[English] 日本語
Yorodumi
- EMDB-34468: Human ATAD2 Walker B mutant, ATP state -

+
Open data


ID or keywords:

Loading...

-
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


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / 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

-
Structure visualization

Supplemental images

emd_34468.png

Downloads & links

-
Map

FileDownload / File: emd_34468.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
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 °

-
Supplemental data

-
Half map: #1

Fileemd_34468_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34468_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
Supramolecule #1: ATAD2

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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more