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- PDB-7n6d: HLA peptide complex -

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基本情報

登録情報
データベース: PDB / ID: 7n6d
タイトルHLA peptide complex
要素
  • Beta-2-microglobulin
  • MHC class I antigen
  • Spike protein S1
キーワードIMMUNE SYSTEM/VIRAL PROTEIN / peptide HLA complex / IMMUNE SYSTEM-VIRAL PROTEIN complex
機能・相同性
機能・相同性情報


antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / symbiont-mediated disruption of host tissue / protein homotetramerization / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / amyloid fibril formation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / learning or memory / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / Amyloid fiber formation / receptor ligand activity / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome
類似検索 - 分子機能
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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
Spike glycoprotein / Beta-2-microglobulin / MHC class I antigen
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: 2.3 Å
データ登録者Chaurasia, P. / Petersen, J. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)#1194036 オーストラリア
引用ジャーナル: J.Biol.Chem. / 年: 2021
タイトル: Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein.
著者: Chaurasia, P. / Nguyen, T.H.O. / Rowntree, L.C. / Juno, J.A. / Wheatley, A.K. / Kent, S.J. / Kedzierska, K. / Rossjohn, J. / Petersen, J.
履歴
登録2021年6月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年7月28日Provider: repository / タイプ: Initial release
改定 1.12021年8月25日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22021年9月22日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.32023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024年10月16日Group: Structure summary
カテゴリ: 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

ダウンロードとリンク

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集合体

登録構造単位
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
E: MHC class I antigen
F: Beta-2-microglobulin
G: Spike protein S1
I: MHC class I antigen
J: Beta-2-microglobulin
K: Spike protein S1
M: MHC class I antigen
N: Beta-2-microglobulin
O: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)181,68029
ポリマ－180,62512
非ポリマー1,05517
水3,603200
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,4047
ポリマ－45,1563
非ポリマー2484
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-8 kcal/mol
Surface area19000 Å2
手法PISA
2
E: MHC class I antigen
F: Beta-2-microglobulin
G: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,4047
ポリマ－45,1563
非ポリマー2484
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-7 kcal/mol
Surface area18930 Å2
手法PISA
3
I: MHC class I antigen
J: Beta-2-microglobulin
K: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,4678
ポリマ－45,1563
非ポリマー3105
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-13 kcal/mol
Surface area19170 Å2
手法PISA
4
M: MHC class I antigen
N: Beta-2-microglobulin
O: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,4047
ポリマ－45,1563
非ポリマー2484
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-6 kcal/mol
Surface area18860 Å2
手法PISA
単位格子
Length a, b, c (Å)85.197, 85.197, 442.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-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 1 through 13 or resid 18...
d_2ens_1(chain "E" and (resid 1 through 13 or resid 18...
d_3ens_1(chain "I" and (resid 1 through 13 or resid 18...
d_4ens_1(chain "M" and (resid 1 through 13 or resid 18...
d_1ens_2(chain "B" and (resid 1 through 40 or (resid 41...
d_2ens_2(chain "F" and (resid 1 through 40 or (resid 41...
d_3ens_2(chain "J" and (resid 1 through 40 or (resid 41...
d_4ens_2(chain "N" and (resid 1 through 44 or resid 46...
d_1ens_3(chain "C" and (resid 1 through 4 or resid 6 through 9))
d_2ens_3(chain "G" and (resid 1 through 4 or resid 6 through 9))
d_3ens_3(chain "K" and (resid 1 through 4 or resid 6 through 9))
d_4ens_3(chain "O" and (resid 1 through 4 or resid 6 through 9))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYSERA1 - 13
d_12ens_1GLYALAA18 - 40
d_13ens_1SERGLNA42 - 43
d_14ens_1METILEA45 - 52
d_15ens_1GLUPROA55 - 57
d_16ens_1TYRSERA59 - 71
d_17ens_1THRHISA73 - 74
d_18ens_1VALTYRA76 - 85
d_19ens_1GLNGLNA87
d_110ens_1GLYLEUA91 - 110
d_111ens_1GLYLYSA112 - 127
d_112ens_1ASPLEUA129 - 130
d_113ens_1SERALAA132 - 140
d_114ens_1THRLYSA142 - 144
d_115ens_1LYSGLYA146 - 175
d_116ens_1GLUVALA177 - 231
d_117ens_1THRGLUA233 - 254
d_118ens_1ARGHISA256 - 263
d_119ens_1GLYPROA265 - 267
d_120ens_1PROGLUA269 - 275
d_21ens_1GLYSERD1 - 13
d_22ens_1GLYALAD18 - 40
d_23ens_1SERGLND42 - 43
d_24ens_1METILED45 - 52
d_25ens_1GLUPROD55 - 57
d_26ens_1TYRSERD59 - 71
d_27ens_1THRHISD73 - 74
d_28ens_1VALTYRD76 - 85
d_29ens_1GLNGLND87
d_210ens_1GLYLEUD91 - 110
d_211ens_1GLYLYSD112 - 127
d_212ens_1ASPLEUD129 - 130
d_213ens_1SERALAD132 - 140
d_214ens_1THRLYSD142 - 144
d_215ens_1LYSGLYD146 - 175
d_216ens_1GLUVALD177 - 231
d_217ens_1THRGLUD233 - 254
d_218ens_1ARGHISD256 - 263
d_219ens_1GLYPROD265 - 267
d_220ens_1PROGLUD269 - 275
d_31ens_1GLYSERG1 - 13
d_32ens_1GLYALAG18 - 40
d_33ens_1SERGLNG42 - 43
d_34ens_1METILEG45 - 52
d_35ens_1GLUPROG55 - 57
d_36ens_1TYRSERG59 - 71
d_37ens_1THRHISG73 - 74
d_38ens_1VALTYRG76 - 85
d_39ens_1GLNGLNG87
d_310ens_1GLYLEUG91 - 110
d_311ens_1GLYLYSG112 - 127
d_312ens_1ASPLEUG129 - 130
d_313ens_1SERALAG132 - 140
d_314ens_1THRLYSG142 - 144
d_315ens_1LYSGLYG146 - 175
d_316ens_1GLUVALG177 - 231
d_317ens_1THRGLUG233 - 254
d_318ens_1ARGHISG256 - 263
d_319ens_1GLYPROG265 - 267
d_320ens_1PROGLUG269 - 275
d_41ens_1GLYSERJ1 - 13
d_42ens_1GLYALAJ18 - 40
d_43ens_1SERGLNJ42 - 43
d_44ens_1METILEJ45 - 52
d_45ens_1GLUPROJ55 - 57
d_46ens_1TYRSERJ59 - 71
d_47ens_1THRHISJ73 - 74
d_48ens_1VALTYRJ76 - 85
d_49ens_1GLNGLNJ87
d_410ens_1GLYLEUJ91 - 110
d_411ens_1GLYLYSJ112 - 127
d_412ens_1ASPLEUJ129 - 130
d_413ens_1SERALAJ132 - 140
d_414ens_1THRLYSJ142 - 144
d_415ens_1LYSGLYJ146 - 175
d_416ens_1GLUVALJ177 - 231
d_417ens_1THRGLUJ233 - 254
d_418ens_1ARGHISJ256 - 263
d_419ens_1GLYPROJ265 - 267
d_420ens_1PROGLUJ269 - 275
d_11ens_2ILEGLUB1 - 44
d_12ens_2ILEILEB46
d_13ens_2VALSERB49 - 57
d_14ens_2ASPTHRB59 - 73
d_15ens_2LYSSERB75 - 88
d_16ens_2PROPROB90
d_17ens_2ILEASPB92 - 96
d_18ens_2ASPMETB98 - 99
d_21ens_2ILEGLUE2 - 45
d_22ens_2ILEILEE47
d_23ens_2VALSERE50 - 58
d_24ens_2ASPTHRE60 - 74
d_25ens_2LYSSERE76 - 89
d_26ens_2PROPROE91
d_27ens_2ILEASPE93 - 97
d_28ens_2ASPMETE99 - 100
d_31ens_2ILEGLUH2 - 45
d_32ens_2ILEILEH47
d_33ens_2VALSERH50 - 58
d_34ens_2ASPTHRH60 - 74
d_35ens_2LYSSERH76 - 89
d_36ens_2PROPROH91
d_37ens_2ILEASPH93 - 97
d_38ens_2ASPMETH99 - 100
d_41ens_2ILEGLUK2 - 45
d_42ens_2ILEILEK47
d_43ens_2VALSERK50 - 58
d_44ens_2ASPTHRK60 - 74
d_45ens_2LYSSERK76 - 89
d_46ens_2PROPROK91
d_47ens_2ILEASPK93 - 97
d_48ens_2ASPMETK99 - 100
d_11ens_3TYRPROC1 - 4
d_12ens_3THRLEUC6 - 9
d_21ens_3TYRPROF1 - 4
d_22ens_3THRLEUF6 - 9
d_31ens_3TYRPROI1 - 4
d_32ens_3THRLEUI6 - 9
d_41ens_3TYRPROL1 - 4
d_42ens_3THRLEUL6 - 9

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

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要素

#1: タンパク質
MHC class I antigen


分子量: 32125.473 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q861F7
#2: タンパク質
Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769
#3: タンパク質・ペプチド
Spike protein S1


分子量: 1151.377 Da / 分子数: 4 / Fragment: epitope YLQPRTFLL (UNP residues 269-277) / 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: 17 / 由来タイプ: 合成 / 式: C2H6O2
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 200 / 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
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: 2.57 Å3/Da / 溶媒含有率: 52.12 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 20% PEG3350, 0.2 M sodium thiocyanate

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データ収集

回折平均測定温度: 100 K / Ambient temp details: 293.15 / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX2 / 波長: 0.953731 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年10月9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: 0.953731 Å / 相対比: 1
反射解像度: 2.3→49.21 Å / Num. obs: 82685 / % possible obs: 99.89 % / 冗長度: 14 % / Biso Wilson estimate: 47.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.06 / Rrim(I) all: 0.16 / Net I/σ(I): 10.3
反射 シェル解像度: 2.3→2.34 Å / 冗長度: 14.4 % / Rmerge(I) obs: 1.782 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4473 / CC1/2: 0.997 / Rpim(I) all: 0.482 / % possible all: 99.95

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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
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3GSO

3gso


解像度: 2.3→44.28 Å / SU ML: 0.3318 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 30.202
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.247 4268 5.17 %
Rwork0.2126 78222 -
obs0.2144 82490 99.9 %
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: 64.53 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→44.28 Å
タンパク質核酸リガンド溶媒全体
原子数12605 0 68 200 12873
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003313092
X-RAY DIFFRACTIONf_angle_d0.653717747
X-RAY DIFFRACTIONf_chiral_restr0.04461804
X-RAY DIFFRACTIONf_plane_restr0.00492318
X-RAY DIFFRACTIONf_dihedral_angle_d12.53994774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.577916167592
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.685958479241
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.685986718605
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.444035557059
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.635947547816
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.629070908292
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.901345627026
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.416944994572
ens_3d_4CX-RAY DIFFRACTIONTorsion NCS0.137806723033
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.36081220.32872536X-RAY DIFFRACTION99.77
2.33-2.350.37771470.33382585X-RAY DIFFRACTION99.78
2.35-2.380.35681320.32112585X-RAY DIFFRACTION100
2.38-2.410.36331390.30462590X-RAY DIFFRACTION99.82
2.41-2.440.33531340.29112600X-RAY DIFFRACTION99.85
2.44-2.480.35081530.2912546X-RAY DIFFRACTION99.82
2.48-2.510.3541570.28122597X-RAY DIFFRACTION100
2.51-2.550.28431440.28292570X-RAY DIFFRACTION99.89
2.55-2.590.30911210.28012635X-RAY DIFFRACTION99.82
2.59-2.630.32621290.32554X-RAY DIFFRACTION99.96
2.63-2.680.36551860.2852581X-RAY DIFFRACTION99.93
2.68-2.730.35281510.28742576X-RAY DIFFRACTION99.93
2.73-2.780.3511340.27582584X-RAY DIFFRACTION100
2.78-2.840.30321380.25932640X-RAY DIFFRACTION99.78
2.84-2.90.25961240.26132570X-RAY DIFFRACTION99.93
2.9-2.970.32341190.25282606X-RAY DIFFRACTION99.93
2.97-3.040.28931690.25232595X-RAY DIFFRACTION99.86
3.04-3.120.27371510.25022597X-RAY DIFFRACTION99.93
3.12-3.210.31321390.26012568X-RAY DIFFRACTION100
3.21-3.320.29671520.26232624X-RAY DIFFRACTION100
3.32-3.440.28241370.22822608X-RAY DIFFRACTION99.96
3.44-3.570.24861510.21012639X-RAY DIFFRACTION100
3.57-3.740.23591280.1962599X-RAY DIFFRACTION100
3.74-3.930.24831290.19722623X-RAY DIFFRACTION100
3.93-4.180.21391410.17832629X-RAY DIFFRACTION100
4.18-4.50.17061220.15492680X-RAY DIFFRACTION100
4.5-4.950.17381720.14952605X-RAY DIFFRACTION100
4.95-5.670.19211510.16232653X-RAY DIFFRACTION99.96
5.67-7.140.21681500.18792691X-RAY DIFFRACTION100
7.14-44.280.16571460.16212756X-RAY DIFFRACTION99.45
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)
13.272102637080.1024787664440.14615024162.85156430417-0.5048784174061.09099754926-0.163320466671-0.2258818547880.3402577755630.2277092922140.165238885444-0.483301519973-0.1089447279180.0352602196632-0.002603283283780.4586286511910.202689697628-0.1101707777460.377859778003-0.06590418300090.619908897649-18.8437379758-24.09298931357.0980741697
23.587640781140.330734727097-0.08220669584454.299974739850.5652903992894.064619563320.04079132227940.0394495396730.3801550797670.1165059818630.147697160102-0.436338828405-0.524958066962-0.337445897029-0.07940462625680.5344553287790.1337965749320.02891757624290.3207042185940.07190822052230.645130175017-28.52259365848.5998649833250.8577379876
32.00000911986.319984538342.000083201261.999926460271.999954027041.99994281117-0.191939730827-4.3951470495-1.423872488234.94960950185-0.458632621987-0.00810694035856-4.6034294081-6.158702323550.7291238903410.908454433449-0.297123588741-0.4405133194650.9890297647180.09301323701211.64717849717-29.532600282323.040248176946.8146936018
45.10841880630.768428552214-0.8721397813392.503162709810.9793422987672.06920140762-0.0118352096333-0.407784698191-0.378594399166-0.1066364211450.02755885204820.03105673623340.243159498077-0.0738197656050.05617574123610.3816681485090.154085962797-0.005607160775090.5033507421950.09719131835880.523241707589-32.9404364555-9.976299301243.0124045067
55.187874263332.10751773309-0.3400981935345.30156605063-0.2330312937676.553901923580.1162174851220.1677507058030.907989954168-0.590770682999-0.166195118785-0.437495004041-1.015534369960.641816876392-0.03471337936650.5753019859240.06566249502060.07806059195780.3285864930850.1266572525860.817609423429-21.4142243374-1.4812042807536.7566177898
64.293891681410.59460675659-2.842710785353.95884954831.853319464394.576609868-0.3381544956970.4471002332760.0204880400936-0.4542462980840.337932295755-0.2117662004480.389731011412-0.006499712242550.1726438701520.3931702786080.128944419404-0.09547143577150.3110847146290.006780240446190.497438412826-29.3018171925-15.382583219835.6874898333
75.13593007781-1.023559776034.375024630034.550786585-4.311522198726.83440007331-0.4292620158511.68579742118-0.04184851464340.21163184356-0.267376215991-0.782747988692-1.014227816170.05759986663050.6199653817950.5589086783760.07111068752730.1530991283540.5680267783290.2038460778170.752053563975-26.7187190016-9.1705727794723.7066907234
85.18702773-1.917707229231.310031991424.03882631607-2.327772545469.941123195170.5832171753270.6551850988990.000634500653359-0.399000348556-0.0143511071787-0.452450199039-0.1543629052470.583603413195-0.3889656442050.4677609356280.1749218749420.04333705245570.401519367947-0.005235033718340.768866936397-20.2130069278-15.036972697138.6101013884
93.859704068872.16627614989-1.885801102628.34344720233-5.025324288863.72598318774-0.09943096330380.7070999092830.369551055976-0.008154473718410.473602515657-0.172103612267-0.521087814263-0.634617933777-0.3102993038970.4707892796550.121547417389-0.01008844299270.372474607465-0.07953283307660.582728282092-24.0333245162-11.084017156442.9647253535
107.823412022353.24470380811-1.542145969012.561370043770.9672087275752.54761616215-0.3289546341480.7854910535940.713536358282-1.068896582330.383880424672-0.1772450975040.224028985323-0.0699200719097-0.02688416042940.50186121430.173098604399-0.04018578278240.5041800182720.1188928246130.689868173545-31.8306336997-7.644595428130.5167658898
115.02652269665-0.433393466104-1.947378002342.067210388712.404092022017.43769688706-0.0460667296792-1.033155070231.30517325756-0.5045510025010.087626496799-0.364074688034-1.87042767126-0.2465018906710.03649487519320.731156697710.315578144668-0.1448133569430.5707530735590.1377741637150.901639378655-30.83242573271.1553506035233.6851559292
120.3934394546320.425592056197-0.02548099052350.504817652188-0.127449012210.726048046486-0.216971122373-0.0397561622420.3513591322350.5282659895940.1063251687-0.3435944427390.04497889808650.02576046072390.1666309424620.5239442605380.326266603803-0.1858425365270.318790098487-0.1764923082970.764264420357-15.5003545625-29.996935274561.09598953
133.196944515980.6677332559071.153767530464.612686852511.966557073314.17283028411-0.188674957561-0.0117826279983-0.3323738519890.2831977305440.1532920092550.03973414646810.06924350857220.1719967216750.1360449904180.277982451890.08606434738110.01736095147060.4930388116190.0845411955450.684979146556-29.847729186-47.868650236226.0551585424
141.90919954947-0.381323694423-0.7801325879442.635136475-0.484028279281.875582653750.014151566050.4128810306140.0267965315429-0.0454254875026-0.0486868416879-0.166244945188-0.0128900005728-0.028825906240.08358256689190.2488804818640.0667794652273-0.004794398054490.6343563940670.1059253116260.745685239097-28.9262835987-38.54012421216.4513092994
153.678629512330.106179453635-0.9230660873632.35605346765-0.9412896224342.09761391549-0.1193035049850.467152337938-0.375308754763-0.0941400217891-0.0387894910484-0.3602118657290.1768263645110.08117072579140.2152809209340.2743190454370.0588784674148-0.1033824911860.594275766626-0.06157649807220.396687394699-38.3484379337-47.998129700915.1286467957
162.183357574630.496027836939-0.6007824230082.466342406290.08305212308872.885275470110.1253121926730.20453603823-0.175591558094-0.01358881573690.03845845108240.181401056835-0.100933053864-0.648313421986-0.07291232553610.2965879157390.0316783141364-0.00424505975140.6406094382760.08774657897110.703009304809-62.9869200091-49.496436851622.8423677005
175.282110710067.25896178534-0.5321238874229.96405345068-0.7304093744630.06257031728920.1098505877510.321505909530.5105494214550.3054846414230.1130566955950.3828431342350.1897002658970.074227708125-0.3651824104880.5556950632910.1503195181120.07100739751860.611353616120.2295899568910.710079595858-43.2333749632-28.314878398127.6801247486
183.83655381155-1.29387972771-0.813225160510.839784902550.1241563823053.420776819110.0341276919356-0.298769312364-0.1874872057780.154442830446-0.06939290612110.2903797592450.2502262606370.05563440171240.01648643187270.347349586290.0263949133548-0.04846861837040.4304561795930.1100467332460.536733100083-46.5349510486-45.725691585139.7431186952
193.15950373931.82060763956-2.025203857074.79022848309-3.510501156183.189272139070.02406093925590.172714915849-0.152725555310.223749874046-0.0845153779376-0.3355437873980.172418418630.2283939649290.02907151910230.3288559568410.0866590555897-0.05057179031630.4454225561660.04309906803190.559005262161-41.5341900392-44.172533777630.9834031801
204.33873531021-0.266424300775-1.29399803835.91428700394-2.965875153598.66379611656-0.270438017181-0.131372935514-0.3960909855620.4386701728530.09239698979680.706166292859-0.0680582083977-1.16871270190.01990676082740.3266735565780.11397834570.02885138947720.513894984937-0.001979543508290.703918121081-52.3976180698-40.936934547542.7861324954
210.4947725229781.91012920868-0.7237842255628.32359778162-3.176816468631.198319764180.09456912144260.1251807513660.359704468746-0.263811873453-0.430210667161-1.269244323930.00989085348820.2415744512260.4763887820160.3217732133850.09450822040550.009479252549650.5965628836090.04674358311740.828149223161-21.8844183602-41.976391602514.5766328252
221.04418377198-0.7276860160460.1156444087774.45132454701-2.696789987855.56393388759-0.04477302203930.0603129219949-0.124149134376-0.1350117809750.1712332107030.6550825094540.0199006642128-0.674619449587-0.1322173413050.3269373174860.129307745762-0.08580332784440.426546235498-0.01302123091810.676793822729-26.7894961826-56.928937931960.2030385518
232.63162803786-0.67744950630.1805936154213.69980494044-0.9003560622452.002588341990.0737423370134-0.02114474993750.512356805590.02468125851660.0398379459835-0.147071579127-0.1136213842210.0995569610797-0.07100877184090.4525019209010.171628735405-0.07217970576550.347816449211-0.01999963804990.65273265133-14.7528368194-48.767258776962.5862586203
245.35790994723-4.61139307748-2.777280803154.993550219914.787258601596.8897546196-0.831995370198-0.410730345703-1.157443627711.072887301580.3222594892861.577094326551.330647308830.5268550212770.13542766720.7651332958170.1223494158420.1745638531570.5035703111610.2509469629860.964686991502-17.402675235-84.071289903466.7814459723
256.05101737589-3.530537204910.2151411584543.766624019041.745640460692.08177468036-0.516655602199-0.595975196462-0.6946290295180.4996811525820.6357642263310.932318920180.583478172520.607296673312-0.1165568565850.5572024791640.2192774323640.03370306358350.5715404791910.1263155477120.718469704539-8.88988256727-85.146396122563.1380922537
260.573901580760.16417680492-0.1119033298743.58667687203-0.7902904942610.827581550040.121551436487-0.280359499840.000379517103288-0.46582354068-0.143829015461-0.533193051823-0.012193398276-0.277646330473-0.2210862722931.294126229171.216941879310.2405635832810.8351622363960.4151353996380.788482863821-11.1476487699-87.507855993972.8935110646
272.20662117159-0.6449301147370.732742106264.58977811748-0.03730038809182.754450391060.1860658857590.137426241955-0.629791937425-0.670295629929-0.1561705211330.9641453132460.456693014667-0.5672185901790.2735552263070.5875290292620.133758775464-0.1948216213250.40676543702-0.08417002710240.88500071312-21.8469966418-76.441050141553.1787856973
284.022141394780.723328567579-1.044690260543.85656011521-0.04521268054134.54480003150.1804948482710.412608861327-0.640385876477-0.694938186924-0.4085021789510.6656341069080.302972013235-1.065210130830.05178348837840.6867574073450.184842249614-0.3311457476460.662725384573-0.1692747927410.782690131798-27.2384840878-70.600796272847.1366552404
295.57088379822.31470193194-1.499542964978.137586067771.292234985173.21177664873-0.1127485467710.463674556496-0.940814023011-0.8386714254830.008579403719560.2595653720710.106935715061-0.2499953822430.2346219777880.4953944529340.162893678609-0.2523236424670.3847206455910.02550404733820.738798387338-21.4167590214-68.677316989654.4359003863
303.708661214810.183030234275-1.974963482357.163549830760.1789284047915.04269190835-0.3254581383220.904837235899-1.62303220243-1.29955512135-0.4900837844090.7964239820921.07578150464-1.340326690380.5367420462161.158295457460.199998519953-0.3456890810920.778274462632-0.3048007788531.1603656313-23.0505841467-81.050351179245.0129776573
310.4726273596810.674383994959-0.3254109988882.00373413046-1.142392500693.174327995580.3822529956230.4403550397780.5998420105640.0597890085410.219009917789-0.670812062803-0.650910288461-0.001476191193-0.09806020690280.3446660762830.203907850643-0.1208411625870.3965134047760.02455023235190.678076094887-19.4008326192-43.874246882363.4293136545
325.26777128465-0.356907707478-0.8755911307422.82006344943-1.432015532463.94271273801-0.0309196324666-0.1857688919560.7761490109130.4255318861660.09238280816680.373106761862-0.757192001673-0.315615340887-0.05451303111030.3566357617180.143090881273-0.02568267647850.527690010781-0.01706801936030.867046044389-4.15080162057-20.100739133912.0462026319
333.70454375268-0.665132352801-1.728714185176.67683766458-5.265170868986.788376653780.13853419228-0.06409479860210.2471031627660.06220811536380.3403862854961.01667784709-0.035577543975-0.455029861458-0.3109598436780.2892839814620.0728554419470.007459203047570.6753522376310.008725853248670.886391533302-12.822898804-27.595031658614.6572300742
343.25970224794-0.09923475992250.8100832016863.07197400229-0.7560246577073.85357618978-0.230656424545-0.255693202695-0.802271357996-0.01588840349060.1771045597970.2470287022910.39061934882-0.08757568538190.07431111894320.2636856612070.0819930282620.03394361014140.576224469132-0.02716259814350.768195458958-2.68294681576-39.070975674711.475897893
356.945046838330.001379709519121.859801228022.02791167368-0.6547442161682.65589692385-0.3050633654761.246815243691.20282581766-0.205676188141-0.001278735304430.408850070916-0.404347334955-0.1969454717240.2783781290520.3645776015360.122961966398-0.01958993386230.7096975673470.09777014672460.7325850089352.42660809009-20.5266324529-4.07317237444
362.72996825512-1.747370373352.729795416094.225609421390.2622431188585.104799756810.07100883720680.8029493470751.220014463940.287830692886-0.055535317748-0.2690176084340.00345113636210.9721188491730.131163846670.3931737624620.0896309050697-0.02746755602380.771622506180.1894066502450.95175113337230.2874471455-17.972102773811.2758619775
373.545206065850.703606434022-0.7385347589812.532541376622.188858902342.328917304630.3642516039641.363111802950.766916892349-0.198211018199-0.231087501967-0.228904825321-0.1103978394770.756835041389-0.1747363059880.3784703525810.1425831475910.01587421422580.9154789184720.2495962361290.83221168544530.2593934125-21.02686079868.75084421781
386.111531298121.68565551275-2.641768209460.739781060247-0.6853585494512.43630748659-0.0271064344294-1.439177014370.7551477497450.498260713716-0.231016437140.111110186068-0.868817015051-0.2267152384780.4575647046350.2861296550230.0856532350037-0.1436771303410.843533228004-0.1844695961120.73948901138613.1229776959-23.034713015824.6375250153
394.626080893650.656374780501-0.4702207131665.1707896069-2.064707074494.80330675223-0.0411351238837-0.9144984208721.425583045830.168157591626-0.70799657504-0.0780874476414-0.7712289498180.4560370356380.2640808192740.5396474980940.0419016037968-0.1650395333930.651463144532-0.2568117498541.2262197415512.7655980148-11.150220595521.0523328547
403.45942340734-0.917907062447-2.095080346624.74369734444-2.707293537294.010037172050.15583078154-0.92121697299-0.1783325834691.03238924446-0.0909262541868-0.689166022303-1.230798896070.439087940146-1.054317643630.8088391149540.136585128449-0.1316901186621.02623032742-0.3211879569091.623967314487.81917220638-4.4243314251726.6221512717
415.71519996042.885202609170.8169569353111.55661450360.03116485722244.69489309452-0.268804121898-0.7363888854550.8538096193540.02096927182050.0417327871811-0.0117383561926-0.5926655002020.04748922570840.07434616805240.3352223185720.152355814969-0.04944103019320.611644967336-0.2002281310420.8719470606087.40018452435-18.273183795218.1767199841
425.709229834284.138321147941.499089856667.51935819306-0.2874916152726.13980132335-0.86619695322-0.8296217889142.172472696410.3392743328940.3781222616560.245785966252-1.207153163680.05013137082410.2967777250120.6646889873750.103740238178-0.3167508760890.894514714141-0.3270163874321.3063572720818.2880896779-11.175158663627.8504308
432.781088706513.81296205114-4.014818511346.41105782505-4.619771905346.61699153873-0.09656339901730.638911515311-0.207799383315-0.0116304157220.6135351406250.4374411613320.0821548286315-1.42900539773-0.2303264412150.269648606780.08356387819540.02668501025340.63979398192-0.01028056536750.65831004096-11.7516174394-33.30810732668.64338234944
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 174 )AA1 - 1741 - 174
22chain 'A' and (resid 175 through 274 )AA175 - 274175 - 274
33chain 'A' and (resid 275 through 275 )AA275275
44chain 'B' and (resid 1 through 11 )BB1 - 111 - 11
55chain 'B' and (resid 12 through 30 )BB12 - 3012 - 30
66chain 'B' and (resid 31 through 41 )BB31 - 4131 - 41
77chain 'B' and (resid 42 through 46 )BB42 - 4642 - 46
88chain 'B' and (resid 47 through 56 )BB47 - 5647 - 56
99chain 'B' and (resid 57 through 71 )BB57 - 7157 - 71
1010chain 'B' and (resid 72 through 90 )BB72 - 9072 - 90
1111chain 'B' and (resid 91 through 99 )BB91 - 9991 - 99
1212chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
1313chain 'E' and (resid 1 through 56 )ED1 - 561 - 56
1414chain 'E' and (resid 57 through 137 )ED57 - 13757 - 137
1515chain 'E' and (resid 138 through 197 )ED138 - 197138 - 197
1616chain 'E' and (resid 198 through 276 )ED198 - 276198 - 276
1717chain 'F' and (resid 0 through 5 )FE0 - 51 - 6
1818chain 'F' and (resid 6 through 51 )FE6 - 517 - 52
1919chain 'F' and (resid 52 through 71 )FE52 - 7153 - 72
2020chain 'F' and (resid 72 through 99 )FE72 - 9973 - 100
2121chain 'G' and (resid 1 through 9 )GF1 - 91 - 9
2222chain 'I' and (resid 1 through 56 )IG1 - 561 - 56
2323chain 'I' and (resid 57 through 174 )IG57 - 17457 - 174
2424chain 'I' and (resid 175 through 197 )IG175 - 197175 - 197
2525chain 'I' and (resid 198 through 262 )IG198 - 262198 - 262
2626chain 'I' and (resid 263 through 276 )IG263 - 276263 - 276
2727chain 'J' and (resid 0 through 30 )JH0 - 301 - 31
2828chain 'J' and (resid 31 through 56 )JH31 - 5632 - 57
2929chain 'J' and (resid 57 through 70 )JH57 - 7058 - 71
3030chain 'J' and (resid 71 through 99 )JH71 - 9972 - 100
3131chain 'K' and (resid 1 through 9 )KI1 - 91 - 9
3232chain 'M' and (resid 1 through 56 )MJ1 - 561 - 56
3333chain 'M' and (resid 57 through 84 )MJ57 - 8457 - 84
3434chain 'M' and (resid 85 through 162 )MJ85 - 16285 - 162
3535chain 'M' and (resid 163 through 185 )MJ163 - 185163 - 185
3636chain 'M' and (resid 186 through 219 )MJ186 - 219186 - 219
3737chain 'M' and (resid 220 through 276 )MJ220 - 276220 - 276
3838chain 'N' and (resid 0 through 11 )NK0 - 111 - 12
3939chain 'N' and (resid 12 through 41 )NK12 - 4113 - 42
4040chain 'N' and (resid 42 through 51 )NK42 - 5143 - 52
4141chain 'N' and (resid 52 through 71 )NK52 - 7153 - 72
4242chain 'N' and (resid 72 through 99 )NK72 - 9973 - 100
4343chain 'O' and (resid 1 through 9 )OL1 - 91 - 9

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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