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- EMDB-13046: Cryo-EM structure of Brr2 in complex with Jab1/MPN and C9ORF78 -

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Basic information

Entry
Database: EMDB / ID: EMD-13046
TitleCryo-EM structure of Brr2 in complex with Jab1/MPN and C9ORF78
Map data
Sample
  • Complex: Trimeric complex of Brr2, the Jab1/MPN domain of Prp8 and a N-terminal fragment of C9ORF78
    • Complex: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2)
      • Protein or peptide: U5 small nuclear ribonucleoprotein 200 kDa helicase
    • Complex: Telomere length and silencing protein 1 homolog (C9ORF78)
      • Protein or peptide: Telomere length and silencing protein 1 homolog
    • Complex: Pre-mRNA-processing-splicing factor 8 (Prp8) Jab1/MPN Domain
      • Protein or peptide: Pre-mRNA-processing-splicing factor 8
Function / homology
Function and homology information


regulation of homologous chromosome segregation / cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway ...regulation of homologous chromosome segregation / cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / chromosome, centromeric region / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / chromosome segregation / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / RNA helicase activity / RNA helicase / nuclear speck / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
Telomere length and silencing protein 1 / Hepatocellular carcinoma-associated antigen 59 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease ...Telomere length and silencing protein 1 / Hepatocellular carcinoma-associated antigen 59 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / 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 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing-splicing factor 8 / Splicing factor C9orf78
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsBergfort A / Hilal T / Weber G / Wahl MC
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)TRR186-A15 Germany
Citation
Journal: Nucleic Acids Res / Year: 2022
Title: The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling.
Authors: Alexandra Bergfort / Tarek Hilal / Benno Kuropka / İbrahim Avşar Ilik / Gert Weber / Tuğçe Aktaş / Christian Freund / Markus C Wahl /
Abstract: Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. ...Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. The intrinsically disordered TSSC4 protein has been identified as a nuclear-localized U5 snRNP and U4/U6-U5 tri-snRNP assembly/recycling factor, but how TSSC4's intrinsic disorder supports TSSC4 functions remains unknown. Using diverse interaction assays and cryogenic electron microscopy-based structural analysis, we show that TSSC4 employs four conserved, non-contiguous regions to bind the PRPF8 Jab1/MPN domain and the SNRNP200 helicase at functionally important sites. It thereby inhibits SNRNP200 helicase activity, spatially aligns the proteins, coordinates formation of a U5 sub-module and transiently blocks premature interaction of SNRNP200 with at least three other spliceosomal factors. Guided by the structure, we designed a TSSC4 variant that lacks stable binding to the PRPF8 Jab1/MPN domain or SNRNP200 in vitro. Comparative immunoprecipitation/mass spectrometry from HEK293 nuclear extract revealed distinct interaction profiles of wild type TSSC4 and the variant deficient in PRPF8/SNRNP200 binding with snRNP proteins, other spliceosomal proteins as well as snRNP assembly/recycling factors and chaperones. Our findings elucidate molecular strategies employed by an intrinsically disordered protein to promote snRNP assembly, and suggest multiple TSSC4-dependent stages during snRNP assembly/recycling.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Liebschner D / Afonine PV / Baker ML / Bunkoczi G / Chen VB / Croll TI / Hintze B / Hung LW / Jain S / McCoy AJ / Moriarty NW / Oeffner RD / Poon BK / Prisant MG / Read RJ / Richardson JS / ...Authors: Liebschner D / Afonine PV / Baker ML / Bunkoczi G / Chen VB / Croll TI / Hintze B / Hung LW / Jain S / McCoy AJ / Moriarty NW / Oeffner RD / Poon BK / Prisant MG / Read RJ / Richardson JS / Richardson DC / Sammito MD / Sobolev OV / Stockwell DH / Terwilliger TC / Urzhumtsev AG / Videau LL / Williams CJ / Adams PD
History
DepositionJun 7, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.2
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  • Surface view with fitted model
  • Atomic models: PDB-7os2
  • Surface level: 0.2
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13046.png

Downloads & links

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Map

FileDownload / File: emd_13046.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.657 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.0 - 1.4427326
Average (Standard dev.)0.005394726 (±0.04373509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 252.288 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6570.6570.657
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z252.288252.288252.288
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0001.4430.005

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Supplemental data

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Sample components

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Entire : Trimeric complex of Brr2, the Jab1/MPN domain of Prp8 and a N-ter...

EntireName: Trimeric complex of Brr2, the Jab1/MPN domain of Prp8 and a N-terminal fragment of C9ORF78
Components
  • Complex: Trimeric complex of Brr2, the Jab1/MPN domain of Prp8 and a N-terminal fragment of C9ORF78
    • Complex: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2)
      • Protein or peptide: U5 small nuclear ribonucleoprotein 200 kDa helicase
    • Complex: Telomere length and silencing protein 1 homolog (C9ORF78)
      • Protein or peptide: Telomere length and silencing protein 1 homolog
    • Complex: Pre-mRNA-processing-splicing factor 8 (Prp8) Jab1/MPN Domain
      • Protein or peptide: Pre-mRNA-processing-splicing factor 8

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Supramolecule #1: Trimeric complex of Brr2, the Jab1/MPN domain of Prp8 and a N-ter...

SupramoleculeName: Trimeric complex of Brr2, the Jab1/MPN domain of Prp8 and a N-terminal fragment of C9ORF78
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #2: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2)

SupramoleculeName: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: Telomere length and silencing protein 1 homolog (C9ORF78)

SupramoleculeName: Telomere length and silencing protein 1 homolog (C9ORF78)
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: Pre-mRNA-processing-splicing factor 8 (Prp8) Jab1/MPN Domain

SupramoleculeName: Pre-mRNA-processing-splicing factor 8 (Prp8) Jab1/MPN Domain
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: U5 small nuclear ribonucleoprotein 200 kDa helicase

MacromoleculeName: U5 small nuclear ribonucleoprotein 200 kDa helicase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 198.785797 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAEFDLDQGG EALAPRQVLD LEDLVFTQGS HFMANKRCQL PDGSFRRQRK GYEEVHVPAL KPKPFGSEEQ LLPVEKLPKY AQAGFEGFK TLNRIQSKLY RAALETDENL LLCAPTGAGK TNVALMCMLR EIGKHINMDG TINVDDFKII YIAPMRSLVQ E MVGSFGKR ...String:
GAEFDLDQGG EALAPRQVLD LEDLVFTQGS HFMANKRCQL PDGSFRRQRK GYEEVHVPAL KPKPFGSEEQ LLPVEKLPKY AQAGFEGFK TLNRIQSKLY RAALETDENL LLCAPTGAGK TNVALMCMLR EIGKHINMDG TINVDDFKII YIAPMRSLVQ E MVGSFGKR LATYGITVAE LTGDHQLCKE EISATQIIVC TPEKWDIITR KGGERTYTQL VRLIILDEIH LLHDDRGPVL EA LVARAIR NIEMTQEDVR LIGLSATLPN YEDVATFLRV DPAKGLFYFD NSFRPVPLEQ TYVGITEKKA IKRFQIMNEI VYE KIMEHA GKNQVLVFVH SRKETGKTAR AIRDMCLEKD TLGLFLREGS ASTEVLRTEA EQCKNLELKD LLPYGFAIHH AGMT RVDRT LVEDLFADKH IQVLVSTATL AWGVNLPAHT VIIKGTQVYS PEKGRWTELG ALDILQMLGR AGRPQYDTKG EGILI TSHG ELQYYLSLLN QQLPIESQMV SKLPDMLNAE IVLGNVQNAK DAVNWLGYAY LYIRMLRSPT LYGISHDDLK GDPLLD QRR LDLVHTAALM LDKNNLVKYD KKTGNFQVTE LGRIASHYYI TNDTVQTYNQ LLKPTLSEIE LFRVFSLSSE FKNITVR EE EKLELQKLLE RVPIPVKESI EEPSAKINVL LQAFISQLKL EGFALMADMV YVTQSAGRLM RAIFEIVLNR GWAQLTDK T LNLCKMIDKR MWQSMCPLRQ FRKLPEEVVK KIEKKNFPFE RLYDLNHNEI GELIRMPKMG KTIHKYVHLF PKLELSVHL QPITRSTLKV ELTITPDFQW DEKVHGSSEA FWILVEDVDS EVILHHEYFL LKAKYAQDEH LITFFVPVFE PLPPQYFIRV VSDRWLSCE TQLPVSFRHL ILPEKYPPPT ELLDLQPLPV SALRNSAFES LYQDKFPFFN PIQTQVFNTV YNSDDNVFVG A PTGSGKTI CAEFAILRML LQSSEGRCVY ITPMEALAEQ VYMDWYEKFQ DRLNKKVVLL TGETSTDLKL LGKGNIIIST PE KWDILSR RWKQRKNVQN INLFVVDEVH LIGGENGPVL EVICSRMRYI SSQIERPIRI VALSSSLSNA KDVAHWLGCS ATS TFNFHP NVRPVPLELH IQGFNISHTQ TRLLSMAKPV YHAITKHSPK KPVIVFVPSR KQTRLTAIDI LTTCAADIQR QRFL HCTEK DLIPYLEKLS DSTLKETLLN GVGYLHEGLS PMERRLVEQL FSSGAIQVVV ASRSLCWGMN VAAHLVIIMD TQYYN GKIH AYVDYPIYDV LQMVGHANRP LQDDEGRCVI MCQGSKKDFF KKFLYEPLPV ESHLDHCMHD HFNAEIVTKT IENKQD AVD YLTWTFLYRR MTQNPNYYNL QGISHRHLSD HLSELVEQTL SDLEQSKCIS IEDEMDVAPL NLGMIAAYYY INYTTIE LF SMSLNAKTKV RGLIEIISNA AEYENIPIRH HEDNLLRQLA QKVPHKLNNP KFNDPHVKTN LLLQAHLSRM QLSAELQS D TEEILSKAIR LIQACVDVLS SNGWLSPALA AMELAQMVTQ AMWSKDSYLK QLPHFTSEHI KRCTDKGVES VFDIMEMED EERNALLQLT DSQIADVARF CNRYPNIELS YEVVDKDSIR SGGPVVVLVQ LEREEEVTGP VIAPLFPQKR EEGWWVVIGD AKSNSLISI KRLTLQQKAK VKLDFVAPAT GAHNYTLYFM SDAYMGCDQE YKFSVDVKEA

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Macromolecule #2: Telomere length and silencing protein 1 homolog

MacromoleculeName: Telomere length and silencing protein 1 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.081516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMAMPVVRK IFRRRRGDSE SEEDEQDSEE VRLKLEETRE VQNLRKRPNG VSAVALLVGE KVQEETTLVD DPFQMKTGGM VDMKKLKER GKDKISEEED LHLGTSFSAE TNRRDEDADM MKYIETELKK RKGIVEHEEQ KVKPKNAEDC LYELPENIRV S SAKKTEEM ...String:
GAMAMPVVRK IFRRRRGDSE SEEDEQDSEE VRLKLEETRE VQNLRKRPNG VSAVALLVGE KVQEETTLVD DPFQMKTGGM VDMKKLKER GKDKISEEED LHLGTSFSAE TNRRDEDADM MKYIETELKK RKGIVEHEEQ KVKPKNAEDC LYELPENIRV S SAKKTEEM LSNQMLSGIP EVDLGIDAKI KNIISTEDAK ARLLAEQQNK KKDSETSFVP TNMAVNYVQH NRFYHEELNA PI RRNKEEP KARPLRVGDT EKPEPERSPP NRKRPANEKA TDDYHYEKFK KMNRRY

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Macromolecule #3: Pre-mRNA-processing-splicing factor 8

MacromoleculeName: Pre-mRNA-processing-splicing factor 8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.860984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMTQTF SSKTEWRVRA ISAANLHLRT NHIYVSSDDI KETGYTYILP KNVLKKFICI SDLRAQIAGY LYGVSPPDNP QVKEIRCIV MVPQWGTHQT VHLPGQLPQH EYLKEMEPLG WIHTQPNESP QLSPQDVTTH AKIMADNPSW DGEKTIIITC S FTPGSCTL ...String:
GPLGSMTQTF SSKTEWRVRA ISAANLHLRT NHIYVSSDDI KETGYTYILP KNVLKKFICI SDLRAQIAGY LYGVSPPDNP QVKEIRCIV MVPQWGTHQT VHLPGQLPQH EYLKEMEPLG WIHTQPNESP QLSPQDVTTH AKIMADNPSW DGEKTIIITC S FTPGSCTL TAYKLTPSGY EWGRQNTDKG NNPKGYLPSH YERVQMLLSD RFLGFFMVPA QSSWNYNFMG VRHDPNMKYE LQ LANPKEF YHEVHRPSHF LNFALLQEGE VYSADREDLY A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5160 / Average exposure time: 40.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 936716
CTF correctionSoftware - Name: cryoSPARC (ver. 3.1)
Startup modelType of model: OTHER
Details: The structure of Brr2HR in complex with Jab1/MPN (PDB ID 4KIT) was placed in the final cryoEM map of the BRR2HR-Jab1/MPN-C9ORF78 complex employing PHENIX Dock in Map. C9ORF78 was built in ...Details: The structure of Brr2HR in complex with Jab1/MPN (PDB ID 4KIT) was placed in the final cryoEM map of the BRR2HR-Jab1/MPN-C9ORF78 complex employing PHENIX Dock in Map. C9ORF78 was built in the remaining electron density with COOT and the coordinates were refined with PHENIX REAL SPACE REFINE.
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 370493
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4kit

chain_id: B

4kit

chain_id: C
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 102 / Target criteria: CC, R.m.s.d. Bonds / Angles
Output model

PDB-7os2:
Cryo-EM structure of Brr2 in complex with Jab1/MPN and C9ORF78

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