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- PDB-8cmi: 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: 8cmi
タイトルHuman Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) 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 / omicron / BA.1 / immune escape / viral variants
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 / early endosome membrane / Maturation of spike protein / viral translation / adaptive immune response / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / lysosome / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / 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: 2.6 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11月13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: 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)137,88932
ポリマ－136,2579
非ポリマー1,63223
水2,720151
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)46,14213
ポリマ－45,4193
非ポリマー72310
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)45,88810
ポリマ－45,4193
非ポリマー4687
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: Spike protein S2'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,8609
ポリマ－45,4193
非ポリマー4406
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)148.190, 148.190, 129.071
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
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 46 or resid 48...
d_2ens_1(chain "D" and (resid 4 through 46 or resid 48...
d_3ens_1(chain "G" and (resid 4 through 46 or resid 48...
d_1ens_2(chain "B" and (resid 0 through 54 or resid 56...
d_2ens_2(chain "E" and (resid 0 through 54 or resid 56...

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_1GLUGLUGLUGLUAA4 - 465 - 47
d_12ens_1PHEPHELEULEUAA48 - 9949 - 100
d_13ens_1GLUGLULEULEUAA101 - 122102 - 123
d_14ens_1ASNASNTHRTHRAA124 - 129125 - 130
d_15ens_1GLYGLYASPASPAA131 - 171132 - 172
d_16ens_1PROPROALAALAAA173 - 182174 - 183
d_21ens_1GLUGLUGLUGLUDD4 - 465 - 47
d_22ens_1PHEPHELEULEUDD48 - 9949 - 100
d_23ens_1GLUGLULEULEUDD101 - 122102 - 123
d_24ens_1ASNASNTHRTHRDD124 - 129125 - 130
d_25ens_1GLYGLYASPASPDD131 - 171132 - 172
d_26ens_1PROPROALAALADD173 - 182174 - 183
d_31ens_1GLUGLUGLUGLUGG4 - 465 - 47
d_32ens_1PHEPHELEULEUGG48 - 9949 - 100
d_33ens_1GLUGLULEULEUGG101 - 122102 - 123
d_34ens_1ASNASNTHRTHRGG124 - 129125 - 130
d_35ens_1GLYGLYASPASPGG131 - 171132 - 172
d_36ens_1PROPROALAALAGG173 - 182174 - 183
d_11ens_2METMETGLYGLYBB0 - 544 - 58
d_12ens_2PROPROVALVALBB56 - 9160 - 95
d_13ens_2ARGARGPROPROBB93 - 9797 - 101
d_14ens_2VALVALSERSERBB99 - 104103 - 108
d_15ens_2LEULEUILEILEBB114 - 127118 - 131
d_16ens_2VALVALGLUGLUBB129 - 138133 - 142
d_17ens_2ALAALALEULEUBB140 - 161144 - 165
d_18ens_2THRTHRPROPROBB163 - 165167 - 169
d_19ens_2SERSERALAALABB167 - 190171 - 194
d_21ens_2METMETGLYGLYEE0 - 544 - 58
d_22ens_2PROPROVALVALEE56 - 9160 - 95
d_23ens_2ARGARGPROPROEE93 - 9797 - 101
d_24ens_2VALVALSERSEREE99 - 104103 - 108
d_25ens_2LEULEUILEILEEE114 - 127118 - 131
d_26ens_2VALVALGLUGLUEE129 - 138133 - 142
d_27ens_2ALAALALEULEUEE140 - 161144 - 165
d_28ens_2THRTHRPROPROEE163 - 165167 - 169
d_29ens_2SERSERALAALAEE167 - 190171 - 194

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.667445500557, -0.496247696874, 0.555206922808), (-0.407778963291, 0.867429589817, 0.285100374968), (-0.62308331777, -0.0361127409151, -0.78132134814)183.092451031, -0.869703817903, 13.8055772281
2given(-0.999395937965, -0.0320668757225, -0.0133968152806), (0.0289066004933, -0.553038900931, -0.832653819126), (0.019291646539, -0.832538100953, 0.553631775493)165.476985738, -36.8546417764, -19.2141569669
3given(-0.664293014024, -0.511911957346, 0.544665897083), (-0.436184606064, 0.857226050922, 0.273690494999), (-0.60700723303, -0.0557641959227, -0.792737392522)182.968304747, 2.15109474695, 12.0732644163

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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 Spike protein S2' / SARS-CoV-2 Omicron (BA.1) Spike epitope S761-775


分子量: 1644.867 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

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非ポリマー , 3種, 174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: 17 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 6 / 由来タイプ: 合成 / 式: SO4
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 151 / 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 Å3/Da / 溶媒含有率: 59.03 %
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: 7
詳細: 0.1 M TRIS pH 7.0, 28 % PEG8000, 0.2 M ammonium sulphate

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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4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: 2.6→48.67 Å / Num. obs: 50460 / % possible obs: 99.52 % / 冗長度: 21.1 % / Biso Wilson estimate: 55.03 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.358 / Rpim(I) all: 0.0793 / Rrim(I) all: 0.367 / Net I/σ(I): 5.93
反射 シェル解像度: 2.6→2.69 Å / 冗長度: 21.8 % / Rmerge(I) obs: 2.637 / Mean I/σ(I) obs: 0.56 / Num. unique obs: 4998 / CC1/2: 0.522 / CC star: 0.828 / Rpim(I) all: 0.571 / Rrim(I) all: 2.699 / % possible all: 99.09

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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: 2.6→48.51 Å / SU ML: 0.3604 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 24.1286
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2364 2554 5.06 %
Rwork0.1918 47883 -
obs0.194 50437 99.54 %
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: 65.65 Å2
精密化ステップサイクル: LAST / 解像度: 2.6→48.51 Å
タンパク質核酸リガンド溶媒全体
原子数9460 0 98 151 9709
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00259789
X-RAY DIFFRACTIONf_angle_d0.594613280
X-RAY DIFFRACTIONf_chiral_restr0.04511423
X-RAY DIFFRACTIONf_plane_restr0.00461734
X-RAY DIFFRACTIONf_dihedral_angle_d12.65793586
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.669764833284
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.659770387126
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.799606950975
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.32571550.30532629X-RAY DIFFRACTION99.15
2.65-2.70.32971190.27732606X-RAY DIFFRACTION99.2
2.7-2.760.34161290.2852667X-RAY DIFFRACTION99.29
2.76-2.830.32561270.27262619X-RAY DIFFRACTION99.31
2.83-2.90.30791390.26342623X-RAY DIFFRACTION99.46
2.9-2.980.28011420.25912650X-RAY DIFFRACTION99.47
2.98-3.060.34541280.26182638X-RAY DIFFRACTION99.39
3.06-3.160.28011580.24222629X-RAY DIFFRACTION99.32
3.16-3.280.27441410.2252654X-RAY DIFFRACTION99.68
3.28-3.410.26971580.19692616X-RAY DIFFRACTION99.43
3.41-3.560.22211370.19192651X-RAY DIFFRACTION99.82
3.56-3.750.25311130.19122676X-RAY DIFFRACTION99.61
3.75-3.980.2391550.17652654X-RAY DIFFRACTION99.75
3.98-4.290.19121250.15652699X-RAY DIFFRACTION99.86
4.29-4.720.17491720.1362647X-RAY DIFFRACTION99.75
4.72-5.410.18551220.1472724X-RAY DIFFRACTION99.96
5.41-6.810.23521720.17762706X-RAY DIFFRACTION99.97
6.81-48.510.20921620.17512795X-RAY DIFFRACTION99.33
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)
13.268759863832.14835382812-2.724344679677.99598357207-3.16510129972.631143457130.174797770755-0.1365719991310.2787638575130.08783367025990.1453572917350.3427096893920.168899311039-0.185834770502-0.4048961024220.603190668811-0.110435344905-0.113508613680.506337029733-0.08593354434090.501941129413104.0859542429.50759036539-10.9112798357
23.620635264361.411933540040.6337090663891.022991464432.022661512095.980491671250.166648929362-0.107971003574-0.7343651074690.994471977994-0.196161054745-0.5235477489640.450571244233-0.07766867238240.06547020718610.812902724614-0.0527199662922-0.1718120005510.4192154938570.02304347222160.472473042136104.41274952-3.25084252505-5.08270434537
33.85271421719-3.27602784802-2.476419636593.263174449361.005230424253.900098387130.3379752300991.42617431643-1.030281655280.164199739870.103647298273-0.3006712564311.578964261950.671836438177-0.3654594740910.6550850870970.0935318803747-0.229706629860.810215083481-0.2911248321950.731021695206106.02787606-6.00295246451-17.2485032778
44.549828601120.358676871427-1.170262637111.924413176961.043504401253.906664367520.389487564574-0.914941230066-0.323913127180.934734375446-0.420945611286-0.01894852523810.04158643355040.648485524080.03869617012261.2057601078-0.130645178064-0.2290136428780.6292830132480.0839926641860.501903037562107.0865939744.287203349479.59314007973
54.729156043644.254014156356.288309435836.753403897877.26922073259.20550648663-0.09817647839840.1035676828410.13450413274-0.520760397969-0.1456377218730.57674010603-0.979888346141-0.03912099799260.1692634992580.7970124754620.03947974255560.2357067346960.445078362412-0.04452378713060.6200022371178.8044119183-4.2435735977-14.2625278601
65.32897345325.272736339843.020024641675.744355136292.635265264382.513557229080.392554361192-0.3349820494960.08674855941740.568382877687-0.29346504497-0.004840535064520.0467613254763-0.0899810794237-0.08592437690180.715154612421-0.05100130045670.0978461448680.415079583185-0.04520085753930.34757597929288.2895753347-3.76817138207-3.54006134546
73.909967341534.325926611934.814323266728.699856394976.320618004958.706917334161.398542946330.201010394417-0.03034192027241.07279098296-0.309718620147-0.0765537836674-0.00649484838261-0.19151473583-0.8282359090640.698125333091-0.1335675734860.2082323352480.68589738679-0.08990857847690.6023762998276.1965542674-9.03714322741-4.14155497752
83.529104626954.215617520043.315651750045.26183751814.378766578624.201586787760.115901107816-1.274589809430.986493647230.320057142523-0.8432664534070.802313452409-0.993965509267-1.735159305270.7630903965021.01015252899-0.05502883625950.2800280920980.914236258068-0.1473471376990.55907581749278.1485989206-1.924763234490.74943924722
92.174624454190.351641345126-1.463493412362.70397137354-1.239176887615.229304958230.274980957161-0.510301412717-0.09305140285961.02533594101-0.255086170359-0.393680878051-0.1473231236840.5597565335390.01804656958320.882475252249-0.184232367158-0.1583650608560.5101697156550.008973164204890.460822967626110.98573867213.8460821374-0.169799799142
106.153426885920.1029520356731.942212254390.344815837999-0.1529256514731.609946704910.01805187692630.6784212865030.0510367748901-0.05608461880460.0488774712314-0.00958436589820.01738109742060.176382497817-0.09372483874630.488470110143-0.0183333684774-0.008930443332520.342240647092-0.02131296259180.37392575540986.79670681054.19121314101-22.6684432077
117.75214156169-1.712109307211.976516976590.944425774995-1.031771790494.301427501160.145736958833-0.194920460030.2882025842720.1660973268450.09438607693710.002294008353210.0137571328729-0.10144970618-0.1873824541040.465025581392-0.0557209031246-0.01993696519340.283096677003-0.08483513995840.34255541763179.03032139158.29276609197-28.6785055438
127.039868643962.033876301794.642470897142.998182095722.979793786955.42508594893-0.0172440811297-0.61240965906-0.4295349638951.670511235580.087996719975-0.2283952867072.113488838281.48559270930.003195705241260.890619727998-0.0358417431506-0.1917509904310.6003691257280.008781302131560.758366213088116.885156744.48529391496-1.182613062
138.382275897332.32787906443-6.503167010830.921405070491-1.522443001389.07729977516-0.10376836858-0.3740152691870.282129932868-0.02195672610220.153584856428-0.1481940674720.4368292214770.2247827085250.08380246017130.3553791076010.0495312337685-0.04130597769140.332275716090.01717972066440.351750952077109.155527252-41.1851270243-47.7961963428
146.47420421386-1.94345045086-1.82345755854.348824475040.4438980509895.45391386888-0.380901777289-0.626528797038-0.7958076541340.4101761693970.1760698240080.4557839675080.863763367280.4089731625270.2664794441580.4501762600570.0382145037257-0.02763987511280.4355948213010.1305759801660.49582812752108.862072129-52.1090726158-41.9480378349
151.26670318340.0443000458169-0.7797000273872.04046911211-0.9204548698385.14871648317-0.02771165861660.0149615707080.0297583884043-0.0271325792146-0.193312231808-0.0995756457475-0.05918337051880.4793682211820.1786148482420.1809398646150.06203519558830.0581102541550.3407241886440.01120017416790.334770866172118.019697666-38.8809597563-49.0896624498
161.63406022361-1.253097492432.19627878271.93533988404-2.35558385996.322647361860.1745047126130.0749008791969-0.1657493601970.0207709561273-0.155244845849-0.0567480461858-0.042248636330.5725186561340.09950927359210.341058815925-0.01398733518070.03171226833620.4259252983870.0007901002233280.354546021697124.01634832-41.1425402355-38.2285309475
175.95496031847-2.119808352433.542249221778.00131533881-5.012641754144.1798240848-0.009433453486470.4264519249940.05388153203140.227028981598-0.322716280965-0.764043167134-0.02870997944751.160704485350.4074368077230.506184267144-0.0494641677673-0.003235846037620.68891446388-0.06561685883430.523881223966134.480670439-41.3108287646-30.2080368145
188.8595878763-0.5711437213493.176395792747.39289416645-4.306271707023.682001899760.382433517644-0.128233635706-0.1878255415210.575658112595-0.25379923405-0.519893326508-0.9626988744461.73981758096-0.2077551431120.384290289874-0.165783363005-0.001390435250860.510089389877-0.0520522741770.548321769934132.181361374-34.1738470322-35.4726877357
195.074112818420.177128406232-1.245632284111.269458722250.09647536664532.67087863210.08513088388880.174851916089-0.0274648053695-0.123355961910.0192778940110.267173195708-0.137566031326-0.246005956818-0.139885578010.3530962712890.08616730600510.02655965913050.3498697974450.02208800817870.36371539294102.009446672-34.3508694164-55.7282431134
202.68489224041-1.43045319532.379323592450.9673383140560.07819009024256.91811129650.0708100931274-0.714220221866-0.01822145596330.4417461890460.2906593771030.0629311389934-0.0794254342769-0.0605285365369-0.2129161361650.445066448957-0.06349631726070.05504952694910.6097132705990.004261603191660.428263469175104.762692848-42.6758160727-28.3009803991
215.13123270764-1.11737428895-0.6067369884227.728911336521.994151527677.401339432110.345963847767-1.013525411721.170067279020.7513886937460.187258508253-0.483706398705-0.824469233830.13605493106-0.4211966817370.611425165166-0.03987456805250.1531363643420.589388848851-0.129262099920.678831455398111.6089817-32.5614861555-18.0501891964
224.08957370557-1.018855279410.2542642613844.386487754480.2268279584824.98603024437-0.184423945836-1.392790664141.237236183331.48601682028-0.5244065269550.11725331493-0.513003924637-0.3986599892620.4798324235341.07620776734-0.0687874633137-0.02044516481081.04721153482-0.1399938793010.489619730695110.267978556-34.7148355516-7.39140336819
238.073265857920.614772290654-0.8723617066077.61555938986-2.018323590699.958977896170.04320543188671.34941303288-0.550944361135-0.903796442040.3441135249060.3900054504140.454612839206-0.502647490055-0.0630240943090.3670357440670.0161342517922-0.04728035601980.490559001387-0.1905115194540.417960626376101.318988698-45.1521169564-56.8832896189
248.925916150080.746620936986-0.7774428943195.23685320988-4.792084641264.393717360.3123897697660.583254842433-0.00757640585998-0.8249104677941.006251046790.8487176443151.13945412-0.921545410601-1.022731244870.49050512906-0.0507909440303-0.06941286500750.32122841577-0.02840600433660.45353706159461.0161980559-31.093373236-28.2803319765
252.359424458550.530114111458-0.1776745358117.71519997569-1.847641218391.935839694620.145235543817-0.05354924377810.1849212519770.4882455896020.1538076506950.622527943871-0.141750577598-0.369187853979-0.3168233798120.3648838377440.008130393402160.03407706234650.4366229753680.07539315219350.41746188709559.8123218979-32.464049897-17.2012854601
266.113254483472.85760391801-0.4465899104698.34353052595-1.285754840995.363144147590.2798378798750.1522314317950.275568528977-0.67069878125-0.457491911173-0.495396875103-0.5486296477410.01770618405020.2503995065410.4710157938130.0740669458155-0.02570095638690.513632868264-0.05064048068830.52088536122387.3817492679-20.367807494-22.4007528478
276.690966469445.1313359792.018153560455.405973807982.10774268211.870742068640.0646059306917-0.196290859562-0.002842752086010.04306349835270.04688553408120.184864073552-0.413026712899-0.250615970263-0.09810752039640.4425411844850.01762378261020.05748889089410.3164109812560.04005417751450.32073512764477.3534516056-29.1421318676-16.4957271327
286.593159371178.37938427791-4.104974524472.03408617566-5.801712809497.64575103851.46314275335-0.740216926605-1.184765631472.52024787632-1.02232339258-1.21700580913-0.2330706450130.338876095639-0.1106524298320.483143075634-0.0325304052516-0.05484170525830.4794334269860.04311277016020.69414216913689.506554674-26.0073054868-12.3144847539
292.798786413821.572927582713.580692211195.973377066293.088915177034.832218898620.194627303242-0.449451506268-0.9356187069230.102616975155-0.0413598360093-1.392729828570.05034490206630.4203073338750.04967841039520.3441853819180.0922305564705-0.02078947181510.347096858050.004191971331470.63209091741487.3638819777-34.1893643563-15.5979001168
303.86870432223-1.340786940162.233481624188.639983606-5.519067592043.93299400743-0.1391277519190.1066071886880.195612153541-0.8891187069810.2538437190010.4580685957470.55588889504-0.4467864956610.007501809739890.447676613911-0.0309663133109-0.02637616035370.476709118178-0.03011292257730.43725417682859.9282246323-37.9177360756-26.280444267
312.280048611151.98131314587-0.5151018625355.53348882119-1.080134802651.65964908097-0.2200048074860.6009166427190.243074781196-0.7761464561450.7473122747751.083195350560.290042353198-0.668768913757-0.4726981964040.510849326372-0.102675978198-0.1531393115380.6902260811760.1444493257790.55424690316552.9765643265-35.7673345245-31.3420520858
326.100934717453.82006412037-2.093652312754.4449823182-1.160763676699.1157328178-0.544331614024-1.449844611160.7721004718080.01966798310640.225327551025-1.850317677581.817249892881.255751688080.366146413430.801520607360.0487748642913-0.004660263087170.7196886082210.1961973706030.52185901143897.4990895694-22.3785183946-33.2889301394
334.59975581345-0.850410862628-1.833906547883.12237644256-1.546515713764.177064525890.00588173138975-0.01037947943110.119012001015-0.0871045652436-0.0782941757037-0.07646296065320.07516099732380.3907567552120.09092714176180.3637078685130.00567796424682-0.01121448062430.3516429755-0.0189583804330.26308147083486.6133721756-17.6696296632-40.1226514687
347.860465924831.86195313355-4.299692459275.17766430396-5.532209626166.47782696636-0.1291670356720.3791760202180.337574535931-0.5400684887810.5482659711491.676557743120.618225611221-0.597408127518-0.3844777916020.407316454047-0.0525794826241-0.1466965543520.754726526780.09952149740380.57657299169948.6011358908-36.9448647949-21.4410238966
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 14 )AA0 - 141 - 15
22chain 'A' and (resid 15 through 43 )AA15 - 4316 - 44
33chain 'A' and (resid 44 through 55 )AA44 - 5545 - 56
44chain 'A' and (resid 56 through 87 )AA56 - 8757 - 88
55chain 'A' and (resid 88 through 101 )AA88 - 10189 - 102
66chain 'A' and (resid 102 through 154 )AA102 - 154103 - 155
77chain 'A' and (resid 155 through 166 )AA155 - 166156 - 167
88chain 'A' and (resid 167 through 182 )AA167 - 182168 - 183
99chain 'B' and (resid 0 through 77 )BB0 - 771 - 78
1010chain 'B' and (resid 78 through 122 )BB78 - 12279 - 123
1111chain 'B' and (resid 123 through 190 )BB123 - 190124 - 191
1212chain 'C' and (resid 1 through 14 )CC1 - 141 - 14
1313chain 'D' and (resid 2 through 26 )DD2 - 261 - 25
1414chain 'D' and (resid 27 through 55 )DD27 - 5526 - 54
1515chain 'D' and (resid 56 through 101 )DD56 - 10155 - 100
1616chain 'D' and (resid 102 through 154 )DD102 - 154101 - 153
1717chain 'D' and (resid 155 through 166 )DD155 - 166154 - 165
1818chain 'D' and (resid 167 through 182 )DD167 - 182166 - 181
1919chain 'E' and (resid 0 through 77 )EE0 - 771 - 78
2020chain 'E' and (resid 78 through 113 )EE78 - 11379 - 107
2121chain 'E' and (resid 114 through 162 )EE114 - 162108 - 156
2222chain 'E' and (resid 163 through 190 )EE163 - 190157 - 184
2323chain 'F' and (resid 1 through 15 )FF1 - 151 - 15
2424chain 'G' and (resid 2 through 14 )GG2 - 141 - 13
2525chain 'G' and (resid 15 through 87 )GG15 - 8714 - 86
2626chain 'G' and (resid 88 through 101 )GG88 - 10187 - 100
2727chain 'G' and (resid 102 through 154 )GG102 - 154101 - 153
2828chain 'G' and (resid 155 through 166 )GG155 - 166154 - 165
2929chain 'G' and (resid 167 through 182 )GG167 - 182166 - 181
3030chain 'H' and (resid 0 through 32 )HH0 - 321 - 33
3131chain 'H' and (resid 33 through 97 )HH33 - 9734 - 98
3232chain 'H' and (resid 98 through 113 )HH98 - 11399 - 114
3333chain 'H' and (resid 114 through 190 )HH114 - 190115 - 191
3434chain '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