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- PDB-8qr1: Cryo-EM structure of the human Tip60 complex -

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Basic information

Entry
Database: PDB / ID: 8qr1
TitleCryo-EM structure of the human Tip60 complex
Components
  • Actin, cytoplasmic 1, N-terminally processed
  • 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
KeywordsTRANSCRIPTION / Eukaryotic transcription / Histone acetyltransferase / chromatin remodeling / Complex
Function / homology
Function and homology information


ATP-dependent H2AZ histone chaperone activity / piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / histone chaperone activity / sperm DNA condensation ...ATP-dependent H2AZ histone chaperone activity / piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / histone chaperone activity / sperm DNA condensation / establishment of protein localization to chromatin / morphogenesis of a polarized epithelium / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / brahma complex / nBAF complex / protein localization to adherens junction / R2TP complex / postsynaptic actin cytoskeleton / dynein axonemal particle / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / chromatin-protein adaptor activity / Regulation of MITF-M-dependent genes involved in pigmentation / RPAP3/R2TP/prefoldin-like complex / GBAF complex / neural retina development / protein antigen binding / dense body / Swr1 complex / regulation of G0 to G1 transition / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / blastocyst formation / RHOF GTPase cycle / Adherens junctions interactions / tight junction / enzyme-substrate adaptor activity / protein folding chaperone complex / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of gene expression, epigenetic / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / regulation of chromosome organization / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / Transcriptional Regulation by E2F6 / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / somatic stem cell population maintenance / calyx of Held / negative regulation of cell differentiation / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / spermatid development / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of myoblast differentiation / regulation of DNA repair / DNA helicase activity / Deposition of new CENPA-containing nucleosomes at the centromere / EPHB-mediated forward signaling / substantia nigra development
Similarity search - Function
Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / E1A-binding protein p400, N-terminal / Vps72/YL1, N-terminal / E1A-binding protein p400, N-terminal / DNA methyltransferase 1-associated 1 / Vps72/YL1 family / DNA methyltransferase 1-associated protein 1 (DMAP1) / YL1 nuclear protein / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 ...Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / E1A-binding protein p400, N-terminal / Vps72/YL1, N-terminal / E1A-binding protein p400, N-terminal / DNA methyltransferase 1-associated 1 / Vps72/YL1 family / DNA methyltransferase 1-associated protein 1 (DMAP1) / YL1 nuclear 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 protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / Myb-like domain profile. / domain in helicases and associated with SANT domains / 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 / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / 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
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: 2.4 Å
AuthorsLi, C. / Smirnova, E. / Schnitzler, C. / Crucifix, C. / Concordet, J.P. / Brion, A. / Poterszman, A. / Schultz, P. / Papai, G. / Ben-Shem, A.
Funding support France, 1items
OrganizationGrant numberCountry
La ligue contre le cancer France
CitationJournal: Nature / Year: 2024
Title: Structure of human TIP60-C histone exchange and acetyltransferase complex
Authors: Li, C. / Smirnova, E. / Schnitzler, C. / Crucifix, C. / Concordet, J.P. / Brion, A. / Poterszman, A. / Schultz, P. / Papai, G. / Ben-Shem, A.
History
DepositionOct 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: 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
C: Enhancer of polycomb homolog 1
F: DNA methyltransferase 1-associated protein 1
S: Vacuolar protein sorting-associated protein 72 homolog
B: Actin, cytoplasmic 1, N-terminally processed
G: Actin, cytoplasmic 1, N-terminally processed
K: Actin-like protein 6A
L: RuvB-like 1
H: RuvB-like 2
I: RuvB-like 1
D: RuvB-like 2
E: RuvB-like 1
J: RuvB-like 2


Theoretical massNumber of molelcules
Total (without water)966,83913
Polymers966,83913
Non-polymers00
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 ACFSBGKLIEHDJ

#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: K562
References: UniProt: Q96L91, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: 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: K562 / References: UniProt: Q9H2F5
#3: 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: K562 / References: UniProt: Q9NPF5
#4: 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: K562 / References: UniProt: Q15906
#5: Protein Actin, cytoplasmic 1, N-terminally processed


Mass: 41782.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: P60709
#6: 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: K562 / References: UniProt: O96019
#7: 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: K562 / References: UniProt: Q9Y265, DNA helicase
#8: 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: K562 / References: UniProt: Q9Y230, DNA helicase

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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

ComponentName: Tip60 complex / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Strain: K562 / Cellular location: nucleus
Buffer solutionpH: 8
Buffer component
IDConc.FormulaBuffer-ID
120 mMHEPES1
2250 mMNaCl1
32 mMMgCl21
420 mMBiotin1
51 %Trehalose1
62 mMDTT1
70.0125 %DDM1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 279 K

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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: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1140FEI FALCON IV (4k x 4k)
2152GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
14ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 284286
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180397 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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