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- PDB-5mps: Structure of a spliceosome remodeled for exon ligation -

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データベース: PDB / ID: 5mps
タイトルStructure of a spliceosome remodeled for exon ligation
要素
  • (Pre-mRNA-processing ...) x 2
  • (Pre-mRNA-splicing factor ...) x 15
  • (Small nuclear ribonucleoprotein ...) x 6
  • Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence
  • Small nuclear ribonucleoprotein-associated protein B
  • U2 snRNA
  • U5 snRNA
  • UBC4 gene exon
  • Unknown
  • Yeast UBC4 gene for ubiquitin-conjugating enzyme
キーワードSPLICING / pre-mRNA splicing / trans-esterification / lariat intermediate / complex C-star
機能・相同性
機能・相同性情報


U2-type post-spliceosomal complex / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding ...U2-type post-spliceosomal complex / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / Prp19 complex / pICln-Sm protein complex / snRNP binding / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / pre-mRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / Formation of TC-NER Pre-Incision Complex / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / DNA replication origin binding / mRNA 5'-splice site recognition / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA 3'-splice site recognition / Dual incision in TC-NER / spliceosomal tri-snRNP complex assembly / DNA replication initiation / U5 snRNA binding / positive regulation of cell cycle / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / nuclear periphery / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / GTPase activity / mRNA binding / chromatin binding / chromatin / GTP binding / DNA binding / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm
類似検索 - 分子機能
RNA Binding Protein, Prp18; Chain A / Functional domain of the splicing factor Prp18 / Prp18 / Pre-mRNA-splicing factor 18 / Prp18 domain / Pre-mRNA-splicing factor SLU7 domain / Pre-mRNA-splicing factor SLU7 / Pre-mRNA splicing Prp18-interacting factor / cwf21 / Slt11, RNA recognition motif ...RNA Binding Protein, Prp18; Chain A / Functional domain of the splicing factor Prp18 / Prp18 / Pre-mRNA-splicing factor 18 / Prp18 domain / Pre-mRNA-splicing factor SLU7 domain / Pre-mRNA-splicing factor SLU7 / Pre-mRNA splicing Prp18-interacting factor / cwf21 / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / Torus domain / mRNA splicing factor SYF2 / SYF2 splicing factor / : / : / mRNA splicing factor Cwf21 domain / cwf21 domain / Pre-mRNA-processing factor 17 / HAT (Half-A-TPR) repeat / BUD31/G10-related, conserved site / G10 protein signature 1. / G10 protein signature 2. / : / STL11, N-terminal / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Suppressor of forked / Cwf15/Cwc15 cell cycle control protein / Suppressor of forked protein (Suf) / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Pre-mRNA-splicing factor Syf1-like / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / SH3 type barrels. - #100 / : / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Myb-type HTH DNA-binding domain profile. / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Myb domain / Myb-like DNA-binding domain / : / Sm domain profile. / LSM domain superfamily / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8
類似検索 - ドメイン・相同性
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Pre-mRNA-splicing factor BUD31 / Pre-mRNA-processing protein 45 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor 18 / Pre-mRNA-splicing factor SNU114 / Pre-mRNA-splicing factor SLT11 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-splicing factor SYF2 / Pre-mRNA-splicing factor CWC22 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-splicing factor SLU7 / Pre-mRNA-splicing factor CWC21 / Pre-mRNA-splicing factor CEF1 / Pre-mRNA-splicing factor CWC15 / Pre-mRNA-splicing factor SYF1 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor CWC2 / Pre-mRNA-splicing factor CLF1 / Small nuclear ribonucleoprotein E / Pre-mRNA-splicing factor PRP46
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
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: 3.85 Å
データ登録者Fica, S.M. / Oubridge, C. / Galej, W.P. / Wilkinson, M.E. / Newman, A.J. / Bai, X.-C. / Nagai, K.
資金援助 英国, 3件
組織認可番号国
Medical Research Council (United Kingdom)MC-U105184330 英国
European Research CouncilAdG-693087-SPLICE3D
EMBO and Marie Sklodowska-Curie FellowshipRef. S.M.Fica
引用
ジャーナル: Nature / 年: 2017
タイトル: Structure of a spliceosome remodelled for exon ligation.
著者: Sebastian M Fica / Chris Oubridge / Wojciech P Galej / Max E Wilkinson / Xiao-Chen Bai / Andrew J Newman / Kiyoshi Nagai /
要旨: The spliceosome excises introns from pre-mRNAs in two sequential transesterifications-branching and exon ligation-catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently ...The spliceosome excises introns from pre-mRNAs in two sequential transesterifications-branching and exon ligation-catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5' exon and lariat-3'-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5' splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site. Here we present, at 3.8 Å resolution, the cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but before exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75° compared to the C complex and is stabilized in a new position by Prp17, Cef1 and the reoriented Prp8 RNase H-like domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3' exon docking, and restructures the pairing of the 5' splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNase H-like domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3' exon, suggesting a possible basis for mRNA release after exon ligation. Together with the structure of the C complex, our structure of the C* complex reveals the two major conformations of the spliceosome during the catalytic stages of splicing.
#1: ジャーナル: Science / 年: 2015
タイトル: Structural basis of pre-mRNA splicing.
著者: Jing Hang / Ruixue Wan / Chuangye Yan / Yigong Shi /
要旨: Splicing of precursor messenger RNA is performed by the spliceosome. In the cryogenic electron microscopy structure of the yeast spliceosome, U5 small nuclear ribonucleoprotein acts as a central ...Splicing of precursor messenger RNA is performed by the spliceosome. In the cryogenic electron microscopy structure of the yeast spliceosome, U5 small nuclear ribonucleoprotein acts as a central scaffold onto which U6 and U2 small nuclear RNAs (snRNAs) are intertwined to form a catalytic center next to Loop I of U5 snRNA. Magnesium ions are coordinated by conserved nucleotides in U6 snRNA. The intron lariat is held in place through base-pairing interactions with both U2 and U6 snRNAs, leaving the variable-length middle portion on the solvent-accessible surface of the catalytic center. The protein components of the spliceosome anchor both 5' and 3' ends of the U2 and U6 snRNAs away from the active site, direct the RNA sequences, and allow sufficient flexibility between the ends and the catalytic center. Thus, the spliceosome is in essence a protein-directed ribozyme, with the protein components essential for the delivery of critical RNA molecules into close proximity of one another at the right time for the splicing reaction.
#2: ジャーナル: Nature / 年: 2015
タイトル: The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
著者: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-chen Bai / Christos G Savva / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
要旨: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key ...U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome.
#3: ジャーナル: Nature / 年: 2016
タイトル: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
著者: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
要旨: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led ...U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.
#4: ジャーナル: Nature / 年: 2016
タイトル: Cryo-EM structure of the spliceosome immediately after branching.
著者: Wojciech P Galej / Max E Wilkinson / Sebastian M Fica / Chris Oubridge / Andrew J Newman / Kiyoshi Nagai /
要旨: Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat-intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the ...Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat-intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the spliceosome immediately after lariat formation. The 5'-splice site is cleaved but remains close to the catalytic Mg site in the U2/U6 small nuclear RNA (snRNA) triplex, and the 5'-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2'OH. The 5'-exon is held between the Prp8 amino-terminal and linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson-Crick interactions between the branch helix and 5'-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA ACAGAGA sequence. Isy1 and the step-one factors Yju2 and Cwc25 stabilize docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 reverse transcriptase and linker domains and extends towards the Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation.
履歴
登録2016年12月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年1月18日Provider: repository / タイプ: Initial release
改定 1.12017年3月1日Group: Database references
改定 1.22017年7月5日Group: Data collection / カテゴリ: em_imaging / Item: _em_imaging.details
改定 1.32017年8月30日Group: Author supporting evidence / Data collection
カテゴリ: em_image_scans / em_imaging_optics ...em_image_scans / em_imaging_optics / em_software / pdbx_audit_support
Item: _em_imaging_optics.energyfilter_name / _em_software.name / _pdbx_audit_support.funding_organization
改定 1.42018年10月17日Group: Data collection / Refinement description / カテゴリ: refine
改定 1.52019年10月30日Group: Advisory / Data collection / Derived calculations
カテゴリ: pdbx_validate_close_contact / struct_conn / struct_conn_type
改定 1.62019年12月11日Group: Other / カテゴリ: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
改定 2.02020年10月7日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-3539
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
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: Yeast UBC4 gene for ubiquitin-conjugating enzyme
E: UBC4 gene exon
2: U2 snRNA
6: Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence
5: U5 snRNA
A: Pre-mRNA-splicing factor 8
C: Pre-mRNA-splicing factor SNU114
H: Pre-mRNA-splicing factor CWC22
J: Pre-mRNA-splicing factor PRP46
K: Pre-mRNA-processing protein 45
L: Pre-mRNA-splicing factor BUD31
M: Pre-mRNA-splicing factor CWC2
N: Pre-mRNA-splicing factor SLT11
O: Pre-mRNA-splicing factor CEF1
P: Pre-mRNA-splicing factor CWC15
R: Pre-mRNA-splicing factor CWC21
S: Pre-mRNA-splicing factor CLF1
T: Pre-mRNA-splicing factor SYF1
a: Pre-mRNA-splicing factor 18
c: Pre-mRNA-splicing factor SLU7
o: Pre-mRNA-processing factor 17
X: Unknown
y: Pre-mRNA-splicing factor SYF2
b: Small nuclear ribonucleoprotein-associated protein B
d: Small nuclear ribonucleoprotein Sm D3
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
h: Small nuclear ribonucleoprotein Sm D1
j: Small nuclear ribonucleoprotein Sm D2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,696,09543
ポリマ－1,694,36830
非ポリマー1,72713
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1

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要素

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RNA鎖 , 5種, 5分子 IE265

#1: RNA鎖 Yeast UBC4 gene for ubiquitin-conjugating enzyme


分子量: 30200.730 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: Saccharomyces cerevisiae UBC4 pre-mRNA intron, in vitro transcribed.
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
発現宿主: in vitro transcription vector pT7-Fluc(deltai) (その他)
参照: GenBank: 4718
#2: RNA鎖 UBC4 gene exon


分子量: 6518.976 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: Saccharomyces cerevisiae UBC4 pre-mRNA exon, in vitro transcribed.
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: UBC4
発現宿主: in vitro transcription vector pT7-Fluc(deltai) (その他)
#3: RNA鎖 U2 snRNA


分子量: 376267.406 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Saccharomyces cerevisiae U2 snRNA
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 536627
#4: RNA鎖 Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence


分子量: 35883.176 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Saccharomyces cerevisiae U6 snRNA
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1039022925
#5: RNA鎖 U5 snRNA


分子量: 57444.875 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Saccharomyces cerevisiae U5 snRNA
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1039023700

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Pre-mRNA-splicing factor ... , 15種, 15分子 ACHJLMNOPRSTacy

#6: タンパク質 Pre-mRNA-splicing factor 8


分子量: 279867.469 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Prp8 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P33334
#7: タンパク質 Pre-mRNA-splicing factor SNU114 / 114 kDa U5 small nuclear ribonucleoprotein component / Growth inhibitory protein 10


分子量: 114174.008 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: c Snu114 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P36048
#8: タンパク質 Pre-mRNA-splicing factor CWC22 / Complexed with CEF1 protein 22


分子量: 67386.062 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Cwc22 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P53333
#9: タンパク質 Pre-mRNA-splicing factor PRP46 / Complexed with CEF1 protein 1 / PRP nineteen-associated complex protein 50 / PRP19-associated ...Complexed with CEF1 protein 1 / PRP nineteen-associated complex protein 50 / PRP19-associated complex protein 50 / Pre-mRNA-processing protein 46


分子量: 50771.289 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Prp46 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q12417
#11: タンパク質 Pre-mRNA-splicing factor BUD31 / Bud site selection protein 31 / Complexed with CEF1 protein 14


分子量: 18484.502 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Bud31 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P25337
#12: タンパク質 Pre-mRNA-splicing factor CWC2 / Complexed with CEF1 protein 2 / PRP19-associated complex protein 40 / Synthetic lethal with CLF1 protein 3


分子量: 38486.562 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Cwc2 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q12046
#13: タンパク質 Pre-mRNA-splicing factor SLT11 / Extracellular mutant protein 2 / Synthetic lethality with U2 protein 11


分子量: 40988.590 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Ecm2 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P38241
#14: タンパク質 Pre-mRNA-splicing factor CEF1 / PRP nineteen-associated complex protein 85 / PRP19-associated complex protein 85


分子量: 67837.773 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Cef1 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q03654
#15: タンパク質 Pre-mRNA-splicing factor CWC15 / Complexed with CEF1 protein 15


分子量: 19975.195 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Cwc15 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q03772
#16: タンパク質 Pre-mRNA-splicing factor CWC21 / Complexed with CEF1 protein 21


分子量: 15793.596 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Cwc21 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q03375
#17: タンパク質 Pre-mRNA-splicing factor CLF1 / Crooked neck-like factor 1 / PRP19-associated complex protein 77 / Synthetic lethal with CDC40 protein 3


分子量: 82555.859 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Clf1 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q12309
#18: タンパク質 Pre-mRNA-splicing factor SYF1 / PRP19-associated complex protein 90 / Synthetic lethal with CDC40 protein 1


分子量: 101875.852 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Syf1 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q04048
#19: タンパク質 Pre-mRNA-splicing factor 18


分子量: 28414.391 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Prp18 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P33411
#20: タンパク質 Pre-mRNA-splicing factor SLU7 / Synthetic lethal with U2 snRNA protein 17 / Synthetic lethal with U5 snRNA protein 7


分子量: 44722.875 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Slu7 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q02775
#23: タンパク質 Pre-mRNA-splicing factor SYF2 / PRP19 complex protein 31 / Synthetic lethal with CDC40 protein 2


分子量: 24850.719 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Syf2 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P53277

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Pre-mRNA-processing ... , 2種, 2分子 Ko

#10: タンパク質 Pre-mRNA-processing protein 45


分子量: 42548.727 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Prp45 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P28004
#21: タンパク質 Pre-mRNA-processing factor 17 / Cell division control protein 40


分子量: 52128.762 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae Prp17 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P40968

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タンパク質 , 2種, 2分子 Xb

#22: タンパク質 Unknown


分子量: 5805.147 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Unknown protein helices within C-star complex / 由来: (天然) Saccharomyces cerevisiae (パン酵母)
#24: タンパク質 Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB


分子量: 22426.990 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae SmB protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P40018

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Small nuclear ribonucleoprotein ... , 6種, 6分子 defghj

#25: タンパク質 Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


分子量: 11240.139 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae SmD3 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P43321
#26: タンパク質 Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


分子量: 10385.098 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae SmE protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q12330
#27: タンパク質 Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


分子量: 9669.945 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae SmF protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P54999
#28: タンパク質 Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


分子量: 8490.809 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae SmG protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P40204
#29: タンパク質 Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


分子量: 16296.798 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae SmD1 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q02260
#30: タンパク質 Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


分子量: 12876.066 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Saccharomyces cerevisiae SmD2 protein / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q06217

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非ポリマー , 5種, 13分子

#31: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Mg
#32: 化合物 ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 2 / 由来タイプ: 合成 / 式: K
#33: 化合物 ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / フィチン酸


分子量: 660.035 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H18O24P6
#34: 化合物 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#35: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn

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実験情報

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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

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試料調製

構成要素名称: Saccharomyces cerevisiae spliceosome. Complex C just after Prp16-mediated remodeling
タイプ: COMPLEX
詳細: Splicing extract was prepared from Slu7-TAPS yeast strains. An in vitro transcribed yeast UBC4 pre-mRNA substrate (with 2 x MS2 bacteriophage coat protein-binding stem loops at the 5' end and ...詳細: Splicing extract was prepared from Slu7-TAPS yeast strains. An in vitro transcribed yeast UBC4 pre-mRNA substrate (with 2 x MS2 bacteriophage coat protein-binding stem loops at the 5' end and with a 2'-deoxy substitution at the 3'-splice site sequence UAG sequence (UA-2'dG) was pre-bound to an MS2-maltose binding protein fusion protein. This substrate-protein complex was added to the splicing extract. The splicing reaction proceeded through the first step but the second step was blocked by the deoxy substitution. Substrate-bound spliceosomes from the splicing extract were purified on amylose resin and eluted with maltose. Subsequently the spliceosomes were captured on streptactin resin and eluted with desthiobiotin. Purified spliceosomes were concentrated in 20 mM HEPES KOH pH 7.9, 100 mM KCl, 0.25 mM EDTA.
Entity ID: #1-#30 / 由来: MULTIPLE SOURCES
緩衝液pH: 7.9 / 詳細: NP-40 is also called IGEPAL CA-630
緩衝液成分
ID濃度名称式Buffer-ID
120 mMHepes.KOH pH 7.91
2100 mMpotassium chlorideKCl1
3250 micromolarEDTA1
41 % v/vglycerol1
50.0025 % v/vNonidet P-40 (NP-40)1
試料濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3
急速凍結装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K
詳細: 3.5 microlitres sample were applied to the grid, left for 25 seconds and then blotted for 3.0-3.5 seconds before plunging.

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS / 詳細: GIF Quantum energy filter, 20 eV slit width
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 81000 X / 最大 デフォーカス（公称値）: 4500 nm / 最小 デフォーカス（公称値）: 500 nm
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影平均露光時間: 0.8 sec. / 電子線照射量: 2 e/Å2 / 検出モード: SUPER-RESOLUTION
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
実像数: 3596
詳細: Total dose: 40 electrons/Angstrom^2 over 16 seconds. 20 movie frames collected at 1.25 frames per second.
電子光学装置エネルギーフィルター名称: GIF Quantum

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解析

ソフトウェア名称: REFMAC / バージョン: 5.8.0124 / 分類: 精密化
EMソフトウェア
ID名称バージョンカテゴリ詳細
1RELION1.4粒子像選択
4CTFFIND4CTF補正
7Coot0.8.3モデルフィッティングPaul Emsley's experimental version.
9RELION1.4初期オイラー角割当
10RELION1.4最終オイラー角割当
11RELION1.4分類
12RELION1.4３次元再構成
13REFMAC5.8モデル精密化Used "SOURCE EM" command to get correct electron form factors for refinement of electron microscopy structure.
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 350000
詳細: Selected initial particles automatically using C complex 2D class averages, low-pass filtered to 20 Angstrom for automatic particle picking.
3次元再構成解像度: 3.85 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 65824 / クラス平均像の数: 4 / 対称性のタイプ: POINT
原子モデル構築B value: 330 / プロトコル: FLEXIBLE FIT / 空間: RECIPROCAL / Target criteria: Fourier Shell Correlation
詳細: Used secondary structure restraints generated in ProSMART and LibG.
精密化解像度: 3.85→257.4 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 37.73 / SU ML: 0.526 / ESU R: 0.868
立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射
Rwork0.32177 --
obs0.32177 357071 100 %
溶媒の処理溶媒モデル: PARAMETERS FOR MASK CACLULATION
原子変位パラメータBiso mean: 170.644 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.34 Å2-0.53 Å2
2---0.26 Å2-0.07 Å2
3---0.26 Å2
精密化ステップサイクル: 1 / 合計: 59157
拘束条件
Refine-IDタイプDev idealDev ideal target数
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01861218
ELECTRON MICROSCOPYr_bond_other_d0.0020.0253354
ELECTRON MICROSCOPYr_angle_refined_deg1.2871.85984337
ELECTRON MICROSCOPYr_angle_other_deg1.0123122254
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.7535.1836844
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.3223.4852126
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.397158722
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.12915340
ELECTRON MICROSCOPYr_chiral_restr0.0830.2029725
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0263652
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0213902
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.46717.89927134
ELECTRON MICROSCOPYr_mcbond_other5.46717.89827133
ELECTRON MICROSCOPYr_mcangle_it9.5826.79733767
ELECTRON MICROSCOPYr_mcangle_other9.5826.79833768
ELECTRON MICROSCOPYr_scbond_it5.40118.17334084
ELECTRON MICROSCOPYr_scbond_other5.40118.17334085
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other9.74927.20850571
ELECTRON MICROSCOPYr_long_range_B_refined19.018122798
ELECTRON MICROSCOPYr_long_range_B_other19.018122798
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS精密化 シェル解像度: 3.85→3.95 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rwork0.599 26341 -
Rfree-0 -
obs--100 %

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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

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