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- PDB-8trr: T cell recognition of citrullinated vimentin peptide presented by... -

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基本情報

登録情報
データベース: PDB / ID: 8trr
タイトルT cell recognition of citrullinated vimentin peptide presented by HLA-DR4
要素
  • (HLA class II histocompatibility antigen, ...) x 2
  • A03 TCR alpha chain
  • A03 TCR beta chain
  • Vimentin
キーワードIMMUNE SYSTEM / immune receptor complex
機能・相同性
機能・相同性情報


lens fiber cell development / keratin filament binding / intermediate filament organization / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation ...lens fiber cell development / keratin filament binding / intermediate filament organization / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / cellular response to muramyl dipeptide / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / structural constituent of eye lens / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / astrocyte development / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / Striated Muscle Contraction / inflammatory response to antigenic stimulus / positive regulation of kinase activity / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cell leading edge / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Bergmann glial cell differentiation / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / positive regulation of collagen biosynthetic process / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / regulation of mRNA stability / MHC class II antigen presentation / phagocytic vesicle / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / nuclear matrix / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / Aggrephagy / Chaperone Mediated Autophagy / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / neuron projection development / double-stranded RNA binding / Downstream TCR signaling / positive regulation of T cell activation / negative regulation of neuron projection development / peroxisome / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / scaffold protein binding / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / molecular adaptor activity / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / cytoskeleton / positive regulation of protein phosphorylation / immune response / protein domain specific binding / Golgi membrane / lysosomal membrane / external side of plasma membrane / axon / focal adhesion
類似検索 - 分子機能
: / Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / MHC class II, beta chain, N-terminal ...: / Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / 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 / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Vimentin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 2.65 Å
データ登録者Loh, T.J. / Lim, J.J. / Reid, H.H. / Rossjohn, J.
資金援助 オーストラリア, 米国, 2件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)2008981 オーストラリア
Janssen Pharmaceuticals 米国
引用ジャーナル: Nat Commun / 年: 2024
タイトル: T cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4
著者: Lim, J.J. / Loh, T.J. / Rossjohn, J.
履歴
登録2023年8月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年7月31日Provider: repository / タイプ: Initial release

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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: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Vimentin
D: A03 TCR alpha chain
E: A03 TCR beta chain
F: HLA class II histocompatibility antigen, DR alpha chain
G: HLA class II histocompatibility antigen, DRB1 beta chain
H: Vimentin
I: A03 TCR alpha chain
J: A03 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)194,48841
ポリマ－190,11210
非ポリマー4,37731
水1,63991
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Vimentin
D: A03 TCR alpha chain
E: A03 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,34721
ポリマ－95,0565
非ポリマー2,29116
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: HLA class II histocompatibility antigen, DR alpha chain
G: HLA class II histocompatibility antigen, DRB1 beta chain
H: Vimentin
I: A03 TCR alpha chain
J: A03 TCR beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,14220
ポリマ－95,0565
非ポリマー2,08615
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)98.929, 59.970, 379.159
Angle α, β, γ (deg.)90.000, 90.160, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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要素

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HLA class II histocompatibility antigen, ... , 2種, 4分子 AFBG

#1: タンパク質 HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


分子量: 21084.826 Da / 分子数: 2 / 断片: UNP residues 26-206 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DRA, HLA-DRA1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01903
#2: タンパク質 HLA class II histocompatibility antigen, DRB1 beta chain / Human leukocyte antigen DRB1 / HLA-DRB1


分子量: 22275.748 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-DRB1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01911

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タンパク質・ペプチド , 1種, 2分子 CH

#3: タンパク質・ペプチド Vimentin


分子量: 1438.634 Da / 分子数: 2
断片: UNP residues 59-71 with modified residue citrulline (CIR) at position 64
由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P08670

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タンパク質 , 2種, 4分子 DIEJ

#4: タンパク質 A03 TCR alpha chain


分子量: 23059.496 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) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: タンパク質 A03 TCR beta chain


分子量: 27197.115 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) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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糖 , 3種, 5分子

#6: 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: 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
#7: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 627.594 Da / 分子数: 1 / 由来タイプ: 合成
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#10: 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: 2 / 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

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非ポリマー , 3種, 117分子

#8: 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: 10 / 由来タイプ: 合成 / 式: C3H8O3
#9: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 16 / 由来タイプ: 天然 / 式: SO4
#11: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 91 / 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

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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: 3.07 Å3/Da / 溶媒含有率: 59.88 % / 解説: plate-like
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: 20% w/v PEG8000, 0.1 M Tris, pH 8.5, 0.2 M ammonium sulfate

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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: MX2 / 波長: 0.95374 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年10月6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: 0.95374 Å / 相対比: 1
反射解像度: 2.65→49.52 Å / Num. obs: 65371 / % possible obs: 100 % / 冗長度: 7 % / Biso Wilson estimate: 59.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.9
反射 シェル解像度: 2.65→2.72 Å / Rmerge(I) obs: 1.054 / Num. unique obs: 4569 / CC1/2: 0.806

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
PHENIX1.20.1_4487精密化
XDSデータ削減
Aimless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: PDB entry 6V1A

6v1a


解像度: 2.65→47.89 Å / SU ML: 0.3388 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 29.8624
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2441 3273 5.01 %
Rwork0.2086 62060 -
obs0.2103 65333 99.9 %
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: 79.48 Å2
精密化ステップサイクル: LAST / 解像度: 2.65→47.89 Å
タンパク質核酸リガンド溶媒全体
原子数12690 0 266 91 13047
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.008913249
X-RAY DIFFRACTIONf_angle_d0.964518039
X-RAY DIFFRACTIONf_chiral_restr0.05441996
X-RAY DIFFRACTIONf_plane_restr0.00732314
X-RAY DIFFRACTIONf_dihedral_angle_d14.33614643
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.690.35741740.34522659X-RAY DIFFRACTION99.96
2.69-2.730.36461120.32352705X-RAY DIFFRACTION99.82
2.73-2.780.36361360.30832651X-RAY DIFFRACTION99.96
2.78-2.820.32811360.30722724X-RAY DIFFRACTION99.93
2.82-2.880.34381220.29132673X-RAY DIFFRACTION99.89
2.88-2.930.3471580.28322629X-RAY DIFFRACTION99.86
2.93-2.990.36771420.28372730X-RAY DIFFRACTION99.9
2.99-3.060.3171460.28952630X-RAY DIFFRACTION100
3.06-3.130.27751220.26252709X-RAY DIFFRACTION99.79
3.13-3.20.25341520.25082664X-RAY DIFFRACTION99.89
3.21-3.290.28711230.23922708X-RAY DIFFRACTION99.89
3.29-3.390.26721300.2242667X-RAY DIFFRACTION100
3.39-3.50.2651340.22352703X-RAY DIFFRACTION99.86
3.5-3.620.25921380.21772708X-RAY DIFFRACTION99.96
3.62-3.770.25291490.21322687X-RAY DIFFRACTION100
3.77-3.940.24061530.20052660X-RAY DIFFRACTION100
3.94-4.150.241490.19032709X-RAY DIFFRACTION99.97
4.15-4.410.19141520.162701X-RAY DIFFRACTION100
4.41-4.750.19191170.15442736X-RAY DIFFRACTION99.96
4.75-5.220.1841750.15532688X-RAY DIFFRACTION99.93
5.22-5.980.20891510.18192733X-RAY DIFFRACTION99.93
5.98-7.530.20821570.20892739X-RAY DIFFRACTION100
7.53-47.890.24731450.18662847X-RAY DIFFRACTION99.4
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)
14.670711557843.620858115083.355939423126.201774184443.620007254347.007190147980.0974932026314-0.0488172268331-0.00156287920940.48694847765-0.1585080566770.07314575459470.223090437167-0.09748575976610.03106124500980.813855383368-0.00439410808382-0.0343156444870.3041998340020.0501694438560.393279367055-13.122-17.6452.733
28.534186993513.021810356822.436715854279.205174400833.436812527376.318114395290.0242695147432-0.5054850953340.3868713802040.597893104605-0.02147570973060.65067753474-0.752634009022-0.424122010896-0.02003382268180.7485548855140.1108727110350.002219983474470.340897875664-0.01453827621920.34189369063-21.932-9.53856.448
31.47187614819-0.029693634604-0.2447772349770.6326179256880.5613331448172.09798077953-0.00756479459632-0.249709936695-0.172393034260.3452104933820.0192446060619-0.1105270433890.2844181974450.1387905291720.04036199740580.721123721818-0.0176628076931-0.09932903398490.2794817132940.04404687354590.392297677019-15.33-25.98754.464
42.90355361661-0.428795986753-1.857477479911.385942363290.4549203828652.87667714321-0.0525475349474-0.266988757285-0.338750159375-0.0450385579154-0.05087843643470.1322334434840.357748666919-0.1549263303230.08181721388610.702829678029-0.0794552320133-0.1349395961060.3911839684420.07357367379570.360407996689-21.364-26.21566.001
54.98207594476-3.47644568985-3.874136751729.190753075238.649278667692.4227001708-0.797043372341-0.56674109959-0.9754012161740.8165985946850.2200309008110.4147091517962.86785509392-0.6139494791280.3227772655361.21265665025-0.141511967542-0.03787418388580.6890695088610.2291348752380.662788945659-23.539-34.56872.759
63.909078292140.661216240850.2010525955083.53379379532-0.03776344831423.815026042460.108608840772-0.00247238883014-0.233334424410.356158526002-0.0214441978952-0.4375810391370.07255439626150.283934208754-0.04272675284630.5904862397270.0295976288068-0.03584782514280.2673735630560.02285133587690.3319953571-2.839-15.55346.137
74.30152455571-0.2390176917292.536342419491.881554323091.836653711689.594637865670.101678257063-0.498911671494-0.3350836345960.7029758763530.1629528199-0.2036211750860.01152867378490.0331518846023-0.3131609355710.903336274544-0.0543236703313-0.1115241677750.4443812010370.005708744281040.412497484086-8.92-13.24784.79
83.05642208852-5.19252576157-8.237414657177.395010441418.154374821642.369189019290.2763336918520.137224461041-0.00300049035015-0.724730293778-0.2636037108610.307968327797-0.591878074653-0.421187674171-0.3167077540090.8638543640460.0706337714561-0.007175633090460.496720043434-0.04043754101990.389997404572-10.986-11.46643.237
92.937582229862.80618200517-1.780989840558.20324438991-5.37561543488.736095639440.09976527968550.4098131116020.8115799420140.3742660313110.4480211083490.525150818173-0.939552475851-0.624694149525-0.5688748346370.7524203369410.1642876662560.08245076452230.3912626902960.07007939505980.54113994451-14.34114.70134.261
105.304625094920.6844704911360.4365616507177.71685728926-0.6825218240356.003995541980.02612165809950.460532794770.128658998479-0.1976591731830.193070326955-0.0144228585769-0.4242765114610.0859341260354-0.1949909308070.6175518792370.04449295437560.05037635065850.246861942317-0.008626779966770.320848267861-8.1646.14129.219
112.33819058217-0.715176075234-5.1349543245.32712375587-4.748627475299.65099460266-0.219796928-0.1680347545150.6052266558121.497869541270.354354836023-0.246229514568-0.5954171565260.0358132290772-0.6002086418610.9645158682080.004319085862780.01569507442530.403208553624-0.02621835572430.569992530188-6.05112.41537.271
122.845479945222.4103265992-0.2734440298278.41304969324-0.7921851907890.01711063164670.2141012867270.3534422809240.278739292261-0.06551544641780.0001570693128240.298005526636-0.333489473376-0.0196574762298-0.1449511278140.8433816059450.07791558552270.0381759635050.409913365668-0.01962602964450.351995245765-10.7339.32128.79
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177.24257954152-2.215929873020.08775938851782.03970051422-1.498142212674.77613576451-0.328094313135-0.490573940779-0.1059847652460.965013819810.4860939483170.29871244101-0.49890628615-0.24030869343-0.5580593377311.0921768751-0.0551804214044-0.01634753981410.734449234215-0.0140857744730.644727844039-6.31319.6278.199
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225.088789002293.58628262296-2.991967853454.85271867281-1.591794928784.997011050370.1253224291190.5268688972620.529083726933-0.1232611373070.5524736516590.921194513319-0.24707283402-1.04252945605-0.6342974443690.7736871971590.140694487434-0.1185483671240.7863637182190.2452120444260.585405476782-21.60314.199-0.528
234.71762603548-3.32193270152-0.6736781041527.434978110927.116710737579.107206096930.1250719727950.1520227892050.0665092599585-0.0572943871212-0.345355039974-0.0122421091384-0.267114621212-0.006360398536610.2208148368550.767130792638-0.00579450690927-0.1791406893050.3083885899490.08895716385370.500627006784-37.99536.74-70.184
246.29419244445-1.42824522143-3.300147977478.01798820107-0.2140935117118.112017635070.0721598579780.0847335923365-0.373153263262-0.712284061804-0.003269981719610.3916789058280.35415404655-0.597766987738-0.07585050680510.618519149174-0.0225547471726-0.2148167783540.346741625788-0.02325783966190.459521607915-47.6128.42-70.908
252.52288525308-0.4391427525711.313266631131.41634342203-0.4742927798653.5053677589-0.00781294551250.3366132073760.322909267682-0.216584738-0.100734454332-0.216772209077-0.2896445924070.1055669172820.1694510788340.6911149384190.0818236392425-0.05008185689450.3267338511780.04053001316980.482050945566-42.28644.799-73.518
261.28250950863-1.17218130098-0.5573931231281.77683710015-0.5997111294422.707334074070.2175021873640.1220824189690.468511004104-0.182602627693-0.159922730928-0.0482573927416-0.482514851044-0.6351206187080.1470500268290.8574867658040.123419961876-0.08843863775320.4847055360970.01803081434170.484213768198-56.57348.797-77.462
274.962413346650.4684686463341.547473550.953501065074-0.8134137806522.507544047790.0339857514690.312070382607-0.0240682257290.0184604093783-0.274836345571-0.448087295901-0.26689217581-0.03799931305780.112456695190.9263330484910.0104142004275-0.1012718715860.3204899842020.08384845921810.470555866692-39.58342.185-76.325
285.276692264941.520767733842.890946806752.806983136420.3841216537015.03597508913-0.5410435328510.4417410971051.28049949435-0.402959385986-0.247767560034-0.0524212734963-1.24425193977-0.5147107635880.7161313624231.091801251470.203840922394-0.171115223730.532493976960.06278843251870.634244222544-54.09550.169-83.885
293.14302643847-0.547979611687-0.7935869196934.084004302111.169249772622.71253864460.127403600369-0.07554194418940.317607827065-0.187751484814-0.111597376445-0.704061691283-0.2325672341930.317281407824-0.02722105503820.601378258375-0.0383542596599-0.1733503727860.3068429950130.05956139344230.546809050226-26.03534.398-67.701
303.171633218810.543568670033-0.1401032676693.012956623342.852965578056.383943206260.02120687281490.9579205746930.310619566546-1.4433320499-0.037602142291-0.190890650307-1.18853705224-0.276298347625-0.04974907850661.177847493210.0978662102398-0.07507904149770.6456864260740.03203244653740.45345484356-45.25433.351-101.441
313.061179910086.065517364616.886217831168.739841259966.995926392962.63715231778-0.33026692977-0.6990106253321.16731982263-0.578267177883-0.7726935320431.09984364974-0.289733878499-0.54444655340.6608309903110.76540818491-0.113836092098-0.2498280441680.53937072654-0.05625023893090.643612143912-32.41930.934-61.561
324.67937697214-2.385085106450.9646468138873.95558312994-2.438422066825.079691379790.164384596859-0.875378371224-1.357960567070.2476935966120.331092232963-0.0296580915660.697066456063-0.520752411343-0.5825387785550.942470623385-0.155945493533-0.3602000048770.4665009230750.1750604753510.897392804815-32.6734.281-52.247
334.40538423844-1.492480627180.2299344615123.72468304994-1.710329124377.828166375010.536307345816-0.995793690462-0.7599546693560.6126497715710.199280789092-0.0195452137970.3262531159340.268475609125-0.3086963199170.89963703903-0.145324728299-0.3324005366120.4764014853320.132893344810.653383646859-27.14513.052-46.277
347.49757024514-4.075260148624.995702139384.55424480288-5.009190130557.168197264430.6984290059030.513041188915-0.718493996973-0.330893803117-0.0976314083225-0.387574027270.3088539261360.470656065481-0.2492506087840.8908426903040.00370681950295-0.2141138466030.453100795216-0.06014930215520.664753081969-21.99612.469-59.83
358.87848772112-4.574583474032.1114788852110.0272789346-3.654558406696.91058873370.5507456666040.300173541685-0.563842451185-1.39268854282-0.344426386218-0.3533075860420.5815983685320.34518251349-0.08324281214940.9565719094560.0337457347127-0.2952697822110.4107668217990.04740147792150.894648264686-26.2596.431-58.152
363.94720850794-5.45599202377-0.9562688934328.91744977143-1.095059485324.96091243633-0.106722792749-1.6236717245-0.7284010048730.698286789071-0.0505549447602-1.048351290690.7879552398941.1309647870.02175711570950.829253350048-0.123941037724-0.3535627799290.8725943781270.2744800577690.964391531883-19.4721.972-44.152
372.13285733625-4.985318721841.410476310597.55967837363-2.390909655365.10559056810.0767994250035-0.260455063225-0.9836705347690.4290748597720.2114937228630.4910130593650.5220298981460.268801322746-0.207951778150.944532956954-0.189531831617-0.3728786845920.5410420282880.1827786701350.967777582773-29.475.42-44.696
389.413462017353.904183518820.8200490655175.15623585551-4.821881631987.544760562140.129582147683-0.981744956866-2.03883832202-0.537591262088-0.397439239277-1.50956467428-0.147066380448-0.03527589143230.3710372095681.470876027430.004509277116840.1677320702620.8071970377920.2279306741751.03198560856-26.165-9.738-13.985
397.906319567652.21544733538-5.413328830626.74088960099-0.1750887431389.98918939388-1.235030128130.674309069197-0.26047867594-0.04602301159170.3286086539320.4421058534811.58113619534-0.7065995774010.5000611071571.263899008510.155154482347-0.0448771471151.072864954320.04785947104961.12700786008-32.869-13.269-28.063
404.067519464052.91071920644-2.998879351297.71600632199-0.06270780054831.98827280059-0.5722005680220.5607219057330.0453829808509-0.1789263254220.4185576155610.1018438232050.329437152198-0.4007756947610.406260235881.17727981685-0.0949818919485-0.2288171813480.9144395173260.07912943429411.06650926382-32.902-6.811-25.783
414.782742777613.55454569054-1.56107687432.048766084080.5780546750252.05514474879-0.4837481457780.563492353753-0.705024589036-0.3101191360530.473633527536-0.938429398007-0.2308306488290.8404329296880.06000776149160.856875413830.0499618452966-0.2179635907761.10601291568-0.1240486345710.960636369051-16.7210.039-29.762
427.527691525664.75385235603-7.767011582637.43562522939-3.965718831738.8799295678-1.05607640344-0.082513288305-1.80360250929-0.540696230536-0.237243850525-1.493420299520.667888685608-0.1560773558320.6246513169111.17119262099-0.1840767896710.2799787029770.9216259188350.09801602180731.92211485442-33.604-12.506-17.735
437.851473396480.623253584313-6.530032497042.82185164984-1.945856539553.20543909551-0.147289336225-0.7849904258-0.401456890783-0.0185071611098-0.141363318202-0.181272855848-0.2606936718260.4921167165870.313322054510.874475545167-0.0981693616929-0.2258079903480.6040818225830.03958842426560.525429216772-39.2822.481-38.941
444.10479520230.0760039828711-5.387709040242.67871500027-1.638959992898.817362771010.296129668678-0.1358117121990.1712932260910.0991354678704-0.1434341840530.1168314051-0.502578177993-0.466487353612-0.1121157086290.727416221876-0.0993720487037-0.2254159308190.531104817953-0.0240165724230.45717976863-41.04525.335-42.176
453.84090190576-4.930842696237.534020151167.84340903291-9.715089151442.125931337130.163556656342-0.81377308374-0.756463566358-0.2140575882610.4682795786591.025168295051.03128077987-0.862714852613-0.8164184057120.902721073132-0.1832791079980.04033010444790.9818073907990.02860540362830.613177292411-45.112.89-22.41
466.88273662673-1.24807613589-2.235019459991.249155487232.63506618664.30184376101-0.716801487818-0.106345498077-1.759320382210.7256893896970.4187359621530.2285696688670.6011610781910.4437066966470.4451512138331.0751314032-0.0102750154978-0.01397982204680.5780279444150.1799531850960.965551234823-24.97-1.206-17.839
478.05606884303-2.39421628792.796830111363.951018623740.7430909485837.922164615750.4026097982850.674700451238-1.52046706675-0.12536218408-0.2290338984920.6873667086270.978999951361-0.0896445285926-0.1915969610880.865939454901-0.06744854527290.02015863700840.540459325728-0.03745522086670.716005976389-28.6360.591-21.7
488.16461435023-4.222080589271.975415019346.83914591678-0.9927982043695.359396707020.0614730890594-0.753836052086-0.2041941361740.4852691333090.1362055795870.1396561032650.32375791979-0.065076914262-0.1730865194710.882406357186-0.0265628085137-0.0611116497410.6391049440040.1033427853830.388267467917-30.78510.955-13.034
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:26 )A3 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:55 )A27 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:101 )A56 - 101
4X-RAY DIFFRACTION4( CHAIN A AND RESID 102:154 )A102 - 154
5X-RAY DIFFRACTION5( CHAIN A AND RESID 155:181 )A155 - 181
6X-RAY DIFFRACTION6( CHAIN B AND RESID 2:85 )B2 - 85
7X-RAY DIFFRACTION7( CHAIN B AND RESID 86:190 )B86 - 190
8X-RAY DIFFRACTION8( CHAIN C AND RESID 59:70 )C59 - 70
9X-RAY DIFFRACTION9( CHAIN D AND RESID 0:33 )D0 - 33
10X-RAY DIFFRACTION10( CHAIN D AND RESID 34:69 )D34 - 69
11X-RAY DIFFRACTION11( CHAIN D AND RESID 70:88 )D70 - 88
12X-RAY DIFFRACTION12( CHAIN D AND RESID 89:113 )D89 - 113
13X-RAY DIFFRACTION13( CHAIN D AND RESID 114:133 )D114 - 133
14X-RAY DIFFRACTION14( CHAIN D AND RESID 134:152 )D134 - 152
15X-RAY DIFFRACTION15( CHAIN D AND RESID 153:167 )D153 - 167
16X-RAY DIFFRACTION16( CHAIN D AND RESID 168:175 )D168 - 175
17X-RAY DIFFRACTION17( CHAIN D AND RESID 176:186 )D176 - 186
18X-RAY DIFFRACTION18( CHAIN D AND RESID 187:215 )D187 - 215
19X-RAY DIFFRACTION19( CHAIN E AND RESID 2:120 )E2 - 120
20X-RAY DIFFRACTION20( CHAIN E AND RESID 121:135 )E121 - 135
21X-RAY DIFFRACTION21( CHAIN E AND RESID 136:173 )E136 - 173
22X-RAY DIFFRACTION22( CHAIN E AND RESID 174:256 )E174 - 256
23X-RAY DIFFRACTION23( CHAIN F AND RESID 3:26 )F3 - 26
24X-RAY DIFFRACTION24( CHAIN F AND RESID 27:55 )F27 - 55
25X-RAY DIFFRACTION25( CHAIN F AND RESID 56:112 )F56 - 112
26X-RAY DIFFRACTION26( CHAIN F AND RESID 113:133 )F113 - 133
27X-RAY DIFFRACTION27( CHAIN F AND RESID 134:144 )F134 - 144
28X-RAY DIFFRACTION28( CHAIN F AND RESID 145:181 )F145 - 181
29X-RAY DIFFRACTION29( CHAIN G AND RESID 2:85 )G2 - 85
30X-RAY DIFFRACTION30( CHAIN G AND RESID 86:190 )G86 - 190
31X-RAY DIFFRACTION31( CHAIN H AND RESID 59:71 )H59 - 71
32X-RAY DIFFRACTION32( CHAIN I AND RESID 1:33 )I1 - 33
33X-RAY DIFFRACTION33( CHAIN I AND RESID 34:56 )I34 - 56
34X-RAY DIFFRACTION34( CHAIN I AND RESID 57:69 )I57 - 69
35X-RAY DIFFRACTION35( CHAIN I AND RESID 70:88 )I70 - 88
36X-RAY DIFFRACTION36( CHAIN I AND RESID 89:99 )I89 - 99
37X-RAY DIFFRACTION37( CHAIN I AND RESID 100:133 )I100 - 133
38X-RAY DIFFRACTION38( CHAIN I AND RESID 134:152 )I134 - 152
39X-RAY DIFFRACTION39( CHAIN I AND RESID 153:167 )I153 - 167
40X-RAY DIFFRACTION40( CHAIN I AND RESID 168:175 )I168 - 175
41X-RAY DIFFRACTION41( CHAIN I AND RESID 176:186 )I176 - 186
42X-RAY DIFFRACTION42( CHAIN I AND RESID 187:202 )I187 - 202
43X-RAY DIFFRACTION43( CHAIN J AND RESID 3:56 )J3 - 56
44X-RAY DIFFRACTION44( CHAIN J AND RESID 57:120 )J57 - 120
45X-RAY DIFFRACTION45( CHAIN J AND RESID 121:135 )J121 - 135
46X-RAY DIFFRACTION46( CHAIN J AND RESID 136:173 )J136 - 173
47X-RAY DIFFRACTION47( CHAIN J AND RESID 174:213 )J174 - 213
48X-RAY DIFFRACTION48( CHAIN J AND RESID 214:256 )J214 - 256

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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

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