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

ID or keywords:

Entry

Database: PDB / ID: 7zmv

Title

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006

Components

ATP-dependent DNA helicase Q5
Gluebody G5-006

Keywords

HYDROLASE / 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 / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / negative regulation of transcription elongation by RNA polymerase II / DNA unwinding involved in DNA replication ...
Similarity search - Function

Biological species

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.002 Å

Authors

Ye, 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

Citation

Journal: 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. / ...

History

Deposition	Apr 19, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 22, 2022	Provider: repository / Type: Initial release
Revision 2.0	Oct 5, 2022	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary Category: atom_site / pdbx_contact_author ...atom_site / 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_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim / struct_sheet / struct_sheet_order / struct_sheet_range Item: _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance ..._pdbx_distant_solvent_atoms.auth_seq_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 / _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.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _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_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 / _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 2.1	Jan 31, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7zmv.cif.gz	480 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7zmv_validation.pdf.gz	441.2 KB	Display	wwPDB validaton report
Full document	7zmv_full_validation.pdf.gz	460 KB	Display
Data in XML	7zmv_validation.xml.gz	42.9 KB	Display
Data in CIF	7zmv_validation.cif.gz	73.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/7zmv ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zmv	HTTPS FTP

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Related structure data

Related structure data	7zmlC 7zmmC 7zmnC 7zmoC 7zmpC 7zmqC 7zmrC 7zmsC 7zmtC 5lb5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: ATP-dependent DNA helicase Q5

B: ATP-dependent DNA helicase Q5

C: ATP-dependent DNA helicase Q5

D: ATP-dependent DNA helicase Q5

K: Gluebody G5-006

E: Gluebody G5-006

F: Gluebody G5-006

G: Gluebody G5-006

hetero molecules

254 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP-dependent DNA helicase Q5

G: Gluebody G5-006

hetero molecules

defined by author&software
Evidence: gel filtration, RECQL5 and the engineered nanobody G5-006 elute in the same peak on gel filtration
63.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ATP-dependent DNA helicase Q5

F: Gluebody G5-006

hetero molecules

defined by author&software
63.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: ATP-dependent DNA helicase Q5

K: Gluebody G5-006

hetero molecules

defined by author&software
63.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: ATP-dependent DNA helicase Q5

E: Gluebody G5-006

hetero molecules

defined by author&software
63.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	232.589, 89.965, 164.126
Angle α, β, γ (deg.)	90.000, 110.058, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

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

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	A	A	12 - 451	4 - 443
2	1	1	PRO	PRO	B	B	12 - 451	4 - 443
3	2	2	PRO	PRO	A	A	12 - 451	4 - 443
4	2	2	PRO	PRO	C	C	12 - 451	4 - 443
5	3	3	PRO	PRO	A	A	12 - 451	4 - 443
6	3	3	PRO	PRO	D	D	12 - 451	4 - 443
7	4	4	PRO	PRO	B	B	12 - 451	4 - 443
8	4	4	PRO	PRO	C	C	12 - 451	4 - 443
9	5	5	PRO	PRO	B	B	12 - 451	4 - 443
10	5	5	PRO	PRO	D	D	12 - 451	4 - 443
11	6	6	PRO	PRO	C	C	12 - 451	4 - 443
12	6	6	PRO	PRO	D	D	12 - 451	4 - 443
13	7	7	GLN	GLN	K	E	1 - 124	4 - 127
14	7	7	GLN	GLN	E	F	1 - 124	4 - 127
15	8	8	GLN	GLN	K	E	1 - 124	4 - 127
16	8	8	GLN	GLN	F	G	1 - 124	4 - 127
17	9	9	GLN	GLN	K	E	1 - 124	4 - 127
18	9	9	GLN	GLN	G	H	1 - 124	4 - 127
19	10	10	GLN	GLN	E	F	1 - 124	4 - 127
20	10	10	GLN	GLN	F	G	1 - 124	4 - 127
21	11	11	GLN	GLN	E	F	1 - 124	4 - 127
22	11	11	GLN	GLN	G	H	1 - 124	4 - 127
23	12	12	GLN	GLN	F	G	1 - 124	4 - 127
24	12	12	GLN	GLN	G	H	1 - 124	4 - 127

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

#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.: 4 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.: 4 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.: 4 / 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.: 1028 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.23 Å³/Da / Density % sol: 61.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M ammonium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9119 Å / Relative weight: 1
Reflection	Resolution: 2→109.23 Å / Num. obs: 209231 / % possible obs: 97.7 % / Redundancy: 2.9 % / CC_1/2: 1 / Net I/σ(I): 13.9
Reflection shell	Resolution: 2→2.04 Å / Num. unique obs: 9299 / CC_1/2: 0.3 / % possible all: 87.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5LB5

5lb5

Resolution: 2.002→77.687 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.94 / WR_factor R_free: 0.258 / WR_factor R_work: 0.227 / SU B: 6.919 / SU ML: 0.173 / Average fsc free: 0.8093 / Average fsc work: 0.821 / Cross valid method: FREE R-VALUE / ESU R: 0.194 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2747	10399	4.978 %
R_work	0.2431	198492	-
all	0.245	-	-
obs	-	208891	97.572 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.403 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.018 Å²	-0 Å²	0.005 Å²
2-	-	-0.02 Å²	-0 Å²
3-	-	-	-0.002 Å²

Refinement step

Cycle: LAST / Resolution: 2.002→77.687 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17422	0	20	1028	18470

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	17979
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	17033
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.643	24354
X-RAY DIFFRACTION	r_angle_other_deg	1.334	1.58	39153
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.856	5	2294
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.17	21.2	950
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.197	15	3065
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.464	15	149
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	2315
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	20586
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4304
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	3768
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	15473
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	8588
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	9190
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	849
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.035	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	63
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	194
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.145	0.2	28
X-RAY DIFFRACTION	r_mcbond_it	4.158	4.798	9086
X-RAY DIFFRACTION	r_mcbond_other	4.158	4.798	9085
X-RAY DIFFRACTION	r_mcangle_it	5.958	7.19	11365
X-RAY DIFFRACTION	r_mcangle_other	5.958	7.19	11366
X-RAY DIFFRACTION	r_scbond_it	5.121	5.388	8893
X-RAY DIFFRACTION	r_scbond_other	5.084	5.386	8877
X-RAY DIFFRACTION	r_scangle_it	7.681	7.837	12972
X-RAY DIFFRACTION	r_scangle_other	7.672	7.834	12949
X-RAY DIFFRACTION	r_lrange_it	10.888	91.947	74750
X-RAY DIFFRACTION	r_lrange_other	10.892	91.887	74345
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.058	0.05	14268
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.056	0.05	14264
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.059	0.05	14257
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.054	0.05	14296
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.062	0.05	14248
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.056	0.05	14283
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.058	0.05	3757
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.069	0.05	3748
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.078	0.05	3724
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.061	0.05	3761
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.07	0.05	3740
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.061	0.05	3752

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05783	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.05783	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05588	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.05588	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05929	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.05929	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.05422	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.05422	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.0618	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.0618	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.05639	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.05639	0.05009
7	13	K	X-RAY DIFFRACTION	Local ncs	0.0578	0.0501
7	14	E	X-RAY DIFFRACTION	Local ncs	0.0578	0.0501
8	15	K	X-RAY DIFFRACTION	Local ncs	0.06874	0.0501
8	16	F	X-RAY DIFFRACTION	Local ncs	0.06874	0.0501
9	17	K	X-RAY DIFFRACTION	Local ncs	0.07815	0.0501
9	18	G	X-RAY DIFFRACTION	Local ncs	0.07815	0.0501
10	19	E	X-RAY DIFFRACTION	Local ncs	0.06136	0.0501
10	20	F	X-RAY DIFFRACTION	Local ncs	0.06136	0.0501
11	21	E	X-RAY DIFFRACTION	Local ncs	0.07046	0.0501
11	22	G	X-RAY DIFFRACTION	Local ncs	0.07046	0.0501
12	23	F	X-RAY DIFFRACTION	Local ncs	0.06075	0.0501
12	24	G	X-RAY DIFFRACTION	Local ncs	0.06075	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.002-2.054	0.401	669	0.41	13386	X-RAY DIFFRACTION	89.1136
2.054-2.11	0.386	685	0.383	13614	X-RAY DIFFRACTION	93.141
2.11-2.171	0.372	690	0.35	12911	X-RAY DIFFRACTION	91.0863
2.171-2.238	0.355	708	0.325	13582	X-RAY DIFFRACTION	98.5789
2.238-2.311	0.33	719	0.312	13252	X-RAY DIFFRACTION	98.6583
2.311-2.393	0.336	675	0.31	12768	X-RAY DIFFRACTION	99.1006
2.393-2.483	0.333	640	0.294	12439	X-RAY DIFFRACTION	99.1284
2.483-2.584	0.32	638	0.282	11899	X-RAY DIFFRACTION	99.2794
2.584-2.699	0.338	635	0.269	11420	X-RAY DIFFRACTION	99.3326
2.699-2.831	0.312	569	0.257	11011	X-RAY DIFFRACTION	99.4589
2.831-2.984	0.291	575	0.263	10425	X-RAY DIFFRACTION	99.6287
2.984-3.165	0.302	510	0.256	9913	X-RAY DIFFRACTION	99.6177
3.165-3.383	0.287	465	0.252	9320	X-RAY DIFFRACTION	99.522
3.383-3.654	0.276	480	0.238	8664	X-RAY DIFFRACTION	99.5103
3.654-4.003	0.238	409	0.219	8058	X-RAY DIFFRACTION	99.882
4.003-4.475	0.217	367	0.183	7291	X-RAY DIFFRACTION	99.9478
4.475-5.166	0.201	332	0.17	6426	X-RAY DIFFRACTION	99.8965
5.166-6.325	0.226	300	0.205	5444	X-RAY DIFFRACTION	99.913
6.325-8.938	0.221	223	0.187	4270	X-RAY DIFFRACTION	99.7115
8.938-77.687	0.214	110	0.206	2399	X-RAY DIFFRACTION	99.2877

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