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- PDB-5iue: Human leukocyte antigen F (HLA-F) presents peptides and regulates... -

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基本情報

登録情報
データベース: PDB / ID: 5iue
タイトルHuman leukocyte antigen F (HLA-F) presents peptides and regulates immunity through interactions with NK-cell receptors
要素
  • Beta-2-microglobulin
  • Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP
  • cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
キーワードPROTEIN BINDING / MHC-Ib / IMMUNE SYSTEM / PEPTIDE BINDING PROTEIN
機能・相同性
機能・相同性情報


negative regulation of natural killer cell cytokine production / negative regulation of natural killer cell degranulation / positive regulation of natural killer cell degranulation / TAP2 binding / TAP1 binding / negative regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell cytokine production / negative regulation of natural killer cell mediated cytotoxicity ...negative regulation of natural killer cell cytokine production / negative regulation of natural killer cell degranulation / positive regulation of natural killer cell degranulation / TAP2 binding / TAP1 binding / negative regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell cytokine production / negative regulation of natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 14-3-3 protein binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F / HLA class I histocompatibility antigen, alpha chain F / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Trichoplusia ni (イラクサキンウワバ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.62 Å
データ登録者Dulberger, C.L. / Adams, E.J.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI073922 米国
引用ジャーナル: Immunity / 年: 2017
タイトル: Human Leukocyte Antigen F Presents Peptides and Regulates Immunity through Interactions with NK Cell Receptors.
著者: Dulberger, C.L. / McMurtrey, C.P. / Holzemer, A. / Neu, K.E. / Liu, V. / Steinbach, A.M. / Garcia-Beltran, W.F. / Sulak, M. / Jabri, B. / Lynch, V.J. / Altfeld, M. / Hildebrand, W.H. / Adams, E.J.
履歴
登録2016年3月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年6月14日Provider: repository / タイプ: Initial release
改定 1.12017年7月5日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.22017年9月27日Group: Author supporting evidence / Refinement description / カテゴリ: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
改定 1.32019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.52023年9月27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_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.62024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
B: Beta-2-microglobulin
E: cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
F: Beta-2-microglobulin
G: cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
H: Beta-2-microglobulin
I: cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
J: Beta-2-microglobulin
K: Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP
L: Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP
M: Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP
N: Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)215,83213
ポリマ－215,61012
非ポリマー2211
水4,756264
1
A: cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
B: Beta-2-microglobulin
K: Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP


分子量 (理論値)分子数
合計 (水以外)53,9033
ポリマ－53,9033
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-17 kcal/mol
Surface area19160 Å2
手法PISA
2
E: cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
F: Beta-2-microglobulin
L: Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP


分子量 (理論値)分子数
合計 (水以外)53,9033
ポリマ－53,9033
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-9 kcal/mol
Surface area18990 Å2
手法PISA
3
G: cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
H: Beta-2-microglobulin
M: Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP


分子量 (理論値)分子数
合計 (水以外)53,9033
ポリマ－53,9033
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-14 kcal/mol
Surface area18800 Å2
手法PISA
4
I: cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
J: Beta-2-microglobulin
N: Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)54,1244
ポリマ－53,9033
非ポリマー2211
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-18 kcal/mol
Surface area19240 Å2
手法PISA
単位格子
Length a, b, c (Å)102.453, 115.324, 168.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F


分子量: 32769.074 Da / 分子数: 4 / 断片: UNP residues 22-305 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pACgp67a / 細胞株 (発現宿主): High five / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: B3KUD8, UniProt: P30511*PLUS
#2: タンパク質
Beta-2-microglobulin


分子量: 20060.281 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / プラスミド: pACgp67a / 細胞株 (発現宿主): High five / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P61769
#3: タンパク質・ペプチド
Peptide LEU-ILE-LEU-ARG-TRP-GLU-GLN-ASP


分子量: 1073.223 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Trichoplusia ni (イラクサキンウワバ)
細胞株: High five
#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: 1 / 由来タイプ: 組換発現 / 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
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 264 / 由来タイプ: 天然 / 式: H2O
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: 2.31 Å3/Da / 溶媒含有率: 46.67 % / 解説: hexagonal shaped plate crystals
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: PEG 10000, tris-HCl / PH範囲: 8.5-9

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-B / 波長: 1.03318 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2013年12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: 1.03318 Å / 相対比: 1
反射解像度: 2.62→95.144 Å / Num. obs: 60628 / % possible obs: 99.9 % / 冗長度: 6.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.1322 / Net I/σ(I): 2.5

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10_2155: ???)精密化
xia2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: 1HSA

1hsa


解像度: 2.62→95.14 Å / SU ML: 0.36 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 25.63 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.241 3066 5.06 %
Rwork0.197 --
obs0.199 60576 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
精密化ステップサイクル: LAST / 解像度: 2.62→95.14 Å
タンパク質核酸リガンド溶媒全体
原子数12451 0 14 264 12729
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00212819
X-RAY DIFFRACTIONf_angle_d0.67617437
X-RAY DIFFRACTIONf_dihedral_angle_d10.2097597
X-RAY DIFFRACTIONf_chiral_restr0.0441781
X-RAY DIFFRACTIONf_plane_restr0.0042307
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.6610.32061340.28512559X-RAY DIFFRACTION100
2.661-2.70460.34371440.27372589X-RAY DIFFRACTION100
2.7046-2.75120.33911410.26752582X-RAY DIFFRACTION100
2.7512-2.80130.28361540.26372544X-RAY DIFFRACTION100
2.8013-2.85510.36731410.25642602X-RAY DIFFRACTION100
2.8551-2.91340.31661360.24662576X-RAY DIFFRACTION100
2.9134-2.97680.29311200.23512594X-RAY DIFFRACTION100
2.9768-3.0460.27941110.22492630X-RAY DIFFRACTION100
3.046-3.12220.26411320.21712584X-RAY DIFFRACTION100
3.1222-3.20660.24521520.22272589X-RAY DIFFRACTION100
3.2066-3.3010.27751480.22922582X-RAY DIFFRACTION100
3.301-3.40750.26341280.2192637X-RAY DIFFRACTION100
3.4075-3.52930.23821330.20562589X-RAY DIFFRACTION100
3.5293-3.67060.22871530.18962592X-RAY DIFFRACTION100
3.6706-3.83770.23121500.18912594X-RAY DIFFRACTION100
3.8377-4.040.2271340.17562601X-RAY DIFFRACTION100
4.04-4.29320.19711260.15792662X-RAY DIFFRACTION100
4.2932-4.62460.2151400.14652625X-RAY DIFFRACTION100
4.6246-5.090.18271360.14422639X-RAY DIFFRACTION100
5.09-5.82650.2041280.16832679X-RAY DIFFRACTION100
5.8265-7.34030.22781670.19892683X-RAY DIFFRACTION100
7.3403-95.20630.20571580.18752778X-RAY DIFFRACTION99
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)
13.6159-0.06181.21681.81570.60113.6709-0.08980.19670.5469-0.04940.0683-0.0361-0.74520.22910.13410.4489-0.1051-0.02990.36380.1030.37725.8899-5.2317148.3323
22.80840.30471.14181.56830.92234.25620.01920.5330.0001-0.18930.1282-0.2353-0.10960.7829-0.08220.3384-0.08230.00840.57140.05310.389732.4299-17.6231142.2378
33.56221.3602-0.51333.091-0.71131.9965-0.09080.09-0.1176-0.16230.08440.07720.1387-0.09230.00420.3118-0.0378-0.01730.3948-0.04760.195716.1777-31.0792170.7366
46.5911-1.69460.8893.9487-0.83385.73920.6129-0.1730.78940.01440.3921-0.12960.8717-0.9272-0.9120.231-0.0537-0.02960.40530.06020.37738.6371-19.6773154.3893
51.2176-0.2914-1.48322.6511.31042.1601-0.1503-0.80880.16521.62870.26520.31540.1621-0.02930.23940.89670.03080.13651.3223-0.14150.31889.7662-12.5987178.2629
64.4257-0.6569-2.60436.90612.83387.7642-0.2977-0.50470.3906-0.0086-0.15290.298-0.7647-0.36160.23960.34610.0307-0.02650.5898-0.02440.344610.829-13.4902163.4292
75.5075-5.6255-6.40568.67476.0367.54580.28240.47510.6672-0.5235-0.43490.7497-0.973-0.77170.15340.33560.0873-0.05010.609-0.08230.46095.7178-10.2979154.4552
88.8172-3.2859-7.30535.81171.54026.36290.8548-0.08781.8113-0.2869-0.20010.2854-1.3095-0.7424-1.18540.5580.23290.05950.5739-0.15320.48563.3032-3.4533163.1509
98.6062-3.4344-5.6527.54564.27945.8938-0.1285-0.40140.55460.36060.298-0.10180.0302-0.0228-0.17880.28340.0341-0.08920.29480.07920.358515.3577-12.9478157.2836
107.03220.37411.55832.54444.76339.3087-0.0734-0.423-0.9548-0.0788-0.127-0.14760.3059-1.68890.17760.75360.02860.23021.1065-0.24960.7471-2.0903-10.8186176.0512
114.984-1.5548-1.17080.6962-0.7285.84520.06290.2498-0.05890.0192-0.10260.2557-0.6481-1.15750.03960.32250.0831-0.02720.665-0.05050.54910.4936-14.1777154.3271
129.8761-1.74830.89387.5374-2.04366.48540.1776-0.292-0.66880.69360.30580.995-0.1193-0.014-0.52030.3944-0.12930.02920.70930.10960.50811.1851-18.3767167.884
132.34310.5757-0.28652.6292-0.16764.11790.1678-0.2671-0.77380.1434-0.10390.05610.97460.31340.06240.51560.0159-0.03450.32240.08010.478763.29864.8266189.1099
142.51950.5299-0.59490.65440.48327.46880.1582-0.3015-0.28880.14630.0191-0.11670.50640.6852-0.14090.33970.0672-0.0450.46470.06050.361973.813515.4748193.8393
153.9344-0.82912.66822.2225-1.02723.84030.81240.6452-0.2345-0.5042-0.4364-0.02920.40460.1102-0.32380.3026-0.0120.00740.3466-0.07950.295755.91624.6723163.9391
164.43-1.8360.99243.2738-2.31652.7032-0.0705-0.11730.52140.37380.05280.0045-0.3188-0.23250.02290.34060.03340.02550.339-0.1170.322253.211532.4277167.9104
174.0503-0.71950.24985.12942.1320.9699-0.32340.21890.5443-0.05950.3698-0.4501-0.2039-0.5535-0.11560.22690.06330.03510.59240.03570.157359.917532.4805160.0092
185.61713.639-2.09787.44382.02828.42620.34410.4005-0.15450.62610.01830.21910.2742-0.2295-0.13540.2010.0597-0.01380.3927-0.12210.388847.163819.2653181.5302
190.21850.44870.70860.92091.45712.310.04521.1873-0.5611-1.49750.55550.89370.67840.2395-0.51380.6168-0.2253-0.19161.0089-0.11110.600247.224313.7039158.9958
204.93831.1514.03542.62052.08513.84330.12210.4081-0.6109-0.1360.2983-0.29620.57190.55730.20990.429-0.0858-0.01440.3992-0.0280.468348.672513.5886173.7867
218.57033.638.3743.03814.06858.36370.0523-0.7665-0.5240.2079-0.23460.39831.0376-1.2633-0.60360.4128-0.14840.03760.4635-0.07130.603843.605310.1429182.5668
224.5556-3.53113.72023.5367-2.92173.04051.1495-0.9523-1.3788-0.4455-0.02471.67171.3239-1.3418-0.86640.5442-0.2354-0.17970.67040.02660.584634.68286.2316172.6422
236.31840.78986.53132.70371.45936.85860.3717-0.0185-0.6687-0.4616-0.2012-0.63380.0595-0.0775-0.35970.40560.00780.11310.35110.02760.359754.743411.5249182.7432
248.4894-0.49435.7343.2791-1.5458.7280.03230.7675-0.9675-0.59660.26960.24871.3909-0.0734-0.36460.4118-0.0990.01240.2669-0.07680.469749.29239.7445173.9818
254.9754.9442-3.066.7132-1.94522.6549-0.40731.4932-0.0461-0.35480.31190.3094-0.6976-0.1492-0.040.7854-0.3849-0.22570.9210.05260.787235.476312.783162.0606
264.702-1.01713.70121.406-0.63282.94530.0978-0.6302-0.42090.27480.40310.49640.7298-1.8404-0.41530.4837-0.22330.08610.6319-0.07760.560238.748114.4313183.193
274.0157-0.3371-4.9766.0261-0.73817.916-0.4511.66181.057-0.779-0.4632-0.5106-0.5209-0.15010.47450.35550.0216-0.11170.96180.42170.78239.664419.6381170.3527
282.4590.27870.06932.3148-0.81464.83470.18140.4004-0.324-0.48530.01030.4150.8786-0.0706-0.07790.51470.0851-0.13340.6128-0.18440.482466.520510.1771124.0642
294.6193-0.44260.12472.7271.17582.65290.13420.36380.8255-0.4974-0.0714-0.2752-0.2910.0018-0.06830.30450.0480.07120.39570.09650.434968.299133.8332149.8317
302.9347-0.9634-2.2728.62827.30667.8161-0.29160.4043-0.145-0.5638-0.74310.3432-0.69560.21921.02610.40960.04150.01780.67010.04940.271580.218827.9245123.532
317.06513.3374-1.71439.12811.85591.3579-0.07390.16140.234-0.34470.59190.20730.2106-0.3468-0.44910.4220.09860.00880.7010.02570.246681.262126.4959142.2149
325.29372.23180.11392.14890.47830.15610.6033-0.7205-0.14311.52640.18170.2037-0.3917-0.1498-0.2370.84740.17170.05061.16730.10870.335382.710921.1984157.1845
333.4625-0.72730.26061.07870.76890.726-0.20530.02590.1610.0612-0.0638-0.25940.47610.58330.24240.2640.10320.00030.8507-0.14520.357381.614621.0828142.3174
341.44010.378-1.29673.0501-1.06941.35090.3550.9826-0.4237-0.227-0.3949-0.5180.34491.5803-0.07090.34030.14810.01960.8517-0.03040.450987.856620.3121133.5487
354.96732.88045.65482.49623.04486.52180.708-0.166-0.81480.015-0.366-0.86980.55481.1991-0.34970.49970.0829-0.05371.1216-0.01330.443492.661315.2505142.7924
362.4817-0.6281.94752.9645-0.56476.1210.11640.0812-0.3920.46350.17380.5177-0.18610.0059-0.260.33810.1297-0.02130.6654-0.01610.31572.601619.3177129.54
374.0029-0.49973.05731.62631.43195.9760.1194-0.2619-0.39690.19460.1018-0.0110.57620.474-0.45860.33670.1786-0.00510.738-0.03990.352882.658617.2286141.9836
384.356-0.29553.75831.47950.54937.504-0.2721-0.60990.18320.38810.3933-0.3318-1.20480.5953-0.1430.5419-0.003-0.18561.1038-0.09170.484594.017425.1953154.862
394.2293-0.67775.1371.90120.01936.63820.04230.13020.4783-0.2099-0.2506-0.5574-0.24161.85660.09560.3119-0.00860.01941.13160.01840.377390.522326.3076133.4071
405.7339-0.5323-0.21237.1983-6.71476.3568-0.20390.5384-0.07140.77550.3529-0.6253-1.33490.9152-0.17050.4245-0.1871-0.06390.6576-0.0580.376688.134129.9636146.3582
415.9075-1.98013.46913.287-2.5646.393-0.13810.23890.57850.154-0.259-0.2776-0.83530.58380.37620.4187-0.02640.0280.4364-0.06690.302734.9874-9.9019206.0732
423.3791-3.70973.38139.2564-5.7466.7571-0.3797-0.67910.47180.56810.5679-0.2479-1.143-0.4076-0.15250.5001-0.05120.06010.5425-0.18160.432133.7036-7.2349217.6626
432.4011-1.03340.32312.4805-1.24265.1023-0.0571-0.31240.05280.22950.12070.3518-0.3626-0.508-0.07130.30790.00040.05540.4874-0.10660.371222.988-16.6735216.1981
443.82240.2930.28823.18051.95092.77010.1562-0.228-0.61330.29950.0555-0.21590.2236-0.0635-0.17920.3091-0.0007-0.05070.3520.05890.297230.0615-35.3789186.4625
452.1290.3749-2.46161.40760.26363.12630.10480.27190.1498-0.36210.09860.0440.21350.556-0.14390.35890.0491-0.01870.6646-0.04530.265243.2675-25.5777194.351
467.61222.2322-6.77331.7837-2.31296.2831-0.1132-0.98880.05150.072-0.277-0.2078-0.18841.80040.10970.35530.0030.00550.7021-0.03170.292449.5206-23.3592203.505
476.7044-1.2477-5.31551.47960.86064.24220.1311-0.29880.19810.1852-0.2427-0.0405-0.01680.8679-1.81720.1677-0.03050.22111.2505-0.26610.275254.612-17.8098194.8331
484.31270.5354-5.49561.3698-1.14089.4296-0.04010.0080.1231-0.1738-0.0793-0.0378-0.05630.38560.11080.2938-0.0316-0.0130.4689-0.07450.301739.815-20.5889200.8677
493.82621.8243-4.32222.5312-1.744.9572-0.083-0.1271-0.3386-0.4851-0.2268-0.58650.79921.37240.43460.44350.12550.05620.9575-0.030.381853.399-28.3759196.2487
507.5892-4.135.12129.2131-5.35994.40890.3887-0.2643-0.4551-1.00520.14160.2890.8830.5973-0.40450.43760.07530.05660.6152-0.06090.312149.3799-31.554189.9796
516.95182.673-4.93944.2461-1.45073.5741-0.40571.3407-0.2544-0.8830.3154-1.4764-0.35490.102-0.01950.7586-0.09270.03420.39890.14850.649232.4558-8.9933138.9012
528.46543.10221.11215.6152-4.67815.93570.0764-1.7215-0.51030.2716-0.5409-0.904-1.40810.05980.26520.68310.1799-0.190.5841-0.0690.670770.8135.7823197.0713
538.0211-3.3129-0.56874.66444.5235.62711.26940.7157-1.1607-0.84-0.75521.75940.3829-0.8446-0.04740.72760.0344-0.11480.3913-0.20860.768765.2676.4371117.7849
543.76131.42081.0062.63942.1943.80620.3854-0.93811.2991-0.4095-0.4644-0.010.08640.0987-0.1030.61250.14860.05640.4144-0.35410.642727.3852-8.3949219.3517
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 84 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 85 THROUGH 174 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 175 THROUGH 276 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 0 THROUGH 11 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 12 THROUGH 19 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 20 THROUGH 30 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 31 THROUGH 41 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 42 THROUGH 51 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 52 THROUGH 71 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 72 THROUGH 77 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 78 THROUGH 90 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 91 THROUGH 99 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 2 THROUGH 103 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 104 THROUGH 174 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 175 THROUGH 197 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 198 THROUGH 262 )
17X-RAY DIFFRACTION17CHAIN 'E' AND (RESID 263 THROUGH 276 )
18X-RAY DIFFRACTION18CHAIN 'F' AND (RESID 1 THROUGH 11 )
19X-RAY DIFFRACTION19CHAIN 'F' AND (RESID 12 THROUGH 19 )
20X-RAY DIFFRACTION20CHAIN 'F' AND (RESID 20 THROUGH 30 )
21X-RAY DIFFRACTION21CHAIN 'F' AND (RESID 31 THROUGH 41 )
22X-RAY DIFFRACTION22CHAIN 'F' AND (RESID 42 THROUGH 46 )
23X-RAY DIFFRACTION23CHAIN 'F' AND (RESID 47 THROUGH 61 )
24X-RAY DIFFRACTION24CHAIN 'F' AND (RESID 62 THROUGH 71 )
25X-RAY DIFFRACTION25CHAIN 'F' AND (RESID 72 THROUGH 77 )
26X-RAY DIFFRACTION26CHAIN 'F' AND (RESID 78 THROUGH 90 )
27X-RAY DIFFRACTION27CHAIN 'F' AND (RESID 91 THROUGH 99 )
28X-RAY DIFFRACTION28CHAIN 'G' AND (RESID 2 THROUGH 174 )
29X-RAY DIFFRACTION29CHAIN 'G' AND (RESID 175 THROUGH 275 )
30X-RAY DIFFRACTION30CHAIN 'H' AND (RESID 0 THROUGH 5 )
31X-RAY DIFFRACTION31CHAIN 'H' AND (RESID 6 THROUGH 11 )
32X-RAY DIFFRACTION32CHAIN 'H' AND (RESID 12 THROUGH 19 )
33X-RAY DIFFRACTION33CHAIN 'H' AND (RESID 20 THROUGH 30 )
34X-RAY DIFFRACTION34CHAIN 'H' AND (RESID 31 THROUGH 41 )
35X-RAY DIFFRACTION35CHAIN 'H' AND (RESID 42 THROUGH 51 )
36X-RAY DIFFRACTION36CHAIN 'H' AND (RESID 52 THROUGH 61 )
37X-RAY DIFFRACTION37CHAIN 'H' AND (RESID 62 THROUGH 71 )
38X-RAY DIFFRACTION38CHAIN 'H' AND (RESID 72 THROUGH 77 )
39X-RAY DIFFRACTION39CHAIN 'H' AND (RESID 78 THROUGH 90 )
40X-RAY DIFFRACTION40CHAIN 'H' AND (RESID 91 THROUGH 98 )
41X-RAY DIFFRACTION41CHAIN 'I' AND (RESID 1 THROUGH 56 )
42X-RAY DIFFRACTION42CHAIN 'I' AND (RESID 57 THROUGH 84 )
43X-RAY DIFFRACTION43CHAIN 'I' AND (RESID 85 THROUGH 174 )
44X-RAY DIFFRACTION44CHAIN 'I' AND (RESID 175 THROUGH 275 )
45X-RAY DIFFRACTION45CHAIN 'J' AND (RESID 0 THROUGH 30 )
46X-RAY DIFFRACTION46CHAIN 'J' AND (RESID 31 THROUGH 41 )
47X-RAY DIFFRACTION47CHAIN 'J' AND (RESID 42 THROUGH 51 )
48X-RAY DIFFRACTION48CHAIN 'J' AND (RESID 52 THROUGH 71 )
49X-RAY DIFFRACTION49CHAIN 'J' AND (RESID 72 THROUGH 90 )
50X-RAY DIFFRACTION50CHAIN 'J' AND (RESID 91 THROUGH 98 )
51X-RAY DIFFRACTION51CHAIN 'K' AND (RESID 2 THROUGH 8 )
52X-RAY DIFFRACTION52CHAIN 'L' AND (RESID 2 THROUGH 8 )
53X-RAY DIFFRACTION53CHAIN 'M' AND (RESID 2 THROUGH 8 )
54X-RAY DIFFRACTION54CHAIN 'N' AND (RESID 1 THROUGH 8 )

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万見について

-
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