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- PDB-5knm: 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: 5knm
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
  • Leukocyte immunoglobulin-like receptor subfamily B member 1
  • Peptide ILE-LEU-ARG-TRP-GLU-GLN
  • 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 / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / positive regulation of natural killer cell degranulation / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation ...negative regulation of natural killer cell cytokine production / negative regulation of natural killer cell degranulation / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / positive regulation of natural killer cell degranulation / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / TAP2 binding / Fc receptor mediated inhibitory signaling pathway / 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 / MHC class Ib protein binding / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / immune response-regulating signaling pathway / negative regulation of CD8-positive, alpha-beta T cell activation / MHC class I receptor activity / negative regulation of transforming growth factor beta production / interleukin-10-mediated signaling pathway / negative regulation of cytokine production involved in immune response / negative regulation of alpha-beta T cell activation / negative regulation of serotonin secretion / dendritic cell differentiation / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of interleukin-12 production / negative regulation of dendritic cell apoptotic process / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of macrophage cytokine production / negative regulation of interleukin-10 production / beta-2-microglobulin binding / MHC class I protein binding / negative regulation of calcium ion transport / negative regulation of type II interferon production / T cell proliferation involved in immune response / negative regulation of cell cycle / negative regulation of tumor necrosis factor production / 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 / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / 14-3-3 protein binding / SH2 domain binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / response to virus / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / receptor internalization / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling
類似検索 - 分子機能
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 subtype / Immunoglobulin / 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 / Leukocyte immunoglobulin-like receptor subfamily B member 1
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: 3.3 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)R01 AI073922 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6月28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 / カテゴリ: pdbx_audit_support / 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10月16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
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
N: Peptide ILE-LEU-ARG-TRP-GLU-GLN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)83,3635
ポリマ－83,1414
非ポリマー2211
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)231.820, 231.820, 73.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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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: 1 / 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 / Cell (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: 1 / 断片: UNP rrsidues 21-119 / 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 / 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 Leukocyte immunoglobulin-like receptor subfamily B member 1 / Leukocyte immunoglobulin-like receptor 1 / CD85 antigen-like family member J / Immunoglobulin-like ...Leukocyte immunoglobulin-like receptor 1 / CD85 antigen-like family member J / Immunoglobulin-like transcript 2 / ILT-2 / Monocyte/macrophage immunoglobulin-like receptor 7 / MIR-7


分子量: 29467.047 Da / 分子数: 1 / 断片: UNP residues 24-221 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LILRB1, ILT2, LIR1, MIR7 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q8NHL6
#4: タンパク質・ペプチド Peptide ILE-LEU-ARG-TRP-GLU-GLN


分子量: 844.977 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Trichoplusia ni (イラクサキンウワバ)
発現宿主: Trichoplusia ni (イラクサキンウワバ)
#5: 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
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.42 Å3/Da / 溶媒含有率: 67.59 % / 解説: hexagonal plates
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 27% PEG 550 MME .1 M Tris-HCl 300 mM NaCl

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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-D / 波長: 1.03318 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2014年11月20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: 3.304→49.406 Å / Num. obs: 17859 / % possible obs: 99 % / 冗長度: 9.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1413 / Net I/σ(I): 1.57
反射 シェル解像度: 3.304→3.422 Å / 冗長度: 9.8 % / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 1.57 / CC1/2: 0.801 / % possible all: 99

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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データ削減
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: 1PSA

1psa


解像度: 3.3→49.41 Å / SU ML: 0.56 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 39.49 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.326 915 5.12 %
Rwork0.303 --
obs0.305 17858 99.7 %
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: 3.3→49.41 Å
タンパク質核酸リガンド溶媒全体
原子数4514 0 14 0 4528
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0034653
X-RAY DIFFRACTIONf_angle_d0.7746337
X-RAY DIFFRACTIONf_dihedral_angle_d8.0253753
X-RAY DIFFRACTIONf_chiral_restr0.044664
X-RAY DIFFRACTIONf_plane_restr0.006836
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3036-3.47780.37171230.42982349X-RAY DIFFRACTION99
3.4778-3.69560.40681250.40132362X-RAY DIFFRACTION100
3.6956-3.98080.39161290.38352377X-RAY DIFFRACTION100
3.9808-4.38120.33981470.332380X-RAY DIFFRACTION100
4.3812-5.01460.32751520.28582384X-RAY DIFFRACTION100
5.0146-6.31580.33371090.30052472X-RAY DIFFRACTION100
6.3158-49.41190.28521300.25472619X-RAY DIFFRACTION100
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59792.45851.95676.24112.76872.7260.6157-1.17853.0290.3759-0.7581.7697-0.727-0.76790.25111.19370.07510.07871.4993-0.62524.0996-74.1984136.9749121.3148
22.6639-0.3047-3.15924.5589-3.33736.7692-0.5007-2.63461.31731.7834-1.69330.9970.8995-1.16930.78811.2103-0.3412-0.00982.1009-1.06122.2853-64.846134.0467125.1442
35.93436.5216-3.82437.619-2.86596.5593-1.0408-2.07250.0470.35510.1807-1.395-0.39840.82181.18121.0693-0.0217-0.02281.6601-0.88043.1647-67.8627132.591120.222
42.56173.27850.40136.14232.55662.2088-1.60090.39021.6162-3.34020.72741.752-1.17250.0813-0.20682.2580.0467-0.35430.4760.81235.9471-62.6398148.1568100.8539
50.3295-0.7368-0.45114.24621.94480.97930.99451.6442.4761-1.4021-0.99762.3714-0.93850.2479-0.16231.8756-0.3602-0.36681.4841.05323.4953-71.366146.492790.9939
63.49330.3843-0.30656.1463.71036.50440.1476-0.29241.5016-2.2087-0.37481.1929-2.01360.88190.36391.9997-0.6836-1.2061.76530.56693.0136-69.3275139.767596.084
75.6079-0.18071.07919.45322.32725.5434-0.4183-1.57333.06960.95930.5451-1.48670.435-1.5257-0.15711.63790.1607-0.54812.05160.01343.4386-77.4008148.425696.4088
86.6357-5.70131.58114.7504-1.22035.6775-1.40280.13660.25720.26151.03032.0195-1.35490.5838-0.0321.9374-0.2361-0.3341.54620.4373.9422-65.0513145.7224101.8526
96.9135-6.80063.48438.9954-1.50042.7994-1.16610.32223.0736-0.7931.0855-1.0122-0.61350.00360.17882.0651-0.73560.35511.78280.45222.5657-27.3322141.681692.9197
100.07770.24930.44690.85611.61862.9163-0.61670.40830.3635-0.3390.09230.0009-1.99530.0676-0.99452.6125-1.26520.08272.24191.19954.1007-27.9779148.147282.3581
112.3414-1.8080.94293.00140.31322.67480.28942.04512.069-1.307-0.2348-1.2736-0.5335-0.3064-0.14932.6279-0.78180.13962.1330.82292.7252-37.9086137.788282.3442
128.81511.54595.62162.0342.31864.51760.16891.3526-0.4393-2.30462.64891.98280.52792.008-2.47513.7876-1.8754-0.63634.24721.23383.0666-39.8656138.203969.6337
139.03552.0399-2.57354.9354-0.54835.3550.74751.7211.3541-2.02260.1056-1.2841-1.3580.3828-0.66891.81890.11030.47921.23280.06361.8345-31.1896125.711694.2896
147.84051.381-4.14525.17211.68044.6879-0.57791.78880.9757-1.1736-0.17341.5664-0.6653-1.53770.4951.1719-0.2463-0.17421.08610.20781.5124-48.8618119.0403105.9748
153.2817-2.1511-0.5442.02170.53317.5217-0.54090.81741.4866-1.10460.66910.3767-0.2238-0.6604-0.13081.0348-0.1546-0.10250.7735-0.1822.0579-47.8564121.4954108.3889
169.3158-3.8306-3.66177.25435.40625.2106-0.6112-1.3226-1.26410.4290.13752.24491.14990.66940.13740.8727-0.06-0.01260.75250.34221.2899-41.8953112.5073109.2807
176.9263-2.23320.85965.91893.92483.5610.55261.44691.7919-2.5754-0.09710.7689-1.8085-0.567-0.51211.6365-1.15910.03261.3337-0.6484.1841-49.1473142.899296.3834
188.9559-0.3124-7.46588.4021-1.83496.86850.3448-1.71943.55690.38570.41411.47610.16272.2481-0.69571.234-0.2633-0.28391.3826-0.39351.8321-35.9771134.0754115.2108
198.2703-0.8216-0.13553.1014-2.79383.62840.285-0.15954.9498-0.65571.266-0.3678-2.2341-0.6612-1.5361.3959-0.1792-0.06911.17260.20113.3533-43.2309146.901299.9062
207.04040.2367-0.02314.8736-6.31168.3390.6838-0.74882.55281.8891-0.5084-1.3837-3.9292.3479-0.15981.7736-0.44060.00171.7721-1.03262.9992-39.2831148.3585118.5458
215.4839-2.26844.63983.82811.87429.284-1.1286-1.21092.7586-0.40840.6592-1.83280.3294-0.33440.84831.7128-0.6121-0.11051.12740.05133.3656-32.7658143.9876103.6779
220.24730.0256-0.13331.04750.19830.58270.07310.6056-0.3639-0.9357-0.14240.35830.0238-0.4586-0.25372.2593-2.0584-0.23141.10332.57032.4747-41.9187137.818691.9141
239.145-1.38752.8963.6374-0.29010.93440.2574-4.40120.48371.74820.51230.7627-1.0338-0.2270.06790.8134-1.1415-0.19121.0493-0.60762.5177-36.4851140.0991118.1041
249.6281-4.71043.18549.13-5.74593.9848-1.3392-0.30593.936-0.47951.69032.9338-1.6932-1.26250.24861.4407-0.1304-0.10671.04290.20463.9444-47.7932148.4359107.7661
251.33782.02-2.17668.1267-2.61113.6571.2538-0.17721.6710.3040.41240.8912-0.23472.4949-1.67261.2541-0.2029-0.03561.5868-0.51812.4484-45.7889136.5957116.8338
266.40262.8012.6634.92193.33162.3764-0.18860.5576-0.44181.1930.47512.32482.1991-1.89640.47853.8594-1.7155-0.19172.17491.46695.6672-28.1726142.239777.3012
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'D' AND (RESID 1 THROUGH 34 )
2X-RAY DIFFRACTION2CHAIN 'D' AND (RESID 35 THROUGH 57 )
3X-RAY DIFFRACTION3CHAIN 'D' AND (RESID 58 THROUGH 92 )
4X-RAY DIFFRACTION4CHAIN 'D' AND (RESID 93 THROUGH 106 )
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID 107 THROUGH 133 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 134 THROUGH 155 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 156 THROUGH 174 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 175 THROUGH 195 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 1 THROUGH 56 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 57 THROUGH 85 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 86 THROUGH 126 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 127 THROUGH 151 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 152 THROUGH 197 )
14X-RAY DIFFRACTION14CHAIN 'A' AND (RESID 198 THROUGH 227 )
15X-RAY DIFFRACTION15CHAIN 'A' AND (RESID 228 THROUGH 262 )
16X-RAY DIFFRACTION16CHAIN 'A' AND (RESID 263 THROUGH 276 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID -1 THROUGH 8 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 9 THROUGH 27 )
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 28 THROUGH 38 )
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 39 THROUGH 46 )
21X-RAY DIFFRACTION21CHAIN 'B' AND (RESID 47 THROUGH 56 )
22X-RAY DIFFRACTION22CHAIN 'B' AND (RESID 57 THROUGH 63 )
23X-RAY DIFFRACTION23CHAIN 'B' AND (RESID 64 THROUGH 77 )
24X-RAY DIFFRACTION24CHAIN 'B' AND (RESID 78 THROUGH 90 )
25X-RAY DIFFRACTION25CHAIN 'B' AND (RESID 91 THROUGH 99 )
26X-RAY DIFFRACTION26CHAIN 'N' AND (RESID 2 THROUGH 7 )

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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