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- EMDB-21489: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 -

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Basic information

Entry
Database: EMDB / ID: EMD-21489
Titlecryo-EM structure of Sth1-Arp7-Arp9-Rtt102
Map dataCryo-EM map of Sth1-Arp7-Arp9-Rtt102 complex; unsharpened map
Sample
  • Complex: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102
    • Protein or peptide: Actin-related protein 7
    • Protein or peptide: Actin-like protein ARP9
    • Protein or peptide: Nuclear protein STH1/NPS1
    • Protein or peptide: Regulator of Ty1 transposition protein 102
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsChromatin remodeling / Nucleosome / Gene Regulation / MOTOR PROTEIN
Function / homology
Function and homology information


RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / NuA4 histone acetyltransferase complex / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / histone reader activity / meiotic cell cycle / chromosome segregation / helicase activity / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / base-excision repair / double-strand break repair / chromatin organization / DNA helicase / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily ...Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nuclear protein STH1/NPS1 / Regulator of Ty1 transposition protein 102 / Actin-like protein ARP9 / Actin-related protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLeschziner AE / Baker RW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM092895-08 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural insights into assembly and function of the RSC chromatin remodeling complex.
Authors: Richard W Baker / Janice M Reimer / Peter J Carman / Bengi Turegun / Tsutomu Arakawa / Roberto Dominguez / Andres E Leschziner /
Abstract: SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we ...SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we focused on a subcomplex of the Saccharomyces cerevisiae RSC comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9 and the ARP-binding protein Rtt102. Cryo-EM and biochemical analyses of this subcomplex shows that ARP binding induces a helical conformation in the helicase-SANT-associated (HSA) domain of Sth1. Surprisingly, the ARP module is rotated 120° relative to the full RSC about a pivot point previously identified as a regulatory hub in Sth1, suggesting that large conformational changes are part of Sth1 regulation and RSC assembly. We also show that a conserved interaction between Sth1 and the nucleosome acidic patch enhances remodeling. As some cancer-associated mutations dysregulate rather than inactivate SWI/SNF remodelers, our insights into RSC complex regulation advance a mechanistic understanding of chromatin remodeling in disease states.
History
DepositionFeb 28, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vzg
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21489.png

Downloads & links

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Map

FileDownload / File: emd_21489.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Sth1-Arp7-Arp9-Rtt102 complex; unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 240 pix.
= 278.4 Å		1.16 Å/pix.
x 240 pix.
= 278.4 Å		1.16 Å/pix.
x 240 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.015
Minimum - Maximum-0.013791972 - 0.042575225
Average (Standard dev.)-0.00000629925 (±0.0014617345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 278.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z278.400278.400278.400
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0140.043-0.000

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Supplemental data

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Additional map: Cryo-EM map of Sth1-Arp7-Arp9-Rtt102 complex; sharpened map

Fileemd_21489_additional_1.map
AnnotationCryo-EM map of Sth1-Arp7-Arp9-Rtt102 complex; sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of Sth1-Arp7-Arp9-Rtt102 complex; half map 1

Fileemd_21489_half_map_1.map
AnnotationCryo-EM map of Sth1-Arp7-Arp9-Rtt102 complex; half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of Sth1-Arp7-Arp9-Rtt102 complex; half map 2

Fileemd_21489_half_map_2.map
AnnotationCryo-EM map of Sth1-Arp7-Arp9-Rtt102 complex; half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cryo-EM structure of Sth1-Arp7-Arp9-Rtt102

EntireName: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102
Components
  • Complex: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102
    • Protein or peptide: Actin-related protein 7
    • Protein or peptide: Actin-like protein ARP9
    • Protein or peptide: Nuclear protein STH1/NPS1
    • Protein or peptide: Regulator of Ty1 transposition protein 102
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102

SupramoleculeName: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Actin-related protein 7

MacromoleculeName: Actin-related protein 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 53.863016 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTLNRKCVVI HNGSHRTVAG FSNVELPQCI IPSSYIKRTD EGGEAEFIFG TYNMIDAAAE KRNGDEVYTL VDSQGLPYNW DALEMQWRY LYDTQLKVSP EELPLVITMP ATNGKPDMAI LERYYELAFD KLNVPVFQIV IEPLAIALSM GKSSAFVIDI G ASGCNVTP ...String:
MTLNRKCVVI HNGSHRTVAG FSNVELPQCI IPSSYIKRTD EGGEAEFIFG TYNMIDAAAE KRNGDEVYTL VDSQGLPYNW DALEMQWRY LYDTQLKVSP EELPLVITMP ATNGKPDMAI LERYYELAFD KLNVPVFQIV IEPLAIALSM GKSSAFVIDI G ASGCNVTP IIDGIVVKNA VVRSKFGGDF LDFQVHERLA PLIKEENDME NMADEQKRST DVWYEASTWI QQFKSTMLQV SE KDLFELE RYYKEQADIY AKQQEQLKQM DQQLQYTALT GSPNNPLVQK KNFLFKPLNK TLTLDLKECY QFAEYLFKPQ LIS DKFSPE DGLGPLMAKS VKKAGASINS MKANTSTNPN GLGTSHINTN VGDNNSTASS SNISPEQVYS LLLTNVIITG STSL IEGME QRIIKELSIR FPQYKLTTFA NQVMMDRKIQ GWLGALTMAN LPSWSLGKWY SKEDYETLKR DRKQSQATNA TN

UniProtKB: Actin-related protein 7

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Macromolecule #2: Actin-like protein ARP9

MacromoleculeName: Actin-like protein ARP9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 53.13193 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAPFRQDSIL IIYPRSQTTL VQFGLNEETF TVPELEIPTQ IYRTTRQDGS YTYHSTNKDN KAELIKPIQN GEIIDISAFT QFLRLIFVS ILSDRANKNQ DAFEAELSNI PLLLITHHSW SQSDLEIITQ YVFESLEINN LIQLPASLAA TYSMISLQNC C IIDVGTHH ...String:
MAPFRQDSIL IIYPRSQTTL VQFGLNEETF TVPELEIPTQ IYRTTRQDGS YTYHSTNKDN KAELIKPIQN GEIIDISAFT QFLRLIFVS ILSDRANKNQ DAFEAELSNI PLLLITHHSW SQSDLEIITQ YVFESLEINN LIQLPASLAA TYSMISLQNC C IIDVGTHH TDIIPIVDYA QLDHLVSSIP MGGQSINDSL KKLLPQWDDD QIESLKKSPI FEVLSDDAKK LSSFDFGNEN ED EDEGTLN VAEIITSGRD TREVLEERER GQKVKNVKNS DLEFNTFWDE KGNEIKVGKQ RFQGCNNLIK NISNRVGLTL DNI DDINKA KAVWENIIIV GGTTSISGFK EALLGQLLKD HLIIEPEEEK SKREEEAKSV LPAATKKKSK FMTNSTAFVP TIEY VQCPT VIKLAKYPDY FPEWKKSGYS EIIFLGAQIV SKQIFTHPKD TFYITREKYN MKGPAALWDV QF

UniProtKB: Actin-like protein ARP9

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Macromolecule #3: Nuclear protein STH1/NPS1

MacromoleculeName: Nuclear protein STH1/NPS1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 95.077289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPNSVRLA EELERQQLLE KRKKERNLHL QKINSIIDFI KERQSEQWSR QERCFQFGRL GASLHNQMEK DEQKRIEKT AKQRLAALKS NDEEAYLKLL DQTKDTRITQ LLRQTNSFLD SLSEAVRAQQ NEAKILHGEE VQPITDEERE K TDYYEVAH ...String:
MGSSHHHHHH SQDPNSVRLA EELERQQLLE KRKKERNLHL QKINSIIDFI KERQSEQWSR QERCFQFGRL GASLHNQMEK DEQKRIEKT AKQRLAALKS NDEEAYLKLL DQTKDTRITQ LLRQTNSFLD SLSEAVRAQQ NEAKILHGEE VQPITDEERE K TDYYEVAH RIKEKIDKQP SILVGGTLKE YQLRGLEWMV SLYNNHLNGI LADEMGLGKT IQSISLITYL YEVKKDIGPF LV IVPLSTI TNWTLEFEKW APSLNTIIYK GTPNQRHSLQ HQIRVGNFDV LLTTYEYIIK DKSLLSKHDW AHMIIDEGHR MKN AQSKLS FTISHYYRTR NRLILTGTPL QNNLPELWAL LNFVLPKIFN SAKTFEDWFN TPFANTGTQE KLELTEEETL LIIR RLHKV LRPFLLRRLK KEVEKDLPDK VEKVIKCKLS GLQQQLYQQM LKHNALFVGA GTEGATKGGI KGLNNKIMQL RKICN HPFV FDEVEGVVNP SRGNSDLLFR VAGKFELLDR VLPKFKASGH RVLMFFQMTQ VMDIMEDFLR MKDLKYMRLD GSTKTE ERT EMLNAFNAPD SDYFCFLLST RAGGLGLNLQ TADTVIIFDT DWNPHQDLQA QDRAHRIGQK NEVRILRLIT TDSVEEV IL ERAMQKLDID GKVIQAGKFD NKSTAEEQEA FLRRLIESET NRDDDDKAEL DDDELNDTLA RSADEKILFD KIDKERMN Q ERADAKAQGL RVPPPRLIQL DELPKVFRED IEEHFKKEDS EPLGRIRQKK RVYYDDGLTE EQFLEAVEDD NMSLEDAIK KRREARERRR LRQ

UniProtKB: Nuclear protein STH1/NPS1

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Macromolecule #4: Regulator of Ty1 transposition protein 102

MacromoleculeName: Regulator of Ty1 transposition protein 102 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.817615 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDPQTLITKA NKVSYYGNPT SKESWRYDWY QPSKVSSNVQ QPQQQLGDME NNLEKYPFRY KTWLRNQEDE KNLQRESCED ILDLKEFDR RILKKSLMTS HTKGDTSKAT GAPSANQGDE ALSVDDIRGA VGNSEAIPGL SAGVNNDNTK ESKDVKMN

UniProtKB: Regulator of Ty1 transposition protein 102

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

Concentration1 mg/mL
BufferpH: 7.5
GridPretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Details: Glow discharge for 20 seconds, 20 mAmp
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot time, blot force 20.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 7.0 sec. / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1986341
Startup modelType of model: OTHER / Details: Ab initio model generation in cryoSPARC v2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 415957
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4i6m

source_name: PDB, initial_model_type: experimental model

5tgc

source_name: PDB, initial_model_type: experimental model
DetailsInitial model docking was done in Chimera. Sth1-Arp7-Arp9-Rtt102 were refined in Rosetta and the top ten models were deposited.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6vzg:
Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102

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