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- EMDB-19331: DNA helicase RECQL5 in complex with homo Di-Gluebody G5-006 -

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Basic information

Entry
Database: EMDB / ID: EMD-19331
TitleDNA helicase RECQL5 in complex with homo Di-Gluebody G5-006
Map dataEMhancer:RECQL5 in complex with homo Di-Gluebody G5-006
Sample
  • Complex: RECQL5 in complex with G5-006 homo Di-Gluebody
    • Complex: Di-Gluebody G5-006
      • Protein or peptide: Gluebody G5-006
    • Complex: ATP-dependent DNA helicase Q5
      • Protein or peptide: ATP-dependent DNA helicase Q5
  • Ligand: ZINC ION
KeywordsDNA helicase / Di-Gluebody / HYDROLASE
Function / homology
Function and homology information


mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / RNA polymerase II complex binding ...mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / replication fork / helicase activity / double-strand break repair via homologous recombination / cellular response to xenobiotic stimulus / mitotic cell cycle / chromosome / DNA replication / cell division / DNA repair / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent DNA helicase Q5
Similarity search - Component
Biological speciesLama glama (llama) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsYi G / Ye M / Mamalis D / Sauer DB / von Delft F / Davis BG / Gilbert RJC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Nat Chem Biol / Year: 2025
Title: Covalently constrained 'Di-Gembodies' enable parallel structure solutions by cryo-EM.
Authors: Gangshun Yi / Dimitrios Mamalis / Mingda Ye / Loic Carrique / Michael Fairhead / Huanyu Li / Katharina L Duerr / Peijun Zhang / David B Sauer / Frank von Delft / Benjamin G Davis / Robert J C Gilbert /
Abstract: Whilst cryo-electron microscopy(cryo-EM) has become a routine methodology in structural biology, obtaining high-resolution cryo-EM structures of small proteins (<100 kDa) and increasing overall throughput remain challenging. One approach to augment protein size and improve particle alignment involves the use of binding proteins or protein-based scaffolds. However, a given imaging scaffold or linking module may prove inadequate for structure solution and availability of such scaffolds remains limited. Here, we describe a strategy that exploits covalent dimerization of nanobodies to trap an engineered, predisposed nanobody-to-nanobody interface, giving Di-Gembodies as modular constructs created in homomeric and heteromeric forms. By exploiting side-chain-to-side-chain assembly, they can simultaneously display two copies of the same or two distinct proteins through a subunit interface that provides sufficient constraint required for cryo-EM structure determination. We validate this method with multiple soluble and membrane structural targets, down to 14 kDa, demonstrating a flexible and scalable platform for expanded protein structure determination.
History
DepositionJan 2, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19331.png

Downloads & links

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Map

FileDownload / File: emd_19331.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMhancer:RECQL5 in complex with homo Di-Gluebody G5-006
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 420 pix.
= 294. Å		0.7 Å/pix.
x 420 pix.
= 294. Å		0.7 Å/pix.
x 420 pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.204
Minimum - Maximum-0.0050252066 - 2.0217938
Average (Standard dev.)0.0013150914 (±0.026178556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: RECQL5 in complex with homo Di-Gluebody G5-006

Fileemd_19331_additional_1.map
AnnotationRECQL5 in complex with homo Di-Gluebody G5-006
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_19331_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_19331_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RECQL5 in complex with G5-006 homo Di-Gluebody

EntireName: RECQL5 in complex with G5-006 homo Di-Gluebody
Components
  • Complex: RECQL5 in complex with G5-006 homo Di-Gluebody
    • Complex: Di-Gluebody G5-006
      • Protein or peptide: Gluebody G5-006
    • Complex: ATP-dependent DNA helicase Q5
      • Protein or peptide: ATP-dependent DNA helicase Q5
  • Ligand: ZINC ION

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Supramolecule #1: RECQL5 in complex with G5-006 homo Di-Gluebody

SupramoleculeName: RECQL5 in complex with G5-006 homo Di-Gluebody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Two copies of Gluebody G5-006 were assembled by a disulfide to form a homo Di-Gluebody
Molecular weightTheoretical: 126 KDa

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Supramolecule #2: Di-Gluebody G5-006

SupramoleculeName: Di-Gluebody G5-006 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Gluebody G5-006
Source (natural)Organism: Lama glama (llama)

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Supramolecule #3: ATP-dependent DNA helicase Q5

SupramoleculeName: ATP-dependent DNA helicase Q5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: ATP-dependent DNA helicase Q5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gluebody G5-006

MacromoleculeName: Gluebody G5-006 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.775173 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SMAQVQLVEN GGGCVKAGGS LRLSCAASGS IFSINRMTWY RQAPGKEREW VAAITSGGST NYADSVKGRF TISRDNAENT VYLQMNSLK PEDTAVYYCE AYGTYTLAPT GEGEYDDYWG QGTQVMVS

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Macromolecule #2: ATP-dependent DNA helicase Q5

MacromoleculeName: ATP-dependent DNA helicase Q5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.20382 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PERRVRSTLK KVFGFDSFKT PLQESATMAV VKGNKDVFVC MPTGAGKSLC YQLPALLAKG ITIVVSPLIA LIQDQVDHLL TLKVRVSSL NSKLSAQERK ELLADLEREK PQTKILYITP EMAASSSFQP TLNSLVSRHL LSYLVVDEAH CVSQWGHDFR P DYLRLGAL ...String:
PERRVRSTLK KVFGFDSFKT PLQESATMAV VKGNKDVFVC MPTGAGKSLC YQLPALLAKG ITIVVSPLIA LIQDQVDHLL TLKVRVSSL NSKLSAQERK ELLADLEREK PQTKILYITP EMAASSSFQP TLNSLVSRHL LSYLVVDEAH CVSQWGHDFR P DYLRLGAL RSRLGHAPCV ALTATATPQV QEDVFAALHL KKPVAIFKTP CFRANLFYDV QFKELISDPY GNLKDFCLKA LG QEADKGL SGCGIVYCRT REACEQLAIE LSCRGVNAKA YHAGLKASER TLVQNDWMEE KVPVIVATIS FGMGVDKANV RFV AHWNIA KSMAGYYQES GRAGRDGKPS WCRLYYSRND RDQVSFLIRK EVAKLQEKRG NKASDKATIM AFDALVTFCE ELGC RHAAI AKYFGDALPA CAKGCDHCQN PTAVRRRLEA LERSSSW

UniProtKB: ATP-dependent DNA helicase Q5

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
GridModel: C-flat-2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 9247 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 610675
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Details: patch-ctf correction in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction in cryosparc
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 146540
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0) / Details: Non-uniform refinement in Cryosparc
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0) / Details: Non-uniform refinement in Cryosparc
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7zmv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Overall B value: 182.6
Output model

PDB-8rl5:
DNA helicase RECQL5 in complex with homo Di-Gluebody G5-006

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