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- PDB-6yn1: Crystal structure of histone chaperone APLF acidic domain bound t... -

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基本情報

登録情報
データベース: PDB / ID: 6yn1
タイトルCrystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer
要素
  • Aprataxin and PNK-like factor
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
キーワードCHAPERONE / Octamer / aplf / histone
機能・相同性
機能・相同性情報


ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / embryo implantation / protein folding chaperone / DNA endonuclease activity / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / heterochromatin formation / nucleosome / double-strand break repair / nucleosome assembly / site of double-strand break / histone binding / 加水分解酵素; エステル加水分解酵素 / protein heterodimerization activity / DNA repair / nucleotide binding / DNA damage response / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
類似検索 - 分子機能
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / Histone, subunit A / Histone, subunit A / SMAD/FHA domain superfamily / : / Histone H2B signature. ...Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / Histone, subunit A / Histone, subunit A / SMAD/FHA domain superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Histone H2B / Histone H3 / Histone H4 / Histone H2A / Aprataxin and PNK-like factor
類似検索 - 構成要素
生物種Xenopus laevis (アフリカツメガエル)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.35 Å
データ登録者Corbeski, I. / Guo, X. / Van Ingen, H. / Sixma, T.K.
引用ジャーナル: Sci Adv / 年: 2022
タイトル: Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF.
著者: Corbeski, I. / Guo, X. / Eckhardt, B.V. / Fasci, D. / Wiegant, W. / Graewert, M.A. / Vreeken, K. / Wienk, H. / Svergun, D.I. / Heck, A.J.R. / van Attikum, H. / Boelens, R. / Sixma, T.K. / ...著者: Corbeski, I. / Guo, X. / Eckhardt, B.V. / Fasci, D. / Wiegant, W. / Graewert, M.A. / Vreeken, K. / Wienk, H. / Svergun, D.I. / Heck, A.J.R. / van Attikum, H. / Boelens, R. / Sixma, T.K. / Mattiroli, F. / van Ingen, H.
履歴
登録2020年4月10日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年11月17日Provider: repository / タイプ: Initial release
改定 1.12023年10月25日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
改定 1.22024年1月24日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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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: Histone H2A
B: Histone H2B
C: Histone H3
D: Histone H4
E: Aprataxin and PNK-like factor
F: Histone H2A
G: Histone H2B
H: Histone H3
I: Histone H4
J: Aprataxin and PNK-like factor
K: Histone H2A
L: Histone H2B
M: Histone H3
N: Histone H4
O: Aprataxin and PNK-like factor
P: Histone H2A
Q: Histone H2B
R: Histone H3
S: Histone H4
T: Aprataxin and PNK-like factor
U: Histone H2A
V: Histone H2B
W: Histone H3
X: Histone H4
Y: Aprataxin and PNK-like factor
Z: Histone H2A
a: Histone H2B
b: Histone H3
c: Histone H4
d: Aprataxin and PNK-like factor
e: Histone H2A
f: Histone H2B
g: Histone H3
h: Histone H4
i: Aprataxin and PNK-like factor
j: Histone H2A
k: Histone H2B
l: Histone H3
m: Histone H4
n: Aprataxin and PNK-like factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)395,21055
ポリマ－393,88540
非ポリマー1,32515
水7,476415
1
A: Histone H2A
B: Histone H2B
C: Histone H3
D: Histone H4
E: Aprataxin and PNK-like factor
F: Histone H2A
G: Histone H2B
H: Histone H3
I: Histone H4
J: Aprataxin and PNK-like factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,78314
ポリマ－98,47110
非ポリマー3124
水18010
タイプ名称対称操作数
identity operation1_555x,y,z1
2
K: Histone H2A
L: Histone H2B
M: Histone H3
N: Histone H4
O: Aprataxin and PNK-like factor
P: Histone H2A
Q: Histone H2B
R: Histone H3
S: Histone H4
T: Aprataxin and PNK-like factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,84014
ポリマ－98,47110
非ポリマー3684
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
3
U: Histone H2A
V: Histone H2B
W: Histone H3
X: Histone H4
Y: Aprataxin and PNK-like factor
Z: Histone H2A
a: Histone H2B
b: Histone H3
c: Histone H4
d: Aprataxin and PNK-like factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,74813
ポリマ－98,47110
非ポリマー2763
水18010
タイプ名称対称操作数
identity operation1_555x,y,z1
4
e: Histone H2A
f: Histone H2B
g: Histone H3
h: Histone H4
i: Aprataxin and PNK-like factor
j: Histone H2A
k: Histone H2B
l: Histone H3
m: Histone H4
n: Aprataxin and PNK-like factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,84014
ポリマ－98,47110
非ポリマー3684
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)105.224, 189.686, 204.324
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

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要素

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タンパク質 , 4種, 32分子 AFKPUZejBGLQVafkCHMRWbglDINSXchm

#1: タンパク質
Histone H2A


分子量: 11754.768 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
遺伝子: hist1h2aj, h2ac14, LOC494591, XELAEV_18003602mg / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q6AZJ8
#2: タンパク質
Histone H2B


分子量: 11311.154 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
遺伝子: XELAEV_18032685mg / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A1L8FQA5
#3: タンパク質
Histone H3


分子量: 11633.632 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
遺伝子: XELAEV_18002543mg / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A310TTQ1
#4: タンパク質
Histone H4


分子量: 9540.251 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62799

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タンパク質・ペプチド , 1種, 8分子 EJOTYdin

#5: タンパク質・ペプチド
Aprataxin and PNK-like factor / Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1- ...Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1-interacting protein 1


分子量: 4995.819 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APLF, C2orf13, PALF, XIP1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q8IW19, DNA-(apurinic or apyrimidinic site) lyase

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非ポリマー , 3種, 430分子

#6: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物 ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 415 / 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

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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: 2.58 Å3/Da / 溶媒含有率: 52.41 % / 解説: 150um x 150um x 150um
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate

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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: NSLS / ビームライン: X6A / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2020年3月16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 Å / 相対比: 1
反射解像度: 2.2→20 Å / Num. obs: 206799 / % possible obs: 99.8 % / 冗長度: 6.6 % / Biso Wilson estimate: 49 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.058 / Rrim(I) all: 0.151 / Net I/σ(I): 11.1
反射 シェル解像度: 2.2→2.33 Å / Rmerge(I) obs: 3.2 / Mean I/σ(I) obs: 0.54 / Num. unique obs: 23719 / CC1/2: 0.17 / Rrim(I) all: 3.4

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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
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: 2HIO

2hio


解像度: 2.35→19.99 Å / SU ML: 0.3289 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 25.6704
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2325 8284 4.88 %
Rwork0.1769 161494 -
obs0.1796 169778 99.96 %
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: 62.33 Å2
精密化ステップサイクル: LAST / 解像度: 2.35→19.99 Å
タンパク質核酸リガンド溶媒全体
原子数24456 0 85 415 24956
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.008824902
X-RAY DIFFRACTIONf_angle_d0.953733515
X-RAY DIFFRACTIONf_chiral_restr0.05483838
X-RAY DIFFRACTIONf_plane_restr0.00494281
X-RAY DIFFRACTIONf_dihedral_angle_d19.00349568
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.3632670.31365304X-RAY DIFFRACTION99.96
2.38-2.40.34152710.30035364X-RAY DIFFRACTION100
2.4-2.430.35612730.29465310X-RAY DIFFRACTION100
2.43-2.460.34422610.2815400X-RAY DIFFRACTION99.98
2.46-2.50.31592640.26365315X-RAY DIFFRACTION99.96
2.5-2.530.31692820.26185324X-RAY DIFFRACTION99.98
2.53-2.570.2962500.26115362X-RAY DIFFRACTION100
2.57-2.610.33292810.25215321X-RAY DIFFRACTION99.96
2.61-2.650.32072820.24385353X-RAY DIFFRACTION99.98
2.65-2.690.27142420.2375379X-RAY DIFFRACTION99.98
2.69-2.740.30182940.23655297X-RAY DIFFRACTION99.96
2.74-2.790.29672870.22735337X-RAY DIFFRACTION99.98
2.79-2.840.28212790.20955384X-RAY DIFFRACTION99.98
2.84-2.90.23822570.19885328X-RAY DIFFRACTION100
2.9-2.960.25632870.20215353X-RAY DIFFRACTION99.96
2.96-3.030.28712690.20795360X-RAY DIFFRACTION99.98
3.03-3.10.24972730.19685412X-RAY DIFFRACTION100
3.1-3.190.24092620.19435365X-RAY DIFFRACTION100
3.19-3.280.2772880.19795348X-RAY DIFFRACTION99.98
3.28-3.390.28362840.19065386X-RAY DIFFRACTION100
3.39-3.510.2443040.17195356X-RAY DIFFRACTION100
3.51-3.650.21232910.16175351X-RAY DIFFRACTION99.96
3.65-3.810.22332710.15385392X-RAY DIFFRACTION99.96
3.81-4.010.21472980.14965386X-RAY DIFFRACTION100
4.01-4.260.20612890.14475429X-RAY DIFFRACTION99.97
4.26-4.580.17862760.12765441X-RAY DIFFRACTION99.98
4.58-5.040.18472810.12665438X-RAY DIFFRACTION99.98
5.04-5.750.19372720.15655473X-RAY DIFFRACTION100
5.75-7.190.22772900.17395512X-RAY DIFFRACTION99.97
7.19-19.990.16922590.14755714X-RAY DIFFRACTION99.4
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)
11.02985953364-1.22673265195-2.1412115165.65587193075.611861575587.55048646903-0.09984942080130.276955840249-0.908665362266-0.0634097537322-0.600924463146-0.5551943671150.5293442653630.3356999305710.568809123910.7459976405210.2017017494460.1765986629770.4723223070810.02787594276740.72056799059868.0506834667-30.107844189855.6632519405
24.2321183207-1.12476402036-4.167387877462.028100147871.054328555314.19680028136-0.175825987249-0.493388066547-0.653452976613-0.167072299036-0.0102735075995-1.109092869150.4615898175791.053387421470.3234850597380.6323911387230.1653248420750.03220197436860.511757434356-0.01175893530210.58347021660664.0916216099-34.919310843467.2571204215
37.98942925091-0.757591393224-1.742961244315.069404396035.079068877195.163955244050.467265040528-0.77869034122-1.316705730380.118952466562-0.72147273406-0.7409587185431.135718659740.06950502548920.1819877342440.8425186755680.08042919133980.01580250773830.5959144094620.148676829110.61790667954456.424583315-41.047639241468.8624512582
42.418708800171.79865161113-0.3606625368392.164638223930.114518412532.84327690695-0.03828543537050.1077150247920.0198521733988-0.60406165221-0.0242011627187-0.2392576381470.120847072330.2192197883680.001493878658740.5492162578380.07728573607740.06428579196560.383375878556-0.00688178984930.29799868441159.2017743985-18.084359825157.2290934163
56.46081712108-3.196407920822.700820782447.326385850061.211624235154.45867840475-0.106611416851-0.06769765343020.651776438588-0.02629545847190.0118628108565-0.0245642782484-0.0809906800532-0.06738918159120.1353967194810.426848954850.03905445473230.0247962253170.3308057628750.04828368978620.37048278016259.0428066817-4.8606417639763.1425895449
63.040010269161.39527155221-2.934411140042.2003548478-0.8323505846262.981655762240.370131548511.990107635150.528375732374-0.875732691798-0.1132951018850.912208029772-0.561436822884-0.448008065447-0.323800301190.5303625064220.0987541112578-0.0572007682360.496332148430.0673587978450.49043976170346.8988791628-14.463170749860.5618638675
75.905232371972.804413242415.767237746362.295043488842.640073264535.690384692860.681262954878-0.3489515733630.3599940510030.589368421354-0.9453686542081.290671928851.08847651837-0.1026539398310.4752325740330.60200066530.09494064984120.02820827579890.552762941505-0.03286151864290.60766638143849.1124117222-15.187135069170.3669642655
87.1266482573-4.125235938091.569473465374.25318354972-3.129076440593.081575671970.2681946618080.219372839567-0.57144345710.140283236798-0.2799412852610.426123314467-0.1227840180330.1714261245350.1542739447390.4784536776350.02033594791350.04317008257520.445718199139-0.02731171518040.46187850620851.2871391514-2.3091069621968.6819170357
97.169257470845.25095328547-5.045442171643.82948853538-3.728430007844.69357989016-0.246849105429-0.446640580064-0.192023039304-0.8419332908150.41286550181.883410212510.171522453097-0.646311702265-0.2539001544260.6147997052170.124442018908-0.09478166813650.462879615870.00395105008450.63032524580337.2431215579.543249107964.8346086372
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1603.598276361154.10287983482-5.060437641944.69096613528-5.717608393147.088939103541.09102939036-0.2737220141274.507182035511.029219619641.264368907274.04554259023-0.892258305373-1.4583069538-2.388534768830.6397343710040.0219575718570.1259646021170.8492864429330.02905086623781.27684562352-21.607702036.6555482849830.7078255787
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1753.864411370523.46444998673-1.363353252486.58402910229-2.768367620652.47602740936-0.05079049630950.118931657746-0.0698540263291-0.2941694086650.2254839091460.1898742986110.441822625968-0.0559847305484-0.2531710788810.319281189582-0.0107693581908-0.06647171743650.485376356973-0.02631503553220.4248618353117.8339025769-23.591177828431.7583168159
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 73 )
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 89 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 96 )
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 101 )
8X-RAY DIFFRACTION8chain 'A' and (resid 102 through 111 )
9X-RAY DIFFRACTION9chain 'A' and (resid 112 through 118 )
10X-RAY DIFFRACTION10chain 'B' and (resid 35 through 55 )
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 83 )
12X-RAY DIFFRACTION12chain 'B' and (resid 84 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 124 )
14X-RAY DIFFRACTION14chain 'C' and (resid 40 through 56 )
15X-RAY DIFFRACTION15chain 'C' and (resid 57 through 78 )
16X-RAY DIFFRACTION16chain 'C' and (resid 79 through 113 )
17X-RAY DIFFRACTION17chain 'C' and (resid 114 through 133 )
18X-RAY DIFFRACTION18chain 'D' and (resid 26 through 47 )
19X-RAY DIFFRACTION19chain 'D' and (resid 48 through 82 )
20X-RAY DIFFRACTION20chain 'D' and (resid 83 through 101 )
21X-RAY DIFFRACTION21chain 'E' and (resid 459 through 463 )
22X-RAY DIFFRACTION22chain 'E' and (resid 464 through 473 )
23X-RAY DIFFRACTION23chain 'E' and (resid 474 through 487 )
24X-RAY DIFFRACTION24chain 'F' and (resid 16 through 35 )
25X-RAY DIFFRACTION25chain 'F' and (resid 36 through 44 )
26X-RAY DIFFRACTION26chain 'F' and (resid 45 through 73 )
27X-RAY DIFFRACTION27chain 'F' and (resid 74 through 96 )
28X-RAY DIFFRACTION28chain 'F' and (resid 97 through 111 )
29X-RAY DIFFRACTION29chain 'F' and (resid 112 through 118 )
30X-RAY DIFFRACTION30chain 'G' and (resid 36 through 83 )
31X-RAY DIFFRACTION31chain 'G' and (resid 84 through 123 )
32X-RAY DIFFRACTION32chain 'H' and (resid 40 through 56 )
33X-RAY DIFFRACTION33chain 'H' and (resid 57 through 78 )
34X-RAY DIFFRACTION34chain 'H' and (resid 79 through 113 )
35X-RAY DIFFRACTION35chain 'H' and (resid 114 through 133 )
36X-RAY DIFFRACTION36chain 'I' and (resid 26 through 30 )
37X-RAY DIFFRACTION37chain 'I' and (resid 31 through 47 )
38X-RAY DIFFRACTION38chain 'I' and (resid 48 through 82 )
39X-RAY DIFFRACTION39chain 'I' and (resid 83 through 93 )
40X-RAY DIFFRACTION40chain 'I' and (resid 94 through 101 )
41X-RAY DIFFRACTION41chain 'J' and (resid 459 through 468 )
42X-RAY DIFFRACTION42chain 'J' and (resid 469 through 478 )
43X-RAY DIFFRACTION43chain 'J' and (resid 479 through 487 )
44X-RAY DIFFRACTION44chain 'K' and (resid 16 through 36 )
45X-RAY DIFFRACTION45chain 'K' and (resid 37 through 44 )
46X-RAY DIFFRACTION46chain 'K' and (resid 45 through 72 )
47X-RAY DIFFRACTION47chain 'K' and (resid 73 through 89 )
48X-RAY DIFFRACTION48chain 'K' and (resid 90 through 96 )
49X-RAY DIFFRACTION49chain 'K' and (resid 97 through 111 )
50X-RAY DIFFRACTION50chain 'K' and (resid 112 through 118 )
51X-RAY DIFFRACTION51chain 'L' and (resid 36 through 55 )
52X-RAY DIFFRACTION52chain 'L' and (resid 56 through 83 )
53X-RAY DIFFRACTION53chain 'L' and (resid 84 through 123 )
54X-RAY DIFFRACTION54chain 'M' and (resid 39 through 56 )
55X-RAY DIFFRACTION55chain 'M' and (resid 57 through 78 )
56X-RAY DIFFRACTION56chain 'M' and (resid 79 through 113 )
57X-RAY DIFFRACTION57chain 'M' and (resid 114 through 133 )
58X-RAY DIFFRACTION58chain 'N' and (resid 26 through 30 )
59X-RAY DIFFRACTION59chain 'N' and (resid 31 through 40 )
60X-RAY DIFFRACTION60chain 'N' and (resid 41 through 47 )
61X-RAY DIFFRACTION61chain 'N' and (resid 48 through 82 )
62X-RAY DIFFRACTION62chain 'N' and (resid 83 through 93 )
63X-RAY DIFFRACTION63chain 'N' and (resid 94 through 100 )
64X-RAY DIFFRACTION64chain 'O' and (resid 459 through 463 )
65X-RAY DIFFRACTION65chain 'O' and (resid 464 through 473 )
66X-RAY DIFFRACTION66chain 'O' and (resid 482 through 487 )
67X-RAY DIFFRACTION67chain 'P' and (resid 15 through 26 )
68X-RAY DIFFRACTION68chain 'P' and (resid 27 through 44 )
69X-RAY DIFFRACTION69chain 'P' and (resid 45 through 72 )
70X-RAY DIFFRACTION70chain 'P' and (resid 73 through 79 )
71X-RAY DIFFRACTION71chain 'P' and (resid 80 through 89 )
72X-RAY DIFFRACTION72chain 'P' and (resid 90 through 96 )
73X-RAY DIFFRACTION73chain 'P' and (resid 97 through 111 )
74X-RAY DIFFRACTION74chain 'P' and (resid 112 through 118 )
75X-RAY DIFFRACTION75chain 'Q' and (resid 36 through 55 )
76X-RAY DIFFRACTION76chain 'Q' and (resid 56 through 83 )
77X-RAY DIFFRACTION77chain 'Q' and (resid 84 through 90 )
78X-RAY DIFFRACTION78chain 'Q' and (resid 91 through 123 )
79X-RAY DIFFRACTION79chain 'R' and (resid 40 through 56 )
80X-RAY DIFFRACTION80chain 'R' and (resid 57 through 78 )
81X-RAY DIFFRACTION81chain 'R' and (resid 79 through 113 )
82X-RAY DIFFRACTION82chain 'R' and (resid 114 through 133 )
83X-RAY DIFFRACTION83chain 'S' and (resid 25 through 30 )
84X-RAY DIFFRACTION84chain 'S' and (resid 31 through 40 )
85X-RAY DIFFRACTION85chain 'S' and (resid 41 through 47 )
86X-RAY DIFFRACTION86chain 'S' and (resid 48 through 75 )
87X-RAY DIFFRACTION87chain 'S' and (resid 76 through 93 )
88X-RAY DIFFRACTION88chain 'S' and (resid 94 through 101 )
89X-RAY DIFFRACTION89chain 'T' and (resid 459 through 463 )
90X-RAY DIFFRACTION90chain 'T' and (resid 464 through 473 )
91X-RAY DIFFRACTION91chain 'T' and (resid 481 through 487 )
92X-RAY DIFFRACTION92chain 'U' and (resid 15 through 36 )
93X-RAY DIFFRACTION93chain 'U' and (resid 37 through 44 )
94X-RAY DIFFRACTION94chain 'U' and (resid 45 through 72 )
95X-RAY DIFFRACTION95chain 'U' and (resid 73 through 79 )
96X-RAY DIFFRACTION96chain 'U' and (resid 80 through 89 )
97X-RAY DIFFRACTION97chain 'U' and (resid 90 through 96 )
98X-RAY DIFFRACTION98chain 'U' and (resid 97 through 117 )
99X-RAY DIFFRACTION99chain 'V' and (resid 35 through 48 )
100X-RAY DIFFRACTION100chain 'V' and (resid 49 through 55 )
101X-RAY DIFFRACTION101chain 'V' and (resid 56 through 83 )
102X-RAY DIFFRACTION102chain 'V' and (resid 84 through 103 )
103X-RAY DIFFRACTION103chain 'V' and (resid 104 through 123 )
104X-RAY DIFFRACTION104chain 'W' and (resid 40 through 55 )
105X-RAY DIFFRACTION105chain 'W' and (resid 56 through 78 )
106X-RAY DIFFRACTION106chain 'W' and (resid 79 through 113 )
107X-RAY DIFFRACTION107chain 'W' and (resid 114 through 133 )
108X-RAY DIFFRACTION108chain 'X' and (resid 24 through 30 )
109X-RAY DIFFRACTION109chain 'X' and (resid 31 through 47 )
110X-RAY DIFFRACTION110chain 'X' and (resid 48 through 82 )
111X-RAY DIFFRACTION111chain 'X' and (resid 83 through 100 )
112X-RAY DIFFRACTION112chain 'Y' and (resid 459 through 463 )
113X-RAY DIFFRACTION113chain 'Y' and (resid 464 through 468 )
114X-RAY DIFFRACTION114chain 'Y' and (resid 469 through 473 )
115X-RAY DIFFRACTION115chain 'Y' and (resid 474 through 487 )
116X-RAY DIFFRACTION116chain 'Z' and (resid 15 through 26 )
117X-RAY DIFFRACTION117chain 'Z' and (resid 27 through 44 )
118X-RAY DIFFRACTION118chain 'Z' and (resid 45 through 72 )
119X-RAY DIFFRACTION119chain 'Z' and (resid 73 through 88 )
120X-RAY DIFFRACTION120chain 'Z' and (resid 89 through 101 )
121X-RAY DIFFRACTION121chain 'Z' and (resid 102 through 117 )
122X-RAY DIFFRACTION122chain 'a' and (resid 35 through 55 )
123X-RAY DIFFRACTION123chain 'a' and (resid 56 through 83 )
124X-RAY DIFFRACTION124chain 'a' and (resid 84 through 90 )
125X-RAY DIFFRACTION125chain 'a' and (resid 91 through 123 )
126X-RAY DIFFRACTION126chain 'b' and (resid 40 through 56 )
127X-RAY DIFFRACTION127chain 'b' and (resid 57 through 63 )
128X-RAY DIFFRACTION128chain 'b' and (resid 64 through 78 )
129X-RAY DIFFRACTION129chain 'b' and (resid 79 through 113 )
130X-RAY DIFFRACTION130chain 'b' and (resid 114 through 135 )
131X-RAY DIFFRACTION131chain 'c' and (resid 25 through 30 )
132X-RAY DIFFRACTION132chain 'c' and (resid 31 through 47 )
133X-RAY DIFFRACTION133chain 'c' and (resid 48 through 82 )
134X-RAY DIFFRACTION134chain 'c' and (resid 83 through 100 )
135X-RAY DIFFRACTION135chain 'd' and (resid 459 through 463 )
136X-RAY DIFFRACTION136chain 'd' and (resid 464 through 468 )
137X-RAY DIFFRACTION137chain 'd' and (resid 469 through 482 )
138X-RAY DIFFRACTION138chain 'd' and (resid 483 through 487 )
139X-RAY DIFFRACTION139chain 'e' and (resid 16 through 26 )
140X-RAY DIFFRACTION140chain 'e' and (resid 27 through 44 )
141X-RAY DIFFRACTION141chain 'e' and (resid 45 through 72 )
142X-RAY DIFFRACTION142chain 'e' and (resid 73 through 89 )
143X-RAY DIFFRACTION143chain 'e' and (resid 90 through 96 )
144X-RAY DIFFRACTION144chain 'e' and (resid 97 through 117 )
145X-RAY DIFFRACTION145chain 'f' and (resid 36 through 55 )
146X-RAY DIFFRACTION146chain 'f' and (resid 56 through 83 )
147X-RAY DIFFRACTION147chain 'f' and (resid 84 through 90 )
148X-RAY DIFFRACTION148chain 'f' and (resid 91 through 123 )
149X-RAY DIFFRACTION149chain 'g' and (resid 40 through 56 )
150X-RAY DIFFRACTION150chain 'g' and (resid 57 through 78 )
151X-RAY DIFFRACTION151chain 'g' and (resid 79 through 113 )
152X-RAY DIFFRACTION152chain 'g' and (resid 114 through 133 )
153X-RAY DIFFRACTION153chain 'h' and (resid 26 through 30 )
154X-RAY DIFFRACTION154chain 'h' and (resid 31 through 47 )
155X-RAY DIFFRACTION155chain 'h' and (resid 48 through 75 )
156X-RAY DIFFRACTION156chain 'h' and (resid 76 through 93 )
157X-RAY DIFFRACTION157chain 'h' and (resid 94 through 100 )
158X-RAY DIFFRACTION158chain 'i' and (resid 459 through 463 )
159X-RAY DIFFRACTION159chain 'i' and (resid 464 through 473 )
160X-RAY DIFFRACTION160chain 'i' and (resid 482 through 487 )
161X-RAY DIFFRACTION161chain 'j' and (resid 15 through 26 )
162X-RAY DIFFRACTION162chain 'j' and (resid 27 through 36 )
163X-RAY DIFFRACTION163chain 'j' and (resid 37 through 44 )
164X-RAY DIFFRACTION164chain 'j' and (resid 45 through 72 )
165X-RAY DIFFRACTION165chain 'j' and (resid 73 through 79 )
166X-RAY DIFFRACTION166chain 'j' and (resid 80 through 88 )
167X-RAY DIFFRACTION167chain 'j' and (resid 89 through 96 )
168X-RAY DIFFRACTION168chain 'j' and (resid 97 through 111 )
169X-RAY DIFFRACTION169chain 'j' and (resid 112 through 117 )
170X-RAY DIFFRACTION170chain 'k' and (resid 36 through 55 )
171X-RAY DIFFRACTION171chain 'k' and (resid 56 through 83 )
172X-RAY DIFFRACTION172chain 'k' and (resid 84 through 123 )
173X-RAY DIFFRACTION173chain 'l' and (resid 40 through 56 )
174X-RAY DIFFRACTION174chain 'l' and (resid 57 through 78 )
175X-RAY DIFFRACTION175chain 'l' and (resid 79 through 113 )
176X-RAY DIFFRACTION176chain 'l' and (resid 114 through 133 )
177X-RAY DIFFRACTION177chain 'm' and (resid 27 through 40 )
178X-RAY DIFFRACTION178chain 'm' and (resid 41 through 47 )
179X-RAY DIFFRACTION179chain 'm' and (resid 48 through 82 )
180X-RAY DIFFRACTION180chain 'm' and (resid 83 through 93 )
181X-RAY DIFFRACTION181chain 'm' and (resid 94 through 101 )
182X-RAY DIFFRACTION182chain 'n' and (resid 458 through 462 )
183X-RAY DIFFRACTION183chain 'n' and (resid 463 through 482 )
184X-RAY DIFFRACTION184chain 'n' and (resid 483 through 487 )

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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