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- PDB-7st3: Consequences of HLA single chain trimer mutations on peptide pres... -

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基本情報

登録情報
データベース: PDB / ID: 7st3
タイトルConsequences of HLA single chain trimer mutations on peptide presentation and binding affinity
要素
  • Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
  • VHH
キーワードIMMUNE SYSTEM/VIRAL PROTEIN / HLA / VHH / SCT / HPV / IMMUNE SYSTEM-VIRAL PROTEIN complex
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 perturbation of host transcription / symbiont-mediated suppression of host apoptosis / 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 / viral process / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated perturbation of host transcription / symbiont-mediated suppression of host apoptosis / 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 / viral process / 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 / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / early endosome membrane / DNA-binding transcription factor binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / DNA-binding transcription factor activity / protein domain specific binding / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / DNA binding / extracellular space / 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 / 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 ...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 / 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
類似検索 - ドメイン・相同性
MHC class I antigen / Protein E7 / Beta-2-microglobulin
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: 2.78 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)973,05432
ポリマ－973,05432
非ポリマー00
水3,567198
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)60,8162
ポリマ－60,8162
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)117.796, 118.041, 273.507
Angle α, β, γ (deg.)102.449, 102.452, 89.998
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: 48279.074 Da / 分子数: 16 / 変異: Y108C,A163C / 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 sapiens (ヒト)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 198 / 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: 3.72 Å3/Da / 溶媒含有率: 66.96 %
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: 100 mM Tris, pH 7.5, 200 mM Li2SO4, 1.6 M AmSO4

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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: 5.0.1 / 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: 2.78→50.48 Å / Num. obs: 340982 / % possible obs: 98.2 % / 冗長度: 1.8 % / Biso Wilson estimate: 47.42 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.76
反射 シェル解像度: 2.78→2.88 Å / Num. unique obs: 29320 / CC1/2: 0.916

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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: 7SR5

7sr5


解像度: 2.78→50.48 Å / SU ML: 0.3673 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 26.8582
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2747 17167 5.04 %
Rwork0.2376 323689 -
obs0.2395 340856 96.75 %
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: 55.89 Å2
精密化ステップサイクル: LAST / 解像度: 2.78→50.48 Å
タンパク質核酸リガンド溶媒全体
原子数57639 0 0 198 57837
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003259107
X-RAY DIFFRACTIONf_angle_d0.576780530
X-RAY DIFFRACTIONf_chiral_restr0.0418648
X-RAY DIFFRACTIONf_plane_restr0.004510465
X-RAY DIFFRACTIONf_dihedral_angle_d5.15128342
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.810.39083440.34966186X-RAY DIFFRACTION55.81
2.81-2.850.37364880.311410697X-RAY DIFFRACTION96.32
2.85-2.880.33766940.300510911X-RAY DIFFRACTION97.3
2.88-2.920.32526310.294910706X-RAY DIFFRACTION97.57
2.92-2.960.32146890.280810873X-RAY DIFFRACTION97.92
2.96-30.3086250.277910960X-RAY DIFFRACTION98.26
3-3.040.30335640.271810972X-RAY DIFFRACTION98.03
3.04-3.080.30386780.269810791X-RAY DIFFRACTION97.32
3.08-3.130.28825560.263610863X-RAY DIFFRACTION97.76
3.13-3.180.32355590.275310945X-RAY DIFFRACTION97.54
3.18-3.240.30755690.278110676X-RAY DIFFRACTION96.81
3.24-3.30.29285330.245311030X-RAY DIFFRACTION97.72
3.3-3.360.31394870.243910970X-RAY DIFFRACTION98.2
3.36-3.430.28566010.24210974X-RAY DIFFRACTION98.29
3.43-3.50.28155820.238110903X-RAY DIFFRACTION98.19
3.5-3.590.26025350.229411027X-RAY DIFFRACTION97.77
3.59-3.680.29534720.238311035X-RAY DIFFRACTION98.07
3.68-3.780.26946420.233110920X-RAY DIFFRACTION98.56
3.78-3.890.25225940.220910988X-RAY DIFFRACTION98.5
3.89-4.010.26984830.224211048X-RAY DIFFRACTION98.3
4.01-4.150.23576330.212310897X-RAY DIFFRACTION98.01
4.15-4.320.24066190.211911021X-RAY DIFFRACTION99
4.32-4.520.23775600.206311108X-RAY DIFFRACTION99.04
4.52-4.760.23686220.204210957X-RAY DIFFRACTION99.16
4.76-5.050.24476240.210711010X-RAY DIFFRACTION99.22
5.05-5.440.26125780.219510962X-RAY DIFFRACTION98.41
5.44-5.990.29075140.232911104X-RAY DIFFRACTION98.48
5.99-6.850.26455930.250711102X-RAY DIFFRACTION99.46
6.86-8.630.25565200.227311075X-RAY DIFFRACTION98.78
8.63-50.480.28665780.248510978X-RAY DIFFRACTION98.42
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)
10.957838268286-0.008067575231010.003114216338312.24658124182-0.786647968230.2517991833110.110987269693-0.0715350384136-0.004409836954440.333295532347-0.476250726726-0.764972521329-0.0654256633902-0.00521216722070.211560952410.457803345179-0.221631084848-0.06684750686480.4424962982140.1129325259380.43103188823-84.9272218506-61.3088948667-120.153195729
21.727474030620.188363531139-0.5274702852172.726989215420.2305501245562.215818678650.202487683776-0.18272439167-0.1580104703440.409054866467-0.330584245227-0.303123752903-0.198097578869-0.09649657926470.09129599208120.300243438774-0.0306377904798-0.07298197905410.2682256609530.07390079061560.269794470874-90.2550339281-67.5349679782-117.957808002
31.596907154790.72957466252-0.06519619850673.859161802170.7097968868632.60842245815-0.103248848692-0.118355420768-0.578087106047-0.21760980083-0.0260100841733-0.2255021030480.0475554047994-0.2087094611970.163662165740.2645346775020.00216724262170.05082760154770.4005418475450.03779577311630.280357650172-85.9381117245-58.5347053079-135.618929093
41.999686843881.34484777665-0.1523291525662.525292558020.7603159481721.452279931060.0254758350658-0.46802644319-0.366188066433-0.160341969004-0.279671702949-0.01227145183330.00541479646808-0.2684677128960.1621093290450.2395274019420.00689482903767-0.05318326110430.3937773072580.03377113006530.257156748821-89.794858191-52.1284840104-131.560825496
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1421.024405614930.1480613406170.1731379285710.3149337790390.5625815797751.579633892880.158412598423-0.04788484552980.448857199760.537585917805-0.36076909240.992981781218-0.200153786431-0.343920796010.03154508008820.585099159864-0.2061369925710.3470328866060.611914311865-0.1838006755420.762706971463-105.818556504-102.479893414-240.602379017
1430.892076775989-0.1873617627540.2017207783780.247241144596-0.2780247734490.6722892301350.592752692487-0.06965068715280.539422068290.678061550842-0.3883871653211.03143842252-0.226521345179-0.2689110142060.2146091817680.779915297461-0.2061683258170.4349855235680.703729890273-0.2870305831671.06109784692-113.994813892-105.27299581-236.939139364
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1462.896242896360.321333906296-1.084778324132.45470551803-0.3706613290882.147751591120.12818854573-0.107620655160.05753986179220.117764440875-0.264675357407-0.131048503280.160416197325-0.1451297571820.08662378633940.291467253316-0.05437573655890.01743859615640.2984551134110.008386852353360.343064694046-72.1515744657-83.5158687107-253.270772339
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1481.078176895661.288701152840.7539562954122.546222463521.062265230940.9492170238930.0877349723951-0.130282987992-0.0117534149210.0232163672386-0.2187231092-0.01237996543170.0181461337262-0.01510520797760.1271774900850.286736282139-0.04064014900340.019474991760.3686499823520.004383693581780.304775319755-148.106185908-43.3435021287-258.309696274
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1501.58645122654-0.0409828404204-0.2147734057873.42461166396-0.479098764632.20767583644-0.1044376882740.2239060306060.0350835585996-0.538710537362-0.176259944140.137156888719-0.05210339274790.07260566347180.2766579374360.405779613877-0.0589387478896-0.1017208478890.309372791084-0.02418646071430.388606998062-162.256927231-52.1917150435-274.904065482
1510.7818432552650.182361929240.5438306380850.237329930292-0.1297599015160.7166738243280.0636264477808-0.1260173636660.4939155676020.378842956347-0.02266395998110.04891617177760.05213593338510.323562239025-0.10701226980.798716900437-0.5147872434860.2357365121361.03725305598-0.2988259473030.703717384551-163.544236452-51.9924988064-242.120232646
1520.241515050262-0.003207943858580.11947346080.152810306618-0.1965224906430.3280030779040.337723874297-0.3521988431440.4261841555790.846945801472-0.6681765216510.8513457190940.0483881396126-0.7664798860690.2179461152920.693673989185-0.3428150975460.3126312742840.883209925409-0.3607863654670.899089460361-167.178087095-41.5201243071-241.385354028
1536.655047039283.25481762325-3.12746791035.80529284248-3.177229664515.828757690730.23477499007-0.4431803448440.06021393390580.706816147222-0.3138259826320.5927787268870.1509358136980.04712098747650.005735312344710.518314467038-0.1489232824950.1005964803460.47270974063-0.1671391316310.434661391163-134.046334377-13.3388105766-242.587290348
1543.16186604907-2.289009698540.5620224517538.725835725222.967753401841.710658641980.6939410499430.1665560433370.281978452012-0.30206926525-0.375658112196-0.570424096386-0.06328850146640.170146636918-0.1154521566780.5525306564660.05331165625270.1485003358780.3404893284810.07005617119750.377823768801-122.714683964-12.8976434735-262.338797746
1554.50304199311-0.599434769333-4.504770680211.58363074470.5475197974518.08615520160.0133889857144-0.3913970679530.2738897895160.316974323346-0.112303297186-0.0684222001757-0.03417122506490.03237770097420.1359504320220.466950732907-0.135263316050.01530291431790.355842143497-0.0714384798340.402327733382-126.611936551-15.8471883505-246.97631861
1563.8309694502-0.09763959822431.812693832493.44349318001-2.913638334197.812001250230.438514530805-0.440446800282-0.07917220847360.6104470956740.002746221368420.165425574494-0.424040116006-0.436772408546-0.1897896838630.366261787878-0.05315296138050.06285271212720.349410704177-0.05129840874050.29389997463-134.525725728-22.1120216393-245.208103709
1573.21055215266-1.899451882272.434731760822.14845913777-1.197043036012.234540545030.2581917484350.5828439239930.0895052399347-0.41264216049-0.1618212649110.1258953207280.0562505812685-0.4334202988350.02410030533090.306211717981-0.02901419896130.1048118094180.4486414342450.02378760891990.43953357153-140.56310245-22.0940082734-258.143773867
1582.17859816606-0.471775115351.772738912933.42871067621-0.8968980460281.618582124130.3338849086980.111747443196-0.43173933948-0.33982731045-0.622255742497-0.5254268602190.7149480689730.0496739352838-0.08644938152340.3892547713180.03232763870470.03149195764650.3069578644150.02952019381970.437121127018-129.19019874-29.8995123902-250.863835679
1594.45567904767-0.243904596351-3.129761629924.647892547231.396888877686.087245906090.0174149963386-0.218800026625-0.1586693565890.333674456007-0.224252478965-0.3071753794950.3283357939370.4170911642520.1618527441510.2135172754090.0187203587417-0.02960025466540.3875132932760.07021975777610.409979532695-124.251735466-22.2318918961-247.807265355
1603.53466941637-1.047516750891.0444356680.314288377147-0.3154528579640.3160522162580.04867632564870.073704131792-0.331882101895-0.330971887141-0.225261982651-0.1008484516450.4111093784240.1918831140780.07116513811690.4417280063720.029295800214-0.01023788269420.34932222340.03718947003230.420389401261-126.861166983-20.2657418327-265.308703225
1611.027878928040.27505584052-0.8029963864391.4727581316-1.192356439152.459603938940.0766992669154-0.2920875994010.1308047227790.3054820464850.03108100290630.221476644066-0.0853417662977-0.0632505567692-0.08510179446090.277283549504-0.07936212001670.08313015413840.4869688855560.004704277441330.26629588213-138.127591263-20.1702831239-246.246588553
1626.27760476834-1.56779168578-1.005072993855.848673916312.744199794216.464366705920.3168412621190.3451844039440.0526884444201-0.334561075363-0.264194161659-0.290798762676-0.201545194196-0.263606267734-0.1432812216350.455354910738-0.01095113171180.05874550792230.2903492208630.04123571764560.17019635937-129.882068221-12.264292008-260.38609649
1631.20081629945-0.350582455365-0.1425602346242.42114286503-1.003864028470.4755351190140.0471745245159-0.008285521879540.275803630317-0.217831932649-0.153438706299-0.7904044326330.34664731333-0.008055861851260.04932089354420.418749534760.1659781571630.03593203813940.4130029777150.05249742906540.440417875349-84.9154575935-45.2555275656-272.173301303
1641.3354332481-0.6504266832260.1165789348652.641068177-0.6599607520871.107842499670.1136532319940.084980126540.103933186519-0.249986633842-0.162488201769-0.4342535820480.0859647664057-0.09178975770550.02174929261130.3109965190150.07829686624870.01853583820910.3459199413240.01366173054070.251451561812-89.1418474916-40.3890055418-271.74506728
1651.88669451935-0.02603431078320.2262369027292.38513931304-0.119009590851.286388398760.0307640914741-0.2483626336290.03697558676020.217866890938-0.1214041869610.0862562129643-0.204596672102-0.3109978395850.09551851836390.3603224972970.0682579086511-0.02808128996750.352572762179-0.0124412831750.259397366012-88.6554976464-52.6141689352-254.89611964
1661.52229645924-1.097932411440.4812334583633.03894392407-0.3569472152210.5719418306090.0655756479487-0.09004441596040.5072348051530.00152633541913-0.162259925513-1.36376430964-0.389932560806-0.05873720499480.2255695407120.4024087680380.0106039001005-0.06142042051930.3208713158230.08234503433420.659033702373-73.8752531291-50.8771818716-256.519925826
1670.6769341049870.344253449248-0.2843520851320.353317711957-0.4268287759990.5004500826330.06015999325180.270382112310.293884701396-0.867516851413-0.570945000803-1.439675798080.3813121935150.6044017571220.2104359584760.5562233078220.3295921076460.5680835774340.723144753220.4390859081821.30167531244-70.639431768-45.8544052073-281.299918773
1682.733348305740.487510187126-0.1777009828063.02280466812-1.006237926414.46486110261-0.09888556065730.10915897720.406225433618-0.171754177848-0.376700211052-0.0659881948382-0.237059613219-0.1306853145340.372119353540.2249470003850.0765887285443-0.01799141505140.337381244582-0.01535741524820.383827639045-109.668662312-16.6832554163-269.747991511
1695.006147158781.289521221020.06842842996644.557921841040.9353625462222.189146993460.334705039023-0.105763392392-0.0187606616071-0.299280503165-0.294089858175-0.0672358180278-0.232891692395-0.06601327231120.03495504173110.3093240914190.04638967602090.07121658228440.27561499805-0.04564767790270.265851565499-102.521877736-26.4871637522-272.354633306
1704.02667410826-0.0008995126896930.09039811012095.73597978963-2.354209854682.08515510502-0.007371022385430.139001152799-0.286135704566-0.1129407287420.238158024710.2551852571390.287663991655-0.397380190851-0.09090699618980.201753943409-0.03980389756340.04613678531680.213522742544-0.03375960343560.288556248117-111.239835329-28.7472822115-269.33084503
1711.88107976153-0.544724141513-0.6883556900582.3415036690.218378858851.804874895330.08360461136980.02651645993790.126952095786-0.0601997754084-0.21714383072-0.0413192336119-0.1283213177110.05429458885160.09777350733330.3205992290920.03828856933630.01978039991620.358355797274-0.00862096015020.200385894328-104.636875583-21.5304461302-269.410333751
1720.6563718865410.190102900598-0.09747067740782.30912023624-0.9939894148640.42740518104-0.009063545438030.1093551748270.157990966172-0.23979455639-0.710636782617-0.673072484845-0.1304155523830.08657050588850.3744413394330.4267091412850.2563061825390.03312584555550.6495909916080.01542796157320.402524776127-142.353573728-101.48721883-270.007131687
1731.65499525142-0.6812966640291.069690410342.11063618681-0.2820485928551.6427165750.2836102698440.2616802508030.280479945269-0.500366838599-0.395322886712-0.07608735292780.07911250725570.1011411589760.08282926515430.3464609867590.1485875057810.09206252965290.4370537162790.06820294020150.341301408696-147.66278212-95.5201469763-273.022528597
1741.20720606731-0.7254665972180.5744568586122.743971316510.04096131384851.85171183698-0.02764718589320.00817675201243-0.006458787568750.00450435702774-0.1864082926040.229435017966-0.106885920107-0.340528042860.1264139536950.2779074040190.03491817716230.01588403739360.40618696867-0.04890842540310.320376848288-146.677589375-109.005442538-254.502263977
1751.36010771403-0.858588799520.4581879565892.54722442906-0.796544665860.8683352317890.1199849963690.09081654620510.4119860026060.0870802413013-0.398293037812-0.594614938094-0.041075529682-0.1716101594130.1910762728810.229252203550.0522609988609-0.02787109755440.3066446578440.05564014551880.471808815615-133.129480542-107.906120709-254.516786698
1760.340186695593-0.0169953057193-0.5781842628980.05446604758430.111538096851.121398827350.5206792361310.4003416661170.446063244623-0.388057356397-0.493988508388-0.7493239530640.04463942009530.886516543384-0.02428490822880.5675573283670.3396469319390.3173795445771.089550389970.4966062986960.967483093084-127.461757779-102.12159008-279.275160774
1772.007147307760.8806816973010.9462493489473.89015100886-0.5837812059770.7276219225380.1818985026290.2354785988170.4487337146780.271141272112-0.1909479570980.04303473005150.0464200569734-0.03708528100670.07490549664450.3665035947110.06785615038370.0300399224620.2765772490490.05970232676260.426791029222-166.948581412-71.9856386752-269.062701911
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1791.84295610909-0.561266809291-0.4938740807192.579201672710.5755285096932.904699860750.2391509977590.1287492683840.158124368035-0.0852442643217-0.06049951193060.0725155308708-0.03311698203210.150852059087-0.07913093290550.3429286740830.1038294966850.007920272516910.392614774550.0328324317450.281050517431-160.558680982-77.6513953629-269.481406814
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 44 )AA1 - 441 - 25
22chain 'A' and (resid 45 through 144 )AA45 - 14426 - 105
33chain 'A' and (resid 145 through 170 )AA145 - 170106 - 131
44chain 'A' and (resid 171 through 187 )AA171 - 187132 - 148
55chain 'A' and (resid 188 through 229 )AA188 - 229149 - 190
66chain 'A' and (resid 230 through 274 )AA230 - 274191 - 235
77chain 'A' and (resid 275 through 319 )AA275 - 319236 - 280
88chain 'A' and (resid 320 through 349 )AA320 - 349281 - 302
99chain 'A' and (resid 350 through 384 )AA350 - 384303 - 326
1010chain 'A' and (resid 385 through 417 )AA385 - 417327 - 352
1111chain 'B' and (resid 3 through 28 )BB3 - 281 - 26
1212chain 'B' and (resid 29 through 60 )BB29 - 6027 - 58
1313chain 'B' and (resid 61 through 85 )BB61 - 8559 - 83
1414chain 'B' and (resid 86 through 117 )BB86 - 11784 - 115
1515chain 'C' and (resid 1 through 44 )CC1 - 441 - 25
1616chain 'C' and (resid 45 through 144 )CC45 - 14426 - 106
1717chain 'C' and (resid 145 through 170 )CC145 - 170107 - 132
1818chain 'C' and (resid 171 through 229 )CC171 - 229133 - 191
1919chain 'C' and (resid 230 through 274 )CC230 - 274192 - 236
2020chain 'C' and (resid 275 through 319 )CC275 - 319237 - 281
2121chain 'C' and (resid 320 through 342 )CC320 - 342282 - 297
2222chain 'C' and (resid 343 through 384 )CC343 - 384298 - 333
2323chain 'C' and (resid 385 through 417 )CC385 - 417334 - 361
2424chain 'D' and (resid 3 through 28 )DD3 - 281 - 26
2525chain 'D' and (resid 29 through 60 )DD29 - 6027 - 58
2626chain 'D' and (resid 61 through 77 )DD61 - 7759 - 75
2727chain 'D' and (resid 78 through 117 )DD78 - 11776 - 115
2828chain 'E' and (resid 1 through 44 )EE1 - 441 - 25
2929chain 'E' and (resid 45 through 144 )EE45 - 14426 - 106
3030chain 'E' and (resid 145 through 319 )EE145 - 319107 - 281
3131chain 'E' and (resid 320 through 417 )EE320 - 417282 - 368
3232chain 'F' and (resid 3 through 18 )FF3 - 181 - 16
3333chain 'F' and (resid 19 through 28 )FF19 - 2817 - 26
3434chain 'F' and (resid 29 through 60 )FF29 - 6027 - 58
3535chain 'F' and (resid 61 through 77 )FF61 - 7759 - 75
3636chain 'F' and (resid 78 through 85 )FF78 - 8576 - 83
3737chain 'F' and (resid 86 through 110 )FF86 - 11084 - 108
3838chain 'F' and (resid 111 through 117 )FF111 - 117109 - 115
3939chain 'G' and (resid 1 through 64 )GG1 - 641 - 45
4040chain 'G' and (resid 65 through 144 )GG65 - 14446 - 106
4141chain 'G' and (resid 145 through 274 )GG145 - 274107 - 236
4242chain 'G' and (resid 275 through 319 )GG275 - 319237 - 281
4343chain 'G' and (resid 320 through 384 )GG320 - 384282 - 339
4444chain 'G' and (resid 385 through 417 )GG385 - 417340 - 366
4545chain 'H' and (resid 3 through 28 )HH3 - 281 - 26
4646chain 'H' and (resid 29 through 60 )HH29 - 6027 - 58
4747chain 'H' and (resid 61 through 77 )HH61 - 7759 - 75
4848chain 'H' and (resid 78 through 117 )HH78 - 11776 - 115
4949chain 'I' and (resid 1 through 44 )II1 - 441 - 25
5050chain 'I' and (resid 45 through 157 )II45 - 15726 - 117
5151chain 'I' and (resid 158 through 229 )II158 - 229118 - 189
5252chain 'I' and (resid 230 through 349 )II230 - 349190 - 301
5353chain 'I' and (resid 350 through 417 )II350 - 417302 - 358
5454chain 'J' and (resid 3 through 18 )JJ3 - 181 - 16
5555chain 'J' and (resid 19 through 28 )JJ19 - 2817 - 26
5656chain 'J' and (resid 29 through 60 )JJ29 - 6027 - 58
5757chain 'J' and (resid 61 through 77 )JJ61 - 7759 - 75
5858chain 'J' and (resid 78 through 85 )JJ78 - 8576 - 83
5959chain 'J' and (resid 86 through 110 )JJ86 - 11084 - 108
6060chain 'J' and (resid 111 through 117 )JJ111 - 117109 - 115
6161chain 'K' and (resid 1 through 144 )KK1 - 1441 - 105
6262chain 'K' and (resid 145 through 341 )KK145 - 341106 - 300
6363chain 'K' and (resid 342 through 417 )KK342 - 417301 - 376
6464chain 'L' and (resid 3 through 28 )LL3 - 281 - 26
6565chain 'L' and (resid 29 through 60 )LL29 - 6027 - 58
6666chain 'L' and (resid 61 through 77 )LL61 - 7759 - 75
6767chain 'L' and (resid 78 through 117 )LL78 - 11776 - 115
6868chain 'M' and (resid 1 through 44 )MM1 - 441 - 25
6969chain 'M' and (resid 45 through 144 )MM45 - 14426 - 105
7070chain 'M' and (resid 145 through 170 )MM145 - 170106 - 131
7171chain 'M' and (resid 171 through 229 )MM171 - 229132 - 190
7272chain 'M' and (resid 230 through 274 )MM230 - 274191 - 235
7373chain 'M' and (resid 275 through 319 )MM275 - 319236 - 280
7474chain 'M' and (resid 320 through 355 )MM320 - 355281 - 314
7575chain 'M' and (resid 356 through 384 )MM356 - 384315 - 339
7676chain 'M' and (resid 385 through 417 )MM385 - 417340 - 372
7777chain 'N' and (resid 3 through 28 )NN3 - 281 - 26
7878chain 'N' and (resid 29 through 77 )NN29 - 7727 - 75
7979chain 'N' and (resid 78 through 110 )NN78 - 11076 - 108
8080chain 'N' and (resid 111 through 117 )NN111 - 117109 - 115
8181chain 'O' and (resid 1 through 44 )OO1 - 441 - 25
8282chain 'O' and (resid 45 through 144 )OO45 - 14426 - 105
8383chain 'O' and (resid 145 through 229 )OO145 - 229106 - 190
8484chain 'O' and (resid 230 through 349 )OO230 - 349191 - 303
8585chain 'O' and (resid 350 through 417 )OO350 - 417304 - 361
8686chain 'P' and (resid 3 through 28 )PP3 - 281 - 26
8787chain 'P' and (resid 29 through 67 )PP29 - 6727 - 65
8888chain 'P' and (resid 68 through 85 )PP68 - 8566 - 83
8989chain 'P' and (resid 86 through 110 )PP86 - 11084 - 108
9090chain 'P' and (resid 111 through 117 )PP111 - 117109 - 115
9191chain 'Q' and (resid 1 through 44 )QQ1 - 441 - 25
9292chain 'Q' and (resid 45 through 157 )QQ45 - 15726 - 117
9393chain 'Q' and (resid 158 through 229 )QQ158 - 229118 - 189
9494chain 'Q' and (resid 230 through 274 )QQ230 - 274190 - 234
9595chain 'Q' and (resid 275 through 319 )QQ275 - 319235 - 279
9696chain 'Q' and (resid 320 through 417 )QQ320 - 417280 - 375
9797chain 'R' and (resid 3 through 9 )RR3 - 91 - 7
9898chain 'R' and (resid 10 through 18 )RR10 - 188 - 16
9999chain 'R' and (resid 19 through 42 )RR19 - 4217 - 40
100100chain 'R' and (resid 43 through 67 )RR43 - 6741 - 65
101101chain 'R' and (resid 68 through 85 )RR68 - 8566 - 83
102102chain 'R' and (resid 86 through 117 )RR86 - 11784 - 115
103103chain 'S' and (resid 1 through 44 )SS1 - 441 - 25
104104chain 'S' and (resid 45 through 101 )SS45 - 10126 - 82
105105chain 'S' and (resid 102 through 229 )SS102 - 22983 - 189
106106chain 'S' and (resid 230 through 274 )SS230 - 274190 - 234
107107chain 'S' and (resid 275 through 319 )SS275 - 319235 - 279
108108chain 'S' and (resid 320 through 415 )SS320 - 415280 - 345
109109chain 'T' and (resid 3 through 18 )TT3 - 181 - 16
110110chain 'T' and (resid 19 through 28 )TT19 - 2817 - 26
111111chain 'T' and (resid 29 through 50 )TT29 - 5027 - 48
112112chain 'T' and (resid 51 through 60 )TT51 - 6049 - 58
113113chain 'T' and (resid 61 through 85 )TT61 - 8559 - 83
114114chain 'T' and (resid 86 through 110 )TT86 - 11084 - 108
115115chain 'T' and (resid 111 through 117 )TT111 - 117109 - 115
116116chain 'U' and (resid 1 through 44 )UU1 - 441 - 25
117117chain 'U' and (resid 45 through 144 )UU45 - 14426 - 105
118118chain 'U' and (resid 145 through 247 )UU145 - 247106 - 208
119119chain 'U' and (resid 248 through 274 )UU248 - 274209 - 235
120120chain 'U' and (resid 275 through 319 )UU275 - 319236 - 280
121121chain 'U' and (resid 320 through 384 )UU320 - 384281 - 324
122122chain 'U' and (resid 385 through 417 )UU385 - 417325 - 348
123123chain 'V' and (resid 3 through 18 )VV3 - 181 - 16
124124chain 'V' and (resid 19 through 42 )VV19 - 4217 - 40
125125chain 'V' and (resid 43 through 60 )VV43 - 6041 - 58
126126chain 'V' and (resid 61 through 77 )VV61 - 7759 - 75
127127chain 'V' and (resid 78 through 91 )VV78 - 9176 - 89
128128chain 'V' and (resid 92 through 117 )VV92 - 11790 - 115
129129chain 'W' and (resid 1 through 94 )WW1 - 941 - 75
130130chain 'W' and (resid 95 through 144 )WW95 - 14476 - 105
131131chain 'W' and (resid 145 through 229 )WW145 - 229106 - 190
132132chain 'W' and (resid 230 through 349 )WW230 - 349191 - 301
133133chain 'W' and (resid 350 through 417 )WW350 - 417302 - 350
134134chain 'X' and (resid 3 through 28 )XX3 - 281 - 26
135135chain 'X' and (resid 29 through 60 )XX29 - 6027 - 58
136136chain 'X' and (resid 61 through 85 )XX61 - 8559 - 83
137137chain 'X' and (resid 86 through 117 )XX86 - 11784 - 115
138138chain 'Y' and (resid 1 through 44 )YY1 - 441 - 25
139139chain 'Y' and (resid 45 through 144 )YY45 - 14426 - 105
140140chain 'Y' and (resid 145 through 274 )YY145 - 274106 - 235
141141chain 'Y' and (resid 275 through 319 )YY275 - 319236 - 280
142142chain 'Y' and (resid 320 through 395 )YY320 - 395281 - 354
143143chain 'Y' and (resid 396 through 417 )YY396 - 417355 - 376
144144chain 'Z' and (resid 3 through 18 )ZZ3 - 181 - 16
145145chain 'Z' and (resid 19 through 42 )ZZ19 - 4217 - 40
146146chain 'Z' and (resid 43 through 117 )ZZ43 - 11741 - 115
147147chain 'a' and (resid 1 through 44 )aAA1 - 441 - 25
148148chain 'a' and (resid 45 through 229 )aAA45 - 22926 - 190
149149chain 'a' and (resid 230 through 274 )aAA230 - 274191 - 235
150150chain 'a' and (resid 275 through 319 )aAA275 - 319236 - 280
151151chain 'a' and (resid 320 through 334 )aAA320 - 334281 - 295
152152chain 'a' and (resid 339 through 417 )aAA339 - 417296 - 357
153153chain 'b' and (resid 3 through 9 )bAB3 - 91 - 7
154154chain 'b' and (resid 10 through 18 )bAB10 - 188 - 16
155155chain 'b' and (resid 19 through 28 )bAB19 - 2817 - 26
156156chain 'b' and (resid 29 through 42 )bAB29 - 4227 - 40
157157chain 'b' and (resid 43 through 50 )bAB43 - 5041 - 48
158158chain 'b' and (resid 51 through 67 )bAB51 - 6749 - 65
159159chain 'b' and (resid 68 through 85 )bAB68 - 8566 - 83
160160chain 'b' and (resid 86 through 91 )bAB86 - 9184 - 89
161161chain 'b' and (resid 92 through 110 )bAB92 - 11090 - 108
162162chain 'b' and (resid 111 through 117 )bAB111 - 117109 - 115
163163chain 'c' and (resid 1 through 44 )cIB1 - 441 - 25
164164chain 'c' and (resid 45 through 157 )cIB45 - 15726 - 117
165165chain 'c' and (resid 158 through 229 )cIB158 - 229118 - 189
166166chain 'c' and (resid 230 through 349 )cIB230 - 349190 - 302
167167chain 'c' and (resid 350 through 417 )cIB350 - 417303 - 352
168168chain 'd' and (resid 3 through 28 )dJB3 - 281 - 26
169169chain 'd' and (resid 29 through 60 )dJB29 - 6027 - 58
170170chain 'd' and (resid 61 through 77 )dJB61 - 7759 - 75
171171chain 'd' and (resid 78 through 117 )dJB78 - 11776 - 115
172172chain 'e' and (resid 1 through 44 )eKB1 - 441 - 25
173173chain 'e' and (resid 45 through 144 )eKB45 - 14426 - 105
174174chain 'e' and (resid 145 through 229 )eKB145 - 229106 - 190
175175chain 'e' and (resid 230 through 349 )eKB230 - 349191 - 301
176176chain 'e' and (resid 350 through 417 )eKB350 - 417302 - 354
177177chain 'f' and (resid 3 through 18 )fLB3 - 181 - 16
178178chain 'f' and (resid 19 through 85 )fLB19 - 8517 - 83
179179chain 'f' and (resid 86 through 117 )fLB86 - 11784 - 115

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る