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- PDB-9d95: TRAV35/TRBV20 TCR - HLA-B38 complex -

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基本情報

登録情報
データベース: PDB / ID: 9d95
タイトルTRAV35/TRBV20 TCR - HLA-B38 complex
要素
  • (T cell receptor ...) x 2
  • Beta-2-microglobulin
  • Epstein-Barr nuclear antigen 2
  • MHC class I antigen
キーワードIMMUNE SYSTEM / TCR - peptide - HLA complex T cell Human Leucocyte Antigen Epstein Barr virus
機能・相同性
機能・相同性情報


host cell nuclear matrix / protein serine/threonine phosphatase inhibitor activity / DNA-templated viral transcription / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host cell cycle progression / symbiont-mediated suppression of host translation initiation / 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 ...host cell nuclear matrix / protein serine/threonine phosphatase inhibitor activity / DNA-templated viral transcription / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host cell cycle progression / symbiont-mediated suppression of host translation initiation / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / 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 / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / positive regulation of DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / 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, 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 / 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 / Epstein-Barr nuclear antigen 2 / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
human gammaherpesvirus 4 (ヘルペスウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Zhu, S. / 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) オーストラリア
引用ジャーナル: To Be Published
タイトル: The ancient MHC class I molecule HLA-B*38:01 calibrates the immune system to protect against multiple sclerosis
著者: Ladell, K. / Zhu, S. / Kaufmann, M. / Vivian, J. / Petersen, J. / Rossjohn, J. / Fugger, L. / Price, D.
履歴
登録2024年8月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年9月3日Provider: repository / タイプ: Initial release

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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: MHC class I antigen
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 2
D: T cell receptor alpha chain
E: T cell receptor beta chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: Epstein-Barr nuclear antigen 2
I: T cell receptor alpha chain
J: T cell receptor beta chain
K: MHC class I antigen
L: Beta-2-microglobulin
M: Epstein-Barr nuclear antigen 2
N: T cell receptor alpha chain
O: T cell receptor beta chain
P: MHC class I antigen
Q: Beta-2-microglobulin
R: Epstein-Barr nuclear antigen 2
S: T cell receptor alpha chain
T: T cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)394,10343
ポリマ－389,39720
非ポリマー4,70723
水54030
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 2
D: T cell receptor alpha chain
E: T cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,61211
ポリマ－97,3495
非ポリマー1,2636
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: Epstein-Barr nuclear antigen 2
I: T cell receptor alpha chain
J: T cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,1709
ポリマ－97,3495
非ポリマー8214
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
3
K: MHC class I antigen
L: Beta-2-microglobulin
M: Epstein-Barr nuclear antigen 2
N: T cell receptor alpha chain
O: T cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,93013
ポリマ－97,3495
非ポリマー1,5808
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
4
P: MHC class I antigen
Q: Beta-2-microglobulin
R: Epstein-Barr nuclear antigen 2
S: T cell receptor alpha chain
T: T cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,39110
ポリマ－97,3495
非ポリマー1,0425
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)102.789, 124.060, 332.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
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 57 or (resid 58...
d_2ens_1(chain "F" and (resid 1 through 57 or (resid 58...
d_3ens_1(chain "K" and (resid 1 through 97 or resid 99...
d_4ens_1(chain "P" and (resid 1 through 57 or (resid 58...
d_1ens_2(chain "B" and (resid 0 through 2 or resid 4...
d_2ens_2(chain "G" and (resid 0 through 2 or resid 4...
d_3ens_2(chain "L" and (resid 0 through 2 or resid 4...
d_4ens_2(chain "Q" and (resid 0 through 2 or resid 4...
d_1ens_3chain "C"
d_2ens_3chain "H"
d_3ens_3chain "M"
d_4ens_3chain "R"
d_1ens_4(chain "D" and ((resid 3 and (name N or name...
d_2ens_4(chain "I" and ((resid 3 and (name N or name...
d_3ens_4(chain "N" and ((resid 3 and (name N or name...
d_4ens_4(chain "S" and (resid 3 through 47 or (resid 48...
d_1ens_5(chain "E" and (resid 2 through 16 or (resid 17...
d_2ens_5(chain "J" and (resid 2 through 16 or (resid 17...
d_3ens_5(chain "O" and (resid 2 through 16 or (resid 17...
d_4ens_5(chain "T" and (resid 2 through 19 or (resid 20...

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_1GLYGLYARGARGAA1 - 971 - 97
d_12ens_1TYRTYRHISHISAA99 - 19199 - 191
d_13ens_1ARGARGTHRTHRAA202 - 216202 - 216
d_14ens_1GLNGLNALAALAAA226 - 245226 - 245
d_15ens_1VALVALPROPROAA261 - 276261 - 276
d_21ens_1GLYGLYARGARGFF1 - 971 - 97
d_22ens_1TYRTYRHISHISFF99 - 19199 - 191
d_23ens_1ARGARGTHRTHRFF202 - 216202 - 216
d_24ens_1GLNGLNALAALAFF226 - 245226 - 245
d_25ens_1VALVALPROPROFF261 - 276261 - 276
d_31ens_1GLYGLYARGARGKK1 - 971 - 97
d_32ens_1TYRTYRHISHISKK99 - 19199 - 191
d_33ens_1ARGARGTHRTHRKK202 - 216202 - 216
d_34ens_1GLNGLNALAALAKK226 - 245226 - 245
d_35ens_1VALVALPROPROKK261 - 276261 - 276
d_41ens_1GLYGLYARGARGPP1 - 971 - 97
d_42ens_1TYRTYRPROPROPP99 - 27699 - 276
d_11ens_2METMETGLNGLNBB0 - 21 - 3
d_12ens_2THRTHRMETMETBB4 - 995 - 100
d_21ens_2METMETGLNGLNGG0 - 21 - 3
d_22ens_2THRTHRMETMETGG4 - 995 - 100
d_31ens_2METMETGLNGLNLL0 - 21 - 3
d_32ens_2THRTHRMETMETLL4 - 995 - 100
d_41ens_2METMETGLNGLNQQ0 - 21 - 3
d_42ens_2THRTHRMETMETQQ4 - 995 - 100
d_11ens_3TYRTYRLEULEUCC1 - 101 - 10
d_21ens_3TYRTYRLEULEUHH1 - 101 - 10
d_31ens_3TYRTYRLEULEUMM1 - 101 - 10
d_41ens_3TYRTYRLEULEURR1 - 101 - 10
d_11ens_4GLNGLNASPASPDD3 - 1403 - 125
d_12ens_4SERSERSERSERDD147 - 163132 - 148
d_13ens_4SERSERASNASNDD166 - 193151 - 178
d_14ens_4ALAALAPROPRODD198 - 215183 - 200
d_15ens_4NAGNAGNAGNAGDV301
d_21ens_4GLNGLNASPASPII3 - 1403 - 125
d_22ens_4SERSERSERSERII147 - 163132 - 148
d_23ens_4SERSERASNASNII166 - 193151 - 178
d_24ens_4ALAALAPROPROII198 - 215183 - 200
d_25ens_4NAGNAGNAGNAGICA301
d_31ens_4GLNGLNASPASPNN3 - 1403 - 125
d_32ens_4SERSERSERSERNN147 - 163132 - 148
d_33ens_4SERSERASNASNNN166 - 193151 - 178
d_34ens_4ALAALAPROPRONN198 - 215183 - 200
d_35ens_4NAGNAGNAGNAGNHA301
d_41ens_4GLNGLNASPASPSS3 - 1403 - 125
d_42ens_4SERSERASNASNSS147 - 193132 - 178
d_43ens_4ALAALAPROPROSS198 - 215183 - 200
d_44ens_4NAGNAGNAGNAGSOA301
d_11ens_5ALAALAGLUGLUEE2 - 582 - 52
d_12ens_5SERSERSERSEREE63 - 9354 - 83
d_13ens_5PROPROGLNGLNEE96 - 19386 - 183
d_14ens_5SERSERSERSEREE199 - 205189 - 195
d_15ens_5LEULEUASPASPEE207 - 234197 - 224
d_16ens_5ALAALAALAALAEE241 - 256231 - 246
d_21ens_5ALAALAGLUGLUJJ2 - 582 - 52
d_22ens_5SERSERSERSERJJ63 - 9354 - 83
d_23ens_5PROPROGLNGLNJJ96 - 19386 - 183
d_24ens_5SERSERSERSERJJ199 - 205189 - 195
d_25ens_5LEULEUASPASPJJ207 - 234197 - 224
d_26ens_5ALAALAALAALAJJ241 - 256231 - 246
d_31ens_5ALAALASERSEROO2 - 932 - 83
d_32ens_5PROPROGLNGLNOO96 - 19386 - 183
d_33ens_5SERSERSERSEROO199 - 205189 - 195
d_34ens_5LEULEUASPASPOO207 - 234197 - 224
d_35ens_5ALAALAALAALAOO241 - 256231 - 246
d_41ens_5ALAALAGLUGLUTT2 - 582 - 52
d_42ens_5SERSERGLNGLNTT63 - 19354 - 183
d_43ens_5SERSERSERSERTT199 - 205189 - 195
d_44ens_5LEULEUALAALATT207 - 256197 - 246

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixベクター
1given(0.389877859811, -0.261296441547, 0.883017227501), (0.304099604994, -0.86857081017, -0.391290401062), (0.869205778094, 0.421080654217, -0.259176383903)-109.216047679, 24.7817406119, 173.458992623
2given(0.936027185833, 0.344367587574, 0.0725539248436), (-0.348014185536, 0.875074459829, 0.336349247688), (0.0523376924178, -0.340081834833, 0.938938289543)-39.7620608866, -90.0070718141, 74.9364750671
3given(-0.311501333659, -0.0821868638602, -0.946684867597), (0.0965436944913, -0.993834816608, 0.0545130475284), (-0.94532863819, -0.07441556763, 0.317515494286)-46.0158820599, -4.12579360533, 82.2948524621
4given(0.380174270598, -0.257601808111, 0.888317979348), (0.332903399226, -0.857953161624, -0.391269343602), (0.862926909279, 0.44447461223, -0.240415199861)-109.951312413, 26.1087590516, 171.804005053
5given(0.936903581635, 0.331684023829, 0.110441781299), (-0.348793851436, 0.865621327377, 0.359224952906), (0.023548416514, -0.375080559249, 0.92669307009)-42.4881773344, -91.8852472357, 74.2179806178
6given(-0.298060481218, -0.0753029514045, -0.951572075592), (0.113185332865, -0.992638650042, 0.0430997780385), (-0.947812761024, -0.0948576615386, 0.304389543328)-44.9864736906, -2.55839853811, 83.0497798326
7given(0.400643144582, -0.254307822422, 0.880234401824), (0.316522135334, -0.863145831716, -0.39343742963), (0.859824870856, 0.436241681463, -0.265319405267)-108.396688938, 25.4763963574, 174.086913483
8given(0.928105536569, 0.367671025401, 0.0586355700095), (-0.364006593914, 0.862976335532, 0.350386991624), (0.0782260351591, -0.346539840989, 0.934767792572)-38.3627893768, -91.8842539195, 75.9092161785
9given(-0.32513223211, -0.072286477086, -0.942901742958), (0.100770785629, -0.994045451935, 0.0414594772072), (-0.940284148759, -0.0815371370421, 0.330480581693)-46.5857455797, -3.02755236835, 81.1917716933
10given(0.388238685334, -0.248822823772, 0.887331913987), (0.264748115668, -0.892156620466, -0.366012294614), (0.882711254296, 0.377019584277, -0.280494339713)-108.916275496, 21.1693657047, 173.95131935
11given(0.937210065186, 0.337787749087, 0.0868143437481), (-0.346547782882, 0.873913380062, 0.34085193021), (0.0392673896949, -0.349535178079, 0.936100011426)-40.8595624664, -90.5789160459, 74.8593916289
12given(-0.338132600569, -0.0870356101659, -0.93706517756), (0.0867618410808, -0.994356742463, 0.0610495835487), (-0.937090565188, -0.0606586455688, 0.343775800999)-47.7237353896, -4.88469319218, 80.7879109786
13given(0.390544007757, -0.247445836125, 0.886705101028), (0.268024047289, -0.890908199496, -0.366668365347), (0.880703405285, 0.380858422849, -0.281617424292)-108.800203362, 21.4741279517, 174.192851521
14given(0.934430635946, 0.348673863528, 0.0725666831195), (-0.351692720903, 0.871272796097, 0.342338932706), (0.0561392613974, -0.34541316083, 0.93677005271)-39.595908228, -90.4668749908, 75.1387916248
15given(-0.312479380855, -0.0846438726542, -0.946145893276), (0.0805620518786, -0.994795123338, 0.0623892489149), (-0.946502188237, -0.0567281006659, 0.317672048278)-46.7757049468, -5.11492456437, 82.7183020642

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要素

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タンパク質 , 2種, 8分子 AFKPBGLQ

#1: タンパク質
MHC class I antigen / MHC class II antigen


分子量: 32029.297 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-B, HLA-DRB1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: E5FQ58
#2: タンパク質
Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 4 / Fragment: UNP residues 21-119 / 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

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T cell receptor ... , 2種, 8分子 DINSEJOT

#4: タンパク質
T cell receptor alpha chain


分子量: 23604.143 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: タンパク質
T cell receptor beta chain


分子量: 28660.078 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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タンパク質・ペプチド / 糖 , 2種, 18分子 CHMR

#3: タンパク質・ペプチド
Epstein-Barr nuclear antigen 2 / EBNA-2 / EBV nuclear antigen 2


分子量: 1176.297 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) human gammaherpesvirus 4 (ヘルペスウイルス)
遺伝子: EBNA2, BYRF1 / 発現宿主: synthetic construct (人工物) / 参照: UniProt: P12978
#7: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 3種, 39分子

#6: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 5 / 由来タイプ: 合成 / 式: SO4
#8: 化合物
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


分子量: 282.331 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C12H26O7 / コメント: 沈殿剤*YM
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 30 / 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: 2.72 Å3/Da / 溶媒含有率: 54.82 %
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: 0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.95372 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2023年2月24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: 0.95372 Å / 相対比: 1
反射解像度: 2.8→19.97 Å / Num. obs: 96562 / % possible obs: 91.48 % / 冗長度: 4.1 % / CC1/2: 0.994 / CC star: 0.999 / Rpim(I) all: 0.0637 / Net I/σ(I): 9.71
反射 シェル解像度: 2.8→2.9 Å / Mean I/σ(I) obs: 2.12 / Num. unique obs: 9725 / CC1/2: 0.655 / CC star: 0.89 / Rpim(I) all: 0.4374

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
autoPROC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 / 解像度: 2.8→19.97 Å / SU ML: 0.3221 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 24.4288
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2351 4837 5.01 %
Rwork0.2021 91705 -
obs0.2038 96542 91.8 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 66.81 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→19.97 Å
タンパク質核酸リガンド溶媒全体
原子数25175 0 297 30 25502
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001926147
X-RAY DIFFRACTIONf_angle_d0.492835629
X-RAY DIFFRACTIONf_chiral_restr0.05253933
X-RAY DIFFRACTIONf_plane_restr0.00344605
X-RAY DIFFRACTIONf_dihedral_angle_d11.81429163
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.399137114301
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.402506951717
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.351489227073
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.360856691771
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.342921878659
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.310632327809
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.797327899206
ens_3d_3CCX-RAY DIFFRACTIONTorsion NCS0.730213284393
ens_3d_4CCX-RAY DIFFRACTIONTorsion NCS0.810967687352
ens_4d_2DDX-RAY DIFFRACTIONTorsion NCS1.4252300825
ens_4d_3DDX-RAY DIFFRACTIONTorsion NCS4.18125939205
ens_4d_4DDX-RAY DIFFRACTIONTorsion NCS1.39320382748
ens_5d_2EEX-RAY DIFFRACTIONTorsion NCS0.502077485538
ens_5d_3EEX-RAY DIFFRACTIONTorsion NCS0.593119267812
ens_5d_4EEX-RAY DIFFRACTIONTorsion NCS0.719908056542
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.30891620.2953111X-RAY DIFFRACTION93.86
2.83-2.860.37061420.2983070X-RAY DIFFRACTION93.18
2.86-2.90.31561690.29363068X-RAY DIFFRACTION94.07
2.9-2.940.31881710.27933088X-RAY DIFFRACTION92.74
2.94-2.970.33291410.27583091X-RAY DIFFRACTION94.39
2.97-3.020.32761670.28053079X-RAY DIFFRACTION93.09
3.02-3.060.31061550.27693077X-RAY DIFFRACTION93.76
3.06-3.10.29471470.2493114X-RAY DIFFRACTION93.17
3.1-3.150.26781740.24913040X-RAY DIFFRACTION93.46
3.15-3.20.27491390.25443114X-RAY DIFFRACTION92.65
3.2-3.260.27531680.24863046X-RAY DIFFRACTION93.16
3.26-3.320.29271770.24863031X-RAY DIFFRACTION92.18
3.32-3.380.28441670.23333075X-RAY DIFFRACTION93.27
3.38-3.450.27141820.22913050X-RAY DIFFRACTION92.61
3.45-3.520.25051430.22593058X-RAY DIFFRACTION92.41
3.52-3.610.22991570.20333050X-RAY DIFFRACTION92.5
3.61-3.70.25511990.20283042X-RAY DIFFRACTION91.61
3.7-3.790.23491500.19583039X-RAY DIFFRACTION92.09
3.79-3.910.22121760.19463048X-RAY DIFFRACTION92.25
3.91-4.030.26591610.18893057X-RAY DIFFRACTION91.68
4.03-4.170.20171600.17383021X-RAY DIFFRACTION91.12
4.17-4.340.20561580.16853040X-RAY DIFFRACTION90.88
4.34-4.530.17221490.1543030X-RAY DIFFRACTION90.62
4.53-4.770.19731680.14883033X-RAY DIFFRACTION90.22
4.77-5.060.1761620.16192985X-RAY DIFFRACTION89.43
5.06-5.450.20511430.17133034X-RAY DIFFRACTION89.52
5.45-5.980.22481650.18633018X-RAY DIFFRACTION89.64
5.98-6.820.21791740.21383014X-RAY DIFFRACTION89.05
6.82-8.480.19541470.18653077X-RAY DIFFRACTION88.86
8.48-19.970.20291640.17583105X-RAY DIFFRACTION87.27
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)
11.214799681110.0978437228289-0.07977324738812.68284996178-0.4549518167122.80759102348-0.0480142697462-0.2754622198870.03617679226480.582989773496-0.05725530029590.0358037801052-0.180330258250.1620733941050.1077474285580.4737646227190.000917761031642-0.006843288513040.323285933185-0.02809078239760.226122667751-34.799-17.32468.033
24.41188460713-2.669535477940.07909967285514.529140965080.2687684838030.4176959416510.08934682293250.0146099109718-0.123282575918-0.536524652535-0.04373585890090.4323286983990.219634702653-0.3560962515790.02449367286390.820862667416-0.04591817585540.120959875870.602236086346-0.06210511905770.420551513323-64.4290.75674.22
34.150903227291.420284928941.673331524743.901810282681.605343264423.813326994250.1121280082230.41389921219-0.201023134261-0.102962628759-0.344620436550.0163818210528-0.3474545906780.1087949760110.2087421024280.6981109094270.1371965490450.09052936622490.2444904804480.05235583566140.390430570481-44.5933.15563.307
43.20332152542-1.63476628976-0.2294469194144.015972552771.548771203622.88643006058-0.367389078503-1.327099477460.354850693531.03745474044-0.05694339387840.48426907667-0.227624218544-0.4948463392080.269042633231.19091359915-0.06140895326940.3559649473640.807114863163-0.2497135127480.585747918678-52.73410.46186.311
54.30025052022-1.204042794760.1306223006053.466691290481.967086281752.985208604660.154097488943-0.5279537238790.2331220445610.638095391749-0.0864483695240.360909158232-0.08026424670320.1978726254080.2283250497990.831171426755-0.003507985792920.1672380971860.415162621655-0.002392863423770.406605855694-45.3765.34874.968
64.66202587341-4.09369587482-4.387589807873.676669174143.753225892774.186442257350.47208980499-0.3654709463070.224290515933-1.582434556950.211061666037-0.993723195464-1.835852608730.90250777485-0.6580098057590.767392974470.01936746381420.09948547945470.460898027959-0.04597877832980.500137223144-37.2317.86468.312
74.9688416542-1.21699966269-2.579815372975.421440253456.589225860418.45624992790.04925618778770.07966402324050.1260517926571.73150846571-0.0374799172719-0.8568902578690.475469528088-0.38075196647-0.1529201574670.925563099916-0.06276814758740.1103679490380.424600974344-0.01618773200160.352357374739-36.85613.72678.017
82.38646720599-4.19050412842-3.403708318938.518144215037.553320752827.892877124910.184769752579-0.2407370501840.2683745620520.698558904184-0.297100422239-0.00971990553962-0.148810984777-0.2675570246120.2193039691090.691221408352-0.08183322688140.1505170284510.394207478503-0.06011291887230.418975607966-43.2033.43873.864
94.65466169725-2.81631086051-2.361020253986.598068821166.023685538325.505783548070.3998232476180.2194273496050.6935777726020.1214477193560.3234448249930.0907083002336-1.253229134040.489309873351-0.7762008930460.920502396711-0.05163713304580.174763256770.381802460696-0.05091416189490.468130658026-39.95712.41264.524
104.23110372502-0.953969890864-6.440553834857.019527548822.207727755239.900549287190.141984076570.2850651807950.881589424043-0.184795707676-0.1781436644090.906470782154-0.410722804722-0.5803638806940.08612554421860.7497121997310.062426827130.09094018746910.5336828398490.03034689302270.690024833584-51.55914.37672.708
110.975982986764-0.6059807850520.2556604043160.747329665462-0.05058135189580.0977748946824-0.3560185840560.02119720648050.1020244422240.0839774722257-0.23500895881-0.0332600433426-0.15915246788-0.1357107508890.4292877479780.432312522302-0.103550241158-0.04774371644430.583163534994-0.04655135151380.307667890011-29.633-23.54267.482
126.663156892211.00754446682.079737539253.277956140664.688791234486.99824807145-0.105449235411-0.943165478907-1.175326655831.582322444150.217154926075-0.01222678829920.985381143320.0386593515438-0.1170300592790.8788800558960.111989135435-0.05341225487240.7706741217930.1349668622370.532605800618-23.527-55.47674.482
132.717788100180.0524401589765-2.897815357045.386624023161.25216798614.06218100701-0.0254009362031-0.219871820696-0.1160832238550.6538470248210.00803899940110.0486345299812-0.009381836953080.1464060092110.05594176703080.4406527781340.0212882066641-0.08777851386470.3931891263310.02281876657080.216939730841-28.287-43.51769.957
141.94647086804-0.6974530251380.01036637517554.174992853640.9049260217950.639741059581-0.151338515247-0.0415177312936-0.04960117498490.2815004295410.1035136486270.109133616997-0.06359031014790.2121019922970.05977823877240.54270130162-0.0285896832362-0.1534153634080.4618863672410.02536650789660.350125580339-22.409-42.49171.513
157.39616409062-3.84741249809-1.333349411113.70380149790.6595342815371.25267482023-0.1213388057720.118462729262-0.8073188096560.0774464179994-0.0664742331462-0.03678094683040.1799675356410.5078307894070.1413393476870.78614055890.1832399446-0.1342372731220.6799420147410.04493379267610.689556103063-6.009-69.74966.868
164.178947506631.33380615499-3.387752049065.88914795053-0.005643831418862.990101385270.195400855627-1.14791478905-0.6222295295220.5271165135070.0853481736861-0.451729863110.256854425158-0.315655920549-0.004790092678270.6744903723960.245117833128-0.2213461293250.9542393729230.08889345698940.798882990794-6.71-70.40275.506
174.658900283552.174993013591.57216981871.602686734832.302831168175.04685461752-0.431427414218-0.6081560305010.02994408302420.4570065208090.11858060691-0.708363403619-0.00503717734668-0.2394439902530.3906352827051.021732051220.251423681459-0.2777109348030.665274684830.1153803737720.755893724632-2.73-68.7468.585
186.67258215469-2.4535673812-6.574075046153.707323967761.214653371677.00130347128-0.308793292772-0.932638534737-0.8933038764720.09136466488840.027761467328-0.04963523124690.6564116926260.3538668534880.3778609326671.096461464910.0544974711073-0.203378200850.6735081348420.2485014182020.69130173327-5.913-79.83272.597
196.91895371265-0.2334376075165.337693964272.7342189677-0.9184022852798.33281852193-0.1481338907630.418466498294-0.229254937926-0.2832174422170.00126503319409-1.12718543240.3838554463861.287376018970.06917222295950.430106238910.0712395819328-0.02842570412530.612770208499-0.06847904077360.557915967219-1.178-35.62767.848
204.48145631311-1.187066830131.801611709231.80673445611-0.5041818762153.1568081548-0.156735441177-0.270867217880.5549426608040.573039563362-0.0884191246851-0.627943304988-0.2505390023710.2905107303940.3400209357660.678122085962-0.0508904065535-0.2061184187620.571262287335-0.05064639591810.555479471281-9.723-29.85672.745
212.87899478987-2.4544629222-1.057198880252.093406391790.9022525994290.387737850944-0.184965529568-0.5236510990160.002207687594870.742416276477-0.113431792339-0.5961122449150.2934084655070.9410837978450.08028775739930.7509188956090.0195782163465-0.2194394543570.9636729482490.0406300443980.8825008800528.31-43.81477.494
222.058054720570.1853856178741.063402693182.42102728765-0.03985813985552.187798527360.03669872266850.2827090443580.208169840601-0.0384455242539-0.195637949059-0.3615231561230.09950902068630.392183729370.1514131132310.631258826370.175532380963-0.1716656443920.878557493446-0.003980826550050.8162943273275.876-58.71763.104
234.424741950130.153197786247-1.696482068122.366407016940.1615981115323.88447566648-0.205187591587-0.282098366782-0.19488726811-0.2845340334840.0119642630923-0.6323539818350.5994598946730.3249786078050.1395004691650.4106240980880.08626326027480.1033279870280.2682106673150.03194442584560.472297746031-53.241-5.693119.522
243.72043196416-2.52916063142-4.381165510813.557058680121.866258590995.82425852766-0.139440182339-0.832107964479-0.0162276084179-0.0466010244560.108492415744-0.502229859810.008433702246630.806849739704-0.007912280325660.2170235399240.0168831476974-0.0124195873890.3461898855970.006679065903120.356883104455-55.1494.477126.774
253.536862212330.477149016045-1.503809014333.05280454636-1.834031588283.86975770355-0.1044336334170.0685811995050.0748973489899-0.3496065487880.1736833321570.03296450543120.334435004748-0.155884042601-0.06475041766820.277153164103-0.0269073176363-0.0189703723550.2423954563320.01945451749070.270699100287-66.2254.97116.082
264.12082013329-0.854837222545-2.19968820713.27115099580.4669419406112.876849227190.09058216313520.203944537840.468884645597-0.4755622095230.0621061002039-0.240870099068-0.0249397943388-0.0547168004615-0.186647946640.220700674383-0.0428080799061-0.0008349018308650.2645356576210.02351027728270.297908462807-57.89510.51112.985
276.187851942646.591608039861.661981193848.529524595411.980805008972.26803434897-0.3896148579810.269539940763-0.940449332137-0.6312576279130.309042830296-0.8670796207020.202739635223-0.0934976149083-0.04372029135790.7942577379590.0196442311520.1430263528380.403310407689-0.02581844813930.480956249362-62.443-25.18599.906
284.693695378991.350943960071.494417964044.930539837061.625963622144.44754144974-0.0594023566568-0.146945526370.302432622703-0.792111274982-0.247633512470.616666958706-0.206033677028-0.4686676487570.2378353395170.6285988134850.03972101932570.07741986216570.37894964944-0.01674626363610.448166931067-71.482-24.26599.884
294.685861421641.028000591460.7449932247785.430981590490.414356688544.7912071487-0.04872694566560.8518473653820.118072195214-1.39491495857-0.1634589468420.0961619269106-0.2977180027160.2834076083880.180945848880.921992645287-0.02572507817330.03737105530520.5643356995010.004037063479620.469575058329-66.333-25.79691.248
305.56224754432-1.17051123388-0.1176838286793.36961185959-1.428673420483.372545636930.0525663216898-0.004099960161910.259502346799-0.504800770307-0.00763615241893-0.4559356368650.314866795664-0.187768430877-0.07717475517920.275170662981-0.05514541297810.1116652368690.2663463140470.07118160836610.368115606479-66.056-22.857116.237
312.48232096107-2.0720971515-0.5487060308559.38803759039-0.5989160626562.05030227003-0.0349314944954-0.115289444022-0.1998372609450.350604511031-0.1610376823510.02793444444520.06325310068010.08563935062030.1540579783950.364970440352-0.008421071236890.05652255964510.3225125231420.00574095363450.330340468502-61.775-20.162121.475
328.74306678998-6.82385598655-4.332601318565.340673651923.36999588612.15065572928-0.749560049128-0.0937757224992-0.7697101092620.2109362730460.1554387497860.6060823807430.9689089762750.1776316657370.3281184449480.936272178175-0.01223599492580.1549166885610.4145563496580.08851608652290.459296261683-64.234-33.172122.482
334.47173911534-4.31233098905-4.838186239535.280349981346.793429334079.38788081132-0.4611030851780.282627133308-0.536849815991-0.244383679245-0.1763696043950.8367869099030.320795556256-0.5295436464990.8103441004110.701609348166-0.1019208091120.1428516990780.432771108698-0.02207027082560.415884091754-71.724-26.324121.658
343.134229725242.204546183291.822854132124.47945482323-0.3488989171.96262385072-0.3477933767-0.385028121876-0.00872459227965-0.1508854307070.529204577887-0.103727926245-0.193104425225-0.373910917285-0.1082335921480.2598542727440.03931544076190.009335147371940.4310043626320.03937664771590.252425742652-54.8759.875120.441
356.23533033343-1.874083987232.304929869454.18943762793-5.506188152027.249127524450.2718619864720.2389075469610.676405982249-0.88893816574-0.640262493873-1.06061572730.3533030954050.9263763689240.4106189258510.524890614363-0.004324504760610.04808313042540.670996337915-0.03963021255520.601226372683-37.80536.428111.441
362.361639926-0.673599475775-0.627546285137.941310058250.5338940916312.06081601633-0.0296529719527-0.274443715628-0.145394926085-0.4196491406280.0495479750706-0.445234509068-0.1137304757010.335594622122-0.04258988613450.234014509297-0.02004675679690.05273967742730.4450285253760.01071088425740.397543001674-46.24728.193113.907
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878.555253381383.099396017330.6906327771313.128030247220.2482848412343.948519415210.0533810722409-0.692159565401-0.695082011229-0.1208728771910.0001441664166160.4533899753010.1352941284860.0112297337903-0.09333617006850.7136347422040.267148040569-0.1067842258420.574493317734-0.04776059673930.629560396866-102.73464.728112.504
881.16836013893-0.9563646388781.272414940531.28947362198-1.979725932843.12650708676-0.09579492622771.067241493740.504529776466-0.301228612559-0.1926057564191.03842683888-0.554016688758-0.180801743670.2737614519260.9799564459120.358418718417-0.4431304644380.8611680615680.1269358434881.11183051666-114.57674.398106.209
891.462493598241.81013029033-3.557729102438.33999070516-6.369371261689.28785833041-0.07135107629960.09670456224220.4270916230490.2906716604190.574887682370.0463078537236-0.662671475438-1.20238683911-0.5470870120750.743388516010.245682822616-0.03762325752270.9291916934650.02136344582230.923711430716-107.9178.121116.106
902.52361896858-1.668629140731.182231008351.52097199938-0.9096310373162.056332911890.2561717738710.49956549265-0.266077754356-0.465641806464-0.4528966211851.098945367040.180496487133-0.5121051654190.02185294344680.4730660424260.1011833034-0.1985220453880.74848984145-0.09526451056720.957677101721-110.66230.623114.265
911.603809454580.65686761530.5465420849053.635284541741.03109279582.143454195910.3361579001620.669431481692-0.323828433517-0.721485493113-0.3618159487270.9766861176150.06872840183860.1520952469320.02497555963440.735701204940.300999319835-0.3283795499470.853165529621-0.08053156780320.840135288-102.25958.624101.218
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:174 )A1 - 174
2X-RAY DIFFRACTION2( CHAIN A AND RESID 175:276 )A175 - 276
3X-RAY DIFFRACTION3( CHAIN B AND RESID 0:11 )B0 - 11
4X-RAY DIFFRACTION4( CHAIN B AND RESID 12:19 )B12 - 19
5X-RAY DIFFRACTION5( CHAIN B AND RESID 20:30 )B20 - 30
6X-RAY DIFFRACTION6( CHAIN B AND RESID 31:41 )B31 - 41
7X-RAY DIFFRACTION7( CHAIN B AND RESID 42:51 )B42 - 51
8X-RAY DIFFRACTION8( CHAIN B AND RESID 52:77 )B52 - 77
9X-RAY DIFFRACTION9( CHAIN B AND RESID 78:90 )B78 - 90
10X-RAY DIFFRACTION10( CHAIN B AND RESID 91:99 )B91 - 99
11X-RAY DIFFRACTION11( CHAIN C AND RESID 1:10 )C1 - 10
12X-RAY DIFFRACTION12( CHAIN D AND RESID 3:18 )D3 - 18
13X-RAY DIFFRACTION13( CHAIN D AND RESID 19:91 )D19 - 91
14X-RAY DIFFRACTION14( CHAIN D AND RESID 92:119 )D92 - 119
15X-RAY DIFFRACTION15( CHAIN D AND RESID 120:152 )D120 - 152
16X-RAY DIFFRACTION16( CHAIN D AND RESID 153:167 )D153 - 167
17X-RAY DIFFRACTION17( CHAIN D AND RESID 168:204 )D168 - 204
18X-RAY DIFFRACTION18( CHAIN D AND RESID 205:215 )D205 - 215
19X-RAY DIFFRACTION19( CHAIN E AND RESID 2:14 )E2 - 14
20X-RAY DIFFRACTION20( CHAIN E AND RESID 15:121 )E15 - 121
21X-RAY DIFFRACTION21( CHAIN E AND RESID 122:136 )E122 - 136
22X-RAY DIFFRACTION22( CHAIN E AND RESID 137:256 )E137 - 256
23X-RAY DIFFRACTION23( CHAIN F AND RESID 1:56 )F1 - 56
24X-RAY DIFFRACTION24( CHAIN F AND RESID 57:85 )F57 - 85
25X-RAY DIFFRACTION25( CHAIN F AND RESID 86:137 )F86 - 137
26X-RAY DIFFRACTION26( CHAIN F AND RESID 138:174 )F138 - 174
27X-RAY DIFFRACTION27( CHAIN F AND RESID 175:197 )F175 - 197
28X-RAY DIFFRACTION28( CHAIN F AND RESID 198:263 )F198 - 263
29X-RAY DIFFRACTION29( CHAIN F AND RESID 264:276 )F264 - 276
30X-RAY DIFFRACTION30( CHAIN G AND RESID 0:19 )G0 - 19
31X-RAY DIFFRACTION31( CHAIN G AND RESID 20:71 )G20 - 71
32X-RAY DIFFRACTION32( CHAIN G AND RESID 72:83 )G72 - 83
33X-RAY DIFFRACTION33( CHAIN G AND RESID 84:99 )G84 - 99
34X-RAY DIFFRACTION34( CHAIN H AND RESID 1:10 )H1 - 10
35X-RAY DIFFRACTION35( CHAIN I AND RESID 3:18 )I3 - 18
36X-RAY DIFFRACTION36( CHAIN I AND RESID 19:108 )I19 - 108
37X-RAY DIFFRACTION37( CHAIN I AND RESID 109:152 )I109 - 152
38X-RAY DIFFRACTION38( CHAIN I AND RESID 153:215 )I153 - 215
39X-RAY DIFFRACTION39( CHAIN J AND RESID 2:136 )J2 - 136
40X-RAY DIFFRACTION40( CHAIN J AND RESID 137:256 )J137 - 256
41X-RAY DIFFRACTION41( CHAIN K AND RESID 1:103 )K1 - 103
42X-RAY DIFFRACTION42( CHAIN K AND RESID 104:137 )K104 - 137
43X-RAY DIFFRACTION43( CHAIN K AND RESID 138:197 )K138 - 197
44X-RAY DIFFRACTION44( CHAIN K AND RESID 198:276 )K198 - 276
45X-RAY DIFFRACTION45( CHAIN L AND RESID 0:11 )L0 - 11
46X-RAY DIFFRACTION46( CHAIN L AND RESID 12:30 )L12 - 30
47X-RAY DIFFRACTION47( CHAIN L AND RESID 31:51 )L31 - 51
48X-RAY DIFFRACTION48( CHAIN L AND RESID 52:77 )L52 - 77
49X-RAY DIFFRACTION49( CHAIN L AND RESID 78:99 )L78 - 99
50X-RAY DIFFRACTION50( CHAIN M AND RESID 1:10 )M1 - 10
51X-RAY DIFFRACTION51( CHAIN N AND RESID 2:18 )N2 - 18
52X-RAY DIFFRACTION52( CHAIN N AND RESID 19:44 )N19 - 44
53X-RAY DIFFRACTION53( CHAIN N AND RESID 45:56 )N45 - 56
54X-RAY DIFFRACTION54( CHAIN N AND RESID 57:85 )N57 - 85
55X-RAY DIFFRACTION55( CHAIN N AND RESID 86:99 )N86 - 99
56X-RAY DIFFRACTION56( CHAIN N AND RESID 100:119 )N100 - 119
57X-RAY DIFFRACTION57( CHAIN N AND RESID 120:133 )N120 - 133
58X-RAY DIFFRACTION58( CHAIN N AND RESID 134:152 )N134 - 152
59X-RAY DIFFRACTION59( CHAIN N AND RESID 153:167 )N153 - 167
60X-RAY DIFFRACTION60( CHAIN N AND RESID 168:192 )N168 - 192
61X-RAY DIFFRACTION61( CHAIN N AND RESID 193:205 )N193 - 205
62X-RAY DIFFRACTION62( CHAIN N AND RESID 206:215 )N206 - 215
63X-RAY DIFFRACTION63( CHAIN O AND RESID 2:136 )O2 - 136
64X-RAY DIFFRACTION64( CHAIN O AND RESID 137:256 )O137 - 256
65X-RAY DIFFRACTION65( CHAIN P AND RESID 1:118 )P1 - 118
66X-RAY DIFFRACTION66( CHAIN P AND RESID 119:137 )P119 - 137
67X-RAY DIFFRACTION67( CHAIN P AND RESID 138:185 )P138 - 185
68X-RAY DIFFRACTION68( CHAIN P AND RESID 186:227 )P186 - 227
69X-RAY DIFFRACTION69( CHAIN P AND RESID 228:276 )P228 - 276
70X-RAY DIFFRACTION70( CHAIN Q AND RESID 0:11 )Q0 - 11
71X-RAY DIFFRACTION71( CHAIN Q AND RESID 12:30 )Q12 - 30
72X-RAY DIFFRACTION72( CHAIN Q AND RESID 31:41 )Q31 - 41
73X-RAY DIFFRACTION73( CHAIN Q AND RESID 42:51 )Q42 - 51
74X-RAY DIFFRACTION74( CHAIN Q AND RESID 52:77 )Q52 - 77
75X-RAY DIFFRACTION75( CHAIN Q AND RESID 78:90 )Q78 - 90
76X-RAY DIFFRACTION76( CHAIN Q AND RESID 91:99 )Q91 - 99
77X-RAY DIFFRACTION77( CHAIN R AND RESID 1:10 )R1 - 10
78X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )S3 - 17
79X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )S402
80X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )A402 - 403
81X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )E302
82X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )F402
83X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )G102 - 103
84X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )I403
85X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )J301 - 302
86X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )K402 - 406
87X-RAY DIFFRACTION78( CHAIN S AND ( RESID 3:17 OR RESID 402:402 ) ) OR ( CHAIN A AND RESID 402:403 ) OR ( CHAIN E AND RESID 302:302 ) OR ( CHAIN F AND RESID 402:402 ) OR ( CHAIN G AND RESID 102:103 ) OR ( CHAIN I AND RESID 403:403 ) OR ( CHAIN J AND RESID 301:302 ) OR ( CHAIN K AND RESID 402:406 ) OR ( CHAIN O AND RESID 302:302 )O302
88X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )S37 - 44
89X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )S401
90X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )A401
91X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )E301
92X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )F401
93X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )G101
94X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )H101
95X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )I401 - 402
96X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )K401
97X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )N401 - 403
98X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )O301
99X-RAY DIFFRACTION79( CHAIN S AND ( RESID 37:44 OR RESID 401:401 ) ) OR ( CHAIN A AND RESID 401:401 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN F AND RESID 401:401 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN H AND RESID 101:101 ) OR ( CHAIN I AND RESID 401:402 ) OR ( CHAIN K AND RESID 401:401 ) OR ( CHAIN N AND RESID 401:403 ) OR ( CHAIN O AND RESID 301:301 ) OR ( CHAIN T AND RESID 301:301 )T301
100X-RAY DIFFRACTION80( CHAIN S AND RESID 45:56 )S45 - 56
101X-RAY DIFFRACTION81( CHAIN S AND RESID 57:80 )S57 - 80
102X-RAY DIFFRACTION82( CHAIN S AND RESID 81:91 )S81 - 91
103X-RAY DIFFRACTION83( CHAIN S AND RESID 92:108 )S92 - 108
104X-RAY DIFFRACTION84( CHAIN S AND RESID 109:125 )S109 - 125
105X-RAY DIFFRACTION85( CHAIN S AND RESID 126:138 )S126 - 138
106X-RAY DIFFRACTION86( CHAIN S AND RESID 139:162 )S139 - 162
107X-RAY DIFFRACTION87( CHAIN S AND RESID 163:191 )S163 - 191
108X-RAY DIFFRACTION88( CHAIN S AND RESID 192:203 )S192 - 203
109X-RAY DIFFRACTION89( CHAIN S AND RESID 204:215 )S204 - 215
110X-RAY DIFFRACTION90( CHAIN T AND RESID 2:136 )T2 - 136
111X-RAY DIFFRACTION91( CHAIN T AND RESID 137:256 )T137 - 256

+
万見について

-
お知らせ

-
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

+
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

+
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