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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: To Be Published
Title: CONCR lncRNA organizes a 3'-end structural domain that binds DDX11 and is required for sister chromatid cohesion
Authors: Lopez-Perrote A / Martin-Cuevas EM / Merida-Cerro JA / Aicart-Ramos C / Gonzalez-Corpas A / Gonzalez J / Le Coq J / Boskovic J / Chillon I / Llorca O / Moreno-Herrero F / Huarte M
History
DepositionJul 28, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 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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