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- PDB-5ong: X-Ray crystal structure of a nucleosome core particle with its DN... -

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基本情報

登録情報
データベース: PDB / ID: 5ong
タイトルX-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer
要素
  • (DNA (147-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
キーワードDNA BINDING PROTEIN / Nucleosome Core Particle / Histones / Disulfide / Convertible Nucleotide / DNA
機能・相同性
機能・相同性情報


structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
類似検索 - 分子機能
Histone, subunit A / Histone, subunit A / : / 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, subunit A / Histone, subunit A / : / 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
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Xenopus laevis (アフリカツメガエル)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.797 Å
データ登録者Frouws, T.D. / Barth, P.D. / Richmond, T.J.
資金援助 スイス, 1件
組織認可番号国
Louis Jeantet Prize スイス
引用ジャーナル: J. Mol. Biol. / 年: 2018
タイトル: Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability.
著者: Frouws, T.D. / Barth, P.D. / Richmond, T.J.
履歴
登録2017年8月3日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年11月22日Provider: repository / タイプ: Initial release
改定 1.12017年12月27日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.22024年1月17日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
改定 1.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
I: DNA (147-MER)
J: DNA (147-MER)
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)200,32234
ポリマ－199,08210
非ポリマー1,24124
水1,56787
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area60470 Å2
ΔGint-518 kcal/mol
Surface area72040 Å2
手法PISA
単位格子
Length a, b, c (Å)106.240, 183.130, 109.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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DNA鎖 , 2種, 2分子 IJ

#1: DNA鎖 DNA (147-MER)


分子量: 45430.148 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / Variant (発現宿主): DH10B
#2: DNA鎖 DNA (147-MER)


分子量: 45421.133 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / Variant (発現宿主): DH10B

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タンパク質 , 4種, 8分子 AEBFCGDH

#3: タンパク質 Histone H3.2


分子量: 15217.812 Da / 分子数: 2 / Mutation: C110A, R40C / 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 BL21(DE3) (大腸菌) / Variant (発現宿主): pLysS / 参照: UniProt: P84233
#4: タンパク質 Histone H4


分子量: 11394.426 Da / 分子数: 2 / 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 BL21(DE3) (大腸菌) / Variant (発現宿主): pLysS / 参照: UniProt: P62799
#5: タンパク質 Histone H2A


分子量: 13978.241 Da / 分子数: 2 / 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, LOC494591 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): pLysS / 参照: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#6: タンパク質 Histone H2B 1.1 / H2B1.1


分子量: 13524.752 Da / 分子数: 2 / 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 BL21(DE3) (大腸菌) / Variant (発現宿主): pLysS / 参照: UniProt: P02281

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非ポリマー , 3種, 111分子

#7: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 20 / 由来タイプ: 合成 / 式: Mn
#8: 化合物
ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 天然 / 式: Cl
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 87 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY
配列の詳細constructs were all sequenced and the expressed protein MW was confirmed by mass spec: 30268543:42- ...constructs were all sequenced and the expressed protein MW was confirmed by mass spec: 30268543:42-452 Expression vector pET3-H3 H3 gene for Xenopus laevis-like histone H3 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 30268542|emb|CAD89678.1| Xenopus laevis-like histone H2B [Expression vector pET3-H2B] MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFER IAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.01 Å3/Da / 溶媒含有率: 59.09 % / 解説: hollow hexagonal rods
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6
詳細: Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 130-180 mM MnCl2, 100-160 mM KCl and equilibrated against a 1:4 dilution of the same solution

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データ収集

回折平均測定温度: 90 K
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年9月11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: 2.797→29.54 Å / Num. obs: 47952 / % possible obs: 90.3 % / 冗長度: 3.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.7
反射 シェル解像度: 2.797→2.95 Å / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 2.5 / % possible all: 68

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解析

ソフトウェア
名称バージョン分類
PHENIX(dev_2447: ???)精密化
XDSデータ削減
SCALA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: 1KX5

1kx5


解像度: 2.797→29.499 Å / SU ML: 0.35 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.76
Rfactor反射数%反射Selection details
Rfree0.2468 4812 10.07 %random
Rwork0.2057 ---
obs0.2098 47779 89.43 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.797→29.499 Å
タンパク質核酸リガンド溶媒全体
原子数5973 6027 24 87 12111
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00312813
X-RAY DIFFRACTIONf_angle_d0.59718563
X-RAY DIFFRACTIONf_dihedral_angle_d26.1026679
X-RAY DIFFRACTIONf_chiral_restr0.0362109
X-RAY DIFFRACTIONf_plane_restr0.0241473
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7973-2.82910.4036970.3838822X-RAY DIFFRACTION52
2.8291-2.86230.42311180.35081076X-RAY DIFFRACTION69
2.8623-2.89720.33841350.30281145X-RAY DIFFRACTION72
2.8972-2.93390.33391300.27711096X-RAY DIFFRACTION70
2.9339-2.97240.32581490.27721289X-RAY DIFFRACTION82
2.9724-3.01310.30881640.26291450X-RAY DIFFRACTION92
3.0131-3.05610.30141410.2431483X-RAY DIFFRACTION92
3.0561-3.10170.2911630.25281446X-RAY DIFFRACTION92
3.1017-3.15010.28691700.24061431X-RAY DIFFRACTION91
3.1501-3.20170.27141430.24271518X-RAY DIFFRACTION94
3.2017-3.25680.2921660.27031521X-RAY DIFFRACTION96
3.2568-3.3160.28281640.25191528X-RAY DIFFRACTION95
3.316-3.37970.30541510.27261496X-RAY DIFFRACTION95
3.3797-3.44850.29981860.27461464X-RAY DIFFRACTION93
3.4485-3.52340.26721690.24641488X-RAY DIFFRACTION94
3.5234-3.60520.28541560.21241478X-RAY DIFFRACTION94
3.6052-3.69520.25711730.22311510X-RAY DIFFRACTION95
3.6952-3.79490.24521940.21271525X-RAY DIFFRACTION95
3.7949-3.90640.24531700.1961528X-RAY DIFFRACTION96
3.9064-4.03210.22041840.19111492X-RAY DIFFRACTION95
4.0321-4.17590.23361740.1821500X-RAY DIFFRACTION94
4.1759-4.34260.22231500.17441529X-RAY DIFFRACTION93
4.3426-4.53950.2191640.17561480X-RAY DIFFRACTION92
4.5395-4.77790.20181660.16881522X-RAY DIFFRACTION94
4.7779-5.07590.20761760.17221512X-RAY DIFFRACTION94
5.0759-5.46550.21571880.18031508X-RAY DIFFRACTION94
5.4655-6.01130.23861650.19431515X-RAY DIFFRACTION93
6.0113-6.87160.251710.2041497X-RAY DIFFRACTION91
6.8716-8.62150.2271700.171533X-RAY DIFFRACTION92
8.6215-29.50080.20451650.17251585X-RAY DIFFRACTION90
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)
12.07440.15890.26852.10490.71350.21381.1736-0.80870.85272.5658-1.37862.2344-0.1767-0.7504-0.09871.71740.07180.43191.6236-0.0461.67999.6346111.853119.4256
24.0147-3.9246-0.02414.0769-0.65891.86880.35480.5799-1.56570.81150.4421.53240.2-1.13320.34141.0233-0.54490.1481.06030.10661.764514.337865.742919.4159
31.3558-1.04740.04490.9251-0.58011.7551-0.2891-0.4906-0.58620.1569-0.3297-0.92120.90591.1955-2.1260.76140.3555-0.18251.11920.30741.12467.230771.416220.9835
42.23790.26451.41921.1750.69771.91650.1186-0.11711.2973-0.4303-0.1837-0.1339-0.9526-0.1328-0.04530.9237-0.08870.18750.47490.04750.916344.881124.83681.7113
52.05260.10510.14460.91160.38260.15010.14580.4312-0.942-0.0947-0.56671.6580.4609-0.61330.18621.0445-0.283-0.00351.0283-0.13480.946314.438474.639-5.5661
62.1309-0.00680.49320.0282-0.09250.5091-0.2547-0.186-1.5428-1.35920.2786-0.26790.83230.10490.11191.54010.14620.26830.9031-0.16391.531352.496850.0233-2.4507
71.99730.0553-0.11910.6057-1.01411.53650.56590.1519-0.3137-0.3167-1.0556-2.2272-0.01040.9782-0.27021.05140.24950.44431.20010.03491.73782.55592.2212-8.8689
81.3906-0.859-0.27630.7935-0.2521.56140.83890.16570.2923-1.0209-1.4779-1.54670.00950.6523-0.06560.844-0.03710.40861.47440.17751.530285.1536102.8163-11.9129
90.19650.1867-0.39982.09410.12040.8239-0.53370.031-1.5423-0.43620.0165-0.04940.87550.31890.17721.34890.16390.14450.7045-0.12141.620858.082654.3866-3.2055
101.33590.27150.18920.086-0.19561.41980.28230.2528-0.7325-0.0859-0.96641.94120.3839-0.9915-0.62090.6192-0.0845-0.0991.2293-0.30911.029511.078283.2297-6.552
111.2004-0.00061.00171.7757-0.35532.1627-0.14630.0760.80470.0273-0.1103-0.6187-1.05690.383-0.25020.9983-0.25610.06880.5460.06520.887852.5542124.27742.7742
120.0388-0.04390.15751.52080.85941.36960.4998-0.8288-0.42360.34960.0909-1.44650.62930.32814.54290.47310.4392-0.21962.18830.42271.568885.041384.606118.2396
133.8091-1.0505-0.78141.3979-0.35111.448-0.68480.0425-1.55780.28880.53550.14571.10880.0189-0.09221.21420.17570.06370.63560.15991.122249.427757.324922.1767
140.9071-0.51470.24340.5368-0.09211.89510.2234-0.30150.17410.82591.04623.9804-0.6157-1.8657-0.12921.6491-0.21260.13531.19020.40912.6599.192774.129818.0998
150.49020.34190.04980.2120.0388-0.0080.0861-1.18550.61490.363-0.84211.1553-0.0528-0.10330.3431.52290.31540.34311.44480.04511.524511.5047116.159919.1574
160.7788-0.706-0.04920.6497-0.00310.62010.0696-0.1256-0.0862-0.0708-0.3364-0.4092-0.16650.4229-1.24760.3838-0.34240.41670.8281-0.02480.892972.6655113.6031-3.458
172.51430.1244-0.16853.04980.5871.73740.0061-1.0664-0.09260.5993-0.2386-0.9009-0.00680.47690.00190.2024-0.1408-0.02490.78750.01870.666470.395595.214115.7005
180.4588-0.6040.0982.2821-0.53251.8093-0.3216-0.0780.51840.4989-0.1586-1.1876-0.40610.7872-0.00720.1993-0.1139-0.02690.3750.02290.516561.488499.54269.5716
194.8080.74231.27225.19820.49764.14850.4506-1.1945-0.09350.8805-0.76181.0566-0.5565-0.4063-0.02030.4495-0.09190.13860.5133-0.11680.550750.035106.555310.284
200.49550.29560.76851.07170.20492.488-0.0304-0.24750.0610.6098-0.5493-1.1474-0.53680.8307-0.13880.6107-0.2036-0.00660.487-0.02260.797867.3193108.71029.0032
210.72051.7109-0.05666.1909-0.73910.98740.018-0.4520.00711.2143-0.065-0.2736-0.00540.03070.06430.30740.0678-0.06590.5245-0.00240.383259.260194.595317.8604
220.28350.00760.32243.4235-0.81980.5764-0.159-0.18170.0548-0.59150.2293-0.48640.430.31610.12610.26380.0874-0.0230.58970.10890.409660.150682.692511.8279
232.8968-1.05990.5061.60750.72812.5324-0.16660.0808-0.683-0.35730.24070.34880.44280.0151-0.16050.5358-0.02510.04120.31940.02690.405835.684368.440921.3428
243.1947-3.39520.4825.56450.60940.7939-0.434-0.827-0.16480.02590.70270.2206-0.20780.16860.04330.37170.00540.10160.37660.07350.249532.935585.20826.3936
254.6532-1.0052-2.50384.9455-1.52012.2447-0.5635-0.9157-0.16880.2940.7282-0.2767-0.1703-1.3193-0.00520.27030.0626-0.06060.80020.02070.318618.35896.84323.7279
261.6068-0.76010.94231.2179-0.39440.5622-0.28450.2418-0.00970.14920.19910.1188-0.3184-0.5476-0.0480.2541-0.00020.04870.47720.04650.198429.323197.530918.9306
270.99220.6083-0.86893.4427-0.94444.3148-0.1513-0.14370.15010.0008-0.2614-0.5238-0.09360.9181-1.47560.01720.00120.02480.3182-0.06760.460940.443494.775320.7828
281.4505-0.74093.58476.5423-2.4848.9277-0.69040.51890.4384-0.5658-0.0602-1.01250.60170.4569-0.03250.50090.0246-0.00240.3353-0.00190.30437.39892.899411.0128
291.4092-0.40840.14624.55570.2230.5417-0.02880.2258-0.2106-0.31650.5739-0.0451-0.291-0.01880.03410.29080.02880.06190.31950.06570.184329.4864102.880813.6992
301.93240.8505-0.24980.4752-0.45141.6598-0.0272-0.37641.96490.87970.1767-0.1678-1.1065-0.3065-0.16380.93120.1109-0.05550.8985-0.23660.954935.2114123.700514.6502
312.15190.14070.27220.4277-0.69061.6744-0.1299-0.0455-0.24320.3825-0.16580.50130.7047-0.7070.08760.6137-0.16820.02510.40850.06950.296722.642480.620622.7109
326.2435-2.1733-0.0971.97670.23682.25340.03710.6828-0.0967-0.126-0.1759-0.08580.7491-0.1372-0.0640.3998-0.03830.02270.2552-0.01070.241738.481880.239614.6818
331.4887-0.01840.87110.857-0.86861.4152-0.53770.0305-0.08420.42380.4211-0.07270.61290.31640.46630.61760.230.07940.4110.10240.378345.559176.759326.4415
342.52271.2291-0.79865.7478-0.47343.5905-0.1094-0.11050.7131-0.03460.40470.9499-0.6243-0.84440.17150.63430.16730.05340.438-0.12810.432223.8723118.7449.7664
350.6128-0.13811.14483.66141.23182.670.15260.0593-0.1451-1.013-0.10410.5094-0.4714-0.0355-0.04290.3791-0.0038-0.07050.5365-0.040.298123.130496.4902-5.8569
360.70890.2599-0.31972.8843-0.99320.4189-0.38631.0623-0.6338-0.7662-0.7981.11090.6323-0.7022-0.37020.5774-0.0811-0.13140.7442-0.14610.452923.132383.4224-11.3389
370.36080.31650.44091.70150.45211.51540.31890.13390.23540.0887-0.10010.014-0.0633-0.4060.08570.27050.13560.06480.1507-0.03310.34434.5082105.56582.8024
383.3925-1.48711.20061.905-1.70731.5448-0.04470.1901-0.0379-0.2884-0.57250.09960.0903-0.1446-1.2320.38440.19770.16070.196-0.02740.405544.4056108.0556-2.3793
398.417-0.37135.34553.51931.48984.64-0.09411.67130.2386-1.76560.0061-1.8701-0.0210.7368-0.09420.8899-0.02710.24280.40450.02240.684845.8173100.6839-2.483
405.25343.0474-0.87018.2671-2.9713.9294-0.55750.0634-0.318-0.6619-0.43-0.6717-0.0415-0.3308-0.06740.7180.04780.03510.9284-0.06840.329719.875395.7554-19.6522
410.15810.01240.48220.187-0.2622.69440.04920.29370.3982-0.596-0.31040.1734-0.151-0.4767-0.17530.50580.19490.03980.26830.03970.409927.9587110.7331-1.4715
421.83150.29290.02923.84890.90431.0015-0.48670.3802-0.1609-0.2090.788-0.51650.0608-0.27480.07950.3102-0.01920.00550.3891-0.08360.220631.973590.8442-7.4967
433.7-0.32280.96391.29851.16173.59340.3701-0.063-0.30290.28220.04380.31220.9118-0.0093-0.00480.29430.01420.00930.2873-0.05290.293432.769386.16283.6712
442.6838-0.01512.57122.50071.31823.33170.31490.5831-0.87110.0572-0.00640.22240.99120.52041.39790.94810.16050.4070.4517-0.29740.89257.624263.0571-13.7248
455.56630.3944-3.70750.5398-0.49684.24420.0723-0.4527-1.08770.3627-0.4772-0.89610.09780.7302-0.010.84150.11990.10750.38660.01370.718453.515864.8841-1.2892
462.42931.52950.85243.7958-0.16642.1084-0.354-0.16980.13490.2304-0.69190.48960.3196-0.3969-0.05930.69640.25910.11870.7515-0.13050.472344.508265.1070.5924
473.06821.11021.27541.70040.96320.7277-0.62361.4804-0.3494-1.17670.5617-0.4066-0.03410.16210.06740.72860.13180.19770.6901-0.05880.457158.525279.9926-13.7023
482.00560.20330.91230.9491-0.18842.4772-0.01750.30230.5773-0.3284-0.5894-0.4820.06760.0072-1.02870.74490.32080.33670.77850.16460.806473.741988.6878-12.0699
490.7011.32690.66272.50851.25370.6284-0.4460.4596-0.3888-0.56710.09530.16080.40260.8624-0.52780.41830.13430.18770.6297-0.01010.583763.426292.4151-8.8487
504.16320.12190.64443.9034-0.3095.9519-0.0920.80460.4662-0.1242-0.19620.9479-0.0984-0.3505-0.01180.52980.02730.1530.33380.06760.447553.362490.7091-6.3182
510.1690.74110.0143.8293-0.58980.7442-0.20560.08370.21920.1780.0646-0.5961-1.0810.70530.09510.444-0.13240.05190.48130.01580.559864.494498.2274-4.529
521.2659-0.3064-0.88120.22880.41522.0434-0.24960.86380.80720.0566-0.5894-0.69-0.2212-0.506-0.02680.9118-0.06430.16690.73310.22521.072761.1728117.7313-8.5479
533.4174-3.03455.32442.861-4.89968.47050.2744-0.54040.8392-0.3062-0.31240.20850.7005-0.2139-0.00021.22470.04530.00210.5547-0.02810.564965.128368.20141.8873
540.97630.43091.13081.12180.44321.30110.23440.56890.0267-0.49860.1849-0.5605-0.15590.66181.97920.56160.39540.45910.82050.04110.749868.306576.3388-13.9303
553.7580.933-0.07221.2539-0.35421.40310.0835-0.72530.0035-0.3242-0.2289-0.30590.20240.2017-0.03410.4860.11980.090.401-0.0580.391151.877577.5863-1.1694
566.34410.7996-4.66240.1644-0.56633.55580.35530.5399-0.697-0.4898-0.17290.0433-0.21320.19330.06160.60050.09310.00630.2998-0.16860.569937.060566.6074-1.5037
572.7472-2.3492-1.13662.66161.16960.53030.0307-0.12260.4746-0.9739-0.1708-0.0027-0.1516-0.5086-0.12930.512-0.0933-0.06310.2559-0.10960.202742.194777.0195-8.8871
581.8167-0.19761.06047.18741.86961.1581-0.41961.0392-0.0854-1.18740.3928-0.6884-0.4380.18580.08890.82710.01470.0730.4956-0.14780.386248.12872.3466-17.8824
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'I' and (resid -73 through -54 )
2X-RAY DIFFRACTION2chain 'I' and (resid -53 through -44 )
3X-RAY DIFFRACTION3chain 'I' and (resid -43 through -14 )
4X-RAY DIFFRACTION4chain 'I' and (resid -13 through 16 )
5X-RAY DIFFRACTION5chain 'I' and (resid 17 through 36 )
6X-RAY DIFFRACTION6chain 'I' and (resid 37 through 46 )
7X-RAY DIFFRACTION7chain 'I' and (resid 47 through 73 )
8X-RAY DIFFRACTION8chain 'J' and (resid -73 through -54 )
9X-RAY DIFFRACTION9chain 'J' and (resid -53 through -34 )
10X-RAY DIFFRACTION10chain 'J' and (resid -33 through -14 )
11X-RAY DIFFRACTION11chain 'J' and (resid -13 through 16 )
12X-RAY DIFFRACTION12chain 'J' and (resid 17 through 26 )
13X-RAY DIFFRACTION13chain 'J' and (resid 27 through 46 )
14X-RAY DIFFRACTION14chain 'J' and (resid 47 through 56 )
15X-RAY DIFFRACTION15chain 'J' and (resid 57 through 73 )
16X-RAY DIFFRACTION16chain 'A' and (resid 39 through 56 )
17X-RAY DIFFRACTION17chain 'A' and (resid 57 through 77 )
18X-RAY DIFFRACTION18chain 'A' and (resid 78 through 120 )
19X-RAY DIFFRACTION19chain 'A' and (resid 121 through 134 )
20X-RAY DIFFRACTION20chain 'B' and (resid 25 through 49 )
21X-RAY DIFFRACTION21chain 'B' and (resid 50 through 75 )
22X-RAY DIFFRACTION22chain 'B' and (resid 76 through 102 )
23X-RAY DIFFRACTION23chain 'C' and (resid 15 through 44 )
24X-RAY DIFFRACTION24chain 'C' and (resid 45 through 72 )
25X-RAY DIFFRACTION25chain 'C' and (resid 73 through 79 )
26X-RAY DIFFRACTION26chain 'C' and (resid 80 through 89 )
27X-RAY DIFFRACTION27chain 'C' and (resid 90 through 96 )
28X-RAY DIFFRACTION28chain 'C' and (resid 97 through 101 )
29X-RAY DIFFRACTION29chain 'C' and (resid 102 through 111 )
30X-RAY DIFFRACTION30chain 'C' and (resid 112 through 120 )
31X-RAY DIFFRACTION31chain 'D' and (resid 28 through 52 )
32X-RAY DIFFRACTION32chain 'D' and (resid 53 through 81 )
33X-RAY DIFFRACTION33chain 'D' and (resid 82 through 121 )
34X-RAY DIFFRACTION34chain 'E' and (resid 39 through 56 )
35X-RAY DIFFRACTION35chain 'E' and (resid 57 through 78 )
36X-RAY DIFFRACTION36chain 'E' and (resid 79 through 85 )
37X-RAY DIFFRACTION37chain 'E' and (resid 86 through 120 )
38X-RAY DIFFRACTION38chain 'E' and (resid 121 through 130 )
39X-RAY DIFFRACTION39chain 'E' and (resid 131 through 135 )
40X-RAY DIFFRACTION40chain 'F' and (resid 19 through 24 )
41X-RAY DIFFRACTION41chain 'F' and (resid 25 through 49 )
42X-RAY DIFFRACTION42chain 'F' and (resid 50 through 82 )
43X-RAY DIFFRACTION43chain 'F' and (resid 83 through 102 )
44X-RAY DIFFRACTION44chain 'G' and (resid 14 through 26 )
45X-RAY DIFFRACTION45chain 'G' and (resid 27 through 36 )
46X-RAY DIFFRACTION46chain 'G' and (resid 37 through 46 )
47X-RAY DIFFRACTION47chain 'G' and (resid 47 through 72 )
48X-RAY DIFFRACTION48chain 'G' and (resid 73 through 80 )
49X-RAY DIFFRACTION49chain 'G' and (resid 81 through 89 )
50X-RAY DIFFRACTION50chain 'G' and (resid 90 through 101 )
51X-RAY DIFFRACTION51chain 'G' and (resid 102 through 111 )
52X-RAY DIFFRACTION52chain 'G' and (resid 112 through 119 )
53X-RAY DIFFRACTION53chain 'H' and (resid 29 through 34 )
54X-RAY DIFFRACTION54chain 'H' and (resid 35 through 52 )
55X-RAY DIFFRACTION55chain 'H' and (resid 53 through 81 )
56X-RAY DIFFRACTION56chain 'H' and (resid 82 through 87 )
57X-RAY DIFFRACTION57chain 'H' and (resid 88 through 100 )
58X-RAY DIFFRACTION58chain 'H' and (resid 101 through 121 )

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万見について

-
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