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

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Basic information

Entry
Database: PDB / ID: 7zmt
TitleCrystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006
Components
  • ATP-dependent DNA helicase Q5
  • Gluebody G5-006
KeywordsHYDROLASE / Helicase / Apo form / Nanobody complex
Function / homology
Function and homology information


mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / DNA 3'-5' helicase / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA metabolic process / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication ...mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / DNA 3'-5' helicase / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA metabolic process / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / 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 / helicase activity / replication fork / double-strand break repair via homologous recombination / cellular response to xenobiotic stimulus / chromosome / mitotic cell cycle / DNA replication / nucleic acid binding / cell division / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim / struct_sheet_range
Item: _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.asym_id ..._pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _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_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _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_R_factor_all / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _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.d_res_high / _refine_hist.number_atoms_total / _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_restr_ncs.weight_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _struct_mon_prot_cis.pdbx_omega_angle / _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 / _struct_ncs_dom_lim.pdbx_component_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 G5-006
C: Gluebody G5-006
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7566
Polymers126,6254
Non-polymers1312
Water1,49583
1
A: ATP-dependent DNA helicase Q5
C: Gluebody G5-006
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3783
Polymers63,3122
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7 kcal/mol
Surface area26230 Å2
MethodPISA
2
B: ATP-dependent DNA helicase Q5
K: Gluebody G5-006
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3783
Polymers63,3122
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-8 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.355, 90.675, 217.853
Angle α, β, γ (deg.)90.000, 90.754, 90.000
Int Tables number5
Space group name H-MI121
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
111PROPROAA12 - 4514 - 443
211PROPROBB12 - 4514 - 443
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 G5-006


Mass: 13775.173 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium formate -- 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.13→60.94 Å / Num. obs: 89383 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.9 / Net I/σ(I): 9
Reflection shellResolution: 2.13→2.16 Å / Num. unique obs: 4291 / CC1/2: 0.5 / % possible all: 95

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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: 2.3→56.743 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.226 / SU B: 21.447 / SU ML: 0.395 / Average fsc free: 0.5554 / Average fsc work: 0.5784 / Cross valid method: FREE R-VALUE / ESU R: 0.326 / ESU R Free: 0.247
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.291 3471 4.888 %
Rwork0.2636 67544 -
all0.265 --
obs-71015 99.533 %
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: 72.529 Å2
Baniso -1Baniso -2Baniso -3
1-5.36 Å2-0 Å26.029 Å2
2---6.964 Å20 Å2
3---1.444 Å2
Refinement stepCycle: LAST / Resolution: 2.3→56.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8729 0 0 83 8812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138990
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178510
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.64212177
X-RAY DIFFRACTIONr_angle_other_deg1.3041.5819553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76451148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0421.111477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.663151525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4231576
X-RAY DIFFRACTIONr_chiral_restr0.0690.21160
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022155
X-RAY DIFFRACTIONr_nbd_refined0.1990.21625
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.27167
X-RAY DIFFRACTIONr_nbtor_refined0.1610.24199
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24314
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2140
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0590.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.227
X-RAY DIFFRACTIONr_nbd_other0.2450.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.25
X-RAY DIFFRACTIONr_mcbond_it8.5137.484553
X-RAY DIFFRACTIONr_mcbond_other8.4997.4814552
X-RAY DIFFRACTIONr_mcangle_it12.47911.1995693
X-RAY DIFFRACTIONr_mcangle_other12.48111.25694
X-RAY DIFFRACTIONr_scbond_it7.8897.9864437
X-RAY DIFFRACTIONr_scbond_other7.8887.9864437
X-RAY DIFFRACTIONr_scangle_it12.1111.7226477
X-RAY DIFFRACTIONr_scangle_other12.1111.7236478
X-RAY DIFFRACTIONr_lrange_it18.008141.3535950
X-RAY DIFFRACTIONr_lrange_other18.008141.36435931
X-RAY DIFFRACTIONr_ncsr_local_group_10.0760.0513667
X-RAY DIFFRACTIONr_ncsr_local_group_20.1780.053434
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.075620.05008
12BX-RAY DIFFRACTIONLocal ncs0.075620.05008
23KX-RAY DIFFRACTIONLocal ncs0.177890.05006
24CX-RAY DIFFRACTIONLocal ncs0.177890.05006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.4942720.4644952X-RAY DIFFRACTION99.0332
2.36-2.4240.4782530.4614798X-RAY DIFFRACTION99.0781
2.424-2.4950.4042530.4484696X-RAY DIFFRACTION99.1784
2.495-2.5710.42290.4364549X-RAY DIFFRACTION99.2728
2.571-2.6560.4692480.4164452X-RAY DIFFRACTION99.3238
2.656-2.7490.3772120.3884250X-RAY DIFFRACTION99.1776
2.749-2.8520.4022330.3734125X-RAY DIFFRACTION99.6342
2.852-2.9690.4161950.343993X-RAY DIFFRACTION99.6906
2.969-3.1010.3472140.3143817X-RAY DIFFRACTION99.7279
3.101-3.2520.3231710.2893693X-RAY DIFFRACTION99.562
3.252-3.4280.312010.2763478X-RAY DIFFRACTION99.783
3.428-3.6350.2741560.2543328X-RAY DIFFRACTION99.7995
3.635-3.8860.2791400.2433144X-RAY DIFFRACTION99.9391
3.886-4.1970.2261440.2122905X-RAY DIFFRACTION99.9344
4.197-4.5970.2411630.192660X-RAY DIFFRACTION99.9292
4.597-5.1380.1981130.1842437X-RAY DIFFRACTION100
5.138-5.9310.243870.2022186X-RAY DIFFRACTION100
5.931-7.2590.201780.1851835X-RAY DIFFRACTION99.8956
7.259-10.2430.157800.1641429X-RAY DIFFRACTION100
10.243-56.7430.311290.249817X-RAY DIFFRACTION98.9474

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