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- EMDB-34468: Human ATAD2 Walker B mutant, ATP state -

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Basic information

Entry
Database: EMDB / ID: EMD-34468
TitleHuman ATAD2 Walker B mutant, ATP state
Map data
Sample
  • Complex: ATAD2
    • Protein or peptide: ATPase family AAA domain-containing protein 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsHistone chaperone / AAA+ ATPase / GENE REGULATION
Function / homology
Function and homology information


nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsCho C / Song J
Funding support Korea, Republic Of, 5 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2022R1C1C2003419 Korea, Republic Of
National Research Foundation (NRF, Korea)2019R1A6A1A1007388 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A2B5B03001517 Korea, Republic Of
National Research Foundation (NRF, Korea)2020M3E5E2037170 Korea, Republic Of
National Research Foundation (NRF, Korea)2021K2A9A2A08000088 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2023
Title: Structure of the human ATAD2 AAA+ histone chaperone reveals mechanism of regulation and inter-subunit communication.
Authors: Carol Cho / Christian Ganser / Takayuki Uchihashi / Koichi Kato / Ji-Joon Song /
Abstract: ATAD2 is a non-canonical ATP-dependent histone chaperone and a major cancer target. Despite widespread efforts to design drugs targeting the ATAD2 bromodomain, little is known about the overall ...ATAD2 is a non-canonical ATP-dependent histone chaperone and a major cancer target. Despite widespread efforts to design drugs targeting the ATAD2 bromodomain, little is known about the overall structural organization and regulation of ATAD2. Here, we present the 3.1 Å cryo-EM structure of human ATAD2 in the ATP state, showing a shallow hexameric spiral that binds a peptide substrate at the central pore. The spiral conformation is locked by an N-terminal linker domain (LD) that wedges between the seam subunits, thus limiting ATP-dependent symmetry breaking of the AAA+ ring. In contrast, structures of the ATAD2-histone H3/H4 complex show the LD undocked from the seam, suggesting that H3/H4 binding unlocks the AAA+ spiral by allosterically releasing the LD. These findings, together with the discovery of an inter-subunit signaling mechanism, reveal a unique regulatory mechanism for ATAD2 and lay the foundation for developing new ATAD2 inhibitors.
History
DepositionOct 8, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34468.png

Downloads & links

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Map

FileDownload / File: emd_34468.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.07910037 - 0.17844081
Average (Standard dev.)0.0003351729 (±0.0040478064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34468_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34468_half_map_2.map
Projections & Slices
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Sample components

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Entire : ATAD2

EntireName: ATAD2
Components
  • Complex: ATAD2
    • Protein or peptide: ATPase family AAA domain-containing protein 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: ATAD2

SupramoleculeName: ATAD2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATPase family AAA domain-containing protein 2

MacromoleculeName: ATPase family AAA domain-containing protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.690406 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DRMKIGASLA DVDPMQLDSS VRFDSVGGLS NHIAALKEMV VFPLLYPEVF EKFKIQPPRG CLFYGPPGTG KTLVARALAN ECSQGDKRV AFFMRKGADC LSKWVGESER QLRLLFDQAY QMRPSIIFFD QIDGLAPVRS SRQDQIHSSI VSTLLALMDG L DSRGEIVV ...String:
DRMKIGASLA DVDPMQLDSS VRFDSVGGLS NHIAALKEMV VFPLLYPEVF EKFKIQPPRG CLFYGPPGTG KTLVARALAN ECSQGDKRV AFFMRKGADC LSKWVGESER QLRLLFDQAY QMRPSIIFFD QIDGLAPVRS SRQDQIHSSI VSTLLALMDG L DSRGEIVV IGATNRLDSI DPALRRPGRF DREFLFSLPD KEARKEILKI HTRDWNPKPL DTFLEELAEN CVGYCGADIK SI CAEAALC ALRRRYPQIY TTSEKLQLDL SSINISAKDF EVAMQKMIPA SQRAVTSPGQ ALSTVVKPLL QNTVDKILEA LQR VFPHAE FRTNKTLDSD ISCPLLESDL AYSDDDVPSV YENGLSQKSS HKAKDNFNFL HLNRNACYQP MSFRPRILIV GEPG FGQGS HLAPAVIHAL EKFTVYTLDI PVLFGVSTTS PEETCAQVIR EAKRTAPSIV YVPHIHVWWE IVGPTLKATF TTLLQ NIPS FAPVLLLATS DKPHSALPEE VQELFIRDYG EIFNVQLPDK EERTKFFEDL ILKQAAKPPI SKKKAVLQAL EVLPVA PPP EPRSLTAEEV KRLEEQEEYA PSYYHVMPKQ NSTLVGDKRS DPEQNEKLKT PSTPVACSTP AQLKRKIRKK SNWYLGT IK KRRKISQAKD DSQNAIDHKI ESDTEETQDT SVDHNETGNT GESSVEENEK QQNASESKLE LRNNSNTCNI ENELEDSR K TTACTELRDK IACNGDASSS QIIHISDENE GKEMCVLRMT QPTPSLVVDH ERLKNLLKTV VKKSQNYNIF QLENLYAVI SQCIYRHRKD HDKTSLIQKM EQEVENFSCS R

UniProtKB: ATPase family AAA domain-containing protein 2, ATPase family AAA domain-containing protein 2, ATPase family AAA domain-containing protein 2

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212925
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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