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- PDB-9cac: Cryo-EM structure of the RuvBL lobe of the native human TIP60 com... -

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Basic information

Entry
Database: PDB / ID: 9cac
TitleCryo-EM structure of the RuvBL lobe of the native human TIP60 complex (composite structure)
Components
  • Actin, cytoplasmic 1
  • Actin-like protein 6A
  • DNA methyltransferase 1-associated protein 1
  • E1A-binding protein p400
  • Enhancer of polycomb homolog 1
  • RuvB-like 1
  • RuvB-like 2
  • Vacuolar protein sorting-associated protein 72 homolog
KeywordsGENE REGULATION / histone acetyltransferase / chromatin regulator / transcription regulation
Function / homology
Function and homology information


piccolo histone acetyltransferase complex / RPAP3/R2TP/prefoldin-like complex / promoter-enhancer loop anchoring activity / sperm DNA condensation / telomerase RNA localization to Cajal body / npBAF complex / positive regulation of norepinephrine uptake / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / histone chaperone activity ...piccolo histone acetyltransferase complex / RPAP3/R2TP/prefoldin-like complex / promoter-enhancer loop anchoring activity / sperm DNA condensation / telomerase RNA localization to Cajal body / npBAF complex / positive regulation of norepinephrine uptake / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / histone chaperone activity / R2TP complex / dynein axonemal particle / cellular response to cytochalasin B / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / protein antigen binding / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Swr1 complex / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBP-mediated host defense / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / establishment of protein localization to chromatin / protein localization to adherens junction / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / dense body / Tat protein binding / Folding of actin by CCT/TriC / Ino80 complex / postsynaptic actin cytoskeleton / Regulation of CDH1 Function / apical protein localization / Adherens junctions interactions / microtubule nucleation / Prefoldin mediated transfer of substrate to CCT/TriC / SWI/SNF complex / RHOF GTPase cycle / adherens junction assembly / regulation of double-strand break repair / box C/D snoRNP assembly / chromatin-protein adaptor activity / Sensory processing of sound by outer hair cells of the cochlea / tight junction / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / spermatid development / spinal cord development / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / positive regulation of T cell differentiation / maintenance of blood-brain barrier / Interaction between L1 and Ankyrins / apical junction complex / regulation of nucleotide-excision repair / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / Transcriptional Regulation by E2F6 / transporter regulator activity / Recycling pathway of L1 / positive regulation of double-strand break repair / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / MLL1 complex / negative regulation of cell differentiation / establishment or maintenance of cell polarity / regulation of DNA replication / TFIID-class transcription factor complex binding / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / brush border / EPH-ephrin mediated repulsion of cells / protein folding chaperone complex / Telomere Extension By Telomerase / regulation of synaptic vesicle endocytosis / enzyme-substrate adaptor activity / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / kinesin binding / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / axonogenesis / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / replication fork / regulation of embryonic development / Deposition of new CENPA-containing nucleosomes at the centromere / telomere maintenance
Similarity search - Function
Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / Enhancer of polycomb protein / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 ...Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / Enhancer of polycomb protein / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Vps72/YL1, N-terminal / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / Myb-like domain profile. / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT/Myb domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Actin-like protein 6A / Actin, cytoplasmic 1 / Vacuolar protein sorting-associated protein 72 homolog / E1A-binding protein p400 / Enhancer of polycomb homolog 1 / DNA methyltransferase 1-associated protein 1 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsLouder, R.K. / Park, G. / Patel, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60
Authors: Park, G. / Patel, A.B. / Wu, C. / Louder, R.K.
History
DepositionJun 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E1A-binding protein p400
B: Vacuolar protein sorting-associated protein 72 homolog
C: Enhancer of polycomb homolog 1
E: RuvB-like 1
F: RuvB-like 2
G: RuvB-like 1
H: RuvB-like 2
I: RuvB-like 1
J: RuvB-like 2
K: Actin, cytoplasmic 1
L: Actin, cytoplasmic 1
M: Actin-like protein 6A
N: DNA methyltransferase 1-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)970,53129
Polymers966,83913
Non-polymers3,69216
Water00
1


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

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Components

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Protein , 8 types, 13 molecules ABCEGIFHJKLMN

#1: Protein E1A-binding protein p400 / CAG repeat protein 32 / Domino homolog / hDomino / Trinucleotide repeat-containing gene 12 protein ...CAG repeat protein 32 / Domino homolog / hDomino / Trinucleotide repeat-containing gene 12 protein / p400 kDa SWI2/SNF2-related protein


Mass: 343867.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW
References: UniProt: Q96L91, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Vacuolar protein sorting-associated protein 72 homolog / Protein YL-1 / Transcription factor-like 1


Mass: 40658.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: Q15906
#3: Protein Enhancer of polycomb homolog 1


Mass: 93589.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONEMARROW / References: UniProt: Q9H2F5
#4: Protein RuvB-like 1 / 49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa ...49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa erythrocyte cytosolic protein / ECP-54 / INO80 complex subunit H / Nuclear matrix protein 238 / NMP 238 / Pontin 52 / TIP49a / TIP60-associated protein 54-alpha / TAP54-alpha


Mass: 50296.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: Q9Y265, DNA helicase
#5: Protein RuvB-like 2 / 48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa ...48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa erythrocyte cytosolic protein / ECP-51 / INO80 complex subunit J / Repressing pontin 52 / Reptin 52 / TIP49b / TIP60-associated protein 54-beta / TAP54-beta


Mass: 51222.465 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: Q9Y230, DNA helicase
#6: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: P60709
#7: Protein Actin-like protein 6A / 53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor ...53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A / INO80 complex subunit K


Mass: 47509.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: O96019
#8: Protein DNA methyltransferase 1-associated protein 1 / DNMAP1 / DNMT1-associated protein 1


Mass: 53090.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: Q9NPF5

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Non-polymers , 3 types, 16 molecules

#9: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#11: 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

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1TIP60 complexCOMPLEX#1-#80NATURAL
2RuvBL lobe of the TIP60 complexCOMPLEX#1-#81NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.8 MDaNO
22
Source (natural)

Cellular location: NUCLEOPLASM / Ncbi tax-ID: 9606 / Organ: BLOOD / Organelle: NUCLEUS / Organism: Homo sapiens (human) / Strain: K-562 / Tissue: BONE MARROW

IDEntity assembly-ID
21
32
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61163 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 96.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002641572
ELECTRON MICROSCOPYf_angle_d0.533756164
ELECTRON MICROSCOPYf_chiral_restr0.04166364
ELECTRON MICROSCOPYf_plane_restr0.00767187
ELECTRON MICROSCOPYf_dihedral_angle_d12.772615887

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