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- PDB-8cmd: 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: 8cmd
タイトルHuman Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S761-775
要素
  • HLA class II histocompatibility antigen, DR alpha chain
  • Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
  • Spike protein S2'
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 / Spike
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 / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / early endosome membrane / adaptive immune response / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / lysosome / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / immune response / Golgi membrane / fusion of virus membrane with host plasma membrane / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular exosome / identical protein binding / membrane / plasma membrane
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 / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 / Spike glycoprotein
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: 2.54 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: Spike protein S2'
D: HLA class II histocompatibility antigen, DR alpha chain
E: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
F: Spike protein S2'
G: HLA class II histocompatibility antigen, DR alpha chain
H: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
I: Spike protein S2'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,83319
ポリマ－136,2129
非ポリマー62110
水2,972165
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: Spike protein S2'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,7148
ポリマ－45,4043
非ポリマー3105
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: Spike protein S2'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,6527
ポリマ－45,4043
非ポリマー2484
水362
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: Spike protein S2'
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
単位格子
Length a, b, c (Å)113.023, 156.120, 164.852
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-103-

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 4 through 37 or resid 40...
d_2ens_1(chain "D" and (resid 4 through 37 or resid 40...
d_3ens_1(chain "G" and (resid 4 through 37 or resid 40...
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 14)
d_2ens_3(chain "F" and resid 1 through 14)
d_3ens_3(chain "I" and resid 1 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_1GLUGLUALAALAAA4 - 375 - 38
d_12ens_1GLUGLULEULEUAA40 - 4541 - 46
d_13ens_1PHEPHEGLYGLYAA48 - 4949 - 50
d_14ens_1PHEPHEPHEPHEAA51 - 5452 - 55
d_15ens_1ALAALAALAALAAA5657
d_16ens_1GLYGLYTHRTHRAA58 - 9359 - 94
d_17ens_1SERSERVALVALAA95 - 9796 - 98
d_18ens_1LEULEULEULEUAA99100
d_19ens_1PROPROGLYGLYAA102 - 125103 - 126
d_110ens_1PROPROARGARGAA127 - 140128 - 141
d_111ens_1ASPASPPHEPHEAA142 - 145143 - 146
d_112ens_1LYSLYSASPASPAA147 - 181148 - 182
d_21ens_1GLUGLUALAALADD4 - 375 - 38
d_22ens_1GLUGLULEULEUDD40 - 4541 - 46
d_23ens_1PHEPHEGLYGLYDD48 - 4949 - 50
d_24ens_1PHEPHEPHEPHEDD51 - 5452 - 55
d_25ens_1ALAALAALAALADD5657
d_26ens_1GLYGLYTHRTHRDD58 - 9359 - 94
d_27ens_1SERSERVALVALDD95 - 9796 - 98
d_28ens_1LEULEULEULEUDD99100
d_29ens_1PROPROGLYGLYDD102 - 125103 - 126
d_210ens_1PROPROARGARGDD127 - 140128 - 141
d_211ens_1ASPASPPHEPHEDD142 - 145143 - 146
d_212ens_1LYSLYSASPASPDD147 - 181148 - 182
d_31ens_1GLUGLUALAALAGG4 - 375 - 38
d_32ens_1GLUGLULEULEUGG40 - 4541 - 46
d_33ens_1PHEPHEGLYGLYGG48 - 4949 - 50
d_34ens_1PHEPHEPHEPHEGG51 - 5452 - 55
d_35ens_1ALAALAALAALAGG5657
d_36ens_1GLYGLYTHRTHRGG58 - 9359 - 94
d_37ens_1SERSERVALVALGG95 - 9796 - 98
d_38ens_1LEULEULEULEUGG99100
d_39ens_1PROPROGLYGLYGG102 - 125103 - 126
d_310ens_1PROPROARGARGGG127 - 140128 - 141
d_311ens_1ASPASPPHEPHEGG142 - 145143 - 146
d_312ens_1LYSLYSASPASPGG147 - 181148 - 182
d_11ens_2GLYGLYGLUGLUBB1 - 225 - 26
d_12ens_2VALVALGLNGLNBB24 - 3428 - 38
d_13ens_2GLUGLUTHRTHRBB36 - 5140 - 55
d_14ens_2LEULEUSERSERBB53 - 10457 - 108
d_15ens_2THRTHRGLNGLNBB106 - 110110 - 114
d_16ens_2HISHISPROPROBB112 - 165116 - 169
d_17ens_2SERSERALAALABB167 - 190171 - 194
d_21ens_2GLYGLYGLUGLUEE1 - 225 - 26
d_22ens_2VALVALGLNGLNEE24 - 3428 - 38
d_23ens_2GLUGLUTHRTHREE36 - 5140 - 55
d_24ens_2LEULEUSERSEREE53 - 10457 - 108
d_25ens_2THRTHRGLNGLNEE106 - 110110 - 114
d_26ens_2HISHISPROPROEE112 - 165116 - 169
d_27ens_2SERSERALAALAEE167 - 190171 - 194
d_31ens_2GLYGLYGLUGLUHH1 - 225 - 26
d_32ens_2VALVALGLNGLNHH24 - 3428 - 38
d_33ens_2GLUGLUTHRTHRHH36 - 5140 - 55
d_34ens_2LEULEUSERSERHH53 - 10457 - 108
d_35ens_2THRTHRGLNGLNHH106 - 110110 - 114
d_36ens_2HISHISPROPROHH112 - 165116 - 169
d_37ens_2SERSERALAALAHH167 - 190171 - 194
d_11ens_3THRTHRGLNGLNCC1 - 141 - 14
d_21ens_3THRTHRGLNGLNFF1 - 141 - 14
d_31ens_3THRTHRGLNGLNII1 - 141 - 14

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.315385917033, 0.94718208058, -0.0581190981102), (-0.946700894817, 0.318270040358, 0.0496144854079), (0.0654915192167, 0.0393736922085, 0.997076011783)-34.6764964052, -34.3007531592, 28.8120188534
2given(0.788981114984, -0.606989298682, -0.0952512020059), (-0.601827139073, -0.794693436196, 0.0791608308595), (-0.12374528223, -0.00513164219819, -0.992300746434)-12.0548493449, -41.3623972458, 26.6366013371
3given(0.324566219281, 0.943934960443, -0.0603619064872), (-0.943352086128, 0.327691671785, 0.0520097091098), (0.0688738767601, 0.0400619357557, 0.996820661104)-34.4710423879, -34.1511255312, 28.7780625517
4given(0.792989042671, -0.602528908962, -0.0901514951036), (-0.597946875209, -0.798081125247, 0.0743374195922), (-0.116738650977, -0.00504295440439, -0.99314986582)-12.1293836621, -41.0587267744, 26.9179728653
5given(0.302410017023, 0.952987947669, -0.0190303232335), (-0.94716453027, 0.30268138109, 0.106128856299), (0.106899645472, -0.0140695820737, 0.994170263415)-36.1610052166, -36.1450147722, 29.5628518539
6given(0.799032707865, -0.578070877552, -0.165471424386), (-0.578961348976, -0.813951550142, 0.0478187244929), (-0.162328334415, 0.0575928341615, -0.985054606253)-9.3479649392, -39.7783176519, 25.8413705156

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要素

#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)
#3: タンパク質・ペプチド Spike protein S2' / SARS-Cov-2 Spike epitope S761-775


分子量: 1629.790 Da / 分子数: 3 / 由来タイプ: 合成
由来: (合成) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
参照: UniProt: P0DTC2
#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: 10 / 由来タイプ: 合成 / 式: C2H6O2
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 165 / 由来タイプ: 天然 / 式: H2O
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: 2.67 Å3/Da / 溶媒含有率: 53.92 %
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 % 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: 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: 2.54→91.56 Å / Num. obs: 48332 / % possible obs: 99.69 % / 冗長度: 35.6 % / Biso Wilson estimate: 53.04 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.808 / Rpim(I) all: 0.137 / Rrim(I) all: 0.82 / Net I/σ(I): 8.05
反射 シェル解像度: 2.54→2.63 Å / 冗長度: 36.8 % / Rmerge(I) obs: 8.588 / Mean I/σ(I) obs: 0.88 / Num. unique obs: 4754 / CC1/2: 0.356 / CC star: 0.725 / Rrim(I) all: 8.707 / % possible all: 99.22

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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
DIALSデータスケーリング
DIALS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: 2.54→47.27 Å / SU ML: 0.3934 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.1242
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2381 2452 5.09 %
Rwork0.1933 45738 -
obs0.1955 48190 99.71 %
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: 56.11 Å2
精密化ステップサイクル: LAST / 解像度: 2.54→47.27 Å
タンパク質核酸リガンド溶媒全体
原子数9511 0 40 165 9716
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00419832
X-RAY DIFFRACTIONf_angle_d0.744313359
X-RAY DIFFRACTIONf_chiral_restr0.05051435
X-RAY DIFFRACTIONf_plane_restr0.00581756
X-RAY DIFFRACTIONf_dihedral_angle_d12.80053615
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.595995867259
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.54309846867
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.716561520239
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.811588028072
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.917580673406
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS1.04548613175
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.590.32651100.34292482X-RAY DIFFRACTION98.93
2.59-2.640.39731440.34712511X-RAY DIFFRACTION99.48
2.64-2.70.36521520.32342494X-RAY DIFFRACTION99.29
2.7-2.760.36121490.30712497X-RAY DIFFRACTION99.7
2.76-2.830.32221310.2732537X-RAY DIFFRACTION99.89
2.83-2.910.29511320.25922501X-RAY DIFFRACTION99.81
2.91-2.990.33541560.25962510X-RAY DIFFRACTION99.78
2.99-3.090.26471350.24322513X-RAY DIFFRACTION99.74
3.09-3.20.28191300.24062545X-RAY DIFFRACTION99.85
3.2-3.330.30521490.24262536X-RAY DIFFRACTION99.93
3.33-3.480.24231140.19212513X-RAY DIFFRACTION99.92
3.48-3.660.24251360.17762574X-RAY DIFFRACTION99.93
3.66-3.890.21621430.18012536X-RAY DIFFRACTION99.89
3.89-4.190.23081180.16892572X-RAY DIFFRACTION99.96
4.19-4.610.18691300.13522567X-RAY DIFFRACTION100
4.61-5.280.17741400.13362573X-RAY DIFFRACTION100
5.28-6.650.22211420.16862601X-RAY DIFFRACTION99.89
6.65-47.270.17111410.16152676X-RAY DIFFRACTION98.77
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)
10.123650668931-0.1070668941620.0311979412460.2719248232070.0628110129942-0.01578405125180.101518653508-0.0565219564467-0.03922328103610.064784197629-0.1504789811990.142531006835-0.0621470848465-0.1048588706862.04828143646E-50.3894295985670.01236293685490.006107480884280.3353677798090.006202791601150.339386682821-12.1064060356-6.2599642869826.8550566356
20.665095001063-0.5219399495660.1284982598450.44937372544-0.01802093903050.08702472809010.151443892605-0.0822295051445-0.06464257870050.508816371978-0.170297982132-0.4064621228670.3477292914480.0802023572530.006328437043890.477025024853-0.0860241406939-0.1064276225350.416330862122-0.02845738185440.314990239478-3.65559778434-1.9037838766635.9608048146
30.221610175006-0.352013502116-0.09473014557941.08081620663-0.4735449536930.3909310573510.08246905266780.1034977520680.0191422511760.22363425883-0.0732981452865-0.03321999325670.26806135256-0.00523313997721-0.004125497695330.3527938093820.000395757301556-0.05136195411360.324518811924-0.07975514624220.270006311833-6.04618745611-18.349298948929.287831272
40.307333619758-0.108056721706-0.3585944512630.008396961035690.001997551905930.04504302045910.0427231310675-0.0762063987336-0.07523980996610.00597170112459-0.02398267576140.07013457056680.18467019067-0.03360446217011.78940755574E-50.429475737540.0216433601332-0.1150908566850.390526562329-0.03519890396940.450366965851.50704475953-19.132310045126.9126130157
50.123983562931-0.0675752490304-0.1061544080780.1199852985090.0374061647679-0.00516241086002-0.05766357978550.917351578781-0.5121453432240.08573350429540.012112276609-0.115512735659-0.069109474534-0.0481907918439-0.0004406879760790.477661939771-0.0170515162124-0.1453504869730.419692025607-0.05563135657430.4954459735972.59314046256-28.6149397423.1392825936
61.06305089155-0.4852391368330.1070406980050.7353349897340.02234297863310.8150554494570.0852435672475-0.1252045894850.1100758576950.0732943402129-0.07316515907620.265760722382-0.0714265905683-0.0652068269968-7.04881514222E-50.3426561306490.0108915853825-0.05352697901260.333308316497-0.03239283596310.385094902163-19.3082667066-0.74296112466823.5301841315
70.729707834139-0.01057755154580.215848522650.5694237270780.03647243614810.5710637255220.1803126431260.1204729185760.061925699182-0.0742469442305-0.189370003748-0.256142936355-0.1490023021450.03058146721640.0001932159918040.3796145456630.066044915706-0.006313355484280.402484439827-0.008812636766110.47592249030216.7959909225-9.312390330268.33456100735
80.0720995359835-0.114258827175-0.1293534252970.1262809069850.0429470113290.07708748765550.173012112177-0.248329042229-0.02713684670670.0780456138629-0.2393605067890.309855579843-0.179593989159-0.0051331609977-9.67335772038E-60.436927041711-0.08473937865870.04596722886580.456945235264-0.1130930806840.562553680312-21.75982258220.55692154798333.5955301487
90.4568156038480.0527645242583-0.3267244329820.08822428113310.335104088451.47027670044-0.6487345434790.414119919305-0.0573254793118-0.07055533557310.1506079411780.563097112009-0.07915990202240.503403613013-0.1296157429150.389817147952-0.0289214625157-0.1027730137360.2634458499980.001902344398840.486902942127-46.0720933395-23.58256241654.6959460998
100.1345728857190.0719342484532-0.2649606078040.106765277082-0.2077590119790.183616276644-0.132849594628-0.1838003793730.1767347757620.1221168531510.007686382647930.1339729810910.09416135833970.103006146921-1.10449349234E-50.4212836019990.00956569553448-0.09784430358570.434585273571-0.000583453256160.436538400664-39.8080676727-29.358944628564.577599045
111.28769142910.9494205793210.2200429151740.198199436230.1533385025180.869180945041-0.185710992022-0.03371252788870.414191407064-0.05292534605550.08014649632590.3870183455980.0617424863621-0.0275654164979-0.105770618670.2866702940440.0141741028923-0.1049624078520.2430482984570.006853620653980.464326822983-54.9894439058-26.813950619756.1036371193
120.2989797114870.1255515764660.06911280849780.1843469524720.160296557130.127067261215-0.0256199564789-0.09616866017770.166390037258-0.05348203123610.02637502934690.2584316980890.1092490978640.158101123973.55879687623E-50.390145565773-0.0332500960023-0.1009009742260.385692773823-0.004983601182930.359530191972-56.2956348049-42.005507575757.8260247302
130.0882271830586-0.0311994239393-0.03672855515310.08052874528960.02372347334150.0494064686697-0.342494063874-0.2559895781820.465425522746-0.1848733929090.2341011945710.305904969610.01452819806160.149430336643-0.01219467575870.488191629983-0.0392649296215-0.2036254580720.4679498323830.07271631872960.477231450585-51.2038471328-27.341862149751.1204693287
140.250963710162-0.217163299360.2097379838590.2500788462760.04815437179840.3408462043640.0131226022949-0.08181015570380.163784578893-0.0314118430711-0.1438018862750.2981986493130.114112034389-0.0667879933351-4.72090660478E-60.3897909758680.00470991793358-0.07398065862550.3918658694950.04260092344440.365692378873-58.1988711304-45.822000508454.0268038846
152.32767255136-0.481078796741-0.7218880044661.111435137650.6787309398661.8787020608-0.407888032791-0.1228915497550.0986722782257-0.1002470301740.1137024595970.7017945491020.105923046198-0.144213541366-0.5334462530130.3722167983760.00990751996558-0.1666554419820.373404462180.08980680098160.778665938265-53.9211104957-20.434287636354.1633777482
160.293650659903-0.07554918908330.02036120095280.08018128169520.1768572302480.5036157623750.1642443523610.2359212130970.432029819135-0.709586583517-0.07021052878320.361270689985-0.112309139130.1335042749170.02548104211080.462027747814-0.04929437997-0.2466021354590.4302116287620.2197398093980.796574364627-39.7916834139-16.346207084147.0125538613
172.094532962480.474644344009-0.004727649913961.531387632130.3412738473552.69318377499-0.4174545872060.03981642062520.470932241927-0.327532910155-0.2708581789310.294248909064-0.085810690595-0.004341004184-1.644632338120.523737144468-0.0164043466771-0.523626061990.5139620413150.2673017167430.841117477093-49.0524459981-9.7454164237646.069483864
180.2156128307530.477918074080.1410241986771.062942779940.7612086470154.90369370241-0.0153524245498-0.2000258855080.6815862562110.1512071908650.563171141750.541764568716-0.562189039571.348291818650.4553937967720.531283163574-0.183083140426-0.245952074718-0.1994157099610.2305833088171.27377280869-42.1842727657-3.6097425901952.9473907739
190.734292548977-0.552692065648-0.4114822643420.3336956884310.2007546856950.38436218759-0.1335160008490.1804358623750.1564457304130.2482937605740.06341077997810.1151558615650.2008988729950.192341273925-0.005143653019470.357562754176-0.0150036594596-0.1220866445630.3519864363180.09283816520510.232281834461-37.3182020818-44.53262679645.8082814768
20-0.02986278143640.02830800445740.00428109052793-0.01788949239070.07121723734910.0718677384148-0.08596135632840.6399096517950.494914658824-0.1901631352180.0556300796165-0.236523631196-0.5061240747760.3360683475420.003854285043340.344800719864-0.0259922056573-0.04110765691810.6435072875060.02448011284290.477983827884-34.4475056516-46.301519855837.1960068743
210.0217174483567-0.02911547910330.04792148930110.024257598383-0.0640380300780.0609837890578-0.3621473553790.523684956388-0.312959434189-0.2747666757520.2604708325270.2924994070780.05568226324640.08031727131164.8019076947E-50.459665329623-0.0283845707034-0.02177970670780.544677047706-0.01654414713740.455651205559-37.5490124491-51.808815692728.223889486
220.1114589642940.008262949214240.08540236550040.0771079880461-0.1073013958320.0670757183296-0.02556922289480.1107478601610.04536153553890.201462249708-0.1280663818310.05827163252570.167535783852-0.0653704734689-0.0001993958231350.4126561710990.0113668291649-0.1127106309250.3602092731240.03064493153640.330552391571-42.7664018082-45.329775688643.0581533465
230.634493896316-0.281823777071-0.303497803820.06831431831790.1162427390360.1394751747830.1984501956290.131739225655-0.140799403316-0.133776276710.16270120835-0.5563581810880.08620770988580.304403387101-1.19231719693E-50.4399393448220.0426331069731-0.0893338244870.540501905954-0.1108665965960.614381484134-32.3614343976-55.6048772237.0363741986
240.0153660192066-0.0128449135085-0.2104588726630.0234424386413-0.2226219028821.25212768955-0.0747903901494-0.1005198558390.5994853107150.243270634539-0.1209653865660.504908888551-0.3280693110280.355482015449-0.09954304866110.536448194287-0.0232025617913-0.05312090186230.355173745421-0.0697171709860.821033375139-42.9237731497-11.804779276660.6696629164
250.02666514713330.2213487179530.1542364808550.1172321428170.1040934242270.06690009747520.0729817605815-0.02936128189240.0748817931001-0.0759629891447-0.29401355885-0.3067650312920.1295661349770.0748872832098-0.0001970927295670.403741113284-0.06645470474280.03221945464080.404868656027-0.05517346759970.401262565029-21.8186507137-29.39916283934.21993013416
260.351187602312-0.2723375851990.05441946032010.1382440387090.04300962481860.0100537955872-0.127382308010.1389626606840.1247414613070.180091646524-0.000733056628553-0.18975157667-0.0972536883964-0.128226666082-1.65382997433E-50.4340615296340.00321294871224-0.04943446092450.475792502125-0.03191665083190.356724379945-17.4549254355-27.88713758-6.60527860731
270.09294835867870.0856071237760.01785326185580.1085789193150.1281799131280.1318114209370.08686370214170.05857078779510.15829674652-0.170066778135-0.3246428055440.382588713739-0.761568642820.375010583127-0.0001714077836370.552376921063-0.0244979249260.0003298605244080.598178429537-0.06483038589190.481455277833-18.3467091386-40.5171008081-9.71901822414
280.2554093259320.0838579946437-0.2231708107690.276266645362-0.2409652465030.1702742025270.06600525610360.2563633522880.6783494443320.03713763855850.2009501380290.297747902453-0.04405737849840.1470057751420.004748952012920.4894302237520.0142364474795-0.01421384024240.48581027446-0.005078654600670.534887724177-24.8096785071-12.8416842953-1.8968687753
290.05461126953320.01586723921840.101296063639-0.02232107223390.1001736464810.0466105483629-0.244060744389-0.139296297257-0.1415250008130.3040272100240.06761992389040.4617128991890.181145530080.278923312542-0.0002507675505080.4677346956060.0889817904474-0.03245096994960.470004652492-0.02731660208820.4602277654597.71816270251-33.94393906511.51673732808
300.1437629711476.76705233949E-50.00432364922317-0.0226309741240.0839720242852-0.03586374580110.09483576379710.02712289501910.04573093654330.051067653554-0.1299653176930.0948527887470.164132232770.164540255524-1.60656033157E-50.4028141300440.0190828224946-0.08332263609170.48896875504-0.03080585154570.415101650174-2.29202468097-22.1048141498-0.226255378584
310.503060689936-0.1124764989030.506998814358-0.0478626971918-0.116498698050.203389831830.0554618072639-0.00688053937166-0.1024162211190.0613180166898-0.05930541112590.001233665635870.072336475811-0.009672993672592.44254708772E-50.510798170399-0.00964245325143-0.03975832627510.505957922226-0.07927047440370.298994219778-4.87607736147-24.8879299354-1.55983396585
320.0176079698276-0.0618964396266-0.03387954049970.015226086244-0.07453219485320.1127455632320.3859117115480.6966672902730.123766352624-0.161755975503-0.375619013221-0.248196546933-0.181068552031-0.0908255230087-6.63954622933E-50.4098019476080.0615020167362-0.01569980840590.497719816973-0.02602145909930.58078559627510.2346192988-24.4089510283-2.64959879679
330.1036129964390.0703958868708-0.1710663678020.0213950375995-0.05158627822850.28231881856-0.1969761844660.1155469032690.581713777592-0.01495400816270.142475909397-0.365995647632-0.04849878195650.0846652731129-3.33408756026E-50.543685922965-0.0189921872292-0.07123834817780.471740282282-0.08770880952830.6030564047964.45025672448-17.80194361513.29134041419
340.770152806757-0.0492620038085-0.1148462705770.546803883721-0.5726923772490.5968680235860.197454638176-0.001514652904620.2301870548390.0992343703401-0.1042772909070.2393714837480.02451459986690.05743313543533.87666578662E-50.435758483632-0.0389020747540.00245290160520.438343584374-0.06723492680980.413958514375-31.0427691007-23.17002378696.82018217062
350.2555100368030.06319284391180.3723884732270.6802590409970.09977064393770.2832871946390.2694080185960.113436952637-0.5917229035920.1419989803010.0447015127443-0.08249726694850.191810621965-0.001775395300178.15328102761E-70.4711432171370.00933330293636-0.1254464577470.430583247611-0.05012559730390.4968602550220.970272396561-43.037473932813.9757827384
360.05676302457470.071013079681-0.1691463107310.0344054301069-0.09419985267780.1795638173440.235755622679-0.1452715063870.1213807809990.0587897991141-0.1037830469050.1516371659180.187806966558-0.0429520968187-0.0001148437094710.6632791122640.01603671029080.02439746650890.530606818551-0.08626718274810.498644002463-32.6165510296-25.962075891-3.83409020645
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 0 through 26 )AA0 - 261 - 27
22chain 'A' and (resid 27 through 55 )AA27 - 5528 - 56
33chain 'A' and (resid 56 through 133 )AA56 - 13357 - 134
44chain 'A' and (resid 134 through 166 )AA134 - 166135 - 167
55chain 'A' and (resid 167 through 182 )AA167 - 182168 - 183
66chain 'B' and (resid 1 through 97 )BB1 - 971 - 97
77chain 'B' and (resid 98 through 190 )BB98 - 19098 - 190
88chain 'C' and (resid 1 through 15 )CC1 - 151 - 15
99chain 'D' and (resid 0 through 26 )DD0 - 261 - 27
1010chain 'D' and (resid 27 through 55 )DD27 - 5528 - 56
1111chain 'D' and (resid 56 through 101 )DD56 - 10157 - 102
1212chain 'D' and (resid 102 through 134 )DD102 - 134103 - 135
1313chain 'D' and (resid 135 through 144 )DD135 - 144136 - 145
1414chain 'D' and (resid 145 through 182 )DD145 - 182146 - 183
1515chain 'E' and (resid 0 through 18 )EE0 - 181 - 19
1616chain 'E' and (resid 19 through 32 )EE19 - 3220 - 33
1717chain 'E' and (resid 33 through 54 )EE33 - 5434 - 55
1818chain 'E' and (resid 55 through 77 )EE55 - 7756 - 78
1919chain 'E' and (resid 78 through 122 )EE78 - 12279 - 123
2020chain 'E' and (resid 123 through 133 )EE123 - 133124 - 134
2121chain 'E' and (resid 134 through 144 )EE134 - 144135 - 145
2222chain 'E' and (resid 145 through 164 )EE145 - 164146 - 165
2323chain 'E' and (resid 165 through 190 )EE165 - 190166 - 191
2424chain 'F' and (resid 1 through 15 )FF1 - 151 - 15
2525chain 'G' and (resid 2 through 14 )GG2 - 141 - 13
2626chain 'G' and (resid 15 through 45 )GG15 - 4514 - 44
2727chain 'G' and (resid 46 through 55 )GG46 - 5545 - 54
2828chain 'G' and (resid 56 through 87 )GG56 - 8755 - 86
2929chain 'G' and (resid 88 through 102 )GG88 - 10287 - 101
3030chain 'G' and (resid 103 through 123 )GG103 - 123102 - 122
3131chain 'G' and (resid 124 through 153 )GG124 - 153123 - 152
3232chain 'G' and (resid 154 through 166 )GG154 - 166153 - 165
3333chain 'G' and (resid 167 through 181 )GG167 - 181166 - 180
3434chain 'H' and (resid 1 through 77 )HH1 - 771 - 77
3535chain 'H' and (resid 78 through 190 )HH78 - 19078 - 190
3636chain '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://pdbjlc1.pdbj.org/emnavi/covid19.php

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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