY DIFFRACTION99.66
1.8-1.860.32391390.26524866X-RAY DIFFRACTION99.07
1.86-1.920.32261410.26574911X-RAY DIFFRACTION99.12
1.92-1.980.28121420.24414906X-RAY DIFFRACTION99.35
1.98-2.060.28961410.21264931X-RAY DIFFRACTION99.43
2.06-2.160.22571420.18284929X-RAY DIFFRACTION99.33
2.16-2.270.20461420.17684949X-RAY DIFFRACTION99.36
2.27-2.410.21491430.15834956X-RAY DIFFRACTION99.75
2.41-2.60.18761440.16054999X-RAY DIFFRACTION99.67
2.6-2.860.19781430.16554993X-RAY DIFFRACTION99.65
2.86-3.280.19411430.17144998X-RAY DIFFRACTION99.44
3.28-4.130.17971460.14465059X-RAY DIFFRACTION99.39
4.13-33.280.16481520.13765282X-RAY DIFFRACTION99.63
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)
10.30928980763-0.22903203640.1202120921011.147799184890.9479874749981.14691496791-0.3019244889-0.381252264451-0.383623912779-0.0511517973484-0.111015220542-0.4691914239030.1464238822650.60834392634-0.007412789784350.2719931622970.014095209516-0.01382802972760.346186367221-0.01214495697910.4240522816376.73979952459-8.0400098466937.0170538158
20.5736159455550.4533725184360.6236987633010.531793771110.7252735052830.9864991141340.24434978159-0.644255640479-0.592107809280.3409085797160.0376699735534-0.009695279185810.442930817028-0.00679025361146-0.0003798993364910.3262343794720.0067231309883-0.04168103197940.3352043853020.01075434224430.3341437829163.80366710754-21.001679437745.9813522848
31.41947307018-0.120758724224-0.737484690530.287298457553-0.4126533494911.728844197350.09993858638310.115370729684-0.834345769574-0.22892381221-0.2431447114390.1559261413930.796195451599-0.65123249488-0.01702643796770.426848046673-0.0628347503032-0.01018101917590.244388229832-0.0523159449570.3843941928585.04409930095-26.970285504739.4829304881
40.1139332104760.0300583910557-0.1392283415860.1147315511660.08064358057230.294768388932-0.286528948186-0.1268314580240.1296485716180.960234024876-0.3919163906111.281367653220.0439999284367-0.365492550482-0.006350793555920.706108142346-0.001626656757380.1383246121230.454310129715-0.1639106888730.8628728691863.46964905617-6.283773566854.7885147433
50.9525906245050.14013483315-0.01081706526020.575210724303-0.6543167587720.7673468693830.002167520294320.01137466380670.112758014859-0.04524298211760.0144859457297-0.112639604469-0.00258038843854-0.056468746176-0.0002663310894890.2759128762190.00763082752816-0.02079901206960.245560634591-0.02411480963020.3364205115343.8221809051-17.080232687738.2510241089
60.9331004266090.1055219225750.480451185550.657044028882-0.07624990654190.88909894005-0.2348436453940.234748697353-0.02074508486920.02702231145470.0234356293196-0.2611346114850.2537549026070.01538551706950.0001895539171320.311306556272-0.03808290294280.01478211719220.33250857418-0.02865959561870.3505507575167.00914154192-10.675921850334.5419322149
71.22394901914-0.2227138670970.2035479556820.0672977924167-0.2385020761291.59045708936-0.0795251011387-0.1643651787751.051729115150.828607279884-0.0831729077196-0.0387633546064-1.36117496189-0.493438037308-0.004866019383030.9071919493010.193586299496-0.03506677846430.584413108287-0.1188638971720.66479374159-8.700854323638.1157095024844.748206659
81.468145311340.1250103184890.6174822794741.741348646790.6017779131461.81563623662-0.0827619483504-0.143832043410.1780054023270.0292279834718-0.05145985147360.00807409590435-0.173291887044-0.169621919751-7.44848483663E-50.2467562206350.0235787175761-0.02639716247430.196871979003-0.04467077577310.267522248148-5.82880933499-3.7902440497733.8691305521
94.617871048070.1678920077261.845206729940.0416479967154-0.09896365211231.510169212770.1129452515160.611597748801-1.230130784420.00374748591981-0.1091504557360.09531554797440.330438032339-0.5086313433960.0007890936102160.360503835099-0.01323762269030.02330519001290.565951455094-0.08939815844320.452650143633-29.4602048034-21.789600196741.5217414607
101.61335331362-0.302489829242-1.37228411870.4652170518070.2759570392381.167368286230.254401003612-0.05927879604950.2545675815130.01979972765030.2007792197690.0666132056238-0.491167420389-0.294972457380.01315858936650.476863800288-0.01771209789420.03968762942960.595823629505-0.08547268635350.347172149654-27.3999193885-9.3400369926645.4948910552
113.162529344311.10333178653-0.4239139652671.97156470090.303631477293.41088071540.0952012003644-0.676170450113-0.2557708175850.121811950869-0.17193020344-0.0189767881068-0.4291053160870.198963197492-0.002229341354890.374019191797-0.0397969816083-0.01368260191490.5711088252580.008509887717490.313397006536-22.1505792016-15.968340029247.8793475888
120.7186756234070.0806618911373-0.1807623070460.3965080525070.287659075880.825050343134-0.1916770658650.202476603009-0.529924853503-0.231064051580.2836082972630.1837172936510.304689060051-0.1275972117728.06660391279E-50.3807559300960.0141416333518-0.03183828323320.499436680538-0.02322097825250.486268885411-23.0637947465-21.208379742938.9203825137
130.918292885231-0.8756874122660.3342997973211.100642347040.3627776511661.86797793499-0.2315767258960.3099079494360.580677404717-0.4969331695240.03481524731780.230701368366-0.256519313424-0.252871132872-0.0007761065530410.3386852923530.0251101271796-0.04238650236310.240156293352-0.04045120153850.358477903544-5.36136640148-4.1670498658129.6753447119
141.04627218876-0.338186117341-0.3133660089310.485974680750.1980342965051.583075209970.158101982130.3085992221380.2042661759960.1474602539060.0965587492465-0.279651387602-0.3356065687050.161722955491-0.0004085622647130.359982453416-0.03027344161390.0227537122670.308873499868-0.0445331683440.359428565414-0.117869631567-10.140699173621.8617608194
150.18279476903-0.01208827076510.7229483452890.3009185525720.3175172027673.979329607820.0548916862216-0.0564049804539-0.4173071375930.0708885303980.01688648770150.3733909117860.826517230617-0.741502728372-0.07486716065350.2997177146140.00404663889308-0.02870932358790.2354343122540.008292453037310.355811634711-5.33646342302-24.542496425127.0970730451
160.396023850056-0.886841266992-1.150151485424.140185854161.510838593.86695235679-0.7101597573880.34994618222-1.094356628870.06107986339-0.01359918354381.401083706130.762147205543-1.18500502024-0.1355524102610.446229262217-0.0494793732830.06504829830350.466810032128-0.05784521872710.566501128529-8.82274877096-27.51359290737.0179186011
171.29450634089-0.130486157942-0.8390683467770.6470218940810.1113029089542.44338370099-0.0292152960469-0.09573803652620.269056104035-0.333679185814-0.02752913399230.501718349363-0.246325381753-0.464214361044-0.03853073815340.3264829414680.0535631406061-0.09610576007420.343042689887-0.06134862428580.375682304569-29.4219914984-3.797455041777.42544948862
180.0189219136635-0.1110466942510.1419269731181.316713517750.5733126384914.24424660948-0.3457574348080.15696476621-0.0742710343860.108298093243-0.1889170032960.717289893171-0.63138758369-1.46693831713-0.1289597616260.4092472209130.125508058146-0.05145621475460.501408300019-0.06413683230080.452774426465-33.4015979912-1.415661344695.22465375142
191.045776909810.0511941282140.5838067733550.610662122831-0.4769133674790.7558011638230.2560806152030.3435352560750.0586806498394-0.388674367175-0.113814941825-0.680828711281-0.3483985291540.05636146495570.003344340628330.402256297683-0.02261666472210.02624675128440.2838442173680.0241026386180.395560708098-27.7624877698-6.91914744835-10.9784698107
201.072084881570.841076773281-0.1416540926540.686529417379-0.2125188914990.366792065691-0.131467504487-0.1021086528870.155980302433-0.0536532579870.09536223827850.254667218708-0.357461399266-0.43733660475-0.0004173551671270.3874942470380.0700194115488-0.06000038739230.362230083282-0.07305026924990.358571365407-26.52278047950.71128143722914.3318096845
210.554438146773-0.3010262492010.1218069702780.3090148871660.1667996133410.393003071335-0.08682752992050.106709770264-0.350493581411-0.0791511628777-0.0946855122480.230540876579-0.0352888406176-0.112091048492-0.0005620997727860.29282291418-0.00033783969217-0.0133688450540.268019870659-0.02386691997190.267186019694-17.8861205511-10.87616642782.48108550279
221.25430530187-0.1232472782120.2856414947631.031805764960.2500004675911.21290772482-0.050977227565-0.1363901561760.1108694132850.02093495569960.014552710414-0.183363633969-0.0986401800009-0.04489780671929.09934716817E-50.217739223954-0.009461742129190.002214051571750.194881875396-0.02833074544620.229401428854-14.231407457-12.650015763811.6709209658
230.680655484809-0.212592904108-0.01717314837620.4121774478930.3178355742880.3059932026860.268961928491-0.930329458893-0.7268546278330.2890145361230.05782129190930.01382379085460.477160933832-0.1831701709720.007812828732970.4293664163160.0283275244067-0.004272997508270.4963660965770.05895977771110.404388045681-13.2375293628-36.064529587120.1759051158
242.03245711621-0.4807436959160.1444192598280.425762146477-0.4546952218481.194868491620.113098318602-0.11112137578-0.762403387599-0.4081382823620.03323212529810.2300904042990.597727392008-0.07403176664730.02346839785690.427657019944-0.0336862049323-0.03367243444910.2676220899280.01248055487650.347615519367-15.0048888056-38.154232350711.0999738943
250.74000338991-0.706773834132-0.3887326547780.6729543714990.3710407325290.203362124270.09362387901420.1451720517130.145755959839-0.3699685499610.0264350904696-0.165536918306-0.1393444149330.154922490025-7.34192618031E-50.356009677528-0.004408673663420.005177617514830.288732137595-0.02427371357890.278110703038-9.04358063773-28.482796970510.1086188481
260.299615061253-0.0466217308146-0.4855559317321.090401907420.1033403913160.783578908952-0.01225946229520.2858745456330.0931082377616-0.424211273585-0.02888385258560.2903709214910.246571106372-0.368653207742-0.0004536997089010.3551362012-0.0305690259359-0.05598778660.306023611546-0.02168345304970.2944230207-25.1045452839-31.1841886437.75254665912
271.175628375750.657845621787-0.1021947369211.279483346410.1442230520241.07976934841-0.13455699642-0.22562522755-0.1304374410210.2072086385810.1057045616880.5383991895320.370752828725-0.303060088496-0.003429955489390.23614278116-0.0485316009261-0.002987985251740.3099751384140.009280831510640.266522605082-27.2933489302-25.119800440217.4178606745
280.280580370663-0.123131524233-0.03884279725170.273618140215-0.099920233620.2926594718280.0285432516692-0.196590690965-0.4948155473670.413687369112-0.06558716224070.2848536098680.530174808552-0.2532888735290.004258456988260.384852840224-0.01057537330890.0505769690610.4589229440590.03258873392880.338676968362-25.8338654835-30.082161481823.2159342195
291.23473598209-0.7519021356340.08462364448251.144837894980.5951856315981.1003510333-0.0107101143235-0.2755058409460.07637534605570.1548933380980.0673552897009-0.3439590551050.01573227073210.1340477038150.0002075739127570.288591378071-0.044771173032-0.02165070967870.284382900246-0.05477601771180.296906397041-12.9540198163-11.202840167217.6944601061
300.277562688210.4188405148120.1996559147120.881341988164-0.003514157109240.510687204418-0.0214934211366-0.3595170781730.388706276808-0.1085119508460.01354232587180.198556836954-0.2651202085250.1674817277120.0001409168852240.3443307773580.0181510192215-0.03981001814790.341914056258-0.08619440623150.355012950965-16.84894298451.7972275058424.0327319074
310.215689983017-0.5111782127880.3626992419891.63504955672-1.108324069590.756145909277-0.484652759352-1.867694328460.6643054427631.385607753240.3752527467650.0734941298776-0.411644502318-0.5334725921120.01840563191970.4875256286480.118561300223-0.02268096872560.882693909177-0.08538635626420.507166328235-28.6851695871-6.6749110090726.6003444292
322.18754063844-2.17547465796-1.991994566167.564586802457.096918163556.66167382061-0.399117311496-0.534136202913-0.8608211581041.490844992690.3583733428880.7765778641141.6509957894-0.3003004735940.2879417789970.380618864336-0.05309115846950.07118874035690.471483920995-0.009454484134790.394546957887-32.372989323-18.981585396825.0945515155
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 3:12)AA3 - 121 - 10
22(chain A and resid 13:29)AA13 - 2911 - 27
33(chain A and resid 30:44)AA30 - 4428 - 42
44(chain A and resid 45:57)AA45 - 5743 - 55
55(chain A and resid 58:74)AA58 - 7456 - 72
66(chain A and resid 75:90)AA75 - 9073 - 88
77(chain A and resid 91:105)AA91 - 10589 - 103
88(chain A and resid 106:146)AA106 - 146104 - 144
99(chain A and resid 147:162)AA147 - 162145 - 160
1010(chain A and resid 163:189)AA163 - 189161 - 187
1111(chain A and resid 190:235)AA190 - 235188 - 233
1212(chain A and resid 236:246)AA236 - 246234 - 244
1313(chain A and resid 247:257)AA247 - 257245 - 255
1414(chain A and resid 258:272)AA258 - 272256 - 270
1515(chain A and resid 273:283)AA273 - 283271 - 281
1616(chain A and resid 284:287)AA284 - 287282 - 285
1717(chain B and resid 6:29)BE6 - 291 - 24
1818(chain B and resid 30:42)BE30 - 4225 - 37
1919(chain B and resid 43:56)BE43 - 5638 - 51
2020(chain B and resid 57:79)BE57 - 7952 - 74
2121(chain B and resid 80:92)BE80 - 9275 - 87
2222(chain B and resid 93:144)BE93 - 14488 - 139
2323(chain B and resid 145:155)BE145 - 155140 - 150
2424(chain B and resid 156:171)BE156 - 171151 - 166
2525(chain B and resid 172:188)BE172 - 188167 - 183
2626(chain B and resid 189:208)BE189 - 208184 - 203
2727(chain B and resid 209:229)BE209 - 229204 - 224
2828(chain B and resid 230:236)BE230 - 236225 - 231
2929(chain B and resid 237:254)BE237 - 254232 - 249
3030(chain B and resid 255:270)BE255 - 270250 - 265
3131(chain B and resid 271:278)BE271 - 278266 - 273
3232(chain B and resid 279:286)BE279 - 286274 - 281

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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