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

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Basic information

Entry
Database: PDB / ID: 7zmq
TitleCrystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-006
Components
  • ATP-dependent DNA helicase Q5
  • Gluebody G2*-006
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: 2.7 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 2.0Oct 5, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / pdbx_contact_author ...atom_site / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.wR_factor_R_work / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom_lim.pdbx_component_id
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 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 2.2Oct 23, 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 G2*-006
C: Gluebody G2*-006
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,19610
Polymers126,6814
Non-polymers5156
Water93752
1
A: ATP-dependent DNA helicase Q5
K: Gluebody G2*-006
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5985
Polymers63,3402
Non-polymers2583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-38 kcal/mol
Surface area26070 Å2
MethodPISA
2
B: ATP-dependent DNA helicase Q5
C: Gluebody G2*-006
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5985
Polymers63,3402
Non-polymers2583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-39 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.130, 199.086, 174.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32K
42C

NCS domain segments:

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

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETAA10 - 4502 - 442
211METMETBB10 - 4502 - 442
322GLNGLNKC1 - 1244 - 127
422GLNGLNCD1 - 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 G2*-006


Mass: 13803.143 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.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M lithium sulfate -- 25% PEG3350 -- 0.1M tris pH 8.5

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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: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 2.41→99.68 Å / Num. obs: 77373 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.9 / Net I/σ(I): 8.2
Reflection shellResolution: 2.41→2.45 Å / Num. unique obs: 3878 / CC1/2: 0.3

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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: 2.7→99.665 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.203 / SU B: 12.432 / SU ML: 0.246 / Average fsc free: 0.8813 / Average fsc work: 0.8947 / Cross valid method: FREE R-VALUE / ESU R: 0.455 / ESU R Free: 0.294
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2583 2899 5.257 %
Rwork0.225 52251 -
all0.227 --
obs-55150 99.926 %
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: 61.392 Å2
Baniso -1Baniso -2Baniso -3
1-0.557 Å20 Å2-0 Å2
2--2.265 Å20 Å2
3----2.822 Å2
Refinement stepCycle: LAST / Resolution: 2.7→99.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8750 0 20 52 8822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139058
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178563
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.64312278
X-RAY DIFFRACTIONr_angle_other_deg1.2881.5819671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22951155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55221.162482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.074151535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2321576
X-RAY DIFFRACTIONr_chiral_restr0.070.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022181
X-RAY DIFFRACTIONr_nbd_refined0.2080.21707
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.27638
X-RAY DIFFRACTIONr_nbtor_refined0.1630.24279
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2175
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2670.222
X-RAY DIFFRACTIONr_nbd_other0.2420.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.22
X-RAY DIFFRACTIONr_mcbond_it5.2936.344569
X-RAY DIFFRACTIONr_mcbond_other5.2946.344568
X-RAY DIFFRACTIONr_mcangle_it8.1669.5065717
X-RAY DIFFRACTIONr_mcangle_other8.1659.5065718
X-RAY DIFFRACTIONr_scbond_it5.496.7224489
X-RAY DIFFRACTIONr_scbond_other5.4766.7224473
X-RAY DIFFRACTIONr_scangle_it8.4959.8826553
X-RAY DIFFRACTIONr_scangle_other8.499.8826530
X-RAY DIFFRACTIONr_lrange_it13.871119.08237180
X-RAY DIFFRACTIONr_lrange_other13.87119.08337176
X-RAY DIFFRACTIONr_ncsr_local_group_10.0830.0514000
X-RAY DIFFRACTIONr_ncsr_local_group_20.0680.053781
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.083290.05008
12BX-RAY DIFFRACTIONLocal ncs0.083290.05008
23KX-RAY DIFFRACTIONLocal ncs0.067940.05011
24CX-RAY DIFFRACTIONLocal ncs0.067940.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.7-2.770.3532260.34337910.34340240.7620.78799.8260.329
2.77-2.8460.3212090.32637380.32639550.8240.8199.79770.306
2.846-2.9280.3291860.30336270.30438160.8270.84299.92140.279
2.928-3.0180.3311830.27935670.28237560.8640.8799.84030.253
3.018-3.1170.361980.27833960.28335960.8210.85799.94440.25
3.117-3.2270.3141930.26232630.26534580.8580.87799.94220.238
3.227-3.3480.3222000.25331810.25733830.8650.89499.94090.233
3.348-3.4850.2861830.25430930.25632770.8970.90599.96950.233
3.485-3.640.271230.23529730.23730960.9080.9231000.22
3.64-3.8170.2251050.23228900.23229960.9280.92699.96660.217
3.817-4.0230.2331340.20827160.20928530.9350.9499.89480.194
4.023-4.2670.221790.19225330.19427140.950.94999.92630.18
4.267-4.5610.2041170.17324000.17525170.940.9531000.163
4.561-4.9250.1941570.16922050.17123620.9520.9611000.158
4.925-5.3940.2311150.18920980.19122130.9380.951000.177
5.394-6.0290.299790.22119190.22419980.9060.9311000.205
6.029-6.9570.256930.21916560.22117510.910.93799.88580.206
6.957-8.510.187950.16614260.16815210.9580.9611000.161
8.51-11.9910.203660.16211220.16411880.9560.9661000.158
11.991-99.6650.304580.296560.2917160.8820.90899.72070.281

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