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- EMDB-54564: Cryo-EM structure of lncRNA CONCR (nucleotides 419-718) -

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Basic information

Entry
Database: EMDB / ID: EMD-54564
TitleCryo-EM structure of lncRNA CONCR (nucleotides 419-718)
Map dataCryo-EM map of lncRNA CONCR (nt 419-718) (Refine3D)
Sample
  • Complex: CONCR (nt 419-718)
    • RNA: CONCR (nt 419-718)
KeywordslncRNA / CONCR / DDX11 / DNA replication / sister chromatid cohesion / REPLICATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsLopez-Perrote A / Llorca O / Boskovic J / Le Coq J
Funding support Spain, 1 items
OrganizationGrant numberCountry
La Caixa FoundationLCF/PR/HR21/00176 Spain
CitationJournal: Mol Cell / Year: 2026
Title: CONCR lncRNA organizes a 3'-end structural domain that engages DDX11 for DNA replication and sister chromatid cohesion.
Authors: Andrés López-Perrote / Eva María Martín-Cuevas / José Antonio Mérida-Cerro / Clara Aicart-Ramos / Ana González-Corpas / Jovanna González / Johanne Le Coq / Jasminka Boskovic / Isabel ...Authors: Andrés López-Perrote / Eva María Martín-Cuevas / José Antonio Mérida-Cerro / Clara Aicart-Ramos / Ana González-Corpas / Jovanna González / Johanne Le Coq / Jasminka Boskovic / Isabel Chillón / Oscar Llorca / Fernando Moreno-Herrero / Maite Huarte /
Abstract: CONCR (DDX11-AS1) is a long noncoding RNA (lncRNA) necessary for the establishment of sister chromatid cohesion. Despite its activity, whether it contains structural elements essential for its ...CONCR (DDX11-AS1) is a long noncoding RNA (lncRNA) necessary for the establishment of sister chromatid cohesion. Despite its activity, whether it contains structural elements essential for its function remains unknown. We determined CONCR structural organization and its functional relevance by integrating selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), atomic force microscopy (AFM), evolutionary analyses, cryo-electron microscopy (cryo-EM), and cellular genetic studies. We found that CONCR molecular topology is modular, with highly structured domains connected by flexible linkers. A large 3'-end domain is responsible for binding to DDX11 helicase, can trigger DDX11 ATPase activity, and is essential for proper DNA replication and sister chromatid cohesion. This 3' end comprises two helical arms connecting two multiway junctions with structural motifs conserved among all primate groups and required for DDX11 binding and sister chromatid cohesion. Our results highlight the critical role of RNA structure in CONCR function, with a highly structured 3'-end domain acting as a loading and activation platform for DDX11 helicase.
History
DepositionJul 28, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54564.png

Downloads & links

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Map

FileDownload / File: emd_54564.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of lncRNA CONCR (nt 419-718) (Refine3D)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.48 Å		0.84 Å/pix.
x 320 pix.
= 268.48 Å		0.84 Å/pix.
x 320 pix.
= 268.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.006182722 - 0.054088585
Average (Standard dev.)0.0000537633 (±0.0007792701)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened cryo-EM map of lncRNA CONCR (nt 419-718) (Postprocessing)

Fileemd_54564_additional_1.map
AnnotationSharpened cryo-EM map of lncRNA CONCR (nt 419-718) (Postprocessing)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (1) of lncRNA CONCR (nt 419-718) (Refine3D)

Fileemd_54564_half_map_1.map
AnnotationHalf map (1) of lncRNA CONCR (nt 419-718) (Refine3D)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (2) of lncRNA CONCR (nt 419-718) (Refine3D)

Fileemd_54564_half_map_2.map
AnnotationHalf map (2) of lncRNA CONCR (nt 419-718) (Refine3D)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CONCR (nt 419-718)

EntireName: CONCR (nt 419-718)
Components
  • Complex: CONCR (nt 419-718)
    • RNA: CONCR (nt 419-718)

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Supramolecule #1: CONCR (nt 419-718)

SupramoleculeName: CONCR (nt 419-718) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Domain D4 of CONCR lncRNA (nucleotides 419-718)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 970 KDa

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Macromolecule #1: CONCR (nt 419-718)

MacromoleculeName: CONCR (nt 419-718) / type: rna / ID: 1
Details: In vitro transcribed domain 4 (D4) of CONCR lncRNA (nucleotides 419-718)
Source (natural)Organism: Homo sapiens (human)
SequenceString: GGUGUUCCUG GCCCGUGCCG GGCACGACCU UGCAGAGAGC CCAGAAGAUG AAACCCCAGC CUUGCCAGGA GCUCACCUGC UAAUUAGGAG GACAACGAAU CACCUCACCU CCCUAGACUU UGCUUCUCCU UUAUUCAGUG AGGGAUUGGA CUAGCUGGUC CUUGAGGACU ...String:
GGUGUUCCUG GCCCGUGCCG GGCACGACCU UGCAGAGAGC CCAGAAGAUG AAACCCCAGC CUUGCCAGGA GCUCACCUGC UAAUUAGGAG GACAACGAAU CACCUCACCU CCCUAGACUU UGCUUCUCCU UUAUUCAGUG AGGGAUUGGA CUAGCUGGUC CUUGAGGACU UUUCAGAAAG UCUGGUUCUG GGAGAUGACC AAUGGGAUCA UCUUAUGCUA UGAGCUUUCC UGGAAUGACA GGUAAUGGAG AGUGAGGAGA UUUUACCUGA UAUGGUCCUG UUUGCACCAU CAGCCAGCAA CA

GENBANK: GENBANK: AK096360.1

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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

Concentration0.8 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
10.0 mMTrisTris
1.0 mMEDTAEDTA
5.0 mMMgCl2Magnesium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsIn vitro transcribed CONCR lncRNA (nucleotides 419-718) purified in TE buffer and supplemented with 5 mM MgCl2

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 98497
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationSoftware - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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