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- PDB-7khx: Mouse GITR-GITRL complex -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 7khx
タイトルMouse GITR-GITRL complex
要素
  • Tumor necrosis factor ligand superfamily member 18
  • Tumor necrosis factor receptor superfamily member 18
キーワードIMMUNE SYSTEM / TNFRSF / receptor-ligand complex
機能・相同性
機能・相同性情報


regulation of dendritic cell chemotaxis / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / negative regulation of T-helper 17 cell lineage commitment / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / T cell proliferation involved in immune response ...regulation of dendritic cell chemotaxis / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / negative regulation of T-helper 17 cell lineage commitment / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / T cell proliferation involved in immune response / regulation of protein-containing complex assembly / tumor necrosis factor-mediated signaling pathway / positive regulation of cell adhesion / cytokine activity / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / adaptive immune response / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / identical protein binding / plasma membrane
類似検索 - 分子機能
Tumour necrosis factor receptor 18 / Tumour necrosis factor receptor 18, N-terminal / : / Tumor necrosis factor ligand superfamily member 18 / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor-like domain superfamily
類似検索 - ドメイン・相同性
Tumor necrosis factor receptor superfamily member 18 / Tumor necrosis factor ligand superfamily member 18
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.20569845167 Å
データ登録者Wang, F. / Chau, B. / West, S.M. / Strop, P.
引用ジャーナル: Nat Commun / 年: 2021
タイトル: Structures of mouse and human GITR-GITRL complexes reveal unique TNF superfamily interactions.
著者: Wang, F. / Chau, B. / West, S.M. / Kimberlin, C.R. / Cao, F. / Schwarz, F. / Aguilar, B. / Han, M. / Morishige, W. / Bee, C. / Dollinger, G. / Rajpal, A. / Strop, P.
履歴
登録2020年10月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年3月3日Provider: repository / タイプ: Initial release
改定 1.12021年3月17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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22023年10月18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 1.32024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
B: Tumor necrosis factor ligand superfamily member 18
D: Tumor necrosis factor receptor superfamily member 18
A: Tumor necrosis factor ligand superfamily member 18
C: Tumor necrosis factor receptor superfamily member 18
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)60,3868
ポリマ－59,2984
非ポリマー1,0884
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: mass spectrometry
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)70.540, 64.820, 81.230
Angle α, β, γ (deg.)90.000, 91.228, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
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
11CYSCYSLYSLYS(chain 'C' and (resid 29 through 33 or resid 35...CD29 - 3310 - 14
12GLNGLNSERSER(chain 'C' and (resid 29 through 33 or resid 35...CD35 - 4616 - 27
13CYSCYSCYSCYS(chain 'C' and (resid 29 through 33 or resid 35...CD6041
14CYSCYSPROPRO(chain 'C' and (resid 29 through 33 or resid 35...CD62 - 7243 - 53
15CYSCYSCYSCYS(chain 'C' and (resid 29 through 33 or resid 35...CD7455
16ILEILEGLNGLN(chain 'C' and (resid 29 through 33 or resid 35...CD76 - 8657 - 67
17VALVALPHEPHE(chain 'C' and (resid 29 through 33 or resid 35...CD88 - 9869 - 79
18CYSCYSALAALA(chain 'C' and (resid 29 through 33 or resid 35...CD100 - 11081 - 91
19ASPASPTHRTHR(chain 'C' and (resid 29 through 33 or resid 35...CD113 - 13694 - 117
110ASNASNILEILE(chain 'C' and (resid 29 through 33 or resid 35...CD138 - 142119 - 123
21CYSCYSLYSLYS(chain 'D' and (resid 29 through 33 or resid 35...DB29 - 3310 - 14
22GLNGLNSERSER(chain 'D' and (resid 29 through 33 or resid 35...DB35 - 4616 - 27
23CYSCYSCYSCYS(chain 'D' and (resid 29 through 33 or resid 35...DB6041
24CYSCYSPROPRO(chain 'D' and (resid 29 through 33 or resid 35...DB62 - 7243 - 53
25CYSCYSCYSCYS(chain 'D' and (resid 29 through 33 or resid 35...DB7455
26ILEILEGLNGLN(chain 'D' and (resid 29 through 33 or resid 35...DB76 - 8657 - 67
27VALVALPHEPHE(chain 'D' and (resid 29 through 33 or resid 35...DB88 - 9869 - 79
28CYSCYSALAALA(chain 'D' and (resid 29 through 33 or resid 35...DB100 - 11081 - 91
29ASPASPTHRTHR(chain 'D' and (resid 29 through 33 or resid 35...DB113 - 13694 - 117
210ASNASNILEILE(chain 'D' and (resid 29 through 33 or resid 35...DB138 - 142119 - 123

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要素

#1: タンパク質 Tumor necrosis factor ligand superfamily member 18 / GITR ligand / GITRL / Glucocorticoid-induced TNF-related ligand


分子量: 15028.454 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Tnfsf18, Gitrl / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q7TS55
#2: タンパク質 Tumor necrosis factor receptor superfamily member 18 / Glucocorticoid-induced TNFR-related protein


分子量: 14620.600 Da / 分子数: 2 / Mutation: C55S / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Tnfrsf18, Gitr / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O35714
#3: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 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
#4: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
研究の焦点であるリガンドがあるかN
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: 3.13 Å3/Da / 溶媒含有率: 60.72 %
結晶化温度: 295.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 / 詳細: 17% PEG1500 and 0.1 M Bicine pH 8.0

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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: 17-ID / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2019年8月7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 Å / 相対比: 1
反射解像度: 3.2→53.823 Å / Num. obs: 9139 / % possible obs: 90.6 % / 冗長度: 3.3 % / Biso Wilson estimate: 144.16 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.61
反射 シェル解像度: 3.2→3.32 Å / Num. unique obs: 4001 / CC1/2: 0.0279

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2Q8O

2q8o


解像度: 3.20569845167→40.8871824422 Å / SU ML: 0.532213170031 / 交差検証法: FREE R-VALUE / σ(F): 1.33939212946 / 位相誤差: 46.3971880238
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.277675221528 422 4.62719298246 %
Rwork0.243714793741 8698 -
obs0.245402523018 9120 74.5280706055 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 155.453689959 Å2
精密化ステップサイクル: LAST / 解像度: 3.20569845167→40.8871824422 Å
タンパク質核酸リガンド溶媒全体
原子数3585 0 70 0 3655
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003203784932893766
X-RAY DIFFRACTIONf_angle_d0.706896555845110
X-RAY DIFFRACTIONf_chiral_restr0.049221758055558
X-RAY DIFFRACTIONf_plane_restr0.00577661284634649
X-RAY DIFFRACTIONf_dihedral_angle_d14.99000544282265
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2057-3.66930.422472889349590.3736164692971138X-RAY DIFFRACTION29.6213808463
3.6693-4.62190.3352546025431610.3006812541513694X-RAY DIFFRACTION95.0678175092
4.6219-40.880.2538672815762020.2167927869623866X-RAY DIFFRACTION98.2608695652
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)
11.80780306286-1.16156932781-0.3054952009134.156302392951.471676202555.51472935835-0.2767408242621.080345893443.38861564162-1.1751347271-0.246017013089-2.34097364596-0.2469461621080.928780975688-0.03208954643911.12968343571-0.1382203955430.05189741297921.373411960510.7445199872142.4756936504348.9401714956-5.78121484418.206587138
25.266054736154.5680193221-3.404026816965.05984396924-4.321268071923.913821815481.177425495783.67321830815-2.17056808267-3.31790229023-0.793820128866-4.675483242971.350260157172.726392676660.7461337206831.365485116770.3435747347050.7354812365921.578170507660.04070488562391.8827765210247.9214878569-16.64423685968.34534946236
34.65915641846-1.930266055872.911259071116.11084092808-0.8085926114848.17369267253-2.19144558772-1.247436991922.014876170781.95348522464-0.775638310203-1.01961878284-2.60391046522-0.9926526027631.803059641461.283445761980.131888493845-0.2983072321110.773746117726-0.1196978636841.3534682516123.4976984502-2.6592001055812.736905849
40.580650808745-0.8173143666460.8757405375421.66849905626-3.310822581637.99704018294-0.1787695692932.244706651980.15905253822-3.786239686780.1175021386130.7435332453461.147571565131.03316494671-0.5591125310961.49256438641-0.05933023975040.01477687710620.862476360714-0.4749274885521.4787744425634.4370477504-16.50414008653.37563855774
53.42448977027-5.61294027229-2.288818301379.705720784454.745239682053.24217553565-0.4325291874091.6177647678-1.90558960120.183417654084-0.87200640523-0.5084915473011.73131732829-0.392513104980.5830057190011.231594909480.1660791507830.2180609260711.074670077340.1107334279771.6165188906635.3400397419-16.399657176510.6178689151
62.07959961678-2.55888501272-1.651484337753.402352038431.181888712836.650309973751.197449632232.14626596598-0.192311888598-1.65048497931-0.7142926305920.4514496686210.957420611384-1.9598991255-0.5994789553091.26556638484-0.0152367812537-0.1166415900871.379258043580.1137602356621.1345135246330.8051046777-7.747034661944.62398191074
72.02547663277-4.287701568076.263456085734.22168653068-1.92948943484.09080251221-0.89418046472-0.2603717552942.33151139912-0.438752073088-0.0525972661623-2.53140712916-1.670668442250.01136373571850.3864413876010.9200150158150.2000980875910.4689008792570.939796749232-0.1126937859011.8184497358435.6578156551-1.673504785913.1657811223
83.55809678547-2.358594891192.974738073969.18549799231-6.230528312784.850393636320.8329463495320.386677447969-3.23641874440.588281415336-0.1054428346470.739355769772-0.0761478006852-0.147535900198-0.1555149298781.345921630520.386553020772-0.06949920309331.693761924480.4687487305641.8066383494551.2088888734-21.758372418120.1675546172
97.62982523209-1.63637610664-0.5301642560812.201826668571.164702653740.614431933106-1.99531064772.47515071744-0.7633459251040.3348303112221.53862838239-0.3313041467760.33651500673-1.174081277760.5797386265961.892754037210.5359221691530.1094489409922.59435776093-0.09805499048741.5589152997212.6286362197-25.4999138984-14.3167316105
102.017592361885.94705149464-4.194575599894.606520768481.027119738762.01577364273-0.7022191169910.648060435602-0.192320784926-1.283952043560.238350438490.486694349556-1.034539110390.4735556623380.3965904620912.22670725178-0.00387040766443-0.4873830071291.13237772391-0.01194446352631.7188837625813.3143593608-25.3039143186-6.08912663205
116.34691461954.39708194815-5.461148684253.76415599732-3.104835339555.1140691071-1.5552947502-0.414680527979-0.420546299723-0.663685990032-1.14606825707-1.025236822541.43610222704-0.6566848743231.818782946141.387147716770.1000432381560.1347872169051.1738611249-0.2104584807461.5604765551512.5300812685-19.1693965987-7.49015456503
126.90841231851-4.82068138333.019753450094.25040523585-0.04892896577636.20877164481-1.4393399311-0.0200255990060.6641529136623.447429489671.31383104336-0.3657005216580.8816023231151.070805216760.282786932251.399356237480.009492093904190.01081745699821.66657448465-0.05704075868811.1926913737616.8504726246-18.8522424122-1.66415271252
139.25354542546-2.2498676142-1.073571702174.05121948369-5.448699484459.73287084285-2.31277600036-0.9066273237930.479712447995-1.40294050514-1.005250483460.292406655521-0.154413584841-0.9742882633053.088711438261.74943730180.486892941112-0.3296490046911.25592708313-0.6678597714341.570319706845.81081218371-12.34838798581.53564117546
142.720283394450.7160620561780.7144579832454.49433434945-4.153838691934.50051232354-1.169125355891.75150703173-0.2840816377561.14317374577-0.8279018820261.21596682895-2.56467110547-0.008462227102021.187774041341.339740295820.125660733243-0.1598653142371.15128126492-0.2026774463191.3316873849219.1702626656-9.739203431861.26354821923
152.585892601710.192992002233.983904245575.10465962581-0.8717712235788.9196082529-1.711080913110.3904797853970.537889951847-0.9206317095930.779780168461.03454937216-3.4650928034-1.6855712880.6898196565922.054946866030.358150829935-0.3890358978471.44785207415-0.1859422430881.056644718131.80721031523-7.07937662785-8.23733425097
165.00684447442-2.04295224096-1.532162256353.964134345254.54879256055.340099415570.42957329935-0.01917707704170.615210180348-0.921393259492-0.2070268647320.187092059235-0.206502595201-0.1414384443480.3427118286453.06901741785-0.115513219977-0.5537665648432.19571641126-0.203197693881.17066470374-9.25398095341-6.12144986211-24.2057934396
174.986499545632.744968048396.434266982942.079622566452.162462608168.44049179157-0.05562689142372.437542703530.0776576134845-1.552189705610.2365602676850.01456001411880.043856061459-0.0608769042361-0.1112484454871.705571238940.413375027794-0.4227177240052.16663987827-0.4921896617981.26117606107-11.4871228515-5.70424562131-14.7125464494
182.341275252082.32857545118-3.878619058492.42227425794-3.955455112476.480214816-0.0677623223382-2.45452373841-1.423403394130.7177356259330.03720045859741.049182867990.45556914375-0.00390936040596-0.4739954982271.55434652790.2723282609410.04950767110011.228750115650.2780722639132.6358418214549.2011413688-20.595963037625.1752779802
192.58692898861.52275208963-0.7783950059472.146659875911.916568447735.51987863323-0.518831419489-0.484519724642-2.365987424712.183809665831.157736910121.275988711720.5467018865652.812408505450.3208568959131.099382170920.868618339215-0.6027986287611.535101191131.433114738483.0382964644949.2687760697-23.921218016129.5149220895
207.33590433852-2.83506152506-0.6214068970581.636461770771.625388511045.95221012627-1.76569612978-0.894538184112-0.620010278436-0.097217717572-0.511711770065-0.1933406384170.242462734270.927330534158-0.456819273111-0.354696978236-0.127378254898-2.933674199581.923712290150.9889994184820.95406822631646.7956946505-16.878443416635.2339916174
212.67162256263-0.573863006181-3.38967682934.98274012158-0.9607094946116.38044373662-1.041856155072.34660189903-2.10866121834-0.5757808556490.733639140039-1.244367922450.02239641804660.09410297975920.1461554436231.005349702230.2473510520650.144025624690.9321462546660.3043675676281.2444033696533.5831785393-20.817794780922.1959080542
229.140627204371.322625588964.604501562958.353463217060.4467539769448.116742971930.463258280209-2.300848546132.945479678262.57947953671-1.714230782782.73709464840.923131003197-0.9852581716751.231212689081.431952592910.2860492475990.3675082598750.740653321891-0.1844055329860.7904386557826.87083146-16.939382976930.5200720857
239.20141223435-0.735738532248-2.698762834697.390494233660.8227083065999.40310129478-0.5097357776230.3781959339080.8847657567640.8959052962470.2673772610330.03562083491360.6469054655790.7649717591440.2571995745411.16796187592-0.0346740406606-0.1151539159670.6977734366740.1169719975371.4103274015232.5465685147-12.514935358223.9467853314
242.829202268621.54360459542-0.5850631723825.034413120624.932073772196.91802539034-0.837979373605-2.165106048470.8565846283071.7662913923-1.75187973541-1.14036740531-0.3295763063682.023525669021.113161608741.197588427460.0233995466702-0.8345877622161.745953371860.125662773981.8718978364740.4366610099-11.893680064934.9349253861
253.570401738670.721415152235-3.510285101277.113028847020.7630085151883.818886044410.0756554675984-0.824122069138-2.006513288780.451267245598-1.724322708420.2348170195681.857271024760.9187302317161.714401404341.14913904177-0.420188411178-0.1882022416811.581624836750.2528350793241.6783261856629.5055472885-26.187891761727.5885967431
264.53154960495-0.0284904809421.101128638463.005025766291.360152988967.174186333621.486162439041.653498690133.593728526560.4116508723330.361196220307-0.6778304191140.7789264316850.5798388572861.17199297219-0.384274882253-1.241598092120.6247974645820.284256831742.118731479062.297848475949.0115562727-9.659665729119.3263337334
274.267119346790.7466968901880.5554323132756.2132212806-0.7490005994960.18972870615-0.370243786316-0.9359668158551.57817348736-0.1309077545460.09936649141160.175652772084-0.023858312805-0.0760937910228-0.01569485907554.704189223490.0610218777571-0.5083515269561.34120713347-1.409823033122.0360099805313.048731516-0.36280195882749.0120794086
280.303541895536-0.753098661176-0.2621950283124.14609056227-1.20168982511.791485058450.8079972765430.087354541644-0.1317085111440.7177677795150.255281244848-0.248892533864-0.4379117267630.295417852825-0.3889764447633.293986025690.04678806273421.68814303773-0.00654986023104-0.6646275739195.5377398800912.5743524127-1.4548425587839.9585696232
299.31897274942-3.37199578409-6.769660973923.50121490012-0.9857043752689.997077552391.06008395996-0.1349236272610.148426129438-0.325346852988-0.6915702600882.08318334303-0.9747249240570.673349257704-0.06392896786411.332978751640.109547856568-0.09714355174031.31344764260.0130672531211.4571158595811.7513746213-7.587196355343.0388478671
301.05656307630.2773820055031.253107589582.23535268496-1.050334362792.515568007020.595041147213.41055235419-0.3761679878441.47744537935-0.3364595936221.39791539114-0.5755883563340.06116285151070.1260508714831.26802264367-0.08320920619650.08141543679861.72636457115-0.1978304564951.721145275516.3648630209-8.8046415620336.5359445185
314.902955511265.49050201723-4.801502610779.88206055788-5.043209146874.78018117385-0.2422024663920.901683950073-0.264367560694-1.24101679025-0.2807138023740.428573636455-1.21019128619-3.28856666750.3168966008831.72191946899-0.2021671501370.03989232554141.8120282012-0.3741093657751.124692902745.32666274234-15.721843955734.8884122523
321.388584231750.1973341223532.095896103048.717816143923.32895466494.218935436021.22022145554-0.838907011281-0.7563870279291.318176530551.472378541970.6822676230392.55421394179-2.46661621563-1.605700336141.13287100640.05018513916760.3722048632791.558544488740.2231164549641.1275057441218.5819538793-17.771556715435.1942977449
336.075419207852.02349617527-3.706859094195.84915225029-3.897327617537.28373060661-1.11160392150.522768474424-0.1429740713770.4346268482780.415340783254-1.86603713927-0.11947632789-1.597749223460.6629933632741.362797117480.0850313478233-0.1076920666361.72872883094-0.1790112175191.220089760213.08030654809-19.188285598542.0652235511
341.12776361001-1.20364157496-0.4326735215761.399967837510.05386150327281.42888105293-0.493516722796-0.874212704084-0.8918921595961.56873492219-0.5800574203071.116271814750.8918593199280.09148535853510.6223193885161.54637267337-0.4220698289380.9454764189654.19232781984-2.365303811211.66094444685-4.11034191481-17.147419498560.36100617
352.33658776515-0.8672484627562.856346395224.84014006968-3.791630267335.159784455750.6781077656180.0880965735146-0.5894308124521.127480132111.270739995252.51043737957-0.581361036562-0.410955453420.1663058029990.393516975461-0.5626054135870.4471652137472.70354164476-1.368906719382.11442562918-12.0761367102-19.573793006457.8253385321
363.83688695303-0.206869535438-2.694447796935.49849667021-2.563162521394.76911625716-2.062717278641.54891995206-1.01311546464-2.242660920620.756948363573-0.370456531247-0.747793931372-2.021084760151.210790300381.44818471064-0.131175208303-0.0714222217411.74051680754-0.8602532501541.75823147396-8.61861281467-19.992930697250.5902875136
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 50 through 80 )
2X-RAY DIFFRACTION2chain 'B' and (resid 81 through 92 )
3X-RAY DIFFRACTION3chain 'B' and (resid 93 through 109 )
4X-RAY DIFFRACTION4chain 'B' and (resid 110 through 117 )
5X-RAY DIFFRACTION5chain 'B' and (resid 118 through 143 )
6X-RAY DIFFRACTION6chain 'B' and (resid 144 through 153 )
7X-RAY DIFFRACTION7chain 'B' and (resid 154 through 161 )
8X-RAY DIFFRACTION8chain 'B' and (resid 162 through 173 )
9X-RAY DIFFRACTION9chain 'D' and (resid 29 through 36 )
10X-RAY DIFFRACTION10chain 'D' and (resid 37 through 46 )
11X-RAY DIFFRACTION11chain 'D' and (resid 47 through 66 )
12X-RAY DIFFRACTION12chain 'D' and (resid 67 through 76 )
13X-RAY DIFFRACTION13chain 'D' and (resid 77 through 88 )
14X-RAY DIFFRACTION14chain 'D' and (resid 89 through 96 )
15X-RAY DIFFRACTION15chain 'D' and (resid 97 through 124 )
16X-RAY DIFFRACTION16chain 'D' and (resid 125 through 129 )
17X-RAY DIFFRACTION17chain 'D' and (resid 130 through 145 )
18X-RAY DIFFRACTION18chain 'A' and (resid 50 through 57 )
19X-RAY DIFFRACTION19chain 'A' and (resid 58 through 72 )
20X-RAY DIFFRACTION20chain 'A' and (resid 73 through 86 )
21X-RAY DIFFRACTION21chain 'A' and (resid 87 through 102 )
22X-RAY DIFFRACTION22chain 'A' and (resid 103 through 117 )
23X-RAY DIFFRACTION23chain 'A' and (resid 118 through 138 )
24X-RAY DIFFRACTION24chain 'A' and (resid 139 through 147 )
25X-RAY DIFFRACTION25chain 'A' and (resid 148 through 159 )
26X-RAY DIFFRACTION26chain 'A' and (resid 160 through 173 )
27X-RAY DIFFRACTION27chain 'C' and (resid 29 through 36 )
28X-RAY DIFFRACTION28chain 'C' and (resid 37 through 45 )
29X-RAY DIFFRACTION29chain 'C' and (resid 46 through 66 )
30X-RAY DIFFRACTION30chain 'C' and (resid 67 through 76 )
31X-RAY DIFFRACTION31chain 'C' and (resid 77 through 88 )
32X-RAY DIFFRACTION32chain 'C' and (resid 89 through 96 )
33X-RAY DIFFRACTION33chain 'C' and (resid 97 through 119 )
34X-RAY DIFFRACTION34chain 'C' and (resid 120 through 125 )
35X-RAY DIFFRACTION35chain 'C' and (resid 126 through 131 )
36X-RAY DIFFRACTION36chain 'C' and (resid 132 through 143 )

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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