[English] 日本語
Yorodumi
- PDB-9fmd: Integrative model of the human post-catalytic spliceosome (P-complex) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fmd
TitleIntegrative model of the human post-catalytic spliceosome (P-complex)
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 7
  • (Small nuclear ribonucleoprotein ...) x 6
  • (Splicing factor ...) x 3
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • ATP-dependent RNA helicase DHX8
  • Cell division cycle 5-like protein
  • Coiled-coil domain-containing protein 12
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • Exon
  • INTRON
  • Intron-binding protein aquarius
  • NF-kappa-B-activating protein
  • Nitric oxide synthase-interacting protein
  • PRKR-interacting protein 1
  • Peptidylprolyl isomerase domain and WD repeat-containing protein 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • Protein FAM32A
  • Protein FAM50A
  • Protein mago nashi homolog
  • RNA-binding protein 8A
  • SNW domain-containing protein 1
  • STING ER exit protein
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • Splicing regulator SDE2
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
KeywordsSPLICING / P-complex / spliceosome
Function / homology
Function and homology information


regulation of homologous chromosome segregation / second spliceosomal transesterification activity / endoplasmic reticulum membrane organization / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / negative regulation of nitric-oxide synthase activity / cellular response to selenite ion / post-spliceosomal complex / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exon-exon junction complex ...regulation of homologous chromosome segregation / second spliceosomal transesterification activity / endoplasmic reticulum membrane organization / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / negative regulation of nitric-oxide synthase activity / cellular response to selenite ion / post-spliceosomal complex / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exon-exon junction complex / selenocysteine insertion sequence binding / pre-mRNA 3'-splice site binding / negative regulation of catalytic activity / NOSIP mediated eNOS trafficking / regulation of translation at postsynapse, modulating synaptic transmission / protein exit from endoplasmic reticulum / regulation of retinoic acid receptor signaling pathway / granulocyte differentiation / post-mRNA release spliceosomal complex / renal system process / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of toll-like receptor signaling pathway / cis assembly of pre-catalytic spliceosome / histone pre-mRNA 3'end processing complex / regulation of vitamin D receptor signaling pathway / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of lipopolysaccharide-mediated signaling pathway / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / Deadenylation of mRNA / negative regulation of interleukin-8 production / negative regulation of excitatory postsynaptic potential / embryonic cranial skeleton morphogenesis / alternative mRNA splicing, via spliceosome / protein methylation / poly(A) binding / 7-methylguanosine cap hypermethylation / U12-type spliceosomal complex / embryonic brain development / nuclear retinoic acid receptor binding / negative regulation of interferon-beta production / U1 snRNP binding / methylosome / U2-type catalytic step 1 spliceosome / ATP-dependent activity, acting on RNA / pre-mRNA binding / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / RNA splicing, via transesterification reactions / mRNA 3'-end processing / M-decay: degradation of maternal mRNAs by maternally stored factors / sno(s)RNA-containing ribonucleoprotein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / host-mediated activation of viral transcription / positive regulation of vitamin D receptor signaling pathway / snRNP binding / commitment complex / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / regulation of nitric oxide biosynthetic process / oocyte development / telomerase holoenzyme complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / positive regulation of alpha-beta T cell differentiation / RUNX3 regulates NOTCH signaling / telomerase RNA binding / U2-type catalytic step 2 spliceosome / U2-type prespliceosome assembly / U2-type spliceosomal complex / nuclear vitamin D receptor binding / NOTCH4 Intracellular Domain Regulates Transcription / U1 snRNP / RNA Polymerase II Transcription Termination / U2 snRNP / : / U4 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U2-type prespliceosome / negative regulation of type I interferon-mediated signaling pathway / protein peptidyl-prolyl isomerization / positive regulation of neurogenesis / inner cell mass cell proliferation / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding
Similarity search - Function
XAP5 protein / Nitric oxide synthase-interacting protein / STEEP-like / Nitric oxide synthase-interacting protein, zinc-finger / : / : / XAP5, circadian clock regulator C-terminal domain / Zinc-finger of nitric oxide synthase-interacting protein / STEEP1 domain / Telomere length and silencing protein 1 ...XAP5 protein / Nitric oxide synthase-interacting protein / STEEP-like / Nitric oxide synthase-interacting protein, zinc-finger / : / : / XAP5, circadian clock regulator C-terminal domain / Zinc-finger of nitric oxide synthase-interacting protein / STEEP1 domain / Telomere length and silencing protein 1 / Hepatocellular carcinoma-associated antigen 59 / NF-kappa-B-activating protein, C-terminal / NF-kappa-B-activating protein / NF-kappa-B-activating protein C-terminal domain / NF-kappa-B-activating protein / Nuclear protein DGCR14/ESS-2 / : / Nuclear protein Es2 / Vertebrate Splicing regulator sde2, N-terminal ubiquitin domain / Protein FAM32A / Cactin, central domain / Cactin, C-terminal / FAM32A / Cactus-binding C-terminus of cactin protein / Conserved mid region of cactin / PRKR-interacting protein 1 / Protein of unknown function (DUF1168) / mRNA splicing factor Cwf18-like / : / cwf18 pre-mRNA splicing factor / Splicing regulator SDE2, SDE2 domain / Pre-mRNA-splicing factor SLU7 domain / Pre-mRNA-splicing factor SLU7 / Pre-mRNA splicing Prp18-interacting factor / DHX8/ Prp22, DEXH-box helicase domain / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / : / : / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / : / Prp19 WD40 domain / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / : / RBM22 CCCH zinc finger domain / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / mRNA splicing factor SYF2 / SYF2 splicing factor / Helix hairpin bin domain superfamily / Cactus-binding C-terminus of cactin protein / : / : / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / : / Replication stress response SDE2 C-terminal / mRNA splicing factor Cwf21 domain / cwf21 domain / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / G10 protein signature 2. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / BUD31/G10-related, conserved site / G10 protein signature 1. / : / : / : / U-box domain / STL11, N-terminal / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / : / SKIP/SNW domain / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / DNA2/NAM7 helicase, helicase domain / AAA domain / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / Pleiotropic regulator 1 / RNA helicase aquarius / Pre-mRNA-processing factor 17 ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / Pleiotropic regulator 1 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-splicing factor SLU7 / Pre-mRNA-splicing factor SYF2 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / Eukaryotic initiation factor 4A-III / Protein BUD31 homolog / Protein mago nashi homolog / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / SNW domain-containing protein 1 / Protein FAM50A / ATP-dependent RNA helicase DHX8 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing regulator SDE2 / Pre-mRNA-processing-splicing factor 8 / NF-kappa-B-activating protein / Coiled-coil domain-containing protein 12 / Splicing factor Cactin / Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / Splicing factor ESS-2 homolog / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Crooked neck-like protein 1 / STING ER exit protein / PRKR-interacting protein 1 / Pre-mRNA-splicing factor CWC22 homolog / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Splicing factor C9orf78 / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Serine/arginine repetitive matrix protein 2 / Nitric oxide synthase-interacting protein / Peptidyl-prolyl cis-trans isomerase-like 1 / Protein FAM32A / RNA-binding protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
Human adenovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRothe, P. / Plaschka, C. / Vorlaender, M.K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Citation
Journal: Nature / Year: 2024
Title: Mechanism for the initiation of spliceosome disassembly.
Authors: Matthias K Vorländer / Patricia Rothe / Justus Kleifeld / Eric D Cormack / Lalitha Veleti / Daria Riabov-Bassat / Laura Fin / Alex W Phillips / Luisa Cochella / Clemens Plaschka /
Abstract: Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on ...Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on spliceosome assembly and remodelling for catalysis, but the mechanism of disassembly remains unclear. Here we report cryo-electron microscopy structures of nematode and human terminal intron lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 therefore controls both the start and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of the initiation of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes.
#1: Journal: Science / Year: 2019
Title: A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation.
Authors: Sebastian M Fica / Chris Oubridge / Max E Wilkinson / Andrew J Newman / Kiyoshi Nagai /
Abstract: During exon ligation, the spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a ...During exon ligation, the spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo-electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3'SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5'-exon and intron 3'SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP-factors implicated in alternative splicing-further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3'SS selection and to potentially fine-tune alternative splicing at the exon ligation stage.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 2.0Dec 11, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / em_entity_assembly / em_software / entity / entity_poly / entity_src_gen / entity_src_nat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _em_entity_assembly.entity_id_list / _entity.src_method / _entity_poly.type / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.i_auth_seq_id / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.i_auth_seq_id_1 / _ndb_struct_na_base_pair_step.i_auth_seq_id_2 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_auth_seq_id_1 / _ndb_struct_na_base_pair_step.j_auth_seq_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.step_name / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_peptide_omega.omega / _pdbx_validate_planes.rmsd / _struct_asym.entity_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _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.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_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end
Description: Missing anisotropic B-factor / Provider: author / Type: Coordinate replacement

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: PRKR-interacting protein 1
2: U2 snRNA
3: Splicing factor ESS-2 homolog
32: Protein FAM32A
5: U5 snRNA
50: Protein FAM50A
56: STING ER exit protein
6: U6 snRNA
7: Eukaryotic initiation factor 4A-III
8: RNA-binding protein 8A
9: Protein mago nashi homolog
A: Pre-mRNA-processing-splicing factor 8
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: Pre-mRNA-splicing factor ISY1 homolog
E: U5 small nuclear ribonucleoprotein 40 kDa protein
EX: Exon
F: Splicing factor Cactin
H: Pre-mRNA-splicing factor CWC22 homolog
I: Pre-mRNA-splicing factor SYF1
IN: INTRON
J: Crooked neck-like protein 1
K: Pre-mRNA-splicing factor SPF27
L: Cell division cycle 5-like protein
M: Pre-mRNA-splicing factor SYF2
N: Protein BUD31 homolog
NO: Nitric oxide synthase-interacting protein
O: Pre-mRNA-splicing factor RBM22
P: Spliceosome-associated protein CWC15 homolog
Q: Intron-binding protein aquarius
R: SNW domain-containing protein 1
S: Peptidyl-prolyl cis-trans isomerase-like 1
SR: Serine/arginine repetitive matrix protein 2
T: Pleiotropic regulator 1
U: Pre-mRNA-splicing factor SLU7
V: ATP-dependent RNA helicase DHX8
W: Pre-mRNA-processing factor 17
X: Splicing regulator SDE2
Z: Coiled-coil domain-containing protein 12
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated proteins B and B'
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D2
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
h: Small nuclear ribonucleoprotein Sm D3
i: Small nuclear ribonucleoprotein-associated proteins B and B'
j: Small nuclear ribonucleoprotein Sm D1
k: Small nuclear ribonucleoprotein Sm D2
l: Small nuclear ribonucleoprotein E
m: Small nuclear ribonucleoprotein F
n: Small nuclear ribonucleoprotein G
o: U2 small nuclear ribonucleoprotein A'
p: U2 small nuclear ribonucleoprotein B''
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
w: Peptidylprolyl isomerase domain and WD repeat-containing protein 1
x: Splicing factor C9orf78
y: Peptidyl-prolyl cis-trans isomerase E
z: NF-kappa-B-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,373,39679
Polymers3,371,12863
Non-polymers2,26816
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

+
Protein , 24 types, 25 molecules 1325056789ACJLNNOPQRSRTVXZbiwz

#1: Protein PRKR-interacting protein 1


Mass: 21040.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H875
#4: Protein Protein FAM32A / Ovarian tumor-associated gene 12 / OTAG-12


Mass: 13213.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y421
#6: Protein Protein FAM50A / Protein HXC-26 / Protein XAP-5


Mass: 40319.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14320
#7: Protein STING ER exit protein / STEEP


Mass: 25669.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H5V9
#9: Protein Eukaryotic initiation factor 4A-III / eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box ...eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Eukaryotic translation initiation factor 4A isoform 3 / Nuclear matrix protein 265 / hNMP 265


Mass: 46930.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P38919, RNA helicase
#10: Protein RNA-binding protein 8A / Binder of OVCA1-1 / BOV-1 / RNA-binding motif protein 8A / RNA-binding protein Y14 / Ribonucleoprotein RBM8A


Mass: 19925.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5S9
#11: Protein Protein mago nashi homolog


Mass: 17189.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61326
#12: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#14: Protein 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP- ...Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#22: Protein Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#24: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#26: Protein Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#27: Protein Nitric oxide synthase-interacting protein / E3 ubiquitin-protein ligase NOSIP / RING-type E3 ubiquitin transferase NOSIP / eNOS-interacting protein


Mass: 33224.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9Y314, RING-type E3 ubiquitin transferase
#29: Protein Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#30: Protein Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 171502.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60306, RNA helicase
#31: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61770.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#33: Protein Serine/arginine repetitive matrix protein 2 / 300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix ...300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related nuclear matrix protein of 300 kDa / Splicing coactivator subunit SRm300 / Tax-responsive enhancer element-binding protein 803 / TaxREB803


Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#34: Protein Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#36: Protein ATP-dependent RNA helicase DHX8 / DEAH box protein 8 / RNA helicase HRH1


Mass: 139522.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14562, RNA helicase
#38: Protein Splicing regulator SDE2 / Replication stress response regulator SDE2


Mass: 49818.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6IQ49
#39: Protein Coiled-coil domain-containing protein 12


Mass: 19223.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUD4
#41: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#50: Protein Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / Spliceosome-associated cyclophilin


Mass: 73679.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP3, peptidylprolyl isomerase
#53: Protein NF-kappa-B-activating protein


Mass: 47252.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N5F7

+
RNA chain , 5 types, 5 molecules 256EXIN

#2: RNA chain U2 snRNA


Mass: 59825.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#5: RNA chain U5 snRNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#8: RNA chain U6 snRNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#17: RNA chain Exon


Mass: 4437.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 2
#21: RNA chain INTRON


Mass: 27772.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 2

+
Splicing factor ... , 3 types, 3 molecules 3Fx

#3: Protein Splicing factor ESS-2 homolog / DiGeorge syndrome critical region 13 / DiGeorge syndrome critical region 14 / DiGeorge syndrome ...DiGeorge syndrome critical region 13 / DiGeorge syndrome critical region 14 / DiGeorge syndrome protein H / DGS-H / Protein ES2


Mass: 52639.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DF8
#18: Protein Splicing factor Cactin / Renal carcinoma antigen NY-REN-24


Mass: 88860.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUQ7
#51: Protein Splicing factor C9orf78 / Hepatocellular carcinoma-associated antigen 59


Mass: 33751.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZ63

+
U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules BE

#13: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#16: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein ...U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

+
Pre-mRNA-splicing factor ... , 7 types, 7 molecules DHIKMOU

#15: Protein Pre-mRNA-splicing factor ISY1 homolog


Mass: 33046.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULR0
#19: Protein Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8
#20: Protein Pre-mRNA-splicing factor SYF1 / Protein HCNP / XPA-binding protein 2


Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#23: Protein Pre-mRNA-splicing factor SPF27 / Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome- ...Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome-associated protein SPF 27


Mass: 26163.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75934
#25: Protein Pre-mRNA-splicing factor SYF2 / CCNDBP1-interactor / p29


Mass: 28780.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95926
#28: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#35: Protein Pre-mRNA-splicing factor SLU7 / hSlu7


Mass: 68510.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95391

+
Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Sy

#32: Protein Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#52: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 33475.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNP9, peptidylprolyl isomerase

+
Pre-mRNA-processing factor ... , 2 types, 5 molecules Wqrst

#37: Protein Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#49: Protein
Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 ...Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 / Senescence evasion factor


Mass: 55245.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase

+
Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkelfmgn

#40: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#42: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#43: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#44: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#45: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#46: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

+
U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op

#47: Protein U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#48: Protein U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579

+
Non-polymers , 6 types, 16 molecules

#54: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#55: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#56: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#57: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#58: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#59: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6

+
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human post-catalytic spliceosome (P-complex)COMPLEX#1-#530MULTIPLE SOURCES
2Human spliceosomeCOMPLEX#1-#16, #18-#20, #22-#35, #37-#531NATURAL
3ATP-dependent RNA helicase DHX8COMPLEX#361RECOMBINANT
4MINX pre-mRNACOMPLEX#17, #211RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Human adenovirus 210515
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
23Saccharomyces cerevisiae (brewer's yeast)4932
34synthetic construct (others)32630
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103860 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more