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- PDB-6u3m: DQ2-P.fluor-alpha1a -

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基本情報

登録情報
データベース: PDB / ID: 6u3m
タイトルDQ2-P.fluor-alpha1a
要素
  • Alpha1a peptide
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1
キーワードIMMUNE SYSTEM / Immune Complex / Celiac disease / Gliadin epitope / TCR cross-reactivity
機能・相同性
機能・相同性情報


MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / membrane / plasma membrane
類似検索 - 分子機能
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHATE ION / MHC class II HLA-DQ-beta-1 / HLA class II histocompatibility antigen, DQ alpha 1 chain
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Pseudomonas fluorescens (蛍光菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.9 Å
データ登録者Petersen, J. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC)CE140100011 オーストラリア
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2020
タイトル: T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease.
著者: Petersen, J. / Ciacchi, L. / Tran, M.T. / Loh, K.L. / Kooy-Winkelaar, Y. / Croft, N.P. / Hardy, M.Y. / Chen, Z. / McCluskey, J. / Anderson, R.P. / Purcell, A.W. / Tye-Din, J.A. / Koning, F. / ...著者: Petersen, J. / Ciacchi, L. / Tran, M.T. / Loh, K.L. / Kooy-Winkelaar, Y. / Croft, N.P. / Hardy, M.Y. / Chen, Z. / McCluskey, J. / Anderson, R.P. / Purcell, A.W. / Tye-Din, J.A. / Koning, F. / Reid, H.H. / Rossjohn, J.
履歴
登録2019年8月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年12月18日Provider: repository / タイプ: Initial release
改定 1.12020年7月1日Group: Data collection / Database references / カテゴリ: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年10月23日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

ダウンロードとリンク

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集合体

登録構造単位
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: MHC class II HLA-DQ-beta-1
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: MHC class II HLA-DQ-beta-1
E: Alpha1a peptide
F: Alpha1a peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,28914
ポリマ－94,7566
非ポリマー1,5338
水8,629479
1
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: MHC class II HLA-DQ-beta-1
F: Alpha1a peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,5068
ポリマ－47,3783
非ポリマー1,1285
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-37 kcal/mol
Surface area18170 Å2
手法PISA
2
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: MHC class II HLA-DQ-beta-1
E: Alpha1a peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)47,7836
ポリマ－47,3783
非ポリマー4053
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-40 kcal/mol
Surface area17520 Å2
手法PISA
単位格子
Length a, b, c (Å)94.935, 96.276, 105.740
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
12
22
13
23

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
111ILEILEARGARG(chain 'A' and (resid 1 through 181 or resid 1101))AC1 - 523 - 55
121PHEPHEGLUGLU(chain 'A' and (resid 1 through 181 or resid 1101))AC54 - 18156 - 183
131HOHHOHHOHHOH(chain 'A' and (resid 1 through 181 or resid 1101))AQ1101
241ILEILEARGARG(chain 'C' and (resid 1 through 181 or resid 1201))CA1 - 523 - 55
251PHEPHEGLUGLU(chain 'C' and (resid 1 through 181 or resid 1201))CA54 - 18156 - 183
261HOHHOHHOHHOH(chain 'C' and (resid 1 through 181 or resid 1201))CO1201
172SERSERSERSERchain 'B'BD3 - 1049 - 110
182HISHISARGARGchain 'B'BD112 - 189118 - 195
292SERSERSERSER(chain 'D' and resid 3 through 190)DB3 - 1049 - 110
2102HISHISARGARG(chain 'D' and resid 3 through 190)DB112 - 189118 - 195
1113GLNGLNGLNGLNchain 'E'EE-12
1123PROPROPROPROchain 'E'EE1 - 103 - 12
2133GLNGLNGLNGLNchain 'F'FF-12
2143PROPROPROPROchain 'F'FF1 - 103 - 12

NCSアンサンブル:
ID
1
2
3

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要素

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タンパク質 , 2種, 4分子 CADB

#1: タンパク質 HLA class II histocompatibility antigen, DQ alpha 1 chain / DC-1 alpha chain / DC-alpha / HLA-DCA / MHC class II DQA1


分子量: 21501.840 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: HLA-DQA1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P01909
#2: タンパク質 MHC class II HLA-DQ-beta-1


分子量: 23703.496 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: HLA-DQB1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: O19712

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タンパク質・ペプチド , 1種, 2分子 EF

#3: タンパク質・ペプチド Alpha1a peptide


分子量: 2172.461 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Pseudomonas fluorescens (蛍光菌) / 発現宿主: Trichoplusia ni (イラクサキンウワバ)

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糖 , 2種, 3分子

#4: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 2 / 由来タイプ: 天然
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 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: 1 / 由来タイプ: 天然 / 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

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非ポリマー , 3種, 484分子

#5: 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: 4 / 由来タイプ: 合成 / 式: C3H8O3
#6: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 1 / 由来タイプ: 天然 / 式: PO4
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 479 / 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: 2.55 Å3/Da / 溶媒含有率: 51.85 %
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: 18% PEG3350 and 0.15M NH4H2PO4

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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: Australian Synchrotron / ビームライン: MX1 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年5月5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: 0.9537 Å / 相対比: 1
反射解像度: 1.9→47.47 Å / Num. obs: 76918 / % possible obs: 99.62 % / 冗長度: 7.4 % / Biso Wilson estimate: 31.54 Å2 / Rpim(I) all: 0.05776 / Net I/σ(I): 25.38
反射 シェル解像度: 1.9→1.968 Å / Mean I/σ(I) obs: 2.16 / Num. unique obs: 7576 / Rpim(I) all: 0.4427 / % possible all: 96.94

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.9→47.47 Å / SU ML: 0.2039 / 交差検証法: FREE R-VALUE / 位相誤差: 24.3181
Rfactor反射数%反射
Rfree0.22 1800 2.34 %
Rwork0.19 --
obs0.1907 76855 99.92 %
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: 47.44 Å2
精密化ステップサイクル: LAST / 解像度: 1.9→47.47 Å
タンパク質核酸リガンド溶媒全体
原子数6008 0 99 479 6586
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0076273
X-RAY DIFFRACTIONf_angle_d0.86758558
X-RAY DIFFRACTIONf_chiral_restr0.0577961
X-RAY DIFFRACTIONf_plane_restr0.00641092
X-RAY DIFFRACTIONf_dihedral_angle_d12.92223730
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.32671400.28435674X-RAY DIFFRACTION99.88
1.95-2.010.29851320.26845717X-RAY DIFFRACTION99.8
2.01-2.070.30161380.24795701X-RAY DIFFRACTION99.95
2.07-2.150.23791360.22685724X-RAY DIFFRACTION99.95
2.15-2.230.25491360.21135705X-RAY DIFFRACTION99.95
2.23-2.340.2191400.21315734X-RAY DIFFRACTION99.93
2.34-2.460.28051350.21035759X-RAY DIFFRACTION99.97
2.46-2.610.25571410.20495735X-RAY DIFFRACTION99.93
2.61-2.810.24351360.20725774X-RAY DIFFRACTION100
2.81-3.10.21611410.19895786X-RAY DIFFRACTION99.97
3.1-3.550.22091370.18345809X-RAY DIFFRACTION99.97
3.55-4.470.17761420.16015869X-RAY DIFFRACTION100
4.47-47.470.19021460.16226072X-RAY DIFFRACTION99.74
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.69434828107-0.5282129375370.4186838594675.157525462040.2338381310471.86582336624-0.06028308257480.114938828649-0.1073661818810.0919574630317-0.014959890157-0.1619035834530.240845892870.189275644320.07190738949740.1883907811860.02690283176460.03480021367380.2242801784340.01775643691820.144447200954212.614780858-77.3355525601259.137325346
23.75713687626-1.75299300727-2.035916355278.070816536630.1002412073313.88541585202-0.000856111065186-0.760454768180.3394195042791.98274814779-0.200098221222-0.7299011585360.3133235273280.2596272018070.07887820537070.576810782782-0.0190640994873-0.01219730654550.3827061427460.02572564710660.165346062185211.874345266-75.2008525624272.192920819
35.96442249745-1.36761422985-3.739601204863.652635382160.8812819842298.53551943574-0.2792150225230.0970641763546-1.14119051323-0.156870312871-0.090623457531-0.6395481669780.8495641344720.1507476682010.2062604481020.5207628425150.09094278502680.1257254512770.2626786378130.02859409452780.525324350244218.784689121-91.6109098376258.475594442
41.346314571330.7708789983380.8234377673178.34380600652-1.344595193861.232901455350.100492958790.171434085928-0.455267885579-1.20379584953-0.519221780178-0.1270516303630.5257877199320.3680155523290.4305977441870.5122449273210.0070416792230.2367251841080.464096523372-0.1637328341120.553579983744225.606041711-82.4431730464243.32813818
56.5284692143-0.54139023714-2.013295349959.154771268310.7147407513140.885502012632-0.127493699637-0.03873209248050.143753080905-0.526494693321-0.09883126204440.653582648351-0.4705454478860.246176005560.2124260927660.247349426229-0.0341657107133-0.0696362153820.2571119020490.03098771382240.136942326254219.35368356-52.0081986031256.192629363
61.648613369970.04385575122240.0797889751425.627341920650.4240091157371.82020817644-0.1592411745110.075159227138-0.248439668078-0.1461996316670.265193359428-0.7658663935190.08375289041120.323227823145-0.09723364666240.1512047460020.009335153401620.01659286718340.276604432972-0.05755610293920.280194968501224.501744453-64.5288469339254.807065575
75.047511960686.57416237991-5.630772988418.68965899133-7.280224094046.980381471280.230915832767-1.135683260920.05887677683670.780887064464-0.655181439386-0.507075212781-0.9260319392550.8862287902470.3622102162370.4191555437080.0179225618486-0.1380651261830.493635205086-0.005600844313130.335474843263231.498651886-59.089517367262.603588902
84.428036947843.073089393511.927880872067.101094521631.880234050513.33505130995-0.2627290230840.120455227164-0.191019941837-0.2044251219970.295518296381-0.2961717731640.271309988817-0.0189824466360.01147970593630.208319652252-0.00387243148960.03598822073640.2849907741740.009012711908890.204818390398215.964492326-73.7444845818252.207613333
93.98247606686-0.825776292566-0.2731483818935.482364286270.3187131917753.89270277286-0.0783665571819-0.09418901322750.127922967833-0.06127996416690.333793366424-0.971578568637-0.3937597151080.685034738793-0.2350865429270.188744075126-0.0363359031279-0.0001505743060450.371191157327-0.06088257295980.272787541855227.273012907-55.7585360879258.322288538
105.813194249173.18272155859-3.122149710723.419909883720.6738456825465.60924761179-0.23739960990.462569852497-0.0949318501978-1.679989068110.896209538956-1.39854717761-0.4041581592550.219797746068-0.5631062113150.287698107623-0.08938618613910.06188986597050.520238096928-0.03477018784760.350232614543229.848060427-60.3657994815248.957164945
118.891663769990.000485812965667-0.3132718442613.758724500960.9104998109732.98762737343-0.424100517450.228609021808-0.139432237044-0.254294824080.355686641725-0.5315844359590.4098501534560.3152271022150.09426990219260.289180497802-0.02834036169230.08414203537420.217468182116-0.01554943908860.214506369677214.253220627-82.1762709359252.286710939
125.29456734913-0.501442941152-2.073447409435.83285593192.954417543633.68183750933-0.25494986060.622878518577-0.149229596653-0.4908344646350.1491607290820.2486296676310.301206878128-0.3885956713890.1082090172910.42855901664-0.1292268424220.05264762745510.3261502394980.01277429530370.242185930841204.689693682-83.8733727804250.008317939
136.56787053413-1.59222132329-1.501896826791.834022617361.212584644195.10092733291-0.5107364046090.14175557422-0.895239129573-0.4306481697730.271953436620.1228808065661.09885871099-0.005475642581390.2313636261020.73305351516-0.1300309149050.1483346446240.332912737905-0.09875553712540.409131945707205.859795169-95.7474277418248.165160495
144.7716636551-1.327844468641.047628502515.064035683873.220437959776.73262100334-0.222513204195-0.397541263479-1.101473931640.9966214738030.1672409862640.8325500055621.07544823857-0.4383982955930.1114375865970.525423690453-0.1811967399480.1555163117490.3856346130580.02947686066830.494699696018198.052212903-93.5068575627259.280228508
151.751276960742.57289236218-0.56242806747.5923186762-0.5425647282541.43687763484-0.06848873693380.07378666540320.4369799979570.6076134273110.1552394491041.47352307142-0.0445042096739-0.395632876504-0.07435870758890.2058427638070.03263090500360.1071114169860.38678710125-0.01050226531320.472935833945198.429834206-69.9361076348264.816786069
169.61905762677-3.06012200035-0.01533115602195.26258133841-3.213870195799.852247421480.1328705668410.3003137484221.09562657357-0.855202671582-0.186827629158-0.273823049395-1.626793623820.8281465782210.008599225746180.681620309776-0.0869912908707-0.05361514654810.323807850806-0.03474742066010.454571153378209.999918256-43.4436142084251.130889986
172.93446233904-3.222084758770.3562227732467.11399651897-3.938999333764.427558493780.0911094207191-0.3569182885870.352020730203-0.9351168937920.2086837423932.02290007786-0.439733083505-0.700089086046-0.5312572887860.5025468959840.0930631437046-0.2895246052940.219584324223-0.0378260605120.692708667498200.87717474-51.2327060824252.19047329
182.84046744841-1.20496898642-0.03301166638573.596157740030.2500462225483.326156627980.02012918022570.2844541422130.39373528963-1.02313016982-0.3075894294440.656817192666-0.765724793465-0.453555386297-0.05028508478170.5162246396360.120666517446-0.2541070182550.258064428161-0.01907714632720.372966836886205.700932033-53.022514716249.944841513
191.17702950431-0.6499489165470.8919969672431.00920811356-1.17453095331.596934961760.8716195246210.3280173777631.04301394915-1.65321959763-0.9211639104350.104143726645-1.392872947060.3402602776790.0819905394451.456981714850.2496445826530.0136583247160.3754167630280.09802115036420.789709526021206.041340979-37.9567788311244.231840101
205.837498622643.35559526066-1.284492787434.843643611610.7196010010015.881733292990.1759018016230.5313855461090.435557889072-0.3297168476730.2850383290192.69032303112-1.63845243212-0.943973881042-0.2873812263030.4843431242250.256661407508-0.04972013714650.359111806817-0.03160235457970.921854757982199.353958205-44.3746413692255.23785418
213.04842910740.277267859232-0.5290490597856.21489273945-0.685935371042.50524444135-0.042010800069-0.188534751264-0.06260021344470.164960636638-0.0354051673832-0.4216583180720.3768571951380.2363016760540.03015990985760.282626981580.05949834446130.06581125273070.2464686616750.05367915816820.274616662587259.825483055-77.1818821102310.687950658
226.47535536514-5.04269014522-1.983575169433.971111376271.74923067081.20548558607-0.0174650921098-0.7775165714370.1998270451251.578111353760.2616664492780.143037181007-0.1859936616030.132673432468-0.2232681936390.7428332015470.06565500559420.1250232969540.3972228447450.0441977786170.33113923659252.887346398-74.2492509568321.703010509
234.93691466339-2.36932241918-2.303471107271.456148249480.5563363458423.52384844003-0.202906102487-0.0715894039045-1.87688199314-0.213078212698-0.161292085144-1.155343940810.7846384164960.1955189760940.06338325165920.6883671570910.1206123191180.2984145097790.257869102268-0.05774014205150.947877994866265.52825295-91.6095245002307.891733821
241.781978583211.820058719020.4736026860544.704664048991.348048098391.50026556921-0.851545594180.428283330199-0.910467117419-0.596035271407-0.2312034861410.3221336078110.6084442576681.24101411022-0.6149456102070.5983363027190.2314401629610.6350365660530.501010988669-0.2366199184750.921506148652272.889019543-82.4722993645292.820076249
257.78589519505-1.08822444733-1.995999132172.681022024240.7669187924580.947708996759-0.0695663434034-0.0973337450403-0.175543721466-0.514162860046-0.3139029965310.361979306418-0.3770577596350.04694673043840.2641048680270.363014451699-0.0206130803519-0.002554569232870.237671934716-0.005482514802320.174455020637265.549556175-52.0709189912305.112226451
261.45236138530.4290940677550.4264406181182.945184097351.664226964943.27231372478-0.1712870729230.061417814204-0.558070366676-0.1856898123230.277476982038-0.7872968124820.1107508574210.338076225682-0.04326415755640.24230913258-0.01909584265070.1261813496610.312543676845-0.04763693262790.446779190966270.961959413-64.4738336806303.973244308
278.891131768116.46796494019-7.294103191475.106383555-6.103571723667.423789985240.595530563232-1.146270170630.2056356011790.679217375784-0.463765635973-0.646474768216-0.5404124666471.773186970530.01152786323350.467940815735-0.0202307058191-0.03953672877330.710241853058-0.03791627979490.527978103274277.432847181-58.5527610877311.732314663
281.58179633311-0.678002487691-0.4579443421412.615760149930.2950850792173.28056865883-0.220331601035-0.14028538964-0.215704561117-0.1815189741740.38137074195-0.857242388328-0.04688840150910.540427513971-0.1341885092330.230466093450.001616336684550.08345916199080.327857444276-0.02983818669810.331860416516269.38584431-62.6000244278304.959443489
293.800107032851.96189499726-2.878675066192.688453674430.9714313861025.50773434611-0.2109533168850.10190338711-0.01871237097-1.886789496430.807565716779-1.31691651097-0.4582178867760.764260605561-0.4894821577910.432421199902-0.1207216544790.1970366055850.565658629995-0.083189367240.586059247249276.344492309-60.3976905769298.181139593
302.609529338060.238161759687-0.6361082669812.745736044090.5789580502143.19073822389-0.521170692434-0.4372760857190.129404414335-0.6837257425940.45411918419-0.7943107776510.6279692605470.3828356242140.2637750367120.4604348041090.004624477580680.1917784852780.24165781387-0.0226624340440.499389677596261.206260726-82.3769847106301.336729375
318.16607282481.53173521705-1.575306477815.683708961322.45511887173.78152723096-0.4850792949290.451979116480.110456275265-0.8789587303920.4073640747180.2140269964890.5080917455-0.3250740169430.1214430759060.709112160626-0.1584409212290.1172771057010.3141570298870.0579567044710.386962877522251.710112241-84.219282647298.674917903
321.82678994355-0.887110467665-0.5907307182062.27807465421.405772237912.91130273177-0.4669378798840.0678061313154-0.568551742315-0.7123434017710.307327849562-0.06944930425581.62252268569-0.07745999735620.267929270381.33649522542-0.1706899701720.2274818552390.382304160447-0.1051614390320.499999277723253.248800886-96.1180987256296.843316512
333.54343909291-0.4427151538190.2900657163437.03408070992.346348533984.58111530844-0.279948234491-0.0241842010423-0.09221686923671.047107826140.2415300303822.182885513781.07107074054-0.5785082849840.02268664056280.569239092574-0.1914874333630.1811803538480.5196842951710.10095443230.608847936621244.039783284-85.9010524003310.288753129
341.7374139137-1.614994036741.547619126032.625065269710.573878993943.71644010407-0.09547337723920.13178308228-0.02843070865850.6700827738370.2430958156260.558122679068-0.887884320527-0.126424536632-0.1900916994180.3590600276320.07519846239120.08406453839260.31763324528-0.06025291155420.439890967997251.018301194-52.610406579307.07649856
353.19292523539-2.323125674620.3803489453998.459029439-3.177216125456.220852530680.1282318228360.07099056461040.0985467478995-0.6029594144520.06273174613731.0173800404-0.718835565037-0.354387856004-0.2553749626740.4358533656060.0838388813197-0.06942264414090.220582107457-0.0382679982270.363635796045249.752709402-49.9495033563300.051558964
364.20846602073-0.2852943408760.429294264136.10246440911-4.640802205533.615553736840.3152608187080.8562644105280.797838737366-0.257946001967-0.2647575424930.977328221124-0.414802253535-1.11732541319-0.1003531274831.069355781250.269729829478-0.1648716953330.548872143912-0.115997258490.572263663998246.932645429-43.7569023174290.469743674
374.13164889644-4.072379926272.624801308737.53331888883-2.959045098065.29311024804-0.1235700911050.25737099052-0.108584170693-0.393896421697-0.258778642985-0.0914664191598-0.5007511898310.1020141407730.281618119030.297249588650.000677998044587-0.027123767420.189207582689-0.04020155039620.185048221389256.036456192-56.0241913318301.10720347
384.68909068745-1.707775240661.634578890049.565135000490.4171391691060.801495798396-0.01595820694450.2457948464180.95314482828-2.085348950740.2580527938811.32299965498-1.1670364258-0.69551076476-0.2520431433451.277848888820.276906597644-0.03617714144180.414865309547-0.0680045297040.752081265476248.440160919-38.6105791092296.165213111
394.778543911442.652322335791.037257066046.04501270590.6066425202724.4357143664-0.490275590785-0.0535153587911-0.1091584497810.4050803901230.8903310449021.38044659001-1.5066429126-1.04954422962-0.3756816697120.6459806254880.319608807180.1495476294870.4210129931110.1059712366230.831453253965245.275551682-44.2463247824304.867260636
406.64404456655-1.611025944543.679857395493.606675686491.834026365744.48379032877-0.6007801331910.523904057848-1.508516675070.1228522534880.13008035948-0.01138290967621.513788382950.03304302939990.2751988342910.797527169672-0.05161530412890.2907738427050.312573995803-0.0210042885540.577830343963256.415389853-91.6780895063307.661556191
418.88797672577-4.226858478591.254488976398.041326839223.958909189516.22095263531-0.2513300606990.213082101858-1.22244289328-0.06085067418430.0906111572034-0.2190281510910.9439655699680.3352630417030.2940180046590.585782980061-0.02202892443750.2231998185110.2797982938830.008321309175120.502619503807209.624846016-91.519917956258.695660961
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 35 )
2X-RAY DIFFRACTION2chain 'C' and (resid 36 through 55 )
3X-RAY DIFFRACTION3chain 'C' and (resid 56 through 76 )
4X-RAY DIFFRACTION4chain 'C' and (resid 77 through 87 )
5X-RAY DIFFRACTION5chain 'C' and (resid 88 through 101 )
6X-RAY DIFFRACTION6chain 'C' and (resid 102 through 123 )
7X-RAY DIFFRACTION7chain 'C' and (resid 124 through 134 )
8X-RAY DIFFRACTION8chain 'C' and (resid 135 through 146 )
9X-RAY DIFFRACTION9chain 'C' and (resid 147 through 166 )
10X-RAY DIFFRACTION10chain 'C' and (resid 167 through 181 )
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 18 )
12X-RAY DIFFRACTION12chain 'D' and (resid 19 through 41 )
13X-RAY DIFFRACTION13chain 'D' and (resid 42 through 64 )
14X-RAY DIFFRACTION14chain 'D' and (resid 65 through 77 )
15X-RAY DIFFRACTION15chain 'D' and (resid 78 through 97 )
16X-RAY DIFFRACTION16chain 'D' and (resid 98 through 120 )
17X-RAY DIFFRACTION17chain 'D' and (resid 121 through 133 )
18X-RAY DIFFRACTION18chain 'D' and (resid 134 through 156 )
19X-RAY DIFFRACTION19chain 'D' and (resid 157 through 170 )
20X-RAY DIFFRACTION20chain 'D' and (resid 171 through 190 )
21X-RAY DIFFRACTION21chain 'A' and (resid 1 through 45 )
22X-RAY DIFFRACTION22chain 'A' and (resid 46 through 55 )
23X-RAY DIFFRACTION23chain 'A' and (resid 56 through 76 )
24X-RAY DIFFRACTION24chain 'A' and (resid 77 through 87 )
25X-RAY DIFFRACTION25chain 'A' and (resid 88 through 101 )
26X-RAY DIFFRACTION26chain 'A' and (resid 102 through 123 )
27X-RAY DIFFRACTION27chain 'A' and (resid 124 through 134 )
28X-RAY DIFFRACTION28chain 'A' and (resid 135 through 166 )
29X-RAY DIFFRACTION29chain 'A' and (resid 167 through 181 )
30X-RAY DIFFRACTION30chain 'B' and (resid 3 through 18 )
31X-RAY DIFFRACTION31chain 'B' and (resid 19 through 41 )
32X-RAY DIFFRACTION32chain 'B' and (resid 42 through 64 )
33X-RAY DIFFRACTION33chain 'B' and (resid 65 through 88 )
34X-RAY DIFFRACTION34chain 'B' and (resid 89 through 113 )
35X-RAY DIFFRACTION35chain 'B' and (resid 114 through 133 )
36X-RAY DIFFRACTION36chain 'B' and (resid 134 through 144 )
37X-RAY DIFFRACTION37chain 'B' and (resid 145 through 162 )
38X-RAY DIFFRACTION38chain 'B' and (resid 163 through 177 )
39X-RAY DIFFRACTION39chain 'B' and (resid 178 through 190 )
40X-RAY DIFFRACTION40chain 'E' and (resid 2 through 12 )
41X-RAY DIFFRACTION41chain 'F' and (resid 2 through 12 )

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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