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- PDB-7zmo: Crystal structure of human RECQL5 helicase APO form in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7zmo
TitleCrystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-052
Components
  • ATP-dependent DNA helicase Q5
  • Gluebody G3-052
KeywordsHYDROLASE / Helicase / Apo form / Nanobody complex
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 nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase Q5
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsYe, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Aitkenhead, H. / Bountra, C. / Gileadi, O. / von Delft, F.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: To Be Published
Title: Gluebodies improve crystal reliability and diversity through transferable nanobody mutations that introduce constitutive crystal contacts
Authors: Ye, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Wright, N.D. / Koekemoer, L. / Thompson, A. / Bezerra, G.A. / Yi, G. / Li, H. / Rangel, V.L. / Mamalis, D. / ...Authors: Ye, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Wright, N.D. / Koekemoer, L. / Thompson, A. / Bezerra, G.A. / Yi, G. / Li, H. / Rangel, V.L. / Mamalis, D. / Aitkenhead, H. / Gilbert, R.J.C. / Duerr, K. / Davis, B.G. / Bountra, C. / Gileadi, O. / von Delft, F.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase Q5
B: ATP-dependent DNA helicase Q5
K: Gluebody G3-052
C: Gluebody G3-052
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7878
Polymers126,4644
Non-polymers3234
Water724
1
A: ATP-dependent DNA helicase Q5
K: Gluebody G3-052
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3944
Polymers63,2322
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-23 kcal/mol
Surface area25730 Å2
MethodPISA
2
B: ATP-dependent DNA helicase Q5
C: Gluebody G3-052
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3944
Polymers63,2322
Non-polymers1612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-25 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.517, 150.870, 269.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32K
42C

NCS domain segments:

Component-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA12 - 4524 - 444
21PROPROBB12 - 4524 - 444
32GLNGLNKC1 - 1244 - 127
42GLNGLNCD1 - 1244 - 127

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

#1: Protein ATP-dependent DNA helicase Q5 / DNA helicase / RecQ-like type 5 / RecQ5 / RecQ protein-like 5


Mass: 49537.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL5, RECQ5 / Production host: Escherichia coli (E. coli) / References: UniProt: O94762, DNA helicase
#2: Antibody Gluebody G3-052


Mass: 13695.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.25 Å3/Da / Density % sol: 80.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M ammonium sulfate -- 0.5% PEG8000 -- 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 3.03→100.67 Å / Num. obs: 71635 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 1 / Net I/σ(I): 2.5
Reflection shellResolution: 3.03→3.08 Å / Num. unique obs: 3558 / CC1/2: 0.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LB5

5lb5


Resolution: 3.75→100.67 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.901 / SU B: 45.453 / SU ML: 0.589 / Cross valid method: FREE R-VALUE / ESU R: 2.298 / ESU R Free: 0.569
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3063 1891 4.949 %
Rwork0.2832 36322 -
all0.284 --
obs-38213 99.854 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 127.165 Å2
Baniso -1Baniso -2Baniso -3
1-1.068 Å20 Å2-0 Å2
2---1.935 Å20 Å2
3---0.867 Å2
Refinement stepCycle: LAST / Resolution: 3.75→100.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8550 0 10 4 8564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138789
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178110
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.64111949
X-RAY DIFFRACTIONr_angle_other_deg1.3651.57718642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.79351148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.89721.606442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.588151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2151563
X-RAY DIFFRACTIONr_chiral_restr0.0720.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210169
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022073
X-RAY DIFFRACTIONr_nbd_refined0.2320.21982
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.27636
X-RAY DIFFRACTIONr_nbtor_refined0.170.24176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2174
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1750.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3890.225
X-RAY DIFFRACTIONr_nbd_other0.4050.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4840.22
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_mcbond_it13.31813.3414547
X-RAY DIFFRACTIONr_mcbond_other13.31713.3414546
X-RAY DIFFRACTIONr_mcangle_it21.08719.9715686
X-RAY DIFFRACTIONr_mcangle_other21.08519.975687
X-RAY DIFFRACTIONr_scbond_it11.18114.2684241
X-RAY DIFFRACTIONr_scbond_other11.1814.2644233
X-RAY DIFFRACTIONr_scangle_it18.63620.9766242
X-RAY DIFFRACTIONr_scangle_other18.63520.9696231
X-RAY DIFFRACTIONr_lrange_it31.289254.61935984
X-RAY DIFFRACTIONr_lrange_other31.289254.6235983
X-RAY DIFFRACTIONr_ncsr_local_group_10.1220.0513212
X-RAY DIFFRACTIONr_ncsr_local_group_20.1130.053592
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.122410.05008
12BX-RAY DIFFRACTIONLocal ncs0.122410.05008
23KX-RAY DIFFRACTIONLocal ncs0.113480.05009
24CX-RAY DIFFRACTIONLocal ncs0.113480.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.75-3.8470.4931380.472619X-RAY DIFFRACTION99.7107
3.847-3.9530.3981600.4322536X-RAY DIFFRACTION99.7779
3.953-4.0670.381240.42532X-RAY DIFFRACTION99.8496
4.067-4.1920.341360.3572434X-RAY DIFFRACTION99.9222
4.192-4.330.3311170.3162350X-RAY DIFFRACTION99.7574
4.33-4.4810.3041230.2692302X-RAY DIFFRACTION99.8353
4.481-4.650.2571190.2582199X-RAY DIFFRACTION99.9138
4.65-4.840.384910.2712151X-RAY DIFFRACTION100
4.84-5.0550.3391110.282069X-RAY DIFFRACTION99.9542
5.055-5.3010.3351070.3161959X-RAY DIFFRACTION99.8068
5.301-5.5880.3281000.3171880X-RAY DIFFRACTION100
5.588-5.9260.361840.3171772X-RAY DIFFRACTION99.8386
5.926-6.3340.323870.2711678X-RAY DIFFRACTION99.9434
6.334-6.840.245700.2421595X-RAY DIFFRACTION99.8201
6.84-7.4910.27830.2041442X-RAY DIFFRACTION99.869
7.491-8.3720.242640.1671319X-RAY DIFFRACTION99.7116
8.372-9.6610.191670.1781171X-RAY DIFFRACTION100
9.661-11.8170.19410.181028X-RAY DIFFRACTION100
11.817-16.6480.187390.203800X-RAY DIFFRACTION99.881
16.648-100.670.389300.413486X-RAY DIFFRACTION99.2308

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