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- PDB-8wul: Crystal structure of affinity enhanced TCR in complex with HLA-A*... -

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基本情報

登録情報
データベース: PDB / ID: 8wul
タイトルCrystal structure of affinity enhanced TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide (VVGAVGVGK)
要素
  • Beta-2-microglobulin
  • KRAS-G12V nonamer peptide
  • MHC class I antigen
  • TCR alpha chain
  • TCR beta chain
キーワードIMMUNE SYSTEM / T cell receptor / KRAS-G12V / HLA-A*11:01
機能・相同性
機能・相同性情報


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
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. ...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 / 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
MHC class I antigen / Beta-2-microglobulin
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.36 Å
データ登録者Zhang, M.Y. / Luo, L.J. / Xu, W. / Guan, F.H. / Wang, X.Y. / Zhu, P. / Zhang, J.H. / Zhou, X.Y. / Wang, F. / Ye, S.
資金援助 中国, 6件
組織認可番号国
Ministry of Science and Technology (MoST, China)2021YFC2300503 中国
Ministry of Science and Technology (MoST, China)2021YFC2502300 中国
Ministry of Science and Technology (MoST, China)2022YFC2304705 中国
Ministry of Science and Technology (MoST, China)2022YFA0912400 中国
Ministry of Science and Technology (MoST, China)2020YFA0908500 中国
National Natural Science Foundation of China (NSFC)31971127 中国
引用ジャーナル: Commun Biol / 年: 2024
タイトル: Identification and affinity enhancement of T-cell receptor targeting a KRAS G12V cancer neoantigen.
著者: Zhang, M. / Xu, W. / Luo, L. / Guan, F. / Wang, X. / Zhu, P. / Zhang, J. / Zhou, X. / Wang, F. / Ye, S.
履歴
登録2023年10月20日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年5月1日Provider: repository / タイプ: Initial release
改定 1.12024年5月15日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
C: TCR alpha chain
D: TCR beta chain
A: TCR alpha chain
B: TCR beta chain
E: TCR alpha chain
F: TCR beta chain
G: TCR alpha chain
H: TCR beta chain
L: MHC class I antigen
M: Beta-2-microglobulin
N: KRAS-G12V nonamer peptide
I: MHC class I antigen
J: Beta-2-microglobulin
K: KRAS-G12V nonamer peptide
O: MHC class I antigen
P: Beta-2-microglobulin
Q: KRAS-G12V nonamer peptide
R: MHC class I antigen
S: Beta-2-microglobulin
T: KRAS-G12V nonamer peptide


分子量 (理論値)分子数
合計 (水以外)374,75020
ポリマ－374,75020
非ポリマー00
水7,260403
1
C: TCR alpha chain
D: TCR beta chain
L: MHC class I antigen
M: Beta-2-microglobulin
N: KRAS-G12V nonamer peptide


分子量 (理論値)分子数
合計 (水以外)93,6875
ポリマ－93,6875
非ポリマー00
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: TCR alpha chain
B: TCR beta chain
I: MHC class I antigen
J: Beta-2-microglobulin
K: KRAS-G12V nonamer peptide


分子量 (理論値)分子数
合計 (水以外)93,6875
ポリマ－93,6875
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: TCR alpha chain
F: TCR beta chain
O: MHC class I antigen
P: Beta-2-microglobulin
Q: KRAS-G12V nonamer peptide


分子量 (理論値)分子数
合計 (水以外)93,6875
ポリマ－93,6875
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: TCR alpha chain
H: TCR beta chain
R: MHC class I antigen
S: Beta-2-microglobulin
T: KRAS-G12V nonamer peptide


分子量 (理論値)分子数
合計 (水以外)93,6875
ポリマ－93,6875
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)87.752, 96.331, 123.121
Angle α, β, γ (deg.)94.556, 90.630, 93.200
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

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タンパク質 , 4種, 16分子 CAEGDBFHLIORMJPS

#1: タンパク質
TCR alpha chain


分子量: 22105.652 Da / 分子数: 4 / 変異: T159C / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli (大腸菌)
#2: タンパク質
TCR beta chain


分子量: 27321.787 Da / 分子数: 4 / 変異: K51M, E100H, S170C / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli (大腸菌)
#3: タンパク質
MHC class I antigen / HLA-A*1101


分子量: 31725.936 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: A0A6M6CC39
#4: タンパク質
Beta-2-microglobulin


分子量: 11748.160 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 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769

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タンパク質・ペプチド / 非ポリマー , 2種, 407分子 NKQT

#5: タンパク質・ペプチド
KRAS-G12V nonamer peptide


分子量: 785.951 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 403 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.84 Å3/Da / 溶媒含有率: 56.73 %
結晶化温度: 289.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 20% (w/v) PEG 3350, 0.2M ammonium citrate tribasic at pH 7.0

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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: SSRF / ビームライン: BL18U1 / 波長: 1.03845 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2023年4月8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: 1.03845 Å / 相対比: 1
反射解像度: 2.36→30 Å / Num. obs: 161796 / % possible obs: 98.1 % / 冗長度: 3.4 % / Biso Wilson estimate: 53.8 Å2 / CC1/2: 0.99 / Net I/σ(I): 27.1
反射 シェル解像度: 2.36→2.4 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7989 / CC1/2: 0.796

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
HKL-3000データ削減
HKL-3000データスケーリング
PHENIX位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換 / 解像度: 2.36→29.67 Å / SU ML: 0.3398 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 27.9287
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2348 8036 4.97 %
Rwork0.1904 153621 -
obs-161533 97.87 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 74.44 Å2
精密化ステップサイクル: LAST / 解像度: 2.36→29.67 Å
タンパク質核酸リガンド溶媒全体
原子数25613 0 0 403 26016
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001826285
X-RAY DIFFRACTIONf_angle_d0.492835617
X-RAY DIFFRACTIONf_chiral_restr0.04043699
X-RAY DIFFRACTIONf_plane_restr0.0034653
X-RAY DIFFRACTIONf_dihedral_angle_d14.41569697
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.380.37642580.31084648X-RAY DIFFRACTION89.07
2.38-2.410.33222570.2875102X-RAY DIFFRACTION97.19
2.41-2.440.32162450.27815122X-RAY DIFFRACTION97.33
2.44-2.470.3282860.27075088X-RAY DIFFRACTION97.36
2.47-2.510.31652600.25865129X-RAY DIFFRACTION97.45
2.51-2.540.26912600.24695114X-RAY DIFFRACTION97.25
2.54-2.580.28752510.24685110X-RAY DIFFRACTION97.47
2.58-2.610.29972570.2445110X-RAY DIFFRACTION97.8
2.61-2.660.28392940.23875094X-RAY DIFFRACTION97.73
2.66-2.70.2772660.23595082X-RAY DIFFRACTION97.79
2.7-2.750.27972610.24065225X-RAY DIFFRACTION98.03
2.75-2.80.28272500.23875096X-RAY DIFFRACTION97.89
2.8-2.850.32742780.24825146X-RAY DIFFRACTION98.03
2.85-2.910.30842990.25325084X-RAY DIFFRACTION98.18
2.91-2.970.29912860.24235123X-RAY DIFFRACTION98.11
2.97-3.040.29212770.2345156X-RAY DIFFRACTION98.17
3.04-3.120.30132810.23525127X-RAY DIFFRACTION98.11
3.12-3.20.30112580.23445175X-RAY DIFFRACTION98.33
3.2-3.290.30842630.22385102X-RAY DIFFRACTION98.08
3.29-3.40.25352680.21595168X-RAY DIFFRACTION98.41
3.4-3.520.23382820.19555198X-RAY DIFFRACTION98.44
3.52-3.660.252560.18925149X-RAY DIFFRACTION98.58
3.66-3.830.23092860.18375156X-RAY DIFFRACTION98.59
3.83-4.030.2172310.17075194X-RAY DIFFRACTION98.56
4.03-4.280.19732750.15545138X-RAY DIFFRACTION98.6
4.28-4.610.17643060.14145170X-RAY DIFFRACTION98.76
4.61-5.070.17743000.13135149X-RAY DIFFRACTION98.8
5.07-5.80.20122670.14855165X-RAY DIFFRACTION98.75
5.8-7.290.21072080.17985237X-RAY DIFFRACTION98.71
7.29-29.950.17872700.16255064X-RAY DIFFRACTION96.7
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)
11.27285428023-1.911056304541.007466696056.09618739557-2.326932188155.20268352915-0.0277146014843-0.177591640275-0.0699837424309-0.1574212202180.0612029576862-0.3749788031240.977718320785-0.0175623575007-0.0413240081070.468039752252-0.0436063125324-0.0258170479010.4375443485870.02455602811010.4108037523316.928845484417.9053411447-49.4544096468
25.90085830501-0.2417670784192.02451230138.327524926491.38790394733.704588909430.1148571916860.206593450613-0.6605140629130.6232432479470.02547578595880.2062107776830.92700994973-0.0396033236634-0.007445506468831.235609999540.06270128913120.09628844736740.540721464568-0.01945137109080.6238621153472.348344033712.0895948424-18.6665661515
33.40281445757-0.432338726464-0.6950764301682.72563861205-0.6139437849335.607196843230.24084621794-0.2681221700730.3957261719170.05542950850950.2705650600640.26811835184-0.345966266755-0.799263685988-0.3713015730860.243366608862-0.02445183985210.02976086625810.5477974067310.06427785946270.41483700462-6.7124491440237.2612706053-47.0102413577
44.63198861115-1.430671666181.554851201923.18381744637-1.778272711266.18987355484-0.217838937607-0.135071107975-0.103889077640.6774031797120.2767083177630.08815394321770.441507557271-0.528018563283-0.07829867833590.697842036024-0.1836177353870.1053675667230.394889843304-0.1021471566250.432814271636-4.8385003391623.8069227062-18.4079772738
53.92753307208-2.820444664832.254498054.23793616289-0.3114017538666.103499772960.0970097520830.323662063136-0.3618539255250.04527034733130.178091397503-0.06658934311680.8768335275520.0817879636471-0.2847416186670.671208656894-0.02548030548990.07594654770930.445659758758-0.0534967271570.4221111556411.0574380951923.8525727299-19.8306897242
64.91591853746-3.604746009153.26796056935.23331189345-1.292798250448.20462903337-0.453714450049-0.365574370140.8153514349680.5390745188940.163771885032-0.209460681874-0.0993304395759-0.3752092332630.2774510130510.613918968817-0.0340486713660.05486934781890.452491372485-0.1520184499360.496582577301-3.4709358401833.7635759409-14.7206614382
75.7348889575-6.259800906956.622119541166.78956915997-7.10372107637.602523289410.380195883769-0.412868312155-0.608741292979-0.659191204630.4955363332831.128783411681.291367671-0.976200806537-0.8442638570750.681923103886-0.118801230045-0.1931455778260.5548965047560.07800152940560.71255766681143.748608225918.283279545-36.1698522421
81.510711941680.81878536933-1.053303909213.557523001072.030277314892.99786633905-0.4819474639760.33453582305-0.0647631649244-0.7010320727760.2645237682040.6322217900540.206225900847-0.7127178177020.1640204469680.755032002871-0.396767483902-0.2671259097420.6069238127350.2132710040160.86638516059547.558775123522.2623957177-45.3036308393
96.31269698924-0.00300357131875-6.379311813229.19403823553-0.2726475428389.289216407830.0339266405853-0.616508351835-0.048360514970.1116255183230.471802725342-0.2479437992420.5038043240380.562321864761-0.5102680501360.33148415731-0.0797351319186-0.1822522526510.3169470066350.0491961474250.48763533974850.800294336830.3373109473-38.6807358609
103.74285089594-1.14184428183.884519027515.985748021-0.2716973149957.948380962240.2342487801090.0627204094095-1.18745625662-1.713366725730.367724931477-0.9388743093290.623043751463-0.0439088956464-0.6651846799550.78349204543-0.1954804890390.03359271838530.4450664210870.01349439781940.697511032654.916964638921.7378832368-45.1006898896
111.53466529681-3.25845051570.8646572086017.60058902154-3.262584868734.02091973353-0.203519388517-0.0606200751737-0.01699509144540.329771314151-0.0109750503986-0.3586979235230.0818262803125-0.12649181764-0.01400698044380.420951960192-0.231813200141-0.02509317554520.359930231970.003679127746970.48708051970747.858712898128.2953339644-39.2353723293
127.454752525441.24552272564-5.487457897968.32185638241-3.163321298549.31308680241-1.11342202909-0.589533466071-0.1519272628861.549119625410.194752951676-0.2764637139191.17095558150.699630245580.6919822738921.23369296229-0.0217174287451-0.004325653605620.471833417531-0.00567136041460.67450762302653.958206983214.3881251292-19.6132091851
130.7352507688270.1806949934231.595708360367.080908015065.6388305987.4323182657-0.449655292859-0.2420281133070.003127939041531.320129219070.9525171694010.4755258505220.056067035194-0.00466590159122-0.3326270726042.293303473710.1624340835320.5451206072451.064202493470.04586421652150.68851840311540.591636187521.98745020612.88515750846
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736.46551140746-3.92289355432-6.674700472737.746387601634.191233111037.397167810910.6359904415840.07478428176750.3857724053090.367298335225-0.349341280656-0.694748443973-0.55688994480.255917243321-0.3345178126240.502760508156-0.033994410093-0.07624715735230.4574323204750.04744768551110.4758781730028.63854033093-40.3947226518-13.1660186764
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764.944408139253.71746632085-1.771592278844.39044076182-3.851485086865.36377839528-0.9840966543050.311839513267-0.853969461686-0.9725683007660.268042787409-0.7289586214451.61685462515-0.592694962460.8137178675070.807113957724-0.1105299177430.104977081050.388989382161-0.05587857993130.532793904193-0.714637179619-48.0540986179-15.7019986275
777.689235616084.2102111783-5.696126152776.73172626604-7.660198396319.55233734617-1.280847614131.176992670670.02286186453-0.9549995772040.2808814093592.550691151731.04573057910.6401681038330.9939598895830.742101029667-0.2579948090690.1315503306340.647361310286-0.0547880064490.788850730439-9.08272136185-43.4157573721-17.70255583
789.717920711396.57202627735-5.436135710425.53142996356-3.63368214016.38988257076-0.368401488565-0.6869469593070.252096917446-0.3405573454480.072154114780.2089735577870.3549079259420.08718437465190.3249013835030.5505115620370.03872689671540.01127866173770.3643208157480.02090990102290.3750628716131.61856884315-35.3556541055-17.2371909613
799.266609429082.93795130868-4.051528421964.11267342159-4.19694601424.44132755145-1.456069068590.00842900215381-0.697654939678-0.322384333322.098905270360.201251611995-0.7494667640480.225762498498-0.7028582442350.892626744423-0.1792211191690.05665258188120.877783054720.05371666238090.477717567343-9.324752817-49.58192423221.79257472155
805.551029887427.12263692464-5.772404561659.35213324887-7.653629717028.34036694445-0.3435929006650.0693113504922-0.537741871045-0.253447456117-0.0676299674019-0.8729838978930.852113207666-0.01682909637530.4490780729350.660429156071-0.0168433933615-0.03800444455680.3635316568660.00637502008730.4900762841545.85501765827-49.7244979969-14.5698214635
814.20059863548-2.90486840614-2.422016900434.202046612432.461246854672.094484174990.0578113345131-1.73529826470.621081754031.581715852320.460922634809-0.8014403257110.7454873403270.522802823431-0.1010846238260.899189876050.0057738227570.02256667532690.68079148160.07615936532550.4530807664871.19185340515-45.0075496353-1.31998936686
820.9312132092070.623147713820.2463120041424.72268233153-3.858590116093.98124747023-0.595785616275-0.2731752937140.1417421629170.275437877161-0.0401560277061-0.449439247201-0.09409606711290.2512662228910.6476282359420.444584224744-0.019709319906-0.03963005107120.294667579045-0.04210124587270.4968571544936.26298034968-22.1968660294-37.4127459871
830.606697973148-0.0957584171031-0.3096271589721.846864038020.8874578429551.81790694431-0.0154043216986-0.01432044358980.0792731284920.5601486885070.20595994803-0.09809059075220.0398831356389-0.0518184017551-0.1933723720530.5345170516210.0753489260484-0.01965153025640.367028068383-0.01446912759530.48595923263247.3671919212-18.5739657265-20.8746005602
843.36372537388-0.2705914563361.789148049610.363704390057-1.494964229863.419102747030.0180241159284-0.5082741687670.5126613943140.573590708607-0.0316711218082-0.372614347162-0.5684392478190.2506154952480.08915574653661.825471389240.132492998252-0.05261091843220.752876115553-0.1600049225060.71291010123949.2327689412-21.498820048414.2227966623
858.18666592886-0.479675235693-5.726852800485.082964266890.9197700699416.789875465190.184310218548-0.3964137779310.3141876597430.969527855455-0.0175704462039-0.2811081551670.290654329530.465346082125-0.1003232277661.218788761910.260362674353-0.1432049526110.4817712845650.005412987459620.58165042891651.6189488652-34.0173523148-2.32278167041
864.500229384622.05042438591-2.167639016271.77835410116-2.2646716312.98453138019-0.0199058532436-1.26067155810.5821318315161.434646295510.4912969713310.344379875304-0.396818660348-0.040402924353-0.331458309381.640397981840.3079659259450.1451523179650.7911655452560.04604880715410.56761660505637.91625671-32.0496751255.09145948053
873.94062067073.35903518156-1.817806474588.17659478497-7.098409140527.35137441611-0.757162606808-0.2573619409620.1523238026230.3635928877340.508906761202-0.364680259242.16743023474-0.0106578296860.4531568210421.142176137160.126611190058-0.04273510600790.521658125514-0.06435571991910.53687032464245.3449764618-39.7171194618-6.99055213335
885.44975632659-1.578976028710.8356348025043.13990955591-2.994961632742.91971727953-0.09242939785030.401038675703-0.5422582773980.1927232404340.9606802837631.310497788811.3540964523-0.801897501563-0.4114819739951.32177241018-0.01472652150270.1498877424610.608970199723-0.003056463026380.59541489820635.0407129678-42.4802986479-2.68953488512
894.732269129573.16322953594-5.459339020472.72455014742-2.892289725047.135366827830.7174208204750.07275860309941.54150920180.320490488287-0.1997267710021.40534561246-1.08506392335-0.149994531729-0.6138249454641.064124445620.1339229452970.07708408158060.3954738601040.01659989690280.65667239203944.6794158035-27.0146515249-11.5024711635
907.540720720056.465251167370.6682060323026.145542649430.9528735873720.2969799297240.0973010436666-1.805824025810.3394780929781.98226595177-0.539001041255-0.898269172826-1.067176193761.02819772901-0.01011680428030.9837110629020.107890677771-0.1740813273130.743051731765-0.2357441262850.4942252147555.3818907792-23.664845588-10.3089745305
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934.147158270583.73600986869-0.1385662356816.05648795762-3.371611498093.987691634710.6176567567390.3226534021960.5167761259910.317730588460.1881512596840.379843384276-0.173101947548-0.439834368538-1.021666430341.163070082270.07525359572970.004281119595920.487463274396-0.06673731904220.46494631283543.8067605318-42.66668655870.0100486645493
945.91925852715-0.7188212056912.264541862714.14213948713-2.042984924151.64109544849-0.4666771261690.133163198086-1.318112048371.770092668310.195313906296-0.3006506424561.686953774910.7170855746740.3766658095711.133573946490.263105447481-0.01225622776320.464441593994-0.08642467758210.69160678206354.307072124-44.2628781877-6.9208409203
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 3 through 118 )
2X-RAY DIFFRACTION2chain 'C' and (resid 119 through 177 )
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 107 )
4X-RAY DIFFRACTION4chain 'D' and (resid 108 through 138 )
5X-RAY DIFFRACTION5chain 'D' and (resid 139 through 196 )
6X-RAY DIFFRACTION6chain 'D' and (resid 197 through 239 )
7X-RAY DIFFRACTION7chain 'A' and (resid 3 through 14 )
8X-RAY DIFFRACTION8chain 'A' and (resid 15 through 32 )
9X-RAY DIFFRACTION9chain 'A' and (resid 33 through 53 )
10X-RAY DIFFRACTION10chain 'A' and (resid 54 through 76 )
11X-RAY DIFFRACTION11chain 'A' and (resid 77 through 104 )
12X-RAY DIFFRACTION12chain 'A' and (resid 105 through 118 )
13X-RAY DIFFRACTION13chain 'A' and (resid 119 through 131 )
14X-RAY DIFFRACTION14chain 'A' and (resid 132 through 147 )
15X-RAY DIFFRACTION15chain 'A' and (resid 148 through 157 )
16X-RAY DIFFRACTION16chain 'A' and (resid 158 through 168 )
17X-RAY DIFFRACTION17chain 'A' and (resid 169 through 177 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 107 )
19X-RAY DIFFRACTION19chain 'B' and (resid 108 through 122 )
20X-RAY DIFFRACTION20chain 'B' and (resid 123 through 237 )
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 25 )
22X-RAY DIFFRACTION22chain 'E' and (resid 26 through 53 )
23X-RAY DIFFRACTION23chain 'E' and (resid 54 through 76 )
24X-RAY DIFFRACTION24chain 'E' and (resid 77 through 104 )
25X-RAY DIFFRACTION25chain 'E' and (resid 105 through 118 )
26X-RAY DIFFRACTION26chain 'E' and (resid 119 through 131 )
27X-RAY DIFFRACTION27chain 'E' and (resid 132 through 147 )
28X-RAY DIFFRACTION28chain 'E' and (resid 148 through 157 )
29X-RAY DIFFRACTION29chain 'E' and (resid 158 through 167 )
30X-RAY DIFFRACTION30chain 'E' and (resid 168 through 177 )
31X-RAY DIFFRACTION31chain 'F' and (resid 1 through 138 )
32X-RAY DIFFRACTION32chain 'F' and (resid 139 through 239 )
33X-RAY DIFFRACTION33chain 'G' and (resid 1 through 91 )
34X-RAY DIFFRACTION34chain 'G' and (resid 92 through 131 )
35X-RAY DIFFRACTION35chain 'G' and (resid 132 through 161 )
36X-RAY DIFFRACTION36chain 'G' and (resid 162 through 177 )
37X-RAY DIFFRACTION37chain 'H' and (resid 1 through 107 )
38X-RAY DIFFRACTION38chain 'H' and (resid 108 through 138 )
39X-RAY DIFFRACTION39chain 'H' and (resid 139 through 209 )
40X-RAY DIFFRACTION40chain 'H' and (resid 210 through 238 )
41X-RAY DIFFRACTION41chain 'L' and (resid 1 through 174 )
42X-RAY DIFFRACTION42chain 'L' and (resid 175 through 197 )
43X-RAY DIFFRACTION43chain 'L' and (resid 198 through 274 )
44X-RAY DIFFRACTION44chain 'M' and (resid 1 through 11 )
45X-RAY DIFFRACTION45chain 'M' and (resid 12 through 19 )
46X-RAY DIFFRACTION46chain 'M' and (resid 20 through 30 )
47X-RAY DIFFRACTION47chain 'M' and (resid 31 through 46 )
48X-RAY DIFFRACTION48chain 'M' and (resid 47 through 51 )
49X-RAY DIFFRACTION49chain 'M' and (resid 52 through 71 )
50X-RAY DIFFRACTION50chain 'M' and (resid 72 through 77 )
51X-RAY DIFFRACTION51chain 'M' and (resid 78 through 90 )
52X-RAY DIFFRACTION52chain 'M' and (resid 91 through 99 )
53X-RAY DIFFRACTION53chain 'N' and (resid 1 through 9 )
54X-RAY DIFFRACTION54chain 'I' and (resid 1 through 137 )
55X-RAY DIFFRACTION55chain 'I' and (resid 138 through 188 )
56X-RAY DIFFRACTION56chain 'I' and (resid 189 through 274 )
57X-RAY DIFFRACTION57chain 'J' and (resid 1 through 11 )
58X-RAY DIFFRACTION58chain 'J' and (resid 12 through 19 )
59X-RAY DIFFRACTION59chain 'J' and (resid 20 through 30 )
60X-RAY DIFFRACTION60chain 'J' and (resid 31 through 41 )
61X-RAY DIFFRACTION61chain 'J' and (resid 42 through 46 )
62X-RAY DIFFRACTION62chain 'J' and (resid 47 through 51 )
63X-RAY DIFFRACTION63chain 'J' and (resid 52 through 71 )
64X-RAY DIFFRACTION64chain 'J' and (resid 72 through 77 )
65X-RAY DIFFRACTION65chain 'J' and (resid 78 through 83 )
66X-RAY DIFFRACTION66chain 'J' and (resid 84 through 90 )
67X-RAY DIFFRACTION67chain 'J' and (resid 91 through 99 )
68X-RAY DIFFRACTION68chain 'K' and (resid 1 through 9 )
69X-RAY DIFFRACTION69chain 'O' and (resid 1 through 103 )
70X-RAY DIFFRACTION70chain 'O' and (resid 104 through 118 )
71X-RAY DIFFRACTION71chain 'O' and (resid 119 through 174 )
72X-RAY DIFFRACTION72chain 'O' and (resid 175 through 274 )
73X-RAY DIFFRACTION73chain 'P' and (resid 1 through 11 )
74X-RAY DIFFRACTION74chain 'P' and (resid 12 through 19 )
75X-RAY DIFFRACTION75chain 'P' and (resid 20 through 30 )
76X-RAY DIFFRACTION76chain 'P' and (resid 31 through 46 )
77X-RAY DIFFRACTION77chain 'P' and (resid 47 through 51 )
78X-RAY DIFFRACTION78chain 'P' and (resid 52 through 71 )
79X-RAY DIFFRACTION79chain 'P' and (resid 72 through 77 )
80X-RAY DIFFRACTION80chain 'P' and (resid 78 through 90 )
81X-RAY DIFFRACTION81chain 'P' and (resid 91 through 99 )
82X-RAY DIFFRACTION82chain 'Q' and (resid 1 through 9 )
83X-RAY DIFFRACTION83chain 'R' and (resid 1 through 174 )
84X-RAY DIFFRACTION84chain 'R' and (resid 175 through 274 )
85X-RAY DIFFRACTION85chain 'S' and (resid 1 through 11 )
86X-RAY DIFFRACTION86chain 'S' and (resid 12 through 30 )
87X-RAY DIFFRACTION87chain 'S' and (resid 31 through 41 )
88X-RAY DIFFRACTION88chain 'S' and (resid 42 through 51 )
89X-RAY DIFFRACTION89chain 'S' and (resid 52 through 56 )
90X-RAY DIFFRACTION90chain 'S' and (resid 57 through 61 )
91X-RAY DIFFRACTION91chain 'S' and (resid 62 through 71 )
92X-RAY DIFFRACTION92chain 'S' and (resid 72 through 77 )
93X-RAY DIFFRACTION93chain 'S' and (resid 78 through 83 )
94X-RAY DIFFRACTION94chain 'S' and (resid 84 through 90 )
95X-RAY DIFFRACTION95chain 'S' and (resid 91 through 99 )
96X-RAY DIFFRACTION96chain 'T' and (resid 1 through 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