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

ID or keywords:

Entry

Database: PDB / ID: 7zmm

Title

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2-001

Components

ATP-dependent DNA helicase Q5
Gluebody G2-001

Keywords

HYDROLASE / Helicase / Apo form / Nanobody complex

Function / homology

Function and homology information

mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / 3'-5' DNA helicase activity / DNA 3'-5' helicase / DNA metabolic process / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II ...
Similarity search - Function

Biological species

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary Category: atom_site / entity ...atom_site / entity / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_torsion / refine / 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 / _entity.pdbx_description / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_seq_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_validate_torsion.phi / _pdbx_validate_torsion.psi / _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_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_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.R_factor_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.wR_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
Revision 2.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/7zmm ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zmm	HTTPS FTP

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Related structure data

Related structure data	7zmlC 7zmnC 7zmoC 7zmpC 7zmqC 7zmrC 7zmsC 7zmtC 7zmvC 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

B: ATP-dependent DNA helicase Q5

A: ATP-dependent DNA helicase Q5

C: ATP-dependent DNA helicase Q5

D: ATP-dependent DNA helicase Q5

K: Gluebody G2-001

E: Gluebody G2-001

F: Gluebody G2-001

G: Gluebody G2-001

hetero molecules

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

1

B: ATP-dependent DNA helicase Q5

F: Gluebody G2-001

hetero molecules

defined by author&software
Evidence: gel filtration, RECQL5 and the engineered nanobody G2-001 elute in the same peak on gel filtration
64 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: ATP-dependent DNA helicase Q5

K: Gluebody G2-001

hetero molecules

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

3

C: ATP-dependent DNA helicase Q5

E: Gluebody G2-001

hetero molecules

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

4

D: ATP-dependent DNA helicase Q5

G: Gluebody G2-001

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.612, 183.969, 100.947
Angle α, β, γ (deg.)	90.000, 108.124, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	SER	SER	B	A	12 - 450	4 - 442
2	1	1	PRO	PRO	SER	SER	A	B	12 - 450	4 - 442
3	2	2	PRO	PRO	SER	SER	B	A	12 - 452	4 - 444
4	2	2	PRO	PRO	SER	SER	C	C	12 - 452	4 - 444
5	3	3	PRO	PRO	SER	SER	B	A	12 - 452	4 - 444
6	3	3	PRO	PRO	SER	SER	D	D	12 - 452	4 - 444
7	4	4	PRO	PRO	SER	SER	A	B	12 - 450	4 - 442
8	4	4	PRO	PRO	SER	SER	C	C	12 - 450	4 - 442
9	5	5	PRO	PRO	SER	SER	A	B	12 - 450	4 - 442
10	5	5	PRO	PRO	SER	SER	D	D	12 - 450	4 - 442
11	6	6	PRO	PRO	SER	SER	C	C	12 - 452	4 - 444
12	6	6	PRO	PRO	SER	SER	D	D	12 - 452	4 - 444
13	7	7	GLN	GLN	LEU	LEU	K	E	1 - 129	1 - 129
14	7	7	GLN	GLN	LEU	LEU	E	F	1 - 129	1 - 129
15	8	8	GLN	GLN	ALA	ALA	K	E	1 - 125	1 - 125
16	8	8	GLN	GLN	ALA	ALA	F	G	1 - 125	1 - 125
17	9	9	GLN	GLN	ALA	ALA	K	E	1 - 126	1 - 126
18	9	9	GLN	GLN	ALA	ALA	G	H	1 - 126	1 - 126
19	10	10	GLN	GLN	ALA	ALA	E	F	1 - 125	1 - 125
20	10	10	GLN	GLN	ALA	ALA	F	G	1 - 125	1 - 125
21	11	11	GLN	GLN	ALA	ALA	E	F	1 - 126	1 - 126
22	11	11	GLN	GLN	ALA	ALA	G	H	1 - 126	1 - 126
23	12	12	GLN	GLN	ALA	ALA	F	G	1 - 125	1 - 125
24	12	12	GLN	GLN	ALA	ALA	G	H	1 - 125	1 - 125

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 G2-001 Mass: 14364.772 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.5→183.84 Å / Num. obs: 95510 / % possible obs: 99.2 % / Redundancy: 2.7 % / CC_1/2: 1 / Net I/σ(I): 8.6
Reflection shell	Resolution: 2.5→2.55 Å / Num. unique obs: 4769 / CC_1/2: 0.61

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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: 2.5→95.938 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.927 / WR_factor R_free: 0.287 / WR_factor R_work: 0.24 / SU B: 15.088 / SU ML: 0.317 / Average fsc free: 0.8144 / Average fsc work: 0.8387 / Cross valid method: FREE R-VALUE / ESU R: 0.641 / ESU R Free: 0.324
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2806	4407	4.844 %
R_work	0.2356	86568	-
all	0.238	-	-
obs	-	90975	99.371 %

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: 79.866 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.817 Å²	-0 Å²	-2.886 Å²
2-	-	1.73 Å²	-0 Å²
3-	-	-	-0.541 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→95.938 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17546	0	0	95	17641

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	18018
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	17075
X-RAY DIFFRACTION	r_angle_refined_deg	1.411	1.643	24406
X-RAY DIFFRACTION	r_angle_other_deg	1.248	1.579	39251
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.464	5	2306
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.553	21.246	939
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.321	15	3063
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.143	15	145
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	2332
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	20675
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4311
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	3305
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	14645
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	8662
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	9357
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	333
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.143	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.401	0.2	47
X-RAY DIFFRACTION	r_nbd_other	0.327	0.2	97
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.304	0.2	7
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.124	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	8.053	8.275	9159
X-RAY DIFFRACTION	r_mcbond_other	8.047	8.275	9158
X-RAY DIFFRACTION	r_mcangle_it	11.838	12.401	11449
X-RAY DIFFRACTION	r_mcangle_other	11.837	12.402	11450
X-RAY DIFFRACTION	r_scbond_it	7.763	8.781	8859
X-RAY DIFFRACTION	r_scbond_other	7.763	8.78	8857
X-RAY DIFFRACTION	r_scangle_it	11.791	12.921	12931
X-RAY DIFFRACTION	r_scangle_other	11.791	12.921	12931
X-RAY DIFFRACTION	r_lrange_it	18.154	156.628	72296
X-RAY DIFFRACTION	r_lrange_other	18.155	156.629	72291
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.081	0.05	13622
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.085	0.05	13691
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.087	0.05	13665
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.088	0.05	13613
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.081	0.05	13617
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.09	0.05	13661
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.098	0.05	3709
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.094	0.05	3629
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.085	0.05	3654
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.083	0.05	3667
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.097	0.05	3645
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.094	0.05	3637

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.08062	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08062	0.05009
2	3	B	X-RAY DIFFRACTION	Local ncs	0.08507	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.08507	0.05009
3	5	B	X-RAY DIFFRACTION	Local ncs	0.08659	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.08659	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08788	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.08788	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08122	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.08122	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.08971	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.08971	0.05008
7	13	K	X-RAY DIFFRACTION	Local ncs	0.09796	0.05009
7	14	E	X-RAY DIFFRACTION	Local ncs	0.09796	0.05009
8	15	K	X-RAY DIFFRACTION	Local ncs	0.09375	0.0501
8	16	F	X-RAY DIFFRACTION	Local ncs	0.09375	0.0501
9	17	K	X-RAY DIFFRACTION	Local ncs	0.08516	0.05009
9	18	G	X-RAY DIFFRACTION	Local ncs	0.08516	0.05009
10	19	E	X-RAY DIFFRACTION	Local ncs	0.08311	0.0501
10	20	F	X-RAY DIFFRACTION	Local ncs	0.08311	0.0501
11	21	E	X-RAY DIFFRACTION	Local ncs	0.09652	0.0501
11	22	G	X-RAY DIFFRACTION	Local ncs	0.09652	0.0501
12	23	F	X-RAY DIFFRACTION	Local ncs	0.09414	0.0501
12	24	G	X-RAY DIFFRACTION	Local ncs	0.09414	0.0501

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.5-2.565	0.377	331	0.361	6358	0.362	6737	0.606	0.606	99.2875	0.358
2.565-2.635	0.383	344	0.345	6204	0.347	6603	0.665	0.698	99.167	0.339
2.635-2.711	0.38	299	0.333	6038	0.335	6384	0.685	0.716	99.2638	0.324
2.711-2.795	0.386	269	0.309	5938	0.312	6236	0.763	0.797	99.535	0.295
2.795-2.886	0.363	313	0.304	5672	0.307	6022	0.788	0.814	99.3856	0.285
2.886-2.988	0.372	282	0.294	5490	0.298	5800	0.78	0.82	99.5172	0.276
2.988-3.1	0.326	272	0.269	5333	0.272	5638	0.839	0.871	99.4147	0.252
3.1-3.227	0.316	257	0.256	5142	0.259	5432	0.858	0.883	99.3925	0.244
3.227-3.37	0.332	251	0.27	4932	0.273	5213	0.839	0.872	99.4245	0.261
3.37-3.534	0.32	244	0.26	4694	0.263	4961	0.872	0.901	99.5364	0.256
3.534-3.725	0.285	238	0.25	4438	0.252	4703	0.888	0.912	99.4259	0.247
3.725-3.951	0.313	183	0.244	4249	0.247	4476	0.87	0.9	99.017	0.245
3.951-4.223	0.255	195	0.217	4030	0.219	4239	0.915	0.924	99.6697	0.222
4.223-4.561	0.234	194	0.189	3704	0.191	3909	0.929	0.94	99.7186	0.2
4.561-4.995	0.25	170	0.183	3416	0.187	3605	0.935	0.949	99.473	0.197
4.995-5.583	0.267	155	0.212	3099	0.214	3275	0.911	0.931	99.3588	0.225
5.583-6.443	0.277	149	0.225	2722	0.228	2885	0.915	0.926	99.5147	0.24
6.443-7.882	0.248	130	0.201	2284	0.203	2437	0.923	0.934	99.0562	0.218
7.882-11.109	0.198	86	0.176	1822	0.177	1926	0.955	0.955	99.0654	0.198
11.109-95.938	0.207	45	0.257	1003	0.255	1070	0.949	0.928	97.9439	0.325

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