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- EMDB-19335: RECQL5:sfGFP hetero dimer assembled by Di-Gluebody -

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Basic information

Entry
Database: EMDB / ID: EMD-19335
TitleRECQL5:sfGFP hetero dimer assembled by Di-Gluebody
Map dataEMhancer: RECQL5:sfGFP hetero dimer complex assembled by Di-Gluebody
Sample
  • Complex: RECQL5:sfGFP heterodimer assembled by Di-Gluebody
    • Complex: Green fluorescent protein
      • Protein or peptide: Green fluorescent protein
    • Complex: Di-Gluebody
      • Protein or peptide: Gluebody GbEnhancer
      • 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 / GFP / 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 / bioluminescence / replication fork / generation of precursor metabolites and energy / 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) / 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. / Green fluorescent protein, GFP ...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. / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Green fluorescent protein / ATP-dependent DNA helicase Q5
Similarity search - Component
Biological speciesAequorea victoria (jellyfish) / Lama glama (llama) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsYi G / Ye M / Mamalis D / Fairhead M / 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_19335.png

Downloads & links

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Map

FileDownload / File: emd_19335.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMhancer: RECQL5:sfGFP hetero dimer complex assembled by Di-Gluebody
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: 0.26
Minimum - Maximum-0.0022988166 - 2.0883648
Average (Standard dev.)0.001004441 (±0.024006484)
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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Additional map: RECQL5:sfGFP hetero dimer complex assembled by Di-Gluebody

Fileemd_19335_additional_1.map
AnnotationRECQL5:sfGFP hetero dimer complex assembled by Di-Gluebody
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_19335_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_19335_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 : RECQL5:sfGFP heterodimer assembled by Di-Gluebody

EntireName: RECQL5:sfGFP heterodimer assembled by Di-Gluebody
Components
  • Complex: RECQL5:sfGFP heterodimer assembled by Di-Gluebody
    • Complex: Green fluorescent protein
      • Protein or peptide: Green fluorescent protein
    • Complex: Di-Gluebody
      • Protein or peptide: Gluebody GbEnhancer
      • 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:sfGFP heterodimer assembled by Di-Gluebody

SupramoleculeName: RECQL5:sfGFP heterodimer assembled by Di-Gluebody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: GbEnhancer and G5-006 were assembled via a disulfide to form a hetero Di-Gluebody
Molecular weightTheoretical: 103 KDa

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Supramolecule #2: Green fluorescent protein

SupramoleculeName: Green fluorescent protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Green fluorescent protein
Source (natural)Organism: Aequorea victoria (jellyfish)

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Supramolecule #3: Di-Gluebody

SupramoleculeName: Di-Gluebody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: Gluebody GbEnhancer and Gluebody G5-006
Source (natural)Organism: Lama glama (llama)

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Supramolecule #4: ATP-dependent DNA helicase Q5

SupramoleculeName: ATP-dependent DNA helicase Q5 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4 / Details: ATP-dependent DNA helicase Q5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Green fluorescent protein

MacromoleculeName: Green fluorescent protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 26.81923 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATNG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFKIR ...String:
MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATNG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFKIR HNVEDGSVQL ADHYQQNTPI GDGPVLLPDN HYLSTQSVLS KDPNEKRDHM VLLEFVTAAG ITHGMDELYK

UniProtKB: Green fluorescent protein

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Macromolecule #2: Gluebody GbEnhancer

MacromoleculeName: Gluebody GbEnhancer / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.689139 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVENGGA CVKPGGSLRL SCAASGFPVN RYSMRWYRQA PGKEREWVAG MSSAGDRSSY EDSVKGRFTI SRDDARNTVY LQMNSLKPE DTAVYYCNVN VGFEYWGQGT QVMVS

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Macromolecule #3: Gluebody G5-006

MacromoleculeName: Gluebody G5-006 / type: protein_or_peptide / ID: 3 / 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 #4: ATP-dependent DNA helicase Q5

MacromoleculeName: ATP-dependent DNA helicase Q5 / type: protein_or_peptide / ID: 4 / 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 #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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: 3.22 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: non-uniform refinement in cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7zmv

source_name: PDB, initial_model_type: experimental model

3k1k

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Overall B value: 128.5
Output model

PDB-8rl9:
RECQL5:sfGFP hetero dimer assembled by Di-Gluebody

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