SASDC29: Human Rev7 dimer in complex with Rev3 peptide @ 10.6 mg/mL

基本情報

• 登録情報: データベース: SASBDB / ID: SASDC29

試料

Human Rev7 dimer in complex with Rev3 peptide @ 10.6 mg/mL

• Mitotic spindle assembly checkpoint protein MAD2B (protein), hRev7-WT dimer, Homo sapiens
• DNA polymerase zeta catalytic subunit (protein), Rev3-RBM2, Homo sapiens
• DNA polymerase zeta catalytic subunit (protein), Rev3-RBM2, Homo sapiens

機能・相同性

分子機能:

somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / positive regulation of double-strand break repair via nonhomologous end joining / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling / telomere maintenance in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / regulation of cell growth / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / DNA-templated DNA replication / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / chromosome / 4 iron, 4 sulfur cluster binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell division / nucleotide binding / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm

ドメイン・相同性:

Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily

構成要素:

DNA polymerase zeta catalytic subunit / Mitotic spindle assembly checkpoint protein MAD2B

• 生物種: Homo sapiens (ヒト)
• 引用: ジャーナル: Proc Natl Acad Sci U S A / 年: 2018; タイトル: Rev7 dimerization is important for assembly and function of the Rev1/Polζ translesion synthesis complex.; 著者: Alessandro A Rizzo / Faye-Marie Vassel / Nimrat Chatterjee / Sanjay D'Souza / Yunfeng Li / Bing Hao / Michael T Hemann / Graham C Walker / Dmitry M Korzhnev / ; 要旨: The translesion synthesis (TLS) polymerases Polζ and Rev1 form a complex that enables replication of damaged DNA. The Rev7 subunit of Polζ, which is a multifaceted HORMA (Hop1, Rev7, Mad2) protein with roles in TLS, DNA repair, and cell-cycle control, facilitates assembly of this complex by binding Rev1 and the catalytic subunit of Polζ, Rev3. Rev7 interacts with Rev3 by a mechanism conserved among HORMA proteins, whereby an open-to-closed transition locks the ligand underneath the "safety belt" loop. Dimerization of HORMA proteins promotes binding and release of this ligand, as exemplified by the Rev7 homolog, Mad2. Here, we investigate the dimerization of Rev7 when bound to the two Rev7-binding motifs (RBMs) in Rev3 by combining in vitro analyses of Rev7 structure and interactions with a functional assay in a Rev7 cell line. We demonstrate that Rev7 uses the conventional HORMA dimerization interface both to form a homodimer when tethered by the two RBMs in Rev3 and to heterodimerize with other HORMA domains, Mad2 and p31 Structurally, the Rev7 dimer can bind only one copy of Rev1, revealing an unexpected Rev1/Polζ architecture. In cells, mutation of the Rev7 dimer interface increases sensitivity to DNA damage. These results provide insights into the structure of the Rev1/Polζ TLS assembly and highlight the function of Rev7 homo- and heterodimerization.

登録者

• Alex Rizzo (University of Connecticut, Storrs, CT, USA)

モデル

• モデル #1625: ; タイプ: atomic / ダミー原子の半径: 1.90 A; コメント: residues at N- and C-termini that were missing in PDB were built in extended conformation; カイ2乗値: 25.1295213698; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: Human Rev7 dimer in complex with Rev3 peptide @ 10.6 mg/mL; 試料濃度: 10.6 mg/ml / Entity id: 857 / 858 / 859
• バッファ: 名称: 20 mM HEPES, 10 mM DTT, 5% glycerol / pH: 8

要素 #857

名称: hRev7-WT dimer / タイプ: protein / 記述: Mitotic spindle assembly checkpoint protein MAD2B / 分子量: 24.391 / 分子数: 2 / 由来: Homo sapiens / 参照: UniProt: Q9UI95
配列:

GMTTLTRQDL NFGQVVADVL CEFLEVAVHL ILYVREVYPV GIFQKRKKYN VPVQMSCHPE LNQYIQDTLH CVKPLLEKND VEKVVVVILD KEHRPVEKFV FEITQPPLLS ISSDSLLSHV EQLLRAFILK ISVCDAVLDH NPPGCTFTVL VHTREAATRN MEKIQVIKDF PWILADEQDV HMHDPRLIPL KTMTSDILKM QLYVEERAHK GS

要素 #858

名称: Rev3-RBM2 / タイプ: protein / 記述: DNA polymerase zeta catalytic subunit / 分子量: 3.273 / 分子数: 1 / 由来: Homo sapiens / 参照: UniProt: O60673
配列:

MEDKKIVIMP CKCAPSRQLV QVWLQAKE

要素 #859

名称: Rev3-RBM2 / タイプ: protein / 記述: DNA polymerase zeta catalytic subunit / 分子量: 3.273 / 分子数: 1 / 由来: Homo sapiens / 参照: UniProt: O60673
配列:

MEDKKIVIMP CKCAPSRQLV QVWLQAKE

実験情報

• ビーム: 設備名称: Cornell High Energy Synchrotron Source (CHESS) G1; 地域: Ithaca, NY / 国: USA / 線源: X-ray synchrotron / 波長: 0.1267 Å
• 検出器: 名称: Finger Lakes CCD / タイプ: CCD

スキャン

タイトル: Human Rev7 dimer in complex with Rev3 peptide @ 10.6 mg/mL
測定日: 2016年5月14日 / 保管温度: 4 °C / セル温度: 4 °C / 照射時間: 1 sec. / フレーム数: 10 / 単位: 1/A /

	Min	Max
Q	0.0086	0.8019

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 446 /

	Min	Max
Q	0.0194752	0.302274
P(R) point	1	446
R	0	109.6

結果

カーブのタイプ: single_conc
コメント: Model was created by mapping the dimer interface by mutagenesis (9 residues identified) and then docking the dimer with HADDOCK and the mutations. SAXS/WAXS was used for cross-validation.

	実験値	Standard	Standard error	Porod
分子量	53.4 kDa	53.4 kDa	0.04	63.8 kDa
体積	-	-	-	108.4 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	0.369	0.0003	0.366	0.00024
慣性半径, Rg	3.01 nm	0.004	2.93 nm	0.003

	Min	Max
D	-	11
Guinier point	1	63