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

ID or keywords:

Entry

Database: PDB / ID: 7zml

Title

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G1-001

Components

ATP-dependent DNA helicase Q5
Gluebody G1-001

Keywords

HYDROLASE / Helicase / Apo form / Nanobody complex

Function / homology

Function and homology information

mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.79 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_rmsd_angle / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ncs_dom_lim / struct_sheet / struct_sheet_order / 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 / _entity.pdbx_description / _entity.src_method / _pdbx_nonpoly_scheme.auth_seq_num / _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[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_Free / _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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7zml_validation.pdf.gz	501.2 KB	Display	wwPDB validaton report
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Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/7zml ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zml	HTTPS FTP

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Related structure data

Related structure data	7zmmC 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

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 G1-001

E: Gluebody G1-001

F: Gluebody G1-001

G: Gluebody G1-001

hetero molecules

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

1

A: ATP-dependent DNA helicase Q5

F: Gluebody G1-001

hetero molecules

defined by author&software
Evidence: gel filtration, RECQL5 and the engineered nanobody G1-001 elute in the same peak on gel filtration
64 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ATP-dependent DNA helicase Q5

E: Gluebody G1-001

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

K: Gluebody G1-001

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 G1-001

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)	75.740, 185.530, 101.010
Angle α, β, γ (deg.)	90.000, 107.470, 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	A	A	12 - 452	4 - 444
2	1	1	PRO	PRO	SER	SER	B	B	12 - 452	4 - 444
3	2	2	PRO	PRO	SER	SER	A	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	A	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	B	B	12 - 452	4 - 444
8	4	4	PRO	PRO	SER	SER	C	C	12 - 452	4 - 444
9	5	5	PRO	PRO	SER	SER	B	B	12 - 452	4 - 444
10	5	5	PRO	PRO	SER	SER	D	D	12 - 452	4 - 444
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	GLU	GLU	K	E	1 - 127	1 - 127
14	7	7	GLN	GLN	GLU	GLU	E	F	1 - 127	1 - 127
15	8	8	GLN	GLN	LEU	LEU	K	E	1 - 129	1 - 129
16	8	8	GLN	GLN	LEU	LEU	F	G	1 - 129	1 - 129
17	9	9	GLN	GLN	PHE	PHE	K	E	1 - 131	1 - 131
18	9	9	GLN	GLN	PHE	PHE	G	H	1 - 131	1 - 131
19	10	10	GLN	GLN	GLU	GLU	E	F	1 - 127	1 - 127
20	10	10	GLN	GLN	GLU	GLU	F	G	1 - 127	1 - 127
21	11	11	GLN	GLN	GLU	GLU	E	F	1 - 127	1 - 127
22	11	11	GLN	GLN	GLU	GLU	G	H	1 - 127	1 - 127
23	12	12	GLN	GLN	LEU	LEU	F	G	1 - 129	1 - 129
24	12	12	GLN	GLN	LEU	LEU	G	H	1 - 129	1 - 129

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 G1-001 Mass: 14347.761 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.: 19 / 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: 2.68 Å³/Da / Density % sol: 54.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.1M bis-tris pH 5.9 -- 0.1M lithium sulfate -- 30% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.79→96.351 Å / Num. obs: 65889 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC_1/2: 1 / R_rim(I) all: 0.083 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.79→2.84 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3266 / CC_1/2: 0.5

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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: 2.79→96.351 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.892 / WR_factor R_free: 0.258 / WR_factor R_work: 0.218 / SU B: 21.261 / SU ML: 0.385 / Average fsc free: 0.828 / Average fsc work: 0.8397 / Cross valid method: FREE R-VALUE / ESU R Free: 0.394
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.261	3147	4.786 %
R_work	0.2238	62603	-
all	0.226	-	-
obs	-	65750	99.58 %

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: 103.124 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.819 Å²	0 Å²	-2.55 Å²
2-	-	0.1 Å²	0 Å²
3-	-	-	3.609 Å²

Refinement step

Cycle: LAST / Resolution: 2.79→96.351 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17587	0	20	19	17626

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	18068
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	17130
X-RAY DIFFRACTION	r_angle_refined_deg	1.432	1.642	24469
X-RAY DIFFRACTION	r_angle_other_deg	1.237	1.579	39370
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.843	5	2308
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.827	21.265	933
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.808	15	3065
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.924	15	143
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	2337
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	20676
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4311
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	3462
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	15078
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	8687
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	9678
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	328
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.046	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.298	0.2	51
X-RAY DIFFRACTION	r_nbd_other	0.313	0.2	137
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.29	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	10.956	10.748	9176
X-RAY DIFFRACTION	r_mcbond_other	10.949	10.748	9175
X-RAY DIFFRACTION	r_mcangle_it	15.776	16.117	11465
X-RAY DIFFRACTION	r_mcangle_other	15.776	16.117	11466
X-RAY DIFFRACTION	r_scbond_it	10.803	11.292	8892
X-RAY DIFFRACTION	r_scbond_other	10.766	11.29	8877
X-RAY DIFFRACTION	r_scangle_it	16.126	16.659	12979
X-RAY DIFFRACTION	r_scangle_other	16.091	16.656	12956
X-RAY DIFFRACTION	r_lrange_it	23.509	204.687	73502
X-RAY DIFFRACTION	r_lrange_other	23.509	204.687	73502
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.071	0.05	13944
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.075	0.05	13955
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.077	0.05	13910
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.064	0.05	13975
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.068	0.05	13897
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.074	0.05	13929
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.063	0.05	3777
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.11	0.05	3692
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.096	0.05	3814
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.101	0.05	3675
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.087	0.05	3718
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.118	0.05	3661

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	0.07121	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07121	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07455	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.07455	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07686	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07686	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.06441	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.06441	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.0675	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.0675	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.07377	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.07377	0.05009
7	13	K	X-RAY DIFFRACTION	Local ncs	0.06335	0.0501
7	14	E	X-RAY DIFFRACTION	Local ncs	0.06335	0.0501
8	15	K	X-RAY DIFFRACTION	Local ncs	0.11028	0.05009
8	16	F	X-RAY DIFFRACTION	Local ncs	0.11028	0.05009
9	17	K	X-RAY DIFFRACTION	Local ncs	0.09624	0.0501
9	18	G	X-RAY DIFFRACTION	Local ncs	0.09624	0.0501
10	19	E	X-RAY DIFFRACTION	Local ncs	0.10146	0.0501
10	20	F	X-RAY DIFFRACTION	Local ncs	0.10146	0.0501
11	21	E	X-RAY DIFFRACTION	Local ncs	0.08701	0.0501
11	22	G	X-RAY DIFFRACTION	Local ncs	0.08701	0.0501
12	23	F	X-RAY DIFFRACTION	Local ncs	0.11837	0.05009
12	24	G	X-RAY DIFFRACTION	Local ncs	0.11837	0.05009

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
2.79-2.862	0.374	239	0.39	4623	0.389	4871	0.51	0.491	99.8152	0.392
2.862-2.941	0.336	232	0.362	4501	0.361	4744	0.678	0.659	99.7681	0.36
2.941-3.026	0.375	236	0.339	4365	0.341	4604	0.72	0.743	99.9348	0.324
3.026-3.119	0.389	196	0.306	4292	0.31	4488	0.733	0.785	100	0.287
3.119-3.221	0.316	203	0.285	4146	0.286	4349	0.836	0.844	100	0.267
3.221-3.334	0.308	186	0.28	4013	0.282	4200	0.846	0.856	99.9762	0.262
3.334-3.46	0.299	186	0.259	3882	0.26	4069	0.872	0.9	99.9754	0.245
3.46-3.601	0.309	180	0.265	3729	0.267	3910	0.862	0.878	99.9744	0.253
3.601-3.761	0.325	182	0.293	3360	0.295	3735	0.86	0.873	94.8327	0.271
3.761-3.944	0.266	163	0.239	3403	0.241	3571	0.903	0.908	99.86	0.227
3.944-4.157	0.25	183	0.214	3217	0.216	3401	0.923	0.926	99.9706	0.207
4.157-4.409	0.231	147	0.191	3104	0.193	3254	0.934	0.941	99.9078	0.188
4.409-4.712	0.217	136	0.17	2891	0.172	3031	0.938	0.953	99.868	0.17
4.712-5.089	0.228	141	0.174	2680	0.177	2825	0.94	0.954	99.8584	0.173
5.089-5.573	0.233	128	0.188	2470	0.191	2601	0.942	0.95	99.8847	0.189
5.573-6.228	0.272	108	0.208	2257	0.211	2368	0.906	0.934	99.8733	0.209
6.228-7.187	0.242	102	0.211	1964	0.212	2069	0.922	0.933	99.855	0.214
7.187-8.79	0.184	87	0.179	1682	0.179	1771	0.951	0.957	99.8871	0.191
8.79-12.379	0.167	74	0.166	1299	0.166	1383	0.971	0.972	99.2769	0.18
12.379-96.351	0.379	38	0.27	724	0.276	782	0.822	0.859	97.4425	0.323

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi