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

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Entry
Database: PDB / ID: 7zms
TitleCrystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G4-043
Components
  • ATP-dependent DNA helicase Q5
  • Gluebody G4-043
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 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 5, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
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 / _atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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 / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _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_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_label_seq_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: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 6, 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
K: Gluebody G4-043
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2223
Polymers63,1562
Non-polymers651
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, RECQL5 and the engineered nanobody G4-043 elute in the same peak on gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.909, 90.121, 216.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

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Components

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


Mass: 49422.094 Da / Num. of mol.: 1
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 G4-043


Mass: 13734.164 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium chloride -- 25% PEG3350 -- 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.17→41.6 Å / Num. obs: 42737 / % possible obs: 99.6 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 7.2
Reflection shellResolution: 2.17→2.21 Å / Num. unique obs: 1944 / CC1/2: 0.5

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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→40.988 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.21 / SU B: 20.71 / SU ML: 0.376 / Average fsc free: 0.783 / Average fsc work: 0.7911 / Cross valid method: FREE R-VALUE / ESU R: 0.713 / ESU R Free: 0.346
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2762 1151 5.124 %
Rwork0.235 21314 -
all0.237 --
obs-22465 99.929 %
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: 80.715 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0 Å2
2--0.293 Å20 Å2
3---0.047 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4335 0 0 38 4373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134472
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174257
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6436054
X-RAY DIFFRACTIONr_angle_other_deg1.2841.589783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3825569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.33821.017236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08615765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9541538
X-RAY DIFFRACTIONr_chiral_restr0.0670.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021073
X-RAY DIFFRACTIONr_nbd_refined0.2130.2928
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.23849
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22107
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1270.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.217
X-RAY DIFFRACTIONr_nbd_other0.2080.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.23
X-RAY DIFFRACTIONr_mcbond_it7.1898.3072258
X-RAY DIFFRACTIONr_mcbond_other7.188.3062257
X-RAY DIFFRACTIONr_mcangle_it10.81112.4362821
X-RAY DIFFRACTIONr_mcangle_other10.81112.4382822
X-RAY DIFFRACTIONr_scbond_it7.0458.8632214
X-RAY DIFFRACTIONr_scbond_other7.0458.8632214
X-RAY DIFFRACTIONr_scangle_it10.84613.0413229
X-RAY DIFFRACTIONr_scangle_other10.84413.0433230
X-RAY DIFFRACTIONr_lrange_it16.667157.65918202
X-RAY DIFFRACTIONr_lrange_other16.666157.65718199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.411810.4651537X-RAY DIFFRACTION99.8149
2.77-2.8460.419820.4351513X-RAY DIFFRACTION100
2.846-2.9280.367810.4031488X-RAY DIFFRACTION100
2.928-3.0180.374760.3551427X-RAY DIFFRACTION100
3.018-3.1170.367790.3211387X-RAY DIFFRACTION99.7958
3.117-3.2270.328740.3141342X-RAY DIFFRACTION100
3.227-3.3480.295770.2871283X-RAY DIFFRACTION100
3.348-3.4850.288740.2621262X-RAY DIFFRACTION100
3.485-3.640.347660.2471180X-RAY DIFFRACTION100
3.64-3.8170.275640.241159X-RAY DIFFRACTION100
3.817-4.0230.274540.2111105X-RAY DIFFRACTION100
4.023-4.2670.221570.1841033X-RAY DIFFRACTION100
4.267-4.5610.223490.161008X-RAY DIFFRACTION100
4.561-4.9260.255490.171916X-RAY DIFFRACTION100
4.926-5.3950.22430.203856X-RAY DIFFRACTION100
5.395-6.030.275360.225781X-RAY DIFFRACTION100
6.03-6.9590.273350.211691X-RAY DIFFRACTION100
6.959-8.5140.2330.179589X-RAY DIFFRACTION100
8.514-12.0040.21300.162469X-RAY DIFFRACTION100
12.004-40.9880.361110.27288X-RAY DIFFRACTION97.0779

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