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- PDB-8cme: 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: 8cme
タイトルHuman Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Membrane peptide M176-190
要素
  • HLA class II histocompatibility antigen, DR alpha chain
  • Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
  • Membrane protein膜タンパク質
キーワードIMMUNE SYSTEM (免疫系) / HLA-II / HLA-DR / HLA-DR1 / human leukocyte antigen (ヒト白血球型抗原) / major histocompatibility complex (主要組織適合遺伝子複合体) / major histocompatibility complex class 2 / SARS-CoV-2 (SARSコロナウイルス2) / coronavirus (オルトコロナウイルス亜科) / COVID-19 (新型コロナウイルス感染症 (2019年)) / Membrane (生体膜)
機能・相同性
機能・相同性情報


Maturation of protein M / SARS-CoV-2 modulates autophagy / cytoplasmic capsid assembly / 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 ...Maturation of protein M / SARS-CoV-2 modulates autophagy / cytoplasmic capsid assembly / 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 / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / Generation of second messenger molecules / 免疫シナプス / endoplasmic reticulum-Golgi intermediate compartment / PD-1 signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / T cell receptor binding / MHC class II antigen presentation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / VEGFR2 mediated vascular permeability / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / 認識 / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / PIP3 activates AKT signaling / MHC class II protein complex binding / late endosome membrane / TRAF3-dependent IRF activation pathway / early endosome membrane / Translation of Structural Proteins / Virion Assembly and Release / 獲得免疫系 / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / リソソーム / 免疫応答 / lysosomal membrane / virus-mediated perturbation of host defense response / ゴルジ体 / エンベロープ (ウイルス) / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / 細胞膜 / extracellular exosome / identical protein binding / 細胞膜
類似検索 - 分子機能
M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile. / 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 / Immunoglobulin/major histocompatibility complex, conserved site ...M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile. / 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 / 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
HLA class II histocompatibility antigen, DR alpha chain / 膜タンパク質
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.26 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

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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: Membrane protein
D: HLA class II histocompatibility antigen, DR alpha chain
E: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
F: Membrane protein
G: HLA class II histocompatibility antigen, DR alpha chain
H: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
I: Membrane protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,53212
ポリマ－136,2129
非ポリマー3193
水1,60389
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: Membrane protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,6615
ポリマ－45,4043
非ポリマー2572
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: Membrane protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,4664
ポリマ－45,4043
非ポリマー621
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: HLA class II histocompatibility antigen, DR alpha chain
H: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
I: Membrane protein


分子量 (理論値)分子数
合計 (水以外)45,4043
ポリマ－45,4043
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)113.374, 156.766, 165.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDモデル要素
11C-102-

HOH

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 5 through 45 or resid 48...
d_2ens_1(chain "D" and (resid 5 through 45 or resid 48...
d_3ens_1(chain "G" and (resid 5 through 45 or resid 48...
d_1ens_2(chain "B" and (resid 1 through 22 or resid 24...
d_2ens_2(chain "E" and (resid 1 through 22 or resid 24...
d_3ens_2(chain "H" and (resid 1 through 22 or resid 24...
d_1ens_3(chain "C" and (resid 1 through 10 or resid 12 through 14))
d_2ens_3(chain "F" and (resid 1 through 10 or resid 12 through 14))
d_3ens_3(chain "I" and (resid 1 through 10 or resid 12 through 14))

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_1HISHISLEULEUAA5 - 456 - 46
d_12ens_1PHEPHEGLYGLYAA48 - 4949 - 50
d_13ens_1PHEPHETHRTHRAA51 - 9352 - 94
d_14ens_1SERSERLEULEUAA95 - 9996 - 100
d_15ens_1PROPROCYSCYSAA102 - 107103 - 108
d_16ens_1ILEILEGLYGLYAA109 - 125110 - 126
d_17ens_1PROPROASPASPAA127 - 181128 - 182
d_21ens_1HISHISLEULEUDD5 - 456 - 46
d_22ens_1PHEPHEGLYGLYDD48 - 4949 - 50
d_23ens_1PHEPHETHRTHRDD51 - 9352 - 94
d_24ens_1SERSERLEULEUDD95 - 9996 - 100
d_25ens_1PROPROCYSCYSDD102 - 107103 - 108
d_26ens_1ILEILEGLYGLYDD109 - 125110 - 126
d_27ens_1PROPROASPASPDD127 - 181128 - 182
d_31ens_1HISHISLEULEUGG5 - 456 - 46
d_32ens_1PHEPHEGLYGLYGG48 - 4949 - 50
d_33ens_1PHEPHETHRTHRGG51 - 9352 - 94
d_34ens_1SERSERLEULEUGG95 - 9996 - 100
d_35ens_1PROPROCYSCYSGG102 - 107103 - 108
d_36ens_1ILEILEGLYGLYGG109 - 125110 - 126
d_37ens_1PROPROASPASPGG127 - 181128 - 182
d_11ens_2GLYGLYGLUGLUBB1 - 225 - 26
d_12ens_2VALVALGLNGLNBB24 - 3428 - 38
d_13ens_2GLUGLUTHRTHRBB36 - 5140 - 55
d_14ens_2LEULEUGLNGLNBB53 - 6457 - 68
d_15ens_2ASPASPVALVALBB66 - 9170 - 95
d_16ens_2ARGARGPROPROBB93 - 9797 - 101
d_17ens_2VALVALTHRTHRBB99 - 106103 - 110
d_18ens_2PROPROGLNGLNBB108 - 110112 - 114
d_19ens_2HISHISILEILEBB112 - 127116 - 131
d_110ens_2VALVALGLUGLUBB129 - 137133 - 141
d_111ens_2LYSLYSPROPROBB139 - 165143 - 169
d_112ens_2SERSERCYSCYSBB167 - 173171 - 177
d_113ens_2VALVALTRPTRPBB175 - 188179 - 192
d_114ens_2ALAALAALAALABB190194
d_21ens_2GLYGLYGLUGLUEE1 - 225 - 26
d_22ens_2VALVALGLNGLNEE24 - 3428 - 38
d_23ens_2GLUGLUTHRTHREE36 - 5140 - 55
d_24ens_2LEULEUGLNGLNEE53 - 6457 - 68
d_25ens_2ASPASPVALVALEE66 - 9170 - 95
d_26ens_2ARGARGPROPROEE93 - 9797 - 101
d_27ens_2VALVALTHRTHREE99 - 106103 - 110
d_28ens_2PROPROGLNGLNEE108 - 110112 - 114
d_29ens_2HISHISILEILEEE112 - 127116 - 131
d_210ens_2VALVALGLUGLUEE129 - 137133 - 141
d_211ens_2LYSLYSPROPROEE139 - 165143 - 169
d_212ens_2SERSERCYSCYSEE167 - 173171 - 177
d_213ens_2VALVALTRPTRPEE175 - 188179 - 192
d_214ens_2ALAALAALAALAEE190194
d_31ens_2GLYGLYGLUGLUHH1 - 225 - 26
d_32ens_2VALVALGLNGLNHH24 - 3428 - 38
d_33ens_2GLUGLUTHRTHRHH36 - 5140 - 55
d_34ens_2LEULEUGLNGLNHH53 - 6457 - 68
d_35ens_2ASPASPVALVALHH66 - 9170 - 95
d_36ens_2ARGARGPROPROHH93 - 9797 - 101
d_37ens_2VALVALTHRTHRHH99 - 106103 - 110
d_38ens_2PROPROGLNGLNHH108 - 110112 - 114
d_39ens_2HISHISILEILEHH112 - 127116 - 131
d_310ens_2VALVALGLUGLUHH129 - 137133 - 141
d_311ens_2LYSLYSPROPROHH139 - 165143 - 169
d_312ens_2SERSERCYSCYSHH167 - 173171 - 177
d_313ens_2VALVALTRPTRPHH175 - 188179 - 192
d_314ens_2ALAALAALAALAHH190194
d_11ens_3LEULEUGLNGLNCC1 - 101 - 10
d_12ens_3VALVALGLYGLYCC12 - 1412 - 14
d_21ens_3LEULEUGLNGLNFF1 - 101 - 10
d_22ens_3VALVALGLYGLYFF12 - 1412 - 14
d_31ens_3LEULEUGLNGLNII1 - 101 - 10
d_32ens_3VALVALGLYGLYII12 - 1412 - 14

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.317943607386, 0.945634108962, 0.0684689308394), (0.94444596027, 0.322230546086, -0.0647248275238), (-0.0832687855775, 0.044086359985, -0.995551456335)-34.4544032584, -34.9627124547, -52.1702946145
2given(0.783358103363, 0.610344023449, -0.117602104299), (0.602032957475, -0.792095169526, -0.100705315294), (-0.154616946061, 0.00808798213105, -0.987941387197)-23.9421762677, 64.832292334, -18.1929277992
3given(-0.328394366062, 0.941684891305, 0.0733941811558), (0.941349533047, 0.332677279573, -0.0564524958448), (-0.0775770389369, 0.0505508965738, -0.995703977036)-33.2292163377, -35.2377881116, -53.260593559
4given(0.792407618497, 0.601480038179, -0.101547672652), (0.595566340146, -0.79886232317, -0.0843784516616), (-0.131874564014, 0.00638375218218, -0.991245856019)-23.4407666848, 66.3058770428, -20.0366696078
5given(-0.314227441516, 0.948668706044, 0.035899877036), (0.938308271519, 0.316101448679, -0.140205070318), (-0.144356165778, -0.0103711289642, -0.98947144329)-36.0155047134, -36.3381301502, -43.4590127076
6given(0.78120004246, 0.594854987693, -0.189404427816), (0.592040685374, -0.802174764325, -0.0774820904524), (-0.198026060208, -0.0516061149061, -0.978837314564)-24.9347175252, 67.0645197239, -10.2431221807

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要素

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タンパク質 , 2種, 6分子 ADGBEH

#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: 3 / 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: 3 / 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, 3分子 CFI

#3: タンパク質・ペプチド Membrane protein / 膜タンパク質 / M / E1 glycoprotein / Matrix glycoprotein / Membrane glycoprotein


分子量: 1629.814 Da / 分子数: 3 / 由来タイプ: 合成
由来: (合成) Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
参照: UniProt: P0DTC5

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非ポリマー , 3種, 92分子

#4: 化合物 ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸 / MES (緩衝剤)


分子量: 195.237 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H13NO4S / コメント: pH緩衝剤*YM
#5: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル / エチレングリコール


分子量: 62.068 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H6O2
#6: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 89 / 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

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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: 2.7 Å3/Da / 溶媒含有率: 54.42 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5 / 詳細: 0.1 M MES pH 5.0, 20 % PEG3350

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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: 2022年1月28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: 2.26→47.29 Å / Num. obs: 69030 / % possible obs: 99.81 % / 冗長度: 13.7 % / Biso Wilson estimate: 62.91 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0996 / Rpim(I) all: 0.0279 / Rrim(I) all: 0.104 / Net I/σ(I): 16.05
反射 シェル解像度: 2.26→2.34 Å / Rmerge(I) obs: 3.099 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6779 / CC1/2: 0.378 / CC star: 0.741 / Rpim(I) all: 0.867 / Rrim(I) all: 3.219 / % possible all: 98.96

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解析

ソフトウェア
名称バージョン分類
DIALSデータスケーリング
DIALSデータ削減
PHASER位相決定
PHENIX1.19.2-4158精密化
精密化構造決定の手法: 分子置換 / 解像度: 2.26→47.28 Å / SU ML: 0.4203 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.872
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2401 3407 4.94 %
Rwork0.198 65570 -
obs0.2001 68977 99.78 %
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: 74.35 Å2
精密化ステップサイクル: LAST / 解像度: 2.26→47.28 Å
タンパク質核酸リガンド溶媒全体
原子数9520 0 20 89 9629
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00469827
X-RAY DIFFRACTIONf_angle_d0.788113365
X-RAY DIFFRACTIONf_chiral_restr0.05121424
X-RAY DIFFRACTIONf_plane_restr0.00691753
X-RAY DIFFRACTIONf_dihedral_angle_d13.5033613
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.693843788776
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.554098522297
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.796877590522
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.934620605633
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.631271181572
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.71170316758
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.290.43791180.41412606X-RAY DIFFRACTION96.66
2.29-2.330.40051460.37662707X-RAY DIFFRACTION99.79
2.33-2.360.36331490.34612743X-RAY DIFFRACTION99.86
2.36-2.40.3591400.33712689X-RAY DIFFRACTION99.82
2.4-2.440.28881320.30482690X-RAY DIFFRACTION99.89
2.44-2.490.3581500.29042712X-RAY DIFFRACTION99.93
2.49-2.530.31271360.28452714X-RAY DIFFRACTION99.89
2.53-2.590.29991270.27442714X-RAY DIFFRACTION99.89
2.59-2.640.33051440.28452698X-RAY DIFFRACTION99.96
2.64-2.70.30621360.28452746X-RAY DIFFRACTION99.97
2.7-2.770.33491360.28562732X-RAY DIFFRACTION99.97
2.77-2.850.31091360.28112746X-RAY DIFFRACTION99.97
2.85-2.930.31531550.26762702X-RAY DIFFRACTION99.93
2.93-3.020.34351480.26912714X-RAY DIFFRACTION100
3.02-3.130.30571500.26032718X-RAY DIFFRACTION99.93
3.13-3.260.28581350.23442730X-RAY DIFFRACTION100
3.26-3.410.26251670.24232712X-RAY DIFFRACTION100
3.41-3.590.27441510.21072746X-RAY DIFFRACTION100
3.59-3.810.21831380.18732734X-RAY DIFFRACTION100
3.81-4.10.21131290.17742765X-RAY DIFFRACTION100
4.1-4.520.18261490.14052758X-RAY DIFFRACTION100
4.52-5.170.17591370.13332801X-RAY DIFFRACTION100
5.17-6.510.19051460.15622806X-RAY DIFFRACTION100
6.51-47.280.2021520.15172887X-RAY DIFFRACTION99.28
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)
17.86941576419-5.28737029968-3.699738056243.895169320013.613647157916.75765076048-0.497395713198-0.365367586958-0.1448773007180.8756206916160.1883606558320.1486387563280.565756435292-0.05434309960230.2592546731430.679612134772-0.1077456573650.01168720630210.3863032862280.1016421281930.4518926042467.557163746275.4440980207-23.2317818058
24.5011883231-1.702389916550.3059812573864.79815956844-0.5879009986992.461427189540.2356657170890.439023234224-0.0751318495056-0.69154773099-0.279855810059-0.3310820592820.1736165876240.2296266099610.03995055235530.537930723174-0.0366345878351-0.03175851988740.4584418920510.04966500362340.39515401602169.458256067969.8184253383-33.7467020529
36.825351427232.6025793818-0.2200078409291.725434087151.168329851682.09841547928-0.256727571455-0.4298647477540.3715020198570.0906603638129-0.03301751234150.609740342662-0.176917948585-0.2549621580340.3248134221140.626511979108-0.174683373969-0.09735109013010.5089895037290.08728372008110.59847016733242.81520198160.2552884867-22.7246938099
44.582143062280.473463130061-0.2111197805992.12218897841-0.4335212645960.0657472959145-0.02224637095110.2400119868910.0958843082066-0.220322628657-0.0313314134418-0.03815592362890.1285710316-0.09657080328720.004128079429320.613471142437-0.102156369745-0.07361993545720.513174941610.1078273340810.45915265069356.028224705259.6817788937-28.0637924536
57.386684167571.27174760355-0.9196420647631.43468439656-0.4383079606391.995367717730.226448788914-0.348397871409-1.2867919276-0.306524226052-0.1421054307920.02049816754190.522135244141-0.188835796215-0.09081627194430.710913939399-0.112454000614-0.1373451096410.4913897916360.1231025910640.60014328066950.385552209450.3479663206-24.9273789037
62.95985044983-1.74032299321-1.38764909015.286097102881.744216704453.312454839570.0785774949932-0.09038651084020.0324603443980.109999241114-0.347975245629-0.6737903985150.05177484174550.3875057880020.2651405458490.522382968138-0.0628484879687-0.1186430343670.5937878219660.1380742341160.56070054115679.291912562173.1342774664-22.9272035899
75.357123431061.62213909264-1.027215145112.89476281203-1.28886565761.854586853450.1347615433780.3060368743240.09828725499650.2859966139680.0113249403964-0.0682568643571-0.144579986944-0.163626970191-0.1588212399350.532290039757-0.058596214235-0.1339500258040.36848782338-0.06498872902310.30861953870656.867940600677.9434883676-20.179499763
86.66166000731.49121609813-3.771221011052.9979321756-2.710748303315.768251605890.34903710361-0.4563190190420.1218709246680.3809497996270.03719085180330.458871908278-0.400058365249-0.143450548527-0.357633928160.510200572145-0.100998338503-0.07478560156030.4785254501740.05064523922280.54552166951440.695748952770.5842982831-8.14359535753
95.22294877498-5.322050585446.644436666375.68598161866-7.173997810668.063027737071.173998608372.81100671701-0.311280363522-1.28732781791-1.42155194492-0.2963668619720.1401457598880.842956030173-0.096473849730.604490192114-0.05793812236810.01792649960760.578475560697-0.02904814625080.65266793661476.24042330478.9911944097-34.7843602942
100.1065030705540.524715270427-0.3183566494271.086826718980.0640317567392-0.132548033851-0.12033158607-0.0384272184210.125029107369-0.3029620892670.1497428954690.236762569053-0.2752232716560.0908829306367-0.01197545734280.64702471986-0.165772242399-0.2389208488960.6170735007850.1336913442440.7737112699819.5463594476854.8022266707-26.7164201157
114.62441480009-1.7077205853-5.088246080716.926794821452.881498651975.85493613016-0.207360214448-0.4628975862970.01500430891590.3330834629240.225838721344-0.1131729509760.3366828882820.0560493881522-0.01809434817480.591601476524-0.113970394606-0.2352193058420.5896145384020.146643315920.52173482597316.513970242148.6090144813-17.9347853979
121.605532671751.185998344250.3236880803576.237212660140.7703174720941.73309698014-0.1460975033420.04831609864860.619168312602-0.288507766991-0.006540487163220.890072233351-0.426500157476-0.2167897175190.04889350988140.518626274121-0.077723607154-0.172812226620.5331757958190.1286578156220.6084934155531.303480306351.053905512-26.3248726771
131.987486992410.647630211820.9905672942175.282718701470.342505071261.13902093136-0.07000210126780.1082739548280.2914698325670.161496581378-0.1164201015050.116715386766-0.06800752547450.08830152479210.1584933383570.509871300267-0.121892411696-0.1385090564620.5646268693130.0864440411370.419251679669-0.18650783440235.8440230964-27.3613970569
146.999963528970.566558765188-1.829408886581.127600180430.2456797125441.81446872832-0.08394313535610.4635452314340.581288218682-0.3811297430060.08121750555980.50397927805-0.130361546888-0.114818507272-0.0405176894680.779533345068-0.15360150696-0.2994146363280.6384768065220.2692334757370.8234853230428.2325733663959.0700644805-31.278727629
153.017763023612.89332129855-1.937757222645.16077387619-2.930263787224.05590807729-0.4117566437420.6828564202430.861482087405-0.6338960061540.4599932108570.8289044700560.261918771117-0.489983680317-0.09761088479870.913418552136-0.21985536879-0.4191408292380.8039982027080.4216153122181.023527389528.3300905552867.8343114776-36.5956243797
163.612917278293.86021682681-3.243523238757.69848777421-2.245436374963.485601800420.222559893113-0.04329152154911.424944081660.0385980502231-0.1660644947581.81386814145-0.890519811056-0.801785951163-0.4521760846110.9265770715920.00346845897039-0.2047685577750.8424548138720.3904672710391.604455347434.0533074984675.3566938832-32.3550266135
172.76539268198-3.81276959328-0.1466422821786.96750463026-1.02867279291.24480479961-0.173677064679-0.2322908346480.9521132824280.6806702594310.358230613238-0.32689917269-0.6967409309450.0817092471526-0.1198646538620.859661107711-0.254735546722-0.2175879481130.682000987090.1862465705881.0506027963219.389660551472.0128529626-28.4392214561
181.357304116610.6610718296821.296531342096.232731983993.539081264162.36015281212-0.1096932811180.296821580621-0.0551510261883-0.124928069550.27980464639-0.0623034397705-0.05143843517720.285774260389-0.2252136166420.53092781543-0.157495584452-0.1145469645710.5804815600650.1819617931150.47094717662919.027520189532.5052805892-37.1331499539
192.97906836985-1.85405563126-1.690765399354.881738334615.475468303095.188760565880.7613781172340.373196836129-0.0244713950563-0.413694803806-0.273121676576-0.969283836575-0.5628161547160.664204838038-0.5150191850360.6226051823-0.107987032013-0.06613196263080.8920725669230.05210105603570.67822662363221.792297619531.8314453503-45.1024362105
202.267766031770.6875959332741.006822346743.410044486972.995174235184.934740709910.09887405863880.035395027583-0.120230368172-0.287025835435-0.406104893792-0.0376443028304-0.3541945845160.111012465590.1715317767750.577671352967-0.0601197296111-0.1399354531020.6687591042210.09493070153990.52363960093815.415603354730.6786204122-44.2462006537
216.67792009221.207227882812.835365518063.810279497985.417164712892.672537079050.1606955386720.446635722672-0.40814341032-0.8899307997740.388097358885-0.9827428082-0.3772246411751.02911755348-0.5916231582460.604545484569-0.06454091291-0.04500260509170.6238851927590.00726925153930.59188011158624.075552837122.5021088203-45.6086211837
223.82203002331.135806561490.2421636170161.999842128931.796011541663.653006889410.111866340192-0.6646980764110.267432604720.762558885285-0.05039782656570.800034639307-0.243703058738-0.06357794112060.07070491203980.814362998969-0.330138566181-0.1046188311970.7437344515390.05615692180190.87796087457414.052961537364.9249981395-20.7409475793
236.13417228403-1.889549081990.1681548234985.22853930609-1.246693264391.59481099102-0.03373378963380.509338424256-0.00934414363312-0.3978927275740.477802911436-0.5884368200450.3871089108360.458163207668-0.2844672017650.4891241115690.02714444914130.07797646541260.5444705288050.1655438577680.52268805791878.248907659348.4180989586-5.62639439358
242.139002503812.519214999770.1214563499269.264621941041.101220633590.229653255913-0.0556515025621-0.2477267245980.009149947305290.2637540123250.1393917554120.771598172236-0.1227478544720.0158095712843-0.1329321536230.5879686844460.06038616448260.02142783212920.6418126850670.1333077419120.53228528453874.011198473950.50502881016.60846825852
259.075225062875.59021585837-0.3699133068613.91221232721-1.908972906264.15811226705-0.137958864175-0.553438241864-0.1080249412810.8925435923890.352295669990.207358223883-0.472543437979-0.736996513587-0.3996110705730.7474014852780.1953480823270.05755041313150.7738439464780.2188680556960.52001606914174.473234080237.60331426329.42061362725
267.964711628160.819651430121.852819985795.91598803195-0.2757918897313.44183691981-0.0754742872244-0.3787790501760.8945809251610.205201943484-0.0519913457307-0.749357695971-0.2015782978740.2700927907780.1453405832910.38662063010.0542380850670.07951363210180.4723583047130.02006708965340.47214834071281.145618498565.4765989281.60379241174
275.948685562520.0319589294091-0.302836912530.3494436519220.321064539191.611122511660.141728705779-0.585793127645-0.56901575-0.00196103270359-0.0905850548979-0.01457742918930.502233346901-0.220393255707-0.04919534942090.54142541636-0.0330173518094-0.07455748699860.5880749383630.2085006977970.544135136657.719114397652.40481190860.528082804289
283.889282074634.64482566777-0.9419138330649.287924374070.04133417105841.903996185920.172814104593-0.6134689422580.479144956677-0.133582848649-0.2242891307181.0569045535-0.0183804221147-0.3572907021140.02144061716890.4605604863230.0300052117969-0.04780570388640.5983375225310.1624588262810.64904804012449.027302363857.2835232571-0.701492260802
293.70150306401-2.59465246663-1.45117482613.006834260671.239386058192.58479888715-0.176226769444-0.220700919553-0.01326068083910.08952178712760.0883805587917-0.09256461962530.2884375715450.484633357360.196437227260.5404342086120.0229027673830.04438058321890.6448441305620.1670194736870.51084855992180.077410288354.6955529336-5.25353662249
304.42422967523-1.82616985801-0.5839434337322.51766254671.675362082181.234885029850.03217128350920.2844880565720.707570587449-0.4707807996160.0967746068657-0.559153398147-0.05622790523210.350685006828-0.07627008304710.6713252658940.03949672785820.1470133134510.6689067253290.2262301690020.74010154522390.849898242759.6168523015-9.63499311682
313.49325212160.6040015177350.7693448415911.98231137068-0.747950970861.950024827540.280687268309-0.369997856738-0.532975696704-0.218729966535-0.0818742989913-0.2226076150050.381903034726-0.0319822711687-0.2521970462420.6410502192040.08516081275320.07452561046540.4443382217420.03474971138330.49772529588471.184116155239.4058363535-6.67286995986
324.57461988549-1.458419919573.651238312242.61319409523-1.73770770815.377463295910.3716868783110.0659497526336-0.960129505558-0.4416067799350.07366577927210.3428330704590.933292609789-0.112345499102-0.4566512330890.629964159154-0.0914084283922-0.07125028252470.5969954823090.1538632976530.75385688316852.620502835135.1157098761-16.7398358043
338.686888809278.11707747301-1.109572890288.238019260560.567905886534.639381509450.0744256809809-0.3398696126920.376475850850.9091927341130.3219703258690.2454541115410.0005767588046780.274345527221-0.3666572106010.5973223733770.183440396012-0.005570437172860.8088825665820.1092964263680.68739727602588.095250651151.57550843394.20423931904
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 14 )AA1 - 141 - 14
22chain 'A' and (resid 15 through 87 )AA15 - 8715 - 87
33chain 'A' and (resid 88 through 101 )AA88 - 10188 - 101
44chain 'A' and (resid 102 through 154 )AA102 - 154102 - 154
55chain 'A' and (resid 155 through 182 )AA155 - 182155 - 182
66chain 'B' and (resid 0 through 64 )BB0 - 641 - 65
77chain 'B' and (resid 65 through 111 )BB65 - 11166 - 112
88chain 'B' and (resid 112 through 190 )BB112 - 190113 - 191
99chain 'C' and (resid 1 through 15 )CC1 - 151 - 15
1010chain 'D' and (resid 2 through 26 )DD2 - 261 - 25
1111chain 'D' and (resid 27 through 55 )DD27 - 5526 - 54
1212chain 'D' and (resid 56 through 101 )DD56 - 10155 - 100
1313chain 'D' and (resid 102 through 182 )DD102 - 182101 - 181
1414chain 'E' and (resid 0 through 32 )EE0 - 321 - 33
1515chain 'E' and (resid 33 through 51 )EE33 - 5134 - 52
1616chain 'E' and (resid 52 through 62 )EE52 - 6253 - 63
1717chain 'E' and (resid 63 through 78 )EE63 - 7864 - 79
1818chain 'E' and (resid 79 through 122 )EE79 - 12280 - 123
1919chain 'E' and (resid 123 through 133 )EE123 - 133124 - 134
2020chain 'E' and (resid 134 through 164 )EE134 - 164135 - 165
2121chain 'E' and (resid 165 through 190 )EE165 - 190166 - 191
2222chain 'F' and (resid 1 through 15 )FF1 - 151 - 15
2323chain 'G' and (resid 1 through 14 )GG1 - 141 - 14
2424chain 'G' and (resid 15 through 45 )GG15 - 4515 - 45
2525chain 'G' and (resid 46 through 55 )GG46 - 5546 - 55
2626chain 'G' and (resid 56 through 87 )GG56 - 8756 - 87
2727chain 'G' and (resid 88 through 153 )GG88 - 15388 - 153
2828chain 'G' and (resid 154 through 182 )GG154 - 182154 - 182
2929chain 'H' and (resid 0 through 32 )HH0 - 321 - 33
3030chain 'H' and (resid 33 through 64 )HH33 - 6434 - 65
3131chain 'H' and (resid 65 through 111 )HH65 - 11166 - 112
3232chain 'H' and (resid 112 through 190 )HH112 - 190113 - 191
3333chain 'I' and (resid 1 through 15 )II1 - 151 - 15

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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