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- EMDB-19336: RECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5 local... -

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Basic information

Entry
Database: EMDB / ID: EMD-19336
TitleRECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5 local refinement
Map dataEMhancer: RECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5 local refinement
Sample
  • Complex: Local refinement of RECQL5 part of the RECQL5:sfGFP heterodimer assembled by Di-Gluebody
    • Complex: 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 / cytoplasm / cytosol
Similarity search - Function
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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: 3.03 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: To Be Published
Title: Di-Gluebodies: Rigid modular nanobody protein assemblies enabling simultaneous determination of high-resolution cryo-EM structures
Authors: Yi G / Mamalis D / Ye M / Carrique L / Fairhead M / Li H / Duerr K / Zhang P / Sauer DB / von Delft F / Davis BG / Gilbert RJC
History
DepositionJan 2, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19336.png

Downloads & links

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Map

FileDownload / File: emd_19336.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMhancer: RECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5 local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.245
Minimum - Maximum-0.008380524 - 2.4650452
Average (Standard dev.)0.0005608658 (±0.017973075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19336_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: RECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5...

Fileemd_19336_additional_1.map
AnnotationRECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5 local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_19336_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_19336_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Local refinement of RECQL5 part of the RECQL5:sfGFP heterodimer a...

EntireName: Local refinement of RECQL5 part of the RECQL5:sfGFP heterodimer assembled by Di-Gluebody
Components
  • Complex: Local refinement of RECQL5 part of the RECQL5:sfGFP heterodimer assembled by Di-Gluebody
    • Complex: 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: Local refinement of RECQL5 part of the RECQL5:sfGFP heterodimer a...

SupramoleculeName: Local refinement of RECQL5 part of the RECQL5:sfGFP heterodimer assembled by Di-Gluebody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 103 KDa

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Supramolecule #2: Gluebody G5-006

SupramoleculeName: 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: 1 / 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: 1 / 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: 1 / 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

Concentration1.1 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: GATAN K3 (6k x 4k) / Number real images: 10102 / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: 1434365
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 359811
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: Local refinement in cryoSPARC
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: 111.1
Output model

PDB-8rla:
RECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5 local refinement

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