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- PDB-7ciz: Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 di... -

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基本情報

登録情報
データベース: PDB / ID: 7ciz
タイトルCrystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD
要素
  • DNA replication licensing factor MCM2
  • DnaJ homolog subfamily C member 9
  • Histone H3.3
  • Histone H4
キーワードCHAPERONE / Histone chaperone
機能・相同性
機能・相同性情報


Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of chromosome condensation / Barr body / : / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / inner kinetochore / pericentric heterochromatin formation ...Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of chromosome condensation / Barr body / : / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / inner kinetochore / pericentric heterochromatin formation / positive regulation of ATP-dependent activity / MCM complex / muscle cell differentiation / double-strand break repair via break-induced replication / mitotic DNA replication initiation / oocyte maturation / protein folding chaperone complex / regulation of DNA-templated DNA replication initiation / nucleosomal DNA binding / nucleus organization / DNA replication origin binding / cochlea development / spermatid development / Activation of the pre-replicative complex / DNA replication initiation / single fertilization / subtelomeric heterochromatin formation / Activation of ATR in response to replication stress / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / heat shock protein binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / embryo implantation / telomere organization / cellular response to interleukin-4 / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / DNA helicase activity / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Orc1 removal from chromatin / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / multicellular organism growth / male gonad development / Transcriptional regulation of granulopoiesis / HCMV Early Events / osteoblast differentiation / structural constituent of chromatin / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / single-stranded DNA binding / Processing of DNA double-strand break ends / protein-folding chaperone binding / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / Oxidative Stress Induced Senescence / histone binding
類似検索 - 分子機能
: / : / DNAJC9 HTH domain / DNA replication licensing factor MCM2-like, winged-helix domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site ...: / : / DNAJC9 HTH domain / DNA replication licensing factor MCM2-like, winged-helix domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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 / Histone-fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
DNA replication licensing factor MCM2 / Histone H4 / Histone H3.3 / DnaJ homolog subfamily C member 9
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.8 Å
データ登録者Bao, H. / Huang, H.
資金援助 中国, 3件
組織認可番号国
Ministry of Science and Technology (MoST, China)2018YFC1004500 中国
National Natural Science Foundation of China (NSFC)the Thousand Young Talents Program 中国
National Natural Science Foundation of China (NSFC)31800619 中国
引用ジャーナル: Mol.Cell / 年: 2021
タイトル: DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network.
著者: Hammond, C.M. / Bao, H. / Hendriks, I.A. / Carraro, M. / Garcia-Nieto, A. / Liu, Y. / Reveron-Gomez, N. / Spanos, C. / Chen, L. / Rappsilber, J. / Nielsen, M.L. / Patel, D.J. / Huang, H. / Groth, A.
履歴
登録2020年7月8日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年4月14日Provider: repository / タイプ: Initial release
改定 1.12021年4月28日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22021年6月30日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年11月29日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
E: Histone H3.3
F: Histone H4
G: DNA replication licensing factor MCM2
I: Histone H3.3
J: Histone H4
K: DNA replication licensing factor MCM2
D: DnaJ homolog subfamily C member 9
H: DnaJ homolog subfamily C member 9
L: DnaJ homolog subfamily C member 9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)109,98814
ポリマ－109,79612
非ポリマー1922
水13,349741
1
A: Histone H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
H: DnaJ homolog subfamily C member 9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,7916
ポリマ－36,5994
非ポリマー1922
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-63 kcal/mol
Surface area12540 Å2
手法PISA
2
E: Histone H3.3
F: Histone H4
G: DNA replication licensing factor MCM2
D: DnaJ homolog subfamily C member 9


分子量 (理論値)分子数
合計 (水以外)36,5994
ポリマ－36,5994
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-64 kcal/mol
Surface area13160 Å2
手法PISA
3
I: Histone H3.3
J: Histone H4
K: DNA replication licensing factor MCM2
L: DnaJ homolog subfamily C member 9


分子量 (理論値)分子数
合計 (水以外)36,5994
ポリマ－36,5994
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-62 kcal/mol
Surface area13120 Å2
手法PISA
単位格子
Length a, b, c (Å)47.638, 176.816, 202.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDモデル要素
11E-229-

HOH

21F-201-

HOH

31G-238-

HOH

41J-267-

HOH

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要素

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タンパク質 , 4種, 12分子 AEIBFJCGKDHL

#1: タンパク質 Histone H3.3


分子量: 9026.496 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
遺伝子: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: P84243
#2: タンパク質 Histone H4


分子量: 11263.231 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
遺伝子: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, ...遺伝子: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: P62805
#3: タンパク質 DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


分子量: 7860.354 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MCM2, BM28, CCNL1, CDCL1, KIAA0030
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: P49736, DNA helicase
#4: タンパク質 DnaJ homolog subfamily C member 9 / HDJC9 / DnaJ protein SB73


分子量: 8448.566 Da / 分子数: 3 / Mutation: C243S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DNAJC9
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: Q8WXX5

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非ポリマー , 2種, 743分子

#5: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 741 / 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: 1.95 Å3/Da / 溶媒含有率: 36.79 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL18U1 / 波長: 0.97736 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2017年6月23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: 0.97736 Å / 相対比: 1
反射解像度: 1.8→40 Å / Num. obs: 78310 / % possible obs: 97.7 % / 冗長度: 10 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.024 / Net I/σ(I): 31.3
反射 シェル解像度: 1.8→1.83 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3667 / CC1/2: 0.793

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
HKL-3000データ削減
HKL-3000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: 5BNV

5bnv


解像度: 1.8→36.884 Å / SU ML: 0.18 / 交差検証法: FREE R-VALUE / 位相誤差: 20.79 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2138 3911 5.04 %
Rwork0.1706 --
obs0.1727 77571 96.84 %
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
精密化ステップサイクル: LAST / 解像度: 1.8→36.884 Å
タンパク質核酸リガンド溶媒全体
原子数5956 0 10 741 6707
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0066013
X-RAY DIFFRACTIONf_angle_d0.7928055
X-RAY DIFFRACTIONf_dihedral_angle_d7.043762
X-RAY DIFFRACTIONf_chiral_restr0.05906
X-RAY DIFFRACTIONf_plane_restr0.0051059
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8210.30461160.23472149X-RAY DIFFRACTION80
1.821-1.8440.26581180.23112372X-RAY DIFFRACTION88
1.844-1.86830.2931270.22292440X-RAY DIFFRACTION91
1.8683-1.89390.25691300.23032467X-RAY DIFFRACTION92
1.8939-1.92090.26691280.22382522X-RAY DIFFRACTION94
1.9209-1.94960.25931260.20262553X-RAY DIFFRACTION95
1.9496-1.98010.23731530.19332517X-RAY DIFFRACTION94
1.9801-2.01250.20271330.17782570X-RAY DIFFRACTION97
2.0125-2.04720.21691490.17532578X-RAY DIFFRACTION96
2.0472-2.08440.22831240.16662652X-RAY DIFFRACTION97
2.0844-2.12450.21711570.1622600X-RAY DIFFRACTION98
2.1245-2.16790.21461470.1622654X-RAY DIFFRACTION97
2.1679-2.2150.19071380.1632615X-RAY DIFFRACTION98
2.215-2.26650.22481380.15752673X-RAY DIFFRACTION98
2.2665-2.32320.20661490.16032651X-RAY DIFFRACTION99
2.3232-2.3860.20451330.15952709X-RAY DIFFRACTION99
2.386-2.45620.19041680.16052630X-RAY DIFFRACTION99
2.4562-2.53550.21281530.1572705X-RAY DIFFRACTION100
2.5355-2.62610.21611390.16042706X-RAY DIFFRACTION100
2.6261-2.73120.17991550.16492680X-RAY DIFFRACTION100
2.7312-2.85540.19371440.16672742X-RAY DIFFRACTION100
2.8554-3.00590.24881400.16962719X-RAY DIFFRACTION100
3.0059-3.19410.23391290.17772752X-RAY DIFFRACTION100
3.1941-3.44060.20871410.15762755X-RAY DIFFRACTION100
3.4406-3.78650.16731470.15232736X-RAY DIFFRACTION100
3.7865-4.33370.19411480.15322798X-RAY DIFFRACTION100
4.3337-5.45720.2141510.16522781X-RAY DIFFRACTION100
5.4572-36.8840.24821300.20342934X-RAY DIFFRACTION99
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)
15.95321.51.16965.89151.33774.4334-0.07710.59520.0401-0.8845-0.0198-0.3271-0.2807-0.07130.23120.2465-0.01180.01460.23670.01320.2655.821732.8229-13.0939
23.89841.02390.28835.8704-2.523.06780.0194-0.59330.40110.5525-0.2229-0.2479-0.37820.44240.23530.181-0.0327-0.04470.2737-0.03670.236110.652427.36252.8409
30.71420.0605-1.42152.7830.52853.0383-0.0534-0.99640.23050.59870.0637-0.84010.24050.90090.0220.26140.1031-0.08760.54790.07580.231615.103418.70656.7333
47.797-1.88651.26492.6905-1.00762.00340.06010.07580.0203-0.0823-0.01130.3284-0.0367-0.2310.0060.13920.00560.0220.18120.01770.1645-4.491425.4325-7.8559
51.4435-1.35410.0792.21760.67690.65180.1652-0.43050.54510.62610.11610.8215-0.3404-0.5901-0.00490.15610.05720.10020.37070.02270.4296-16.217229.1421-3.3163
64.7282-0.76120.3863.0450.75073.85460.0274-0.00190.50240.0438-0.07530.167-0.4613-0.11330.00210.1960.04470.06630.14480.01090.244-3.754836.4-9.134
72.0144-1.58920.49154.1598-1.07840.9902-0.0894-0.49110.05180.5790.0590.0893-0.2789-0.00630.04120.2046-0.00730.02740.2624-0.00460.09763.6621.06374.1407
86.0104-0.3591-1.3251.94420.24891.1046-0.0078-0.1553-0.24040.0697-0.09360.35420.2756-0.26220.02290.1978-0.01270.01440.30790.05710.1440.874711.8011-1.1112
91.8617-0.42190.78781.4414-0.57112.60340.0519-0.11170.450.1579-0.2695-0.519-1.02380.3610.02850.1676-0.0530.00010.18620.02250.3526.037938.2444-10.0012
100.2747-0.58440.11753.0460.12522.92720.0257-0.1609-0.12220.2008-0.0815-0.19870.07790.01140.03540.2450.0021-0.02610.34260.11890.18327.50996.9256.249
112.41780.40520.7324.27582.27042.8939-0.06240.05680.2012-0.2602-0.09640.2687-0.1549-0.17750.06450.0940.0209-0.01030.09390.04350.1387-9.455730.56333.0877
122.55520.93-1.82244.337-0.34711.57950.08560.52860.1282-0.5945-0.01030.7152-0.1375-0.7515-0.06410.1982-0.0105-0.05880.24480.01450.1582-15.324520.152525.9959
132.53840.29270.56542.46670.23451.4154-0.04410.06360.34640.1104-0.0262-0.3818-0.07680.3007-0.06970.0943-0.0104-0.02010.0990.02590.16517.399130.120140.2645
143.53660.03410.66852.6928-1.37512.53730.26590.40710.234-0.7619-0.3387-0.51550.06320.014-0.11850.12850.04780.06120.28520.03310.262915.587629.265833.321
151.9531-0.84751.2725.4782-1.90721.19010.31871.3938-0.0241-1.2448-0.6805-0.81010.26620.445-0.32350.25980.11610.05080.363-0.02540.225512.452821.899932.0322
169.19154.39516.88093.36763.90225.4443-0.01380.09680.4584-0.8537-0.1190.749-0.443-0.47380.14370.3981-0.0294-0.07840.27650.08050.3487-7.480536.425827.6944
172.84950.5444-0.79653.556-0.04511.6823-0.02240.21840.23620.08060.0278-0.1026-0.35970.3678-0.14930.1299-0.0577-0.0140.05750.06570.14274.735138.889842.027
181.42111.61060.21183.29430.53010.7442-0.15850.22870.0824-0.47680.07160.0182-0.11430.06390.06180.13440.0019-0.00390.13640.03240.0757-3.882422.694428.5571
198.21021.4935-0.41272.7202-0.22642.02260.0110.1527-0.1812-0.0066-0.0279-0.36720.09520.27080.0390.17760.0267-0.00410.135-0.00750.126-1.235713.799434.4546
203.11280.0852-3.06370.4231-0.3343.0477-0.109-0.06230.30540.09590.0174-0.18580.04780.2373-0.02240.2786-0.0716-0.01140.19990.05880.275412.995847.423540.6946
211.27530.1760.720.5764-0.40351.026-0.0876-0.20270.46650.0639-0.24310.5674-0.283-0.28120.25610.1540.0563-0.01060.1713-0.03160.2972-12.200937.53740.6541
224.3456-3.9525-0.20144.93850.17172.4695-0.0781-0.18750.03630.39270.08331.0503-0.0603-0.7091-0.0750.21410.02960.00440.2774-0.01890.3727-19.671510.933633.2167
230.355-0.66570.91565.3102-0.48412.90190.06880.4154-0.205-0.2491-0.1375-0.73170.06350.88860.01820.23690.00150.02240.3383-0.0280.1425-0.80877.260524.0931
245.14894.0078-1.17654.3305-1.57333.5036-0.23920.79690.2174-0.66280.11620.3490.307-0.30160.16820.16060.0018-0.01660.15970.0420.185417.7656.557824.9814
254.01210.918-0.23714.50681.26523.69750.1073-0.3082-0.27770.5811-0.19410.43250.2487-0.4421-0.05430.1251-0.00020.04320.11980.05340.180812.899963.183639.3464
263.5483-0.48330.36092.7218-1.32956.2169-0.1609-0.6524-0.03520.64630.06750.5796-0.3208-0.62180.09630.22930.0360.08630.2087-0.01350.23178.478372.342242.2641
272.5004-0.4987-0.49962.59970.19081.3326-0.0556-0.0721-0.2992-0.0644-0.044-0.24820.07380.2568-0.06450.07970.00890.00640.10640.03660.132231.202261.573928.4076
283.9399-0.9203-0.22746.30150.29031.05920.1701-0.83980.00511.2414-0.2831-0.72280.09680.26730.0790.2038-0.0692-0.05410.30290.03640.230338.486464.514935.4548
293.4595-2.42940.39045.86993.41673.44950.1002-0.137-0.67071.1767-0.32970.4523-0.2793-0.73710.12940.49010.05510.09020.38110.0990.401916.019856.488342.0246
304.1206-0.36340.6933.1667-0.09791.96050.0302-0.0608-0.0887-0.1304-0.0564-0.10060.38920.222-0.06760.1450.044-0.00420.11110.02120.167128.564152.73927.2735
311.7419-3.07-0.23555.44350.68570.2998-0.2778-0.2519-0.19130.61690.1910.1630.13930.08240.04230.1840.0089-0.01180.14280.03590.137622.962967.419439.8998
325.1538-0.1445-0.45113.31330.11142.6086-0.0635-0.0796-0.06340.17370.0299-0.119-0.04160.18540.02590.1713-0.0057-0.01630.1078-0.01020.11918.232678.583635.476
330.9793-0.04460.14181.36540.16640.530.0063-0.0281-0.39960.0048-0.06520.29140.2344-0.05520.02770.203-0.01040.00850.12190.0350.236722.594748.684127.8985
341.61251.9963-0.06922.57550.21971.6392-0.19120.203-0.0138-0.38940.24411.2038-0.4474-0.378-0.0750.088-0.00910.00270.2324-0.03390.53334.033577.51935.1856
353.3262-0.84322.82952.1231-1.70295.9394-0.12480.06060.16460.3259-0.0347-0.4264-0.26260.69540.13890.264-0.0185-0.0290.2006-0.02040.171523.390185.292743.7169
367.44793.18980.02621.91990.31321.0665-0.0540.055-0.18260.0521-0.0098-0.15870.27250.18130.040.23260.018-0.02140.21770.05080.15384.836216.877744.1246
372.5238-1.7197-0.78382.6122-0.84712.0918-0.06090.06760.0327-0.09120.01940.21410.2875-0.17880.05660.2683-0.0143-0.00780.2972-0.01010.1844-5.712914.8745-11.1541
386.1215-2.679-0.2542.41980.83861.3706-0.1606-0.13410.2788-0.05880.017-0.1357-0.33780.10590.08610.2679-0.0277-0.01140.25690.06410.172428.365674.987924.1232
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 134 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 47 )
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 82 )
8X-RAY DIFFRACTION8chain 'B' and (resid 83 through 98 )
9X-RAY DIFFRACTION9chain 'C' and (resid 68 through 95 )
10X-RAY DIFFRACTION10chain 'C' and (resid 96 through 125 )
11X-RAY DIFFRACTION11chain 'E' and (resid 59 through 77 )
12X-RAY DIFFRACTION12chain 'E' and (resid 78 through 85 )
13X-RAY DIFFRACTION13chain 'E' and (resid 86 through 120 )
14X-RAY DIFFRACTION14chain 'E' and (resid 121 through 130 )
15X-RAY DIFFRACTION15chain 'E' and (resid 131 through 135 )
16X-RAY DIFFRACTION16chain 'F' and (resid 22 through 30 )
17X-RAY DIFFRACTION17chain 'F' and (resid 31 through 47 )
18X-RAY DIFFRACTION18chain 'F' and (resid 48 through 82 )
19X-RAY DIFFRACTION19chain 'F' and (resid 83 through 98 )
20X-RAY DIFFRACTION20chain 'G' and (resid 62 through 76 )
21X-RAY DIFFRACTION21chain 'G' and (resid 77 through 96 )
22X-RAY DIFFRACTION22chain 'G' and (resid 97 through 106 )
23X-RAY DIFFRACTION23chain 'G' and (resid 107 through 125 )
24X-RAY DIFFRACTION24chain 'I' and (resid 58 through 63 )
25X-RAY DIFFRACTION25chain 'I' and (resid 64 through 77 )
26X-RAY DIFFRACTION26chain 'I' and (resid 78 through 85 )
27X-RAY DIFFRACTION27chain 'I' and (resid 86 through 120 )
28X-RAY DIFFRACTION28chain 'I' and (resid 121 through 135 )
29X-RAY DIFFRACTION29chain 'J' and (resid 21 through 30 )
30X-RAY DIFFRACTION30chain 'J' and (resid 31 through 47 )
31X-RAY DIFFRACTION31chain 'J' and (resid 48 through 75 )
32X-RAY DIFFRACTION32chain 'J' and (resid 76 through 98 )
33X-RAY DIFFRACTION33chain 'K' and (resid 63 through 92 )
34X-RAY DIFFRACTION34chain 'K' and (resid 93 through 106 )
35X-RAY DIFFRACTION35chain 'K' and (resid 107 through 125 )
36X-RAY DIFFRACTION36chain 'D' and (resid 212 through 245 )
37X-RAY DIFFRACTION37chain 'H' and (resid 212 through 243 )
38X-RAY DIFFRACTION38chain 'L' and (resid 212 through 245 )

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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