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- PDB-8euq: Crystal structure of HLA-DRA*01:01/HLA-DRB1*04:01 in complex with... -

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基本情報

登録情報
データベース: PDB / ID: 8euq
タイトルCrystal structure of HLA-DRA*01:01/HLA-DRB1*04:01 in complex with c44H10 Fab
要素
  • HLA class II histocompatibility antigen, DR alpha chain
  • Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain
  • c44H10 Fab heavy chain
  • c44H10 Fab light chain
キーワードIMMUNE SYSTEM / MHC class II / HLA-DR / Antibody
機能・相同性
機能・相同性情報


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / 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 / positive regulation of T cell activation / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / cognition / endocytic vesicle membrane / Interferon gamma signaling / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / endosome membrane / lysosome / host cell surface receptor binding / immune response / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / extracellular exosome / membrane / plasma membrane
類似検索 - 分子機能
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 / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...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 / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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 / Mainly Beta
類似検索 - ドメイン・相同性
HLA class II histocompatibility antigen DR beta chain / HLA class II histocompatibility antigen, DR alpha chain / Hemagglutinin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Influenza A virus (A型インフルエンザウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.09 Å
データ登録者Kassardjian, A. / Julien, J.-P.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR)PJT-148811 カナダ
引用ジャーナル: Cell Rep / 年: 2023
タイトル: Modular adjuvant-free pan-HLA-DR-immunotargeting subunit vaccine against SARS-CoV-2 elicits broad sarbecovirus-neutralizing antibody responses.
著者: Kassardjian, A. / Sun, E. / Sookhoo, J. / Muthuraman, K. / Boligan, K.F. / Kucharska, I. / Rujas, E. / Jetha, A. / Branch, D.R. / Babiuk, S. / Barber, B. / Julien, J.P.
履歴
登録2022年10月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年4月19日Provider: repository / タイプ: Initial release
改定 1.12023年4月26日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
改定 1.22023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.32024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: HLA class II histocompatibility antigen, DR alpha chain
D: c44H10 Fab light chain
F: HLA class II histocompatibility antigen, DR alpha chain
H: c44H10 Fab light chain
B: Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain
C: c44H10 Fab heavy chain
G: Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain
I: c44H10 Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)192,81228
ポリマ－189,9848
非ポリマー2,82820
水00
1
A: HLA class II histocompatibility antigen, DR alpha chain
D: c44H10 Fab light chain
B: Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain
C: c44H10 Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,59816
ポリマ－94,9924
非ポリマー1,60612
水0
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
H: c44H10 Fab light chain
G: Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain
I: c44H10 Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,21412
ポリマ－94,9924
非ポリマー1,2228
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)169.150, 178.720, 182.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "C" and (resid 2 through 63 or resid 65...
d_2ens_1(chain "I" and (resid 2 through 16 or (resid 17...
d_1ens_2(chain "D" and (resid 1 through 23 or resid 25...
d_2ens_2(chain "H" and (resid 1 through 23 or resid 25...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALLEULEUCF2 - 632 - 63
d_12ens_1SERSERPHEPHECF65 - 7465 - 74
d_13ens_1SERSERSERSERCF76 - 12776 - 134
d_14ens_1THRTHRSERSERCF131 - 215138 - 222
d_15ens_1SO4SO4SO4SO4GW301
d_21ens_1VALVALLEULEUIH2 - 632 - 63
d_22ens_1SERSERPHEPHEIH65 - 7465 - 74
d_23ens_1SERSERSERSERIH76 - 12776 - 134
d_24ens_1THRTHRSERSERIH131 - 215138 - 222
d_25ens_1SO4SO4SO4SO4IBA301
d_11ens_2ASPASPCYSCYSDB1 - 231 - 23
d_12ens_2ALAALAILEILEDB25 - 4425 - 44
d_13ens_2ARGARGPROPRODB46 - 5946 - 59
d_14ens_2ARGARGASPASPDB61 - 12261 - 122
d_15ens_2GLNGLNSERSERDB124 - 159124 - 159
d_16ens_2GLUGLUHISHISDB161 - 189161 - 189
d_17ens_2VALVALGLYGLYDB191 - 212191 - 212
d_21ens_2ASPASPCYSCYSHD1 - 231 - 23
d_22ens_2ALAALAILEILEHD25 - 4425 - 44
d_23ens_2ARGARGPROPROHD46 - 5946 - 59
d_24ens_2ARGARGASPASPHD61 - 12261 - 122
d_25ens_2GLNGLNSERSERHD124 - 159124 - 159
d_26ens_2GLUGLUHISHISHD161 - 189161 - 189
d_27ens_2VALVALGLYGLYHD191 - 212191 - 212

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.545553340327, 0.0305381526401, -0.837519536543), (-0.00456377381415, -0.999429336087, -0.0334690026281), (-0.838063675878, -0.0144368764514, 0.545381381945)-74.0752006144, -62.7236511634, -41.6909236842
2given(-0.551661534585, 0.0355281068192, -0.8333110493), (0.0117610645393, -0.998661688475, -0.0503637700374), (-0.83398514892, -0.0375843796985, 0.550505391239)-74.0733518276, -62.7991437207, -41.7204326812

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要素

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タンパク質 , 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: 21882.576 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-DRA, HLA-DRA1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01903
#3: タンパク質 Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain / MHC class II antigen


分子量: 25935.773 Da / 分子数: 2
Mutation: A3G, C4A in the hemagglutinin peptide that was used
由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (A型インフルエンザウイルス), (組換発現) Homo sapiens (ヒト)
遺伝子: HA, HLA-DRB1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P04664, UniProt: A0A1V1IGJ9

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抗体 , 2種, 4分子 DHCI

#2: 抗体 c44H10 Fab light chain


分子量: 23505.068 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 c44H10 Fab heavy chain


分子量: 23668.643 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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糖 , 2種, 4分子

#5: 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-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: 2 / 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

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非ポリマー , 1種, 16分子

#6: 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: 合成 / 式: SO4

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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: 3.62 Å3/Da / 溶媒含有率: 66.03 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 1.7 M ammonium sulfate, 15% glycerol, 0.085 M HEPES, 1.7% PEG400, with crystal seeds previously grown in 2 M ammonium sulfate, 0.1 M bis-tris pH 5.5

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年3月24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: 1.0332 Å / 相対比: 1
反射解像度: 3.09→40 Å / Num. obs: 50733 / % possible obs: 99.9 % / 冗長度: 16.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.041 / Net I/σ(I): 14.8
反射 シェル解像度: 3.09→3.14 Å / 冗長度: 16.1 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2369 / CC1/2: 0.709 / Rpim(I) all: 0.226 / % possible all: 99.9

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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
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1DLH, 1AJ7

1dlh

1aj7


解像度: 3.09→39.51 Å / SU ML: 0.4394 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 28.6677
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2438 1995 3.94 %
Rwork0.2001 48696 -
obs0.2018 50691 99.91 %
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: 105.25 Å2
精密化ステップサイクル: LAST / 解像度: 3.09→39.51 Å
タンパク質核酸リガンド溶媒全体
原子数12889 0 164 0 13053
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003613357
X-RAY DIFFRACTIONf_angle_d0.718518169
X-RAY DIFFRACTIONf_chiral_restr0.04512012
X-RAY DIFFRACTIONf_plane_restr0.00492319
X-RAY DIFFRACTIONf_dihedral_angle_d12.27914785
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2IX-RAY DIFFRACTIONTorsion NCS0.659133962401
ens_2d_2HX-RAY DIFFRACTIONTorsion NCS0.713052018301
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.170.4111420.37563412X-RAY DIFFRACTION99.83
3.17-3.250.34011550.31583473X-RAY DIFFRACTION99.97
3.25-3.350.34511450.29353404X-RAY DIFFRACTION99.89
3.35-3.460.32161200.26073478X-RAY DIFFRACTION99.92
3.46-3.580.27851400.23343417X-RAY DIFFRACTION99.83
3.58-3.720.29761400.22823478X-RAY DIFFRACTION99.92
3.72-3.890.25171360.22033457X-RAY DIFFRACTION99.86
3.89-4.10.23771380.21863452X-RAY DIFFRACTION99.94
4.1-4.350.25591470.18073488X-RAY DIFFRACTION99.95
4.35-4.690.17771450.15763455X-RAY DIFFRACTION99.94
4.69-5.160.20461300.15663494X-RAY DIFFRACTION99.92
5.16-5.90.22771430.17663525X-RAY DIFFRACTION100
5.91-7.430.22521480.20293517X-RAY DIFFRACTION100
7.43-39.510.22821660.1693646X-RAY DIFFRACTION99.71
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)
10.5164071955820.7858313352870.06900567997481.382988803280.06288119015241.01081274799-0.02096275732170.185200372337-0.0552273884722-0.1708584969-0.0466392131396-0.1101120567110.227259414511-0.199169904765-2.24489445607E-50.583376511090.008025704168580.05941827357050.8665071511970.1447573873550.649759576695-42.287-44.053-89.248
20.532965589105-0.06521648448310.1597547480070.119432694494-0.4808010652470.106912505032-0.014119180780.2492829348680.0166912652637-0.003972912787560.03666591256720.00471573497080.166881087619-0.3060194170652.89570033542E-50.629242366471-0.09058831150980.01759329395770.7671989928040.1107843906340.641385114334-39.855-31.121-94.167
30.135200588766-0.309112917578-0.2728849913260.4423078813660.2511962824340.0512964963962-0.3097561997090.3475129941730.284388459909-0.5002011039830.2412692923630.4385778868070.0216974664597-0.917127009251-0.000296713576180.734394873248-0.059520614757-0.03082454464920.8718837407560.1427354081420.839215827137-43.249-21.582-96.544
40.0630580955567-0.1837759211840.01052227251410.4337340937870.1430747768530.218926681151-0.2408117608750.2284689074490.2430940338490.09379079201070.810945219835-0.52854108892-0.8611922804140.997667118030.009119848905470.790958708292-0.01595596694110.05132001703221.127175648550.07196972550941.0150210533-33.257-17.108-93.833
50.157183626355-0.428251018012-0.253944838890.1638168641460.3605912013280.3831292960810.755092911929-0.041355444491-0.2238152086840.472134122872-0.5370849699740.545110346280.352239150508-0.6188142012330.0003564620681591.25677667708-0.253212816741-0.06041906729981.18739973775-0.004242876542340.990017647254-56.985-31.047-57.646
60.3768427221170.385575161546-0.4797959453441.16140570983-0.06942629372930.8201504291890.334187606009-0.570517483494-0.1078069405130.401901387047-0.284183845331-0.03442388044230.27836610344-0.5460881581450.0001451205914020.753865252179-0.160515920449-0.01311481763880.9301786382980.000950679550080.63286693464-50.965-30.378-64.93
70.110408244422-0.1338595401550.5902346843780.684390787282-0.4249349823170.5154236139520.178054695381-0.3184483358940.09555741994870.289028067612-0.05392080467690.1287027405150.329027705631-0.76226367252-1.70946625037E-50.945678432449-0.05484489816710.07432006405511.0460747143-0.06228978701340.826765507058-46.963-18.317-35.095
84.622715502940.468315939352.658699393942.981158688080.4618227092113.013816861450.0885534790562-0.7488610195190.5918145406380.990927864421-0.206063706044-0.04428952981590.0719346352753-0.00457825465581-1.243249543591.16115110434-0.1226014853690.264480351.32441786609-0.02713367653340.760224108374-45.718-23.206-21.547
90.134266887507-0.3044998583-0.1015135667660.3112276518860.2504874356110.1029448020530.03766350733850.17570958598-0.0360683980132-0.187873178-0.0413213377955-0.269448908948-0.1506108270630.837571837444-3.18957913935E-50.6414323254930.0435299101960.02763236885180.782563644898-0.01672302734090.71011188604821.253-12.937-56.008
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:101 )A3 - 101
2X-RAY DIFFRACTION2( CHAIN A AND RESID 102:154 )A102 - 154
3X-RAY DIFFRACTION3( CHAIN A AND RESID 155:173 )A155 - 173
4X-RAY DIFFRACTION4( CHAIN A AND RESID 174:187 )A174 - 187
5X-RAY DIFFRACTION5( CHAIN D AND RESID 1:20 )D1 - 20
6X-RAY DIFFRACTION6( CHAIN D AND RESID 21:90 )D21 - 90
7X-RAY DIFFRACTION7( CHAIN D AND RESID 91:198 )D91 - 198
8X-RAY DIFFRACTION8( CHAIN D AND RESID 199:212 )D199 - 212
9X-RAY DIFFRACTION9( CHAIN F AND RESID 3:45 )F3 - 45
10X-RAY DIFFRACTION10( CHAIN F AND RESID 46:55 )F46 - 55
11X-RAY DIFFRACTION11( CHAIN F AND RESID 56:87 )F56 - 87
12X-RAY DIFFRACTION12( CHAIN F AND RESID 88:101 )F88 - 101
13X-RAY DIFFRACTION13( CHAIN F AND RESID 102:128 )F102 - 128
14X-RAY DIFFRACTION14( CHAIN F AND RESID 129:154 )F129 - 154
15X-RAY DIFFRACTION15( CHAIN F AND RESID 155:166 )F155 - 166
16X-RAY DIFFRACTION16( CHAIN F AND RESID 167:187 )F167 - 187
17X-RAY DIFFRACTION17( CHAIN H AND RESID 1:75 )H1 - 75
18X-RAY DIFFRACTION18( CHAIN H AND RESID 76:90 )H76 - 90
19X-RAY DIFFRACTION19( CHAIN H AND RESID 91:110 )H91 - 110
20X-RAY DIFFRACTION20( CHAIN H AND RESID 111:213 )H111 - 213
21X-RAY DIFFRACTION21( CHAIN B AND RESID 4:23 )B4 - 23
22X-RAY DIFFRACTION22( CHAIN B AND RESID 32:80 )B32 - 80
23X-RAY DIFFRACTION23( CHAIN B AND RESID 81:106 )B81 - 106
24X-RAY DIFFRACTION24( CHAIN B AND RESID 107:126 )B107 - 126
25X-RAY DIFFRACTION25( CHAIN B AND RESID 127:162 )B127 - 162
26X-RAY DIFFRACTION26( CHAIN B AND RESID 163:198 )B163 - 198
27X-RAY DIFFRACTION27( CHAIN B AND RESID 199:219 )B199 - 219
28X-RAY DIFFRACTION28( CHAIN C AND RESID 1:106 )C1 - 106
29X-RAY DIFFRACTION29( CHAIN C AND RESID 107:130 )C107 - 130
30X-RAY DIFFRACTION30( CHAIN C AND RESID 131:145 )C131 - 145
31X-RAY DIFFRACTION31( CHAIN C AND RESID 146:203 )C146 - 203
32X-RAY DIFFRACTION32( CHAIN C AND RESID 204:215 )C204 - 215
33X-RAY DIFFRACTION33( CHAIN G AND RESID 4:61 )G4 - 61
34X-RAY DIFFRACTION34( CHAIN G AND RESID 62:80 )G62 - 80
35X-RAY DIFFRACTION35( CHAIN G AND RESID 81:106 )G81 - 106
36X-RAY DIFFRACTION36( CHAIN G AND RESID 107:126 )G107 - 126
37X-RAY DIFFRACTION37( CHAIN G AND RESID 127:151 )G127 - 151
38X-RAY DIFFRACTION38( CHAIN G AND RESID 152:219 )G152 - 219
39X-RAY DIFFRACTION39( CHAIN I AND RESID 1:17 )I1 - 17
40X-RAY DIFFRACTION40( CHAIN I AND RESID 18:56 )I18 - 56
41X-RAY DIFFRACTION41( CHAIN I AND RESID 57:87 )I57 - 87
42X-RAY DIFFRACTION42( CHAIN I AND RESID 88:106 )I88 - 106
43X-RAY DIFFRACTION43( CHAIN I AND RESID 107:134 )I107 - 134
44X-RAY DIFFRACTION44( CHAIN I AND RESID 135:145 )I135 - 145
45X-RAY DIFFRACTION45( CHAIN I AND RESID 146:165 )I146 - 165
46X-RAY DIFFRACTION46( CHAIN I AND RESID 166:189 )I166 - 189
47X-RAY DIFFRACTION47( CHAIN I AND RESID 190:215 )I190 - 215

+
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

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