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- PDB-8cmf: Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV... -

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基本情報

登録情報
データベース: PDB / ID: 8cmf
タイトルHuman Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp3 epitope (orf1ab)1350-1364
要素
  • HLA class II histocompatibility antigen, DR alpha chain
  • Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
  • SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
キーワードIMMUNE SYSTEM / HLA-II / HLA-DR / HLA-DR1 / human leukocyte antigen / major histocompatibility complex / major histocompatibility complex class 2 / SARS-CoV-2 / coronavirus / COVID-19 / nsp3 / orf1ab
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 / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / early endosome membrane / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / adaptive immune response / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / lysosome / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / immune response / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / Golgi membrane / lysosomal membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication
類似検索 - 分子機能
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 / MHC classes I/II-like antigen recognition protein / : / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus ...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 / MHC classes I/II-like antigen recognition protein / : / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus
類似検索 - ドメイン・相同性
SUCCINIC ACID / HLA class II histocompatibility antigen, DR alpha chain / Replicase polyprotein 1ab
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者MacLachlan, B.J. / Mason, G.H. / Sourfield, D.O. / Godkin, A.J. / Rizkallah, P.J.
資金援助 英国, 1件
組織認可番号国
Other government 英国
引用ジャーナル: Cell Rep / 年: 2023
タイトル: Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
著者: Chen, Y. / Mason, G.H. / Scourfield, D.O. / Greenshields-Watson, A. / Haigh, T.A. / Sewell, A.K. / Long, H.M. / Gallimore, A.M. / Rizkallah, P. / MacLachlan, B.J. / Godkin, A.
履歴
登録2023年2月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年7月26日Provider: repository / タイプ: Initial release
改定 1.12023年8月2日Group: Database references / Refinement description / カテゴリ: citation / struct_ncs_dom_lim
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.22024年10月9日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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集合体

登録構造単位
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
D: HLA class II histocompatibility antigen, DR alpha chain
E: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
F: SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,45712
ポリマ－90,9736
非ポリマー4846
水3,531196
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,6665
ポリマ－45,4863
非ポリマー1802
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
F: SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,7917
ポリマ－45,4863
非ポリマー3044
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)60.230, 95.490, 202.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,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 "A" and (resid 2 through 49 or resid 51...
d_2ens_1(chain "D" and (resid 2 through 49 or resid 51...
d_1ens_2(chain "B" and (resid 2 through 47 or resid 49...
d_2ens_2(chain "E" and (resid 2 through 47 or resid 49...
d_1ens_3chain "C"
d_2ens_3chain "F"

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_1LYSLYSGLYGLYAA2 - 493 - 50
d_12ens_1PHEPHEALAALAAA51 - 5652 - 57
d_13ens_1GLYGLYTHRTHRAA58 - 7459 - 75
d_14ens_1ARGARGVALVALAA76 - 8977 - 90
d_15ens_1VALVALLEULEUAA91 - 9992 - 100
d_16ens_1PROPROCYSCYSAA102 - 107103 - 108
d_17ens_1ILEILEPHEPHEAA109 - 145110 - 146
d_18ens_1LYSLYSPHEPHEAA147 - 180148 - 181
d_21ens_1LYSLYSGLYGLYDD2 - 493 - 50
d_22ens_1PHEPHEALAALADD51 - 5652 - 57
d_23ens_1GLYGLYTHRTHRDD58 - 7459 - 75
d_24ens_1ARGARGVALVALDD76 - 8977 - 90
d_25ens_1VALVALLEULEUDD91 - 9992 - 100
d_26ens_1PROPROCYSCYSDD102 - 107103 - 108
d_27ens_1ILEILEPHEPHEDD109 - 145110 - 146
d_28ens_1LYSLYSPHEPHEDD147 - 180148 - 181
d_11ens_2ASPASPTYRTYRBB2 - 476 - 51
d_12ens_2ALAALATHRTHRBB49 - 5153 - 55
d_13ens_2LEULEUALAALABB53 - 5857 - 62
d_14ens_2TYRTYRGLNGLNBB60 - 6464 - 68
d_15ens_2ASPASPGLUGLUBB66 - 6970 - 73
d_16ens_2ARGARGVALVALBB71 - 9175 - 95
d_17ens_2ARGARGSERSERBB93 - 10497 - 108
d_18ens_2THRTHRGLNGLNBB106 - 110110 - 114
d_19ens_2HISHISPROPROBB112 - 165116 - 169
d_110ens_2SERSERALAALABB167 - 190171 - 194
d_21ens_2ASPASPTYRTYREE2 - 476 - 51
d_22ens_2ALAALATHRTHREE49 - 5153 - 55
d_23ens_2LEULEUALAALAEE53 - 5857 - 62
d_24ens_2TYRTYRGLNGLNEE60 - 6464 - 68
d_25ens_2ASPASPGLUGLUEE66 - 6970 - 73
d_26ens_2ARGARGVALVALEE71 - 9175 - 95
d_27ens_2ARGARGSERSEREE93 - 10497 - 108
d_28ens_2THRTHRGLNGLNEE106 - 110110 - 114
d_29ens_2HISHISPROPROEE112 - 165116 - 169
d_210ens_2SERSERALAALAEE167 - 190171 - 194
d_11ens_3LYSLYSLYSLYSCC1 - 151 - 15
d_21ens_3LYSLYSLYSLYSFF1 - 151 - 15

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.990036658124, -0.136488704812, -0.0346157338473), (-0.0808432766885, 0.349688000797, 0.933371665904), (-0.115289983022, 0.926870614248, -0.357238133823)-27.9676943071, -41.3560611602, 54.9510774736
2given(-0.992846776376, -0.11375269969, -0.0362712276122), (-0.0721860233779, 0.329922590404, 0.941243997256), (-0.0951023483836, 0.937129344143, -0.335773935375)-27.4267100284, -41.5426436822, 55.6589900053
3given(-0.987100613449, -0.150638668597, -0.0542251828212), (-0.101681139137, 0.328245330232, 0.939103801038), (-0.123666183221, 0.932503616457, -0.339328278254)-28.0951018488, -42.6460114512, 54.7086068801

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要素

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タンパク質 , 2種, 4分子 ADBE

#1: タンパク質 HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


分子量: 21287.102 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: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P01903
#2: タンパク質 Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)


分子量: 22487.186 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: Escherichia coli BL21(DE3) (大腸菌)

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タンパク質・ペプチド , 1種, 2分子 CF

#3: タンパク質・ペプチド SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364


分子量: 1711.996 Da / 分子数: 2 / 由来タイプ: 合成
由来: (合成) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
参照: UniProt: P0DTD1

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非ポリマー , 3種, 202分子

#4: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物 ChemComp-SIN / SUCCINIC ACID / コハク酸


分子量: 118.088 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H6O4
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 196 / 由来タイプ: 天然 / 式: H2O

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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: 3.2 Å3/Da / 溶媒含有率: 61.56 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4.6 / 詳細: 0.1 M SPG pH 4.6, 25 % PEG1500

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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: Diamond / ビームライン: I04 / 波長: 0.9795 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2021年7月5日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9795 Å / 相対比: 1
反射解像度: 2.2→55.11 Å / Num. obs: 60213 / % possible obs: 99.9 % / 冗長度: 27.9 % / Biso Wilson estimate: 44.49 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.0663 / Rrim(I) all: 0.351 / Net I/σ(I): 9.39
反射 シェル解像度: 2.2→2.28 Å / Rmerge(I) obs: 4.163 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 5910 / CC1/2: 0.517 / CC star: 0.914 / Rpim(I) all: 0.818 / Rrim(I) all: 4.244 / % possible all: 98.89

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2-4158精密化
XSCALEデータスケーリング
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.2→55.11 Å / SU ML: 0.2457 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 31.2058
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2397 2972 4.95 %
Rwork0.2072 57057 -
obs0.2088 60029 99.64 %
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: 62.96 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→55.11 Å
タンパク質核酸リガンド溶媒全体
原子数6336 0 32 196 6564
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00556568
X-RAY DIFFRACTIONf_angle_d0.81638928
X-RAY DIFFRACTIONf_chiral_restr0.0538954
X-RAY DIFFRACTIONf_plane_restr0.00681171
X-RAY DIFFRACTIONf_dihedral_angle_d14.40652420
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.645797162631
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.834152045292
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.841456506443
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.3761290.37392642X-RAY DIFFRACTION98.05
2.24-2.270.38161370.36242672X-RAY DIFFRACTION99.65
2.27-2.320.39961410.34392715X-RAY DIFFRACTION99.86
2.32-2.360.34021510.32892632X-RAY DIFFRACTION99.36
2.36-2.410.36721390.32712699X-RAY DIFFRACTION99.27
2.41-2.460.36741580.31182623X-RAY DIFFRACTION99.43
2.46-2.520.31021350.29292716X-RAY DIFFRACTION99.51
2.52-2.580.33151340.28032664X-RAY DIFFRACTION99.89
2.58-2.650.31381520.27642692X-RAY DIFFRACTION99.75
2.65-2.730.2871290.25542718X-RAY DIFFRACTION99.65
2.73-2.820.31811330.23742693X-RAY DIFFRACTION99.61
2.82-2.920.29731390.23172688X-RAY DIFFRACTION99.72
2.92-3.030.26341310.24822718X-RAY DIFFRACTION99.82
3.03-3.170.2681660.25292708X-RAY DIFFRACTION99.86
3.17-3.340.28371530.22982709X-RAY DIFFRACTION99.76
3.34-3.550.2241500.20212725X-RAY DIFFRACTION99.86
3.55-3.820.22241420.19262726X-RAY DIFFRACTION99.93
3.82-4.210.21931240.17112770X-RAY DIFFRACTION99.97
4.21-4.820.16111300.13542796X-RAY DIFFRACTION100
4.82-6.070.14561290.14752831X-RAY DIFFRACTION99.97
6.07-55.110.19891700.16772920X-RAY DIFFRACTION99.68
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.41306561692-2.004946320090.5710983667485.789477476323.695992376279.08926684613-0.0693858623655-0.4323465361880.08367447366722.17331997147-0.00377299804374-0.9187753706610.346934005147-0.8925369947970.1824944775350.8691755987750.0611733015136-0.1504573961390.8206058845570.04640806999070.364803958747-24.2331339929-13.845952873839.7575965678
22.02534018188-0.6030063753451.008236006764.496811594371.297632949924.66533812211-0.01107991001740.0177068976092-0.100865866451-0.0372451074946-0.0371030123462-0.1736688207270.348850243088-0.04450543981750.08057110936680.510301207402-0.02831571091190.002681264787790.4294274815620.008125432342470.297896402062-21.5521281524-26.91957422696.99761027991
34.396050415551.110826084481.787156039022.18063861530.3693084997042.38864327633-0.5854905252020.158952400350.682304897904-0.4597758805390.0531915282571-0.0718543315877-1.558670596370.1230790565640.417801662911.267169807350.019022938196-0.2415911628460.438019216147-0.03084031400190.537935104409-10.98327264826.0458952364125.3188051551
47.07603586231-4.247793928980.03797305894746.831264029612.871501637065.22867463010.101635357140.171534047103-0.8687353563480.282701218144-0.5082532765281.209734935350.692404088302-0.435918001730.3759904231150.430980348396-0.153908103438-0.0201899605410.648299492373-0.05931280482840.3747926213-31.115738721-30.20541174534.70150630129
54.38556339731.48390274028-2.901867980035.56681828504-3.045303164815.22972104766-0.2785296884610.302952076659-0.17121560249-0.117110993160.1449184262940.08076561979120.281109381483-0.3820417129740.1387572246550.4523907951920.0208916667227-0.03271596224370.306955133581-0.02116006391990.2690811864761.55427048297-33.814992977331.561183958
64.18542588865-2.220653680330.5848514692187.652651750521.771683739339.008169162660.129687662103-0.5891376939740.2179889570980.2121584341740.153585981872-0.76184902896-0.1315045696781.1701556697-0.2817692047380.527761215838-0.0587195381634-0.0700829964480.4617987329920.0160433990650.413527471569.56347890153-32.176680735841.8631233483
70.942102986746-0.432954287588-0.4099488939973.213201977831.710528784182.50853790869-0.101034403675-0.03520229260.0814376069945-0.0954895383373-0.0358616454502-0.0404688064853-0.3779063941160.2229822053170.1213368367830.470153394364-0.008726378534180.02582513056220.2729246306440.01083856340.2900782569112.5161862736-20.506862842330.0236236269
81.0366491468-0.1786802321261.146862961196.597262729335.573849687745.89733998953-0.0289408492204-0.008427525622440.03761980484970.1196165401840.20080498805-0.153613130416-0.0852981402030.351417569029-0.04292874090730.4659424702930.0172567799530.02019633892810.2854687946010.01366743345930.3132293273660.0558529130018-15.686403990535.5189315914
91.141161777641.612618180331.416431602327.269542413894.094404333482.483687909230.08410570316460.2800733123930.274025943537-1.53241516805-0.6021510864050.374679855753-1.83420354751-0.6480375024160.6063563960350.8651604763940.117082878589-0.1311765342420.3037339441850.01376847483450.365620234018-3.76236185882-7.3702804983430.6981284638
102.032469473610.417093379265-1.230460730244.34337860248-1.575372433487.183290858370.170870815603-0.074218672892-0.0306208522381-0.335417273299-0.02965482441380.05455710234720.3884871573650.173398635175-0.1310034734220.4204840631740.0330511113435-0.05124453967780.253432070291-0.02365423184620.353184689998-2.87513874777-36.442555011727.8320126886
110.7976016574680.3420019491270.8725555476534.542369573840.789295277013.44073690650.1243973080670.135600911409-0.258592042534-0.307264402055-0.00298086104227-0.1025567335040.9942196753040.0373832602139-0.1166444494850.4227355890620.01218028076140.0171241948740.2862632993640.004282706112260.373086942607-2.99682744343-45.038387591130.7357262779
128.73790988946-5.22159147418-2.723843063165.830423449542.17047669065.86510235162-0.196153295727-0.4385202144120.09435967081620.5663836630480.003254153105850.420504452594-0.671870437203-0.9032485588690.2410024349480.6609654181390.0763740305827-0.02249422178580.4903402353-0.05276500853170.36000868074-18.122647079-14.903227072354.1405807188
135.684573547781.169742465422.023791287136.0862353884-1.363771461091.200421208640.164631796690.366451695183-0.309872737929-0.4936015462940.278586319048-0.4966537561911.120422690670.354803766215-0.426771795660.3709223861590.158305450670.01780113873840.327272358821-0.02695708919440.4946335446666.92704659293-44.975837655628.7892642793
145.535318697512.18774442704-0.3485881713336.8139224144-0.2871959866176.31342485351-0.00893535541064-0.193449295861-0.14454433191-0.0892293031282-0.2544958951950.2622845808770.725252356485-0.4315152276840.2788055568710.615972504702-0.0297904606478-0.03921354428870.524922180002-0.02389005100420.268443260287-27.1540934808-23.164043524814.3057117038
159.387788555092.951134242571.212091904385.637983375391.952402528385.440653803830.072001781777-1.122102422180.5823620759590.0640646110718-0.4372912930990.935531259683-0.391989921178-1.568212954110.3218958301360.6070972182230.217604577679-0.1207645158650.850415635198-0.1547253839830.483550320457-36.4254574083-14.448050327712.0737441517
166.69661337529-3.83992786153.810616641218.135358222220.08724040966646.208612286190.24419870582-0.471730315995-0.4037554163680.155428360628-0.1649941027760.3427312481921.03870597783-1.00811754076-0.1811206093380.722789352953-0.2635609603420.01904806150640.669795604522-0.03835130702540.433162421443-32.4673843978-36.151164219713.8291813286
173.168335991280.7328284856511.300451148533.860523665611.10696298944.58233582788-0.278488924635-0.7779774186660.45641098850.4631662360930.539622214059-0.3651326071480.19387084659-0.88706452874-0.07650768156710.8695330239640.0169770900825-0.03071243358420.696299091136-0.02064467220720.29766853294-23.6020165821-15.763889455830.5722963032
182.376347373690.3153761811010.2812191285084.564753348930.8299392892744.96220341372-0.0998591650773-0.5714648166070.313352307960.503560942353-0.05891048193360.492909449657-0.332764782441-1.551794505690.1417640249940.6708201493490.203678241702-0.05947486538050.882308498207-0.08976941042920.399785726545-30.5759609505-12.758945857733.1453183439
192.86412547151-1.75005148996-0.07101486946886.859923377053.143781292696.94132262377-0.248097253135-0.3861639536580.2804874531280.317257931626-0.04596267279520.490857146521-0.592670938995-0.8812322296390.3044672860890.6050822514930.184877911412-0.08689798986590.740263752262-0.07657728960360.384585317795-27.7472194626-12.66840515130.2409222353
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 167 through 182 )AA167 - 182166 - 181
22chain 'B' and (resid 2 through 97 )BB2 - 971 - 96
33chain 'B' and (resid 98 through 190 )BB98 - 19097 - 189
44chain 'C' and (resid 1 through 15 )CC1 - 151 - 15
55chain 'D' and (resid 2 through 26 )DD2 - 261 - 25
66chain 'D' and (resid 27 through 55 )DD27 - 5526 - 54
77chain 'D' and (resid 56 through 133 )DD56 - 13355 - 132
88chain 'D' and (resid 134 through 166 )DD134 - 166133 - 165
99chain 'D' and (resid 167 through 182 )DD167 - 182166 - 181
1010chain 'E' and (resid 0 through 32 )EE0 - 321 - 33
1111chain 'E' and (resid 33 through 97 )EE33 - 9734 - 98
1212chain 'E' and (resid 98 through 190 )EE98 - 19099 - 191
1313chain 'F' and (resid 1 through 15 )FF1 - 151 - 15
1414chain 'A' and (resid 2 through 26 )AA2 - 261 - 25
1515chain 'A' and (resid 27 through 55 )AA27 - 5526 - 54
1616chain 'A' and (resid 56 through 76 )AA56 - 7655 - 75
1717chain 'A' and (resid 77 through 101 )AA77 - 10176 - 100
1818chain 'A' and (resid 102 through 133 )AA102 - 133101 - 132
1919chain 'A' and (resid 134 through 166 )AA134 - 166133 - 165

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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