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- EMDB-45476: MORC2 PD mutant with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-45476
TitleMORC2 PD mutant with DNA
Map data
Sample
  • Complex: MORC2 PD mutant with DNA
    • Protein or peptide: ATPase MORC2
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsATPase / chromatin remodeller / DNA compaction / 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: 1.95 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

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Structure visualization

Supplemental images

emd_45476.png

Downloads & links

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Map

FileDownload / File: emd_45476.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 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 EMDB: 0.22
Minimum - Maximum-2.5407228 - 5.994812
Average (Standard dev.)-0.00030692894 (±0.061211266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45476_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: #1

Fileemd_45476_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_45476_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_45476_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : MORC2 PD mutant with DNA

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

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Supramolecule #1: MORC2 PD mutant with DNA

SupramoleculeName: MORC2 PD mutant with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 236 KDa

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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: 117.9075 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 EEPVRRPQRP RSPPLPAVIR NAPSRPPSLP TPRPASQ PR KAPVISSTPK LPALAAREEA STSRLLQPPE APRKPANTLV KTASRPAPLV QQLSPSLLPN SKSPREVPSP KVIKTPVV K KTEAPIKLAP ATPSRKRAVA VADEEEVEEE AERRKERCKR GRFVVKEEKK DSNELADAAG EEDSADLKRA QKDKGLHVE VRVNREWYTG RVTAVEVGKH VVRWKVKFDY VPTDTTPRDR WVEKGSEDVR LMKPPSPEHQ SLDTQQEGGE EEVGPVAQQA IAVAEPSTS ECLRIEPDTT ALSTNHETID LLVQILRNCL RYFLPPSFPI SKKQLSAMNS DELISFPLKE YFKQYEVGLQ N LCNSYQSR ADSRAKASEE SLRTSERKLR ETEEKLQKLR TNIVALLQKV QEDIDINTDD ELDAYIEDLI TKGD

UniProtKB: ATPase MORC2

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Macromolecule #2: ZINC ION

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

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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

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Macromolecule #4: MAGNESIUM ION

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

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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

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

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 192.0 K / Max: 310.0 K
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 5494 / 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: 100.0 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

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Image processing

Particle selectionNumber selected: 2222506
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: 1.95 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: 4 / Avg.num./class: 500000
FSC plot (resolution estimation)

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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: 51.7 / Target criteria: Cross-correlation coefficient
Output model

PDB-9cdh:
MORC2 PD mutant with DNA

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