[English] 日本語
Yorodumi
- EMDB-45478: MORC2 ATPase with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45478
TitleMORC2 ATPase with DNA
Map data
Sample
  • Complex: MORC2 ATPase with DNA
    • Protein or peptide: ATPase MORC2
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsChromatin remodeller / DNA / AMP-PNP / DNA BINDING PROTEIN
Function / homology
Function and homology information


constitutive heterochromatin formation / transposable element silencing by heterochromatin formation / Fatty acyl-CoA biosynthesis / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / heterochromatin / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / fatty acid metabolic process / nuclear matrix / chromatin remodeling / DNA damage response ...constitutive heterochromatin formation / transposable element silencing by heterochromatin formation / Fatty acyl-CoA biosynthesis / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / heterochromatin / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / fatty acid metabolic process / nuclear matrix / chromatin remodeling / DNA damage response / chromatin binding / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / ATPase MORC2, chromo domain-like / Morc, S5 domain 2-like / Morc6 ribosomal protein S5 domain 2-like / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsTan W / Shakeel S
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2026635 Australia
National Health and Medical Research Council (NHMRC, Australia)2016827 Australia
CitationJournal: Nat Commun / Year: 2025
Title: MORC2 is a phosphorylation-dependent DNA compaction machine.
Authors: Winnie Tan / Jeongveen Park / Hariprasad Venugopal / Jieqiong Lou / Prabavi Shayana Dias / Pedro L Baldoni / Kyoung-Wook Moon / Toby A Dite / Christine R Keenan / Alexandra D Gurzau / ...Authors: Winnie Tan / Jeongveen Park / Hariprasad Venugopal / Jieqiong Lou / Prabavi Shayana Dias / Pedro L Baldoni / Kyoung-Wook Moon / Toby A Dite / Christine R Keenan / Alexandra D Gurzau / Joonyoung Lee / Timothy M Johanson / Andrew Leis / Jumana Yousef / Vineet Vaibhav / Laura F Dagley / Ching-Seng Ang / Laura D Corso / Chen Davidovich / Stephin J Vervoort / Gordon K Smyth / Marnie E Blewitt / Rhys S Allan / Elizabeth Hinde / Sheena D'Arcy / Je-Kyung Ryu / Shabih Shakeel /
Abstract: The Microrchidia (MORC) family of chromatin-remodelling ATPases is pivotal in forming higher-order chromatin structures that suppress transcription. The exact mechanisms of MORC-induced chromatin ...The Microrchidia (MORC) family of chromatin-remodelling ATPases is pivotal in forming higher-order chromatin structures that suppress transcription. The exact mechanisms of MORC-induced chromatin remodelling have been elusive. Here, we report an in vitro reconstitution of full-length MORC2, the most commonly mutated MORC member, linked to various cancers and neurological disorders. MORC2 possesses multiple DNA-binding sites that undergo structural rearrangement upon DNA binding. MORC2 locks onto the DNA using its C-terminal domain (CTD) and acts as a clamp. A conserved phosphate-interacting motif within the CTD was found to regulate ATP hydrolysis and cooperative DNA binding. Importantly, MORC2 mediates chromatin remodelling via ATP hydrolysis-dependent DNA compaction in vitro, regulated by the phosphorylation state of its CTD. These findings position MORC2 CTD phosphorylation as a critical regulator of chromatin remodelling and a promising therapeutic target.
History
DepositionJun 25, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45478.png

Downloads & links

-
Map

FileDownload / File: emd_45478.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.152
Minimum - Maximum-1.7317207 - 3.1237845
Average (Standard dev.)0.00089392485 (±0.051673487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_45478_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_45478_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_45478_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_45478_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MORC2 ATPase with DNA

EntireName: MORC2 ATPase with DNA
Components
  • Complex: MORC2 ATPase with DNA
    • Protein or peptide: ATPase MORC2
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: MORC2 ATPase with DNA

SupramoleculeName: MORC2 ATPase with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 240 KDa

-
Macromolecule #1: ATPase MORC2

MacromoleculeName: ATPase MORC2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.707641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAFTNYSSLN RAQLTFEYLH TNSTTHEFLF GALAELVDNA RDADATRIDI YAERREDLRG GFMLCFLDDG AGMDPSDAAS VIQFGKSAK RTPESTQIGQ YGNGLKSGSM RIGKDFILFT KKEDTMTCLF LSRTFHEEEG IDEVIVPLPT WNARTREPVT D NVEKFAIE ...String:
MAFTNYSSLN RAQLTFEYLH TNSTTHEFLF GALAELVDNA RDADATRIDI YAERREDLRG GFMLCFLDDG AGMDPSDAAS VIQFGKSAK RTPESTQIGQ YGNGLKSGSM RIGKDFILFT KKEDTMTCLF LSRTFHEEEG IDEVIVPLPT WNARTREPVT D NVEKFAIE TELIYKYSPF RTEEEVMTQF MKIPGDSGTL VIIFNLKLMD NGEPELDIIS NPRDIQMAET SPEGTKPERR SF RAYAAVL YIDPRMRIFI HGHKVQTKRL SCCLYKPRMY KYTSSRFKTR AEQEVKKAEH VARIAEEKAR EAESKARTLE VRL GGDLTR DSRVMLRQVQ NRAITLRREA DVKKRIKEAK QRALKEPKEL NFVFGVNIEH RDLDGMFIYN CSRLIKMYEK VGPQ LEGGM ACGGVVGVVD VPYLVLEPTH NKQDFADAKE YRHLLRAMGE HLAQYWKDIA IAQRGIIKFW DEFGYLSANW NQPPS SELR YKRRRAMEIP TTIQCDLCLK WRTLPFQLSS VEKDYPDTWV CSMNPDPEQD RCEASEQKQK VPLGTFRKDM KTQEEK QKQ LTEKIRQQQE KLEALQKTTP IRSQADLKKL PLEVTTRPST

UniProtKB: ATPase MORC2

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Details: 20 mM HEPES pH 8, 60 mM KCl, 2 mM MgCl2, 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.025 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 196.0 K / Max: 310.0 K
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 6484 / Average exposure time: 1.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 10500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2727046
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 185490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 185000
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5of9


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 79.1 / Target criteria: Cross-correlation coefficient
Output model

PDB-9cdj:
MORC2 ATPase with DNA

+
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://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