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- PDB-7ssh: Single chain trimer HLA-A*02:01 (Y108A) with HPV.16 E7 peptide YM... -

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基本情報

登録情報
データベース: PDB / ID: 7ssh
タイトルSingle chain trimer HLA-A*02:01 (Y108A) with HPV.16 E7 peptide YMLDLQPETTDLYC
要素
  • Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
  • VHH
キーワードIMMUNE SYSTEM (免疫系) / HLA / VHH / HPV / SCT
機能・相同性
機能・相同性情報


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / : / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of actin filament polymerization / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation / viral process ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / : / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of actin filament polymerization / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation / viral process / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / recycling endosome membrane / phagocytic vesicle membrane / early endosome membrane / DNA-binding transcription factor binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 免疫応答 / DNA-binding transcription factor activity / protein domain specific binding / DNA-templated transcription / host cell nucleus / 細胞膜 / DNA binding / zinc ion binding / extracellular region
類似検索 - 分子機能
Papillomavirus E7 / E7 protein, Early protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Β2-ミクログロブリン / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein ...Papillomavirus E7 / E7 protein, Early protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Β2-ミクログロブリン / 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
類似検索 - ドメイン・相同性
MHC class I antigen / Protein E7 / Β2-ミクログロブリン
類似検索 - 構成要素
生物種Human papillomavirus type 16 (パピローマウイルス)
Pongo pygmaeus (オランウータン)
Homo sapiens (ヒト)
Lama glama (ラマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.73 Å
データ登録者Finton, K.A.K. / Rupert, P.B.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI) 米国
引用ジャーナル: Front Immunol / 年: 2023
タイトル: Effects of HLA single chain trimer design on peptide presentation and stability.
著者: Finton, K.A.K. / Rupert, P.B. / Friend, D.J. / Dinca, A. / Lovelace, E.S. / Buerger, M. / Rusnac, D.V. / Foote-McNabb, U. / Chour, W. / Heath, J.R. / Campbell, J.S. / Pierce, R.H. / Strong, R.K.
履歴
登録2021年11月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年11月23日Provider: repository / タイプ: Initial release
改定 1.12023年5月31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
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

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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: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
B: VHH
C: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
D: VHH
E: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
F: VHH
G: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
H: VHH
I: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
J: VHH
K: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
L: VHH
M: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
N: VHH
O: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
P: VHH
Q: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
R: VHH
S: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
T: VHH
U: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
V: VHH
W: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
X: VHH
Y: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
Z: VHH
a: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
b: VHH
c: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
d: VHH
e: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
f: VHH


分子量 (理論値)分子数
合計 (水以外)972,02832
ポリマ－972,02832
非ポリマー00
水5,080282
1
A: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
B: VHH


  • 登録者が定義した集合体
  • 根拠: surface plasmon resonance
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
D: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
F: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
H: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
J: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
L: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
7
M: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
N: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
8
O: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
P: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
9
Q: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
R: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
10
S: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
T: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
11
U: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
V: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
12
W: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
X: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
13
Y: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
Z: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
14
a: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
b: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
15
c: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
d: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
16
e: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
f: VHH


  • 登録者が定義した集合体
  • 60.8 kDa, 2 ポリマー
分子量 (理論値)分子数
合計 (水以外)60,7522
ポリマ－60,7522
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)117.681, 118.924, 274.991
Angle α, β, γ (deg.)77.598, 77.597, 89.947
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

#1: タンパク質
Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera


分子量: 48214.949 Da / 分子数: 16 / 変異: Y108A / 由来タイプ: 組換発現
由来: (組換発現) Human papillomavirus type 16 (パピローマウイルス), (組換発現) Pongo pygmaeus (オランウータン), (組換発現) Homo sapiens (ヒト)
遺伝子: E7, B2M, HLA-A / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: P03129, UniProt: P16213, UniProt: A0A678ZGP6
#2: 抗体
VHH


分子量: 12536.822 Da / 分子数: 16 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Homo (ヒト属)
#3: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 282 / 由来タイプ: 天然 / 式: H2O

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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: 3.77 Å3/Da / 溶媒含有率: 70.67 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 200 mM NaCl, 100 mM HEPES, pH 7.0, 1.45 M (NH4)2SO4

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データ収集

回折平均測定温度: 93 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 5.0.2 / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2021年8月13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 Å / 相対比: 1
反射解像度: 2.73→50 Å / Num. obs: 331873 / % possible obs: 89.7 % / 冗長度: 2.3 % / Biso Wilson estimate: 48.77 Å2 / CC1/2: 0.986 / Net I/σ(I): 15.9
反射 シェル解像度: 2.73→2.83 Å / Mean I/σ(I) obs: 2.33 / Num. unique obs: 28511 / CC1/2: 0.51

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解析

ソフトウェア名称: PHENIX / バージョン: 1.19.1_4122 / 分類: 精密化
精密化構造決定の手法: 分子置換
開始モデル: 7SQP

7sqp


解像度: 2.73→49.19 Å / SU ML: 0.4164 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 29.7146
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2942 -5.11 %
Rwork0.2531 314740 -
obs0.2552 331873 88.26 %
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: 55.94 Å2
精密化ステップサイクル: LAST / 解像度: 2.73→49.19 Å
タンパク質核酸リガンド溶媒全体
原子数56601 0 0 282 56883
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003958052
X-RAY DIFFRACTIONf_angle_d0.523879195
X-RAY DIFFRACTIONf_chiral_restr0.04138560
X-RAY DIFFRACTIONf_plane_restr0.004310308
X-RAY DIFFRACTIONf_dihedral_angle_d4.63938267
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.760.34833470.33475894X-RAY DIFFRACTION49.68
2.76-2.80.34595590.316810443X-RAY DIFFRACTION87.94
2.8-2.830.36946700.31610522X-RAY DIFFRACTION88.99
2.83-2.870.34265830.307110560X-RAY DIFFRACTION89.12
2.87-2.910.33365310.300510636X-RAY DIFFRACTION89.16
2.91-2.940.36075050.291410540X-RAY DIFFRACTION88.56
2.94-2.990.33465920.28710605X-RAY DIFFRACTION88.98
2.99-3.030.31076220.287910643X-RAY DIFFRACTION90.09
3.03-3.080.34615350.29210727X-RAY DIFFRACTION90.42
3.08-3.130.34416660.295410873X-RAY DIFFRACTION91.35
3.13-3.180.34255680.290810897X-RAY DIFFRACTION92.03
3.18-3.240.31896390.274710955X-RAY DIFFRACTION92.49
3.24-3.30.33355710.271911015X-RAY DIFFRACTION92.53
3.3-3.370.30176320.258810914X-RAY DIFFRACTION92.45
3.37-3.440.30236340.254110901X-RAY DIFFRACTION92.04
3.44-3.520.30455450.25911026X-RAY DIFFRACTION92.41
3.52-3.610.27875970.255611031X-RAY DIFFRACTION92.2
3.61-3.710.29356480.252110790X-RAY DIFFRACTION91.04
3.71-3.820.28715460.244310646X-RAY DIFFRACTION89.51
3.82-3.940.27755610.233610536X-RAY DIFFRACTION89.04
3.94-4.080.26275970.23310796X-RAY DIFFRACTION90.35
4.08-4.250.25355270.225210652X-RAY DIFFRACTION89.74
4.25-4.440.26874720.225610688X-RAY DIFFRACTION89.2
4.44-4.670.28015670.223310551X-RAY DIFFRACTION88.55
4.67-4.970.25065980.222310418X-RAY DIFFRACTION88.05
4.97-5.350.29345670.23110396X-RAY DIFFRACTION87.36
5.35-5.890.26724630.250510258X-RAY DIFFRACTION85.84
5.89-6.740.31785090.260910469X-RAY DIFFRACTION87.62
6.74-8.480.27975770.236810368X-RAY DIFFRACTION87.13
8.48-49.190.26445100.25319990X-RAY DIFFRACTION84.04
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)
12.543787869711.52942935555-0.9945190271373.86477034962-1.553739181982.519658925310.237419070923-0.308243951973-0.1902864257040.485243670855-0.236510701633-0.479524666199-0.1150762875040.00319796777562-0.01408236309190.321469445311-0.0681402321789-0.1350510957920.2590454365950.07968032313080.302702979706-88.9076466158-66.1902483872-119.99993911
21.889213928721.01596493132-0.2481683040083.809714091210.000609832034051.75511774090.00559471000101-0.0166080490502-0.403398866861-0.251210802769-0.121323535145-0.6440988776370.2141576884110.07693306136540.1149582234360.278917755395-0.009741150162780.05329087751660.2210660746390.05840577178250.449275825565-79.4548879896-55.7497442754-133.822433681
31.13881169885-0.154799586027-0.70111998961.595990822140.5908897806021.25131014772-0.161785646971-0.4382561231370.1047507837930.6720454787650.0993395925568-0.8727925873640.005708129990440.8182034778010.2952192953841.19198884737-0.284007343792-0.9914148260910.6774174513371.033229591231.45219678725-65.9678588415-63.8648596255-106.4586545
43.16537457674-0.1219322584490.3332027083524.54644125577-0.1835920868113.512750924810.407763592476-0.702191510325-0.6620123865090.775184381827-0.349318660924-0.2082072808940.954264366536-0.344110534205-0.083678188160.340333794113-0.107015643519-0.02729101036850.3238693186860.1090388594560.490164621704-108.698675626-88.7712948721-118.788712079
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1426.30756215108-2.59350823566-1.574491725114.924990579330.8929046123271.246020744660.7148355618560.535090948360.245315367466-0.646898476225-0.5176365900880.0755044143493-0.214013512808-0.0483958589561-0.1244377030740.4959702079230.03535472666710.1718317174730.3406857542680.02169144088670.52538339191-164.472888229-76.3075160814-274.413838826
1433.5325193841.562251900242.624605714112.95257241127-0.4220886676113.069447790360.425497701936-0.4215761211691.021653787550.0256241215303-0.603446599893-0.1622380727760.158920930240.3193118197580.1329636122190.3530361707020.08482599137580.03897879930880.972967699549-0.3087923722010.724581127673-160.252218702-84.9650775107-271.096711994
1442.010932393260.2930428462951.219074934033.49842829595-0.3721774492474.568727914720.2671524889710.197586594695-0.334095399466-0.150772718181-0.2817733715160.5310028765430.458836210410.0600080636058-0.0166105866310.3533887599770.05345670121070.08399675745030.549339794134-0.06356090730810.544242915962-164.65597507-79.7916319455-271.444728487
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 144 )AA1 - 1441 - 110
22chain 'A' and (resid 145 through 384 )AA145 - 384111 - 335
33chain 'A' and (resid 385 through 417 )AA385 - 417336 - 368
44chain 'B' and (resid 3 through 34 )BB3 - 341 - 32
55chain 'B' and (resid 35 through 77 )BB35 - 7733 - 75
66chain 'B' and (resid 78 through 117 )BB78 - 11776 - 115
77chain 'C' and (resid 1 through 156 )CC1 - 1561 - 123
88chain 'C' and (resid 157 through 229 )CC157 - 229124 - 196
99chain 'C' and (resid 230 through 319 )CC230 - 319197 - 286
1010chain 'C' and (resid 320 through 417 )CC320 - 417287 - 366
1111chain 'D' and (resid 3 through 34 )DD3 - 341 - 32
1212chain 'D' and (resid 35 through 77 )DD35 - 7733 - 75
1313chain 'D' and (resid 78 through 117 )DD78 - 11776 - 115
1414chain 'E' and (resid 1 through 144 )EE1 - 1441 - 112
1515chain 'E' and (resid 145 through 319 )EE145 - 319113 - 287
1616chain 'E' and (resid 320 through 417 )EE320 - 417288 - 362
1717chain 'F' and (resid 3 through 28 )FF3 - 281 - 26
1818chain 'F' and (resid 29 through 50 )FF29 - 5027 - 48
1919chain 'F' and (resid 51 through 60 )FF51 - 6049 - 58
2020chain 'F' and (resid 61 through 77 )FF61 - 7759 - 75
2121chain 'F' and (resid 78 through 110 )FF78 - 11076 - 108
2222chain 'F' and (resid 111 through 117 )FF111 - 117109 - 115
2323chain 'G' and (resid 1 through 113 )GG1 - 1131 - 101
2424chain 'G' and (resid 114 through 319 )GG114 - 319102 - 286
2525chain 'G' and (resid 320 through 417 )GG320 - 417287 - 382
2626chain 'H' and (resid 3 through 28 )HH3 - 281 - 26
2727chain 'H' and (resid 29 through 67 )HH29 - 6727 - 65
2828chain 'H' and (resid 68 through 85 )HH68 - 8566 - 83
2929chain 'H' and (resid 86 through 110 )HH86 - 11084 - 108
3030chain 'H' and (resid 111 through 117 )HH111 - 117109 - 115
3131chain 'I' and (resid 1 through 157 )II1 - 1571 - 124
3232chain 'I' and (resid 158 through 319 )II158 - 319125 - 286
3333chain 'I' and (resid 320 through 417 )II320 - 417287 - 359
3434chain 'J' and (resid 3 through 14 )JJ3 - 141 - 12
3535chain 'J' and (resid 15 through 34 )JJ15 - 3413 - 32
3636chain 'J' and (resid 35 through 77 )JJ35 - 7733 - 75
3737chain 'J' and (resid 78 through 110 )JJ78 - 11076 - 108
3838chain 'J' and (resid 111 through 117 )JJ111 - 117109 - 115
3939chain 'K' and (resid 1 through 157 )KK1 - 1571 - 124
4040chain 'K' and (resid 158 through 340 )KK158 - 340125 - 305
4141chain 'K' and (resid 341 through 417 )KK341 - 417306 - 382
4242chain 'L' and (resid 3 through 28 )LL3 - 281 - 26
4343chain 'L' and (resid 29 through 60 )LL29 - 6027 - 58
4444chain 'L' and (resid 61 through 77 )LL61 - 7759 - 75
4545chain 'L' and (resid 78 through 85 )LL78 - 8576 - 83
4646chain 'L' and (resid 86 through 91 )LL86 - 9184 - 89
4747chain 'L' and (resid 92 through 100 )LL92 - 10090 - 98
4848chain 'L' and (resid 101 through 117 )LL101 - 11799 - 115
4949chain 'M' and (resid 1 through 122 )MM1 - 1221 - 111
5050chain 'M' and (resid 145 through 340 )MM145 - 340112 - 305
5151chain 'M' and (resid 341 through 417 )MM341 - 417306 - 378
5252chain 'N' and (resid 3 through 28 )NN3 - 281 - 26
5353chain 'N' and (resid 29 through 117 )NN29 - 11727 - 115
5454chain 'O' and (resid 1 through 170 )OO1 - 1701 - 137
5555chain 'O' and (resid 171 through 280 )OO171 - 280138 - 247
5656chain 'O' and (resid 281 through 319 )OO281 - 319248 - 286
5757chain 'O' and (resid 320 through 417 )OO320 - 417287 - 361
5858chain 'P' and (resid 3 through 28 )PP3 - 281 - 26
5959chain 'P' and (resid 29 through 60 )PP29 - 6027 - 58
6060chain 'P' and (resid 61 through 85 )PP61 - 8559 - 83
6161chain 'P' and (resid 86 through 100 )PP86 - 10084 - 98
6262chain 'P' and (resid 101 through 117 )PP101 - 11799 - 115
6363chain 'Q' and (resid 1 through 157 )QQ1 - 1571 - 124
6464chain 'Q' and (resid 158 through 229 )QQ158 - 229125 - 196
6565chain 'Q' and (resid 230 through 319 )QQ230 - 319197 - 286
6666chain 'Q' and (resid 320 through 417 )QQ320 - 417287 - 384
6767chain 'R' and (resid 3 through 27 )RR3 - 271 - 25
6868chain 'R' and (resid 31 through 77 )RR31 - 7726 - 72
6969chain 'R' and (resid 78 through 117 )RR78 - 11773 - 112
7070chain 'S' and (resid 1 through 35 )SS1 - 351 - 23
7171chain 'S' and (resid 36 through 86 )SS36 - 8624 - 74
7272chain 'S' and (resid 87 through 144 )SS87 - 14475 - 111
7373chain 'S' and (resid 145 through 170 )SS145 - 170112 - 137
7474chain 'S' and (resid 171 through 228 )SS171 - 228138 - 195
7575chain 'S' and (resid 229 through 280 )SS229 - 280196 - 247
7676chain 'S' and (resid 281 through 319 )SS281 - 319248 - 286
7777chain 'S' and (resid 320 through 349 )SS320 - 349287 - 305
7878chain 'S' and (resid 350 through 412 )SS350 - 412306 - 344
7979chain 'T' and (resid 3 through 28 )TT3 - 281 - 26
8080chain 'T' and (resid 29 through 60 )TT29 - 6027 - 58
8181chain 'T' and (resid 61 through 77 )TT61 - 7759 - 75
8282chain 'T' and (resid 78 through 117 )TT78 - 11776 - 115
8383chain 'U' and (resid 1 through 94 )UU1 - 941 - 80
8484chain 'U' and (resid 95 through 157 )UU95 - 15781 - 119
8585chain 'U' and (resid 158 through 280 )UU158 - 280120 - 242
8686chain 'U' and (resid 281 through 319 )UU281 - 319243 - 281
8787chain 'U' and (resid 320 through 402 )UU320 - 402282 - 333
8888chain 'V' and (resid 3 through 28 )VV3 - 281 - 26
8989chain 'V' and (resid 29 through 60 )VV29 - 6027 - 58
9090chain 'V' and (resid 61 through 85 )VV61 - 8559 - 83
9191chain 'V' and (resid 86 through 117 )VV86 - 11784 - 115
9292chain 'W' and (resid 1 through 157 )WW1 - 1571 - 124
9393chain 'W' and (resid 158 through 229 )WW158 - 229125 - 196
9494chain 'W' and (resid 230 through 247 )WW230 - 247197 - 214
9595chain 'W' and (resid 248 through 319 )WW248 - 319215 - 286
9696chain 'W' and (resid 320 through 417 )WW320 - 417287 - 347
9797chain 'X' and (resid 3 through 28 )XX3 - 281 - 26
9898chain 'X' and (resid 29 through 67 )XX29 - 6727 - 65
9999chain 'X' and (resid 68 through 85 )XX68 - 8566 - 83
100100chain 'X' and (resid 86 through 117 )XX86 - 11784 - 115
101101chain 'Y' and (resid 1 through 144 )YY1 - 1441 - 108
102102chain 'Y' and (resid 145 through 225 )YY145 - 225109 - 189
103103chain 'Y' and (resid 233 through 280 )YY233 - 280190 - 237
104104chain 'Y' and (resid 281 through 319 )YY281 - 319238 - 276
105105chain 'Y' and (resid 320 through 355 )YY320 - 355277 - 308
106106chain 'Y' and (resid 356 through 417 )YY356 - 417309 - 365
107107chain 'Z' and (resid 3 through 10 )ZZ3 - 101 - 8
108108chain 'Z' and (resid 11 through 60 )ZZ11 - 609 - 53
109109chain 'Z' and (resid 61 through 85 )ZZ61 - 8554 - 78
110110chain 'Z' and (resid 86 through 117 )ZZ86 - 11779 - 110
111111chain 'a' and (resid 1 through 35 )aAA1 - 351 - 23
112112chain 'a' and (resid 36 through 144 )aAA36 - 14424 - 108
113113chain 'a' and (resid 145 through 280 )aAA145 - 280109 - 244
114114chain 'a' and (resid 281 through 319 )aAA281 - 319245 - 283
115115chain 'a' and (resid 320 through 411 )aAA320 - 411284 - 342
116116chain 'b' and (resid 3 through 28 )bHB3 - 281 - 26
117117chain 'b' and (resid 29 through 34 )bHB29 - 3427 - 32
118118chain 'b' and (resid 35 through 42 )bHB35 - 4233 - 40
119119chain 'b' and (resid 43 through 60 )bHB43 - 6041 - 58
120120chain 'b' and (resid 61 through 77 )bHB61 - 7759 - 75
121121chain 'b' and (resid 78 through 117 )bHB78 - 11776 - 115
122122chain 'c' and (resid 1 through 170 )cIB1 - 1701 - 134
123123chain 'c' and (resid 171 through 260 )cIB171 - 260135 - 220
124124chain 'c' and (resid 261 through 280 )cIB261 - 280221 - 240
125125chain 'c' and (resid 281 through 319 )cIB281 - 319241 - 279
126126chain 'c' and (resid 320 through 410 )cIB320 - 410280 - 327
127127chain 'd' and (resid 3 through 42 )dJB3 - 421 - 37
128128chain 'd' and (resid 43 through 60 )dJB43 - 6038 - 55
129129chain 'd' and (resid 61 through 85 )dJB61 - 8556 - 80
130130chain 'd' and (resid 86 through 117 )dJB86 - 11781 - 112
131131chain 'e' and (resid 1 through 35 )eKB1 - 351 - 23
132132chain 'e' and (resid 36 through 52 )eKB36 - 5224 - 40
133133chain 'e' and (resid 53 through 105 )eKB53 - 10541 - 93
134134chain 'e' and (resid 106 through 170 )eKB106 - 17094 - 137
135135chain 'e' and (resid 171 through 187 )eKB171 - 187138 - 154
136136chain 'e' and (resid 188 through 229 )eKB188 - 229155 - 196
137137chain 'e' and (resid 230 through 260 )eKB230 - 260197 - 227
138138chain 'e' and (resid 261 through 280 )eKB261 - 280228 - 247
139139chain 'e' and (resid 281 through 319 )eKB281 - 319248 - 286
140140chain 'e' and (resid 320 through 362 )eKB320 - 362287 - 315
141141chain 'e' and (resid 372 through 416 )eKB372 - 416316 - 353
142142chain 'f' and (resid 3 through 42 )fLB3 - 421 - 40
143143chain 'f' and (resid 43 through 60 )fLB43 - 6041 - 58
144144chain 'f' and (resid 61 through 117 )fLB61 - 11759 - 115

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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