+ データを開く
データを開く
- 基本情報
基本情報
| 登録情報 | データベース: PDB / ID: 9jc6 | ||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| タイトル | Human H2BW2 nucleosome | ||||||||||||||||||||||||||||||
|  要素 | 
 | ||||||||||||||||||||||||||||||
|  キーワード | DNA BINDING PROTEIN/DNA / Nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||||||||||||||||||||
| 機能・相同性 |  機能・相同性情報 negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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 ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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  / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / epigenetic regulation of gene expression / 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 / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / UCH proteinases / nucleosome / heterochromatin formation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 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 / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane 類似検索 - 分子機能 | ||||||||||||||||||||||||||||||
| 生物種 |  Homo sapiens (ヒト) synthetic construct (人工物) | ||||||||||||||||||||||||||||||
| 手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.34 Å | ||||||||||||||||||||||||||||||
|  データ登録者 | Ding, D.B. / Ishibashi, T. / Nguyen, T.T. | ||||||||||||||||||||||||||||||
| 資金援助 |  中国,  香港, 3件 
 | ||||||||||||||||||||||||||||||
|  引用 |  ジャーナル: Nucleic Acids Res / 年: 2025 タイトル: H2B.W2, a spermatocyte-specific histone variant, disrupts nucleosome stability, and reduces chromatin compaction. 著者: April T T Nguyen / Dongbo Ding / Xingpeng Bai / Matthew Y H Pang / Mingxi Deng / Yue Liu / Tingyu Jin / Zhichun Xu / Yingyi Zhang / Yuanliang Zhai / Yan Yan / Toyotaka Ishibashi /  要旨: Spermatogenesis is a highly regulated process that requires precise chromatin remodeling, which includes the incorporation of testis-specific histone variants. While several of these variants have ...Spermatogenesis is a highly regulated process that requires precise chromatin remodeling, which includes the incorporation of testis-specific histone variants. While several of these variants have been characterized, the role of H2B.W2, a member of the H2BW family, remains largely unclear. Here, we showed that H2B.W2 expression occurs mainly in spermatocytes, slightly later than its paralog H2B.W1. Cryo-electron microscopy analysis of H2B.W2-containing nucleosomes reveals a more relaxed conformation compared to canonical nucleosomes caused by weakened interactions between the outer DNA turn and the histone core. We pinpointed the N-terminal tail and α2 helix of H2B.W2 as critical regions for nucleosome destabilization. Furthermore, we identify G73 within the L1 loop as a key residue involved in disrupting higher-order chromatin structure. Our findings suggest that H2B.W2-mediated nucleosome and chromatin destabilization may play a role in regulating gene expression during spermatogenesis, with potential implications for sperm development and function. | ||||||||||||||||||||||||||||||
| 履歴 | 
 | 
- 構造の表示
構造の表示
| 構造ビューア | 分子:  Molmil  Jmol/JSmol | 
|---|
- ダウンロードとリンク
ダウンロードとリンク
- ダウンロード
ダウンロード
| PDBx/mmCIF形式 |  9jc6.cif.gz | 273.9 KB | 表示 |  PDBx/mmCIF形式 | 
|---|---|---|---|---|
| PDB形式 |  pdb9jc6.ent.gz | 203.3 KB | 表示 |  PDB形式 | 
| PDBx/mmJSON形式 |  9jc6.json.gz | ツリー表示 |  PDBx/mmJSON形式 | |
| その他 |  その他のダウンロード | 
-検証レポート
| 文書・要旨 |  9jc6_validation.pdf.gz | 1.2 MB | 表示 |  wwPDB検証レポート | 
|---|---|---|---|---|
| 文書・詳細版 |  9jc6_full_validation.pdf.gz | 1.3 MB | 表示 | |
| XML形式データ |  9jc6_validation.xml.gz | 39.9 KB | 表示 | |
| CIF形式データ |  9jc6_validation.cif.gz | 61.1 KB | 表示 | |
| アーカイブディレクトリ |  https://data.pdbj.org/pub/pdb/validation_reports/jc/9jc6  ftp://data.pdbj.org/pub/pdb/validation_reports/jc/9jc6 | HTTPS FTP | 
-関連構造データ
| 関連構造データ |  61358MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( | 
|---|---|
| 類似構造データ | 類似検索 - 機能・相同性  F&H 検索 | 
- リンク
リンク
- 集合体
集合体
| 登録構造単位 |  
 | 
|---|---|
| 1 | 
 | 
- 要素
要素
-タンパク質 , 4種, 8分子 AEBFCGDH       
| #1: タンパク質 | 分子量: 15305.969 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現)   Homo sapiens (ヒト) 遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J 発現宿主:   Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P68431 #2: タンパク質 | 分子量: 11263.231 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現)   Homo sapiens (ヒト) 遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, 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 | 分子量: 14034.355 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現)   Homo sapiens (ヒト) / 遺伝子: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE 発現宿主:   Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P04908 #4: タンパク質 | 分子量: 16395.580 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現)   Homo sapiens (ヒト) / 遺伝子: H2BW2, H2BFM 発現宿主:   Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P0C1H6 | 
|---|
-DNA鎖 , 2種, 2分子 IJ 
| #5: DNA鎖 | 分子量: 45138.770 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: 601 DNA / 由来: (合成) synthetic construct (人工物) | 
|---|---|
| #6: DNA鎖 | 分子量: 45610.043 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: 601 Reverse Complementary / 由来: (合成) synthetic construct (人工物) | 
-詳細
| Has protein modification | N | 
|---|
-実験情報
-実験
| 実験 | 手法: 電子顕微鏡法 | 
|---|---|
| EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 | 
- 試料調製
試料調製
| 構成要素 | 名称: Human H2BW2 nucleosome with 601 DNA sequence / タイプ: COMPLEX / Entity ID: all / 由来: MULTIPLE SOURCES | 
|---|---|
| 分子量 | 実験値: NO | 
| 由来(天然) | 生物種:  Homo sapiens (ヒト) | 
| 由来(組換発現) | 生物種:   Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) | 
| 緩衝液 | pH: 7.5 | 
| 試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | 
| 急速凍結 | 凍結剤: ETHANE | 
- 電子顕微鏡撮影
電子顕微鏡撮影
| 顕微鏡 | モデル: TFS TITAN THEMIS | 
|---|---|
| 電子銃 | 電子線源:  FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN | 
| 電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1100 nm / 最小 デフォーカス(公称値): 250 nm | 
| 撮影 | 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) | 
- 解析
解析
| EMソフトウェア | 
 | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
| 3次元再構成 | 解像度: 3.34 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 127551 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
| 精密化 | 立体化学のターゲット値: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) | ||||||||||||||||||||||||
| 拘束条件 | 
 | 
 ムービー
ムービー コントローラー
コントローラー



 PDBj
PDBj










































