PDB-6ftu: Structure of a Quadruplex forming sequence from D. discoideum

Basic information

• Entry: Database: PDB / ID: 6ftu
• Title: Structure of a Quadruplex forming sequence from D. discoideum
• Components: DNA (26-MER)
• Keywords: DNA / Quadruplex / four quartets
• Function / homology: : / DNA / DNA (> 10)
• Biological species: Dictyostelium discoideum (eukaryote)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
• Authors: Guedin, A. / Linda, L. / Armane, S. / Lacroix, L. / Mergny, J.L. / Thore, S. / Yatsunyk, L.A.

Funding support

United States, 1items

Organization	Grant number	Country
National Institutes of Health	1R15CA208676-01A1	United States

• Citation: Journal: Nucleic Acids Res. / Year: 2018; Title: Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome.; Authors: Guedin, A. / Lin, L.Y. / Armane, S. / Lacroix, L. / Mergny, J.L. / Thore, S. / Yatsunyk, L.A.

History

Deposition	Feb 23, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 18, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 25, 2018	Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2	May 9, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3	May 23, 2018	Group: Data collection / Category: diffrn_source Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4	Jun 13, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5	Aug 14, 2019	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.6	Jan 17, 2024	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_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

Assembly

Deposited unit

A: DNA (26-MER)

B: DNA (26-MER)

C: DNA (26-MER)

D: DNA (26-MER)

E: DNA (26-MER)

F: DNA (26-MER)

Z: DNA (26-MER)

hetero molecules

Summary:

• 59 kDa, 7 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	58,951	28
Polymers	58,130	7
Non-polymers	821	21
Water	0	0

1

A: DNA (26-MER)

hetero molecules

Summary:

• defined by author&software
• Evidence: native gel electrophoresis
• 8.42 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,422	4
Polymers	8,304	1
Non-polymers	117	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

2

B: DNA (26-MER)

hetero molecules

Summary:

• defined by author&software
• 8.42 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,422	4
Polymers	8,304	1
Non-polymers	117	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

3

C: DNA (26-MER)

hetero molecules

Summary:

• defined by author&software
• 8.42 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,422	4
Polymers	8,304	1
Non-polymers	117	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

4

D: DNA (26-MER)

hetero molecules

Summary:

• defined by author&software
• 8.42 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,422	4
Polymers	8,304	1
Non-polymers	117	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

5

E: DNA (26-MER)

hetero molecules

Summary:

• defined by author&software
• 8.42 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,422	4
Polymers	8,304	1
Non-polymers	117	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

6

F: DNA (26-MER)

hetero molecules

Summary:

• defined by author&software
• 8.42 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,422	4
Polymers	8,304	1
Non-polymers	117	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

7

Z: DNA (26-MER)

hetero molecules

Summary:

• defined by author&software
• 8.42 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,422	4
Polymers	8,304	1
Non-polymers	117	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

Unit cell

Length a, b, c (Å)	72.060, 135.750, 55.200
Angle α, β, γ (deg.)	90.00, 93.58, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	Z
1	7	B
2	7	C
1	8	B
2	8	D
1	9	B
2	9	E
1	10	B
2	10	F
1	11	B
2	11	Z
1	12	C
2	12	D
1	13	C
2	13	E
1	14	C
2	14	F
1	15	C
2	15	Z
1	16	D
2	16	E
1	17	D
2	17	F
1	18	D
2	18	Z
1	19	E
2	19	F
1	20	E
2	20	Z
1	21	F
2	21	Z

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DG / End label comp-ID: DG / Refine code: _ / Auth seq-ID: 1 - 26 / Label seq-ID: 1 - 26

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	Z	G
1	7	B	B
2	7	C	C
1	8	B	B
2	8	D	D
1	9	B	B
2	9	E	E
1	10	B	B
2	10	F	F
1	11	B	B
2	11	Z	G
1	12	C	C
2	12	D	D
1	13	C	C
2	13	E	E
1	14	C	C
2	14	F	F
1	15	C	C
2	15	Z	G
1	16	D	D
2	16	E	E
1	17	D	D
2	17	F	F
1	18	D	D
2	18	Z	G
1	19	E	E
2	19	F	F
1	20	E	E
2	20	Z	G
1	21	F	F
2	21	Z	G

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

Components

#1: DNA chain

A B C D E F Z
DNA (26-MER)

Details:

Mass: 8304.325 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) Dictyostelium discoideum (eukaryote)

#2: Chemical

A-101 A-102 A-103 B-101 B-102 B-103 C-101 C-102 C-103 D-101 D-102 D-103 E-101 E-102 E-103 F-101 F-102 F-103 Z-101 Z-102 ...
ChemComp-K / POTASSIUM ION

Details:

Mass: 39.098 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: K

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.41 ų/Da / Density % sol: 48.89 %
• Crystal grow: Temperature: 298 K / Method: vapor diffusion, sitting drop; Details: NaCl, MgCl2, sodium cacodylate pH 6.0, 2-methyl-2,4-pentanediol (MPD), spermine tetrahydrochloride

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
• Detector: Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2015
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97857 Å / Relative weight: 1
• Reflection: Resolution: 2.95→67.88 Å / Num. obs: 10099 / % possible obs: 99.7 % / Redundancy: 3.4 % / R_rim(I) all: 0.058 / Net I/σ(I): 17.07
• Reflection shell: Resolution: 2.95→3.05 Å / Redundancy: 3 % / R_merge(I) obs: 0.579 / Num. unique obs: 742 / R_rim(I) all: 0.579 / % possible all: 100

Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JRN

1jrn

Resolution: 2.95→67.88 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.917 / SU B: 23.077 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.537 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.28705	1108	9.9 %	RANDOM
Rwork	0.21775	-	-	-
obs	0.22454	10040	99.73 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 83.096 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.52 Å2	0 Å2	0.48 Å2
2-	-	0.4 Å2	-0 Å2
3-	-	-	-0.97 Å2

Refinement step

Cycle: 1 / Resolution: 2.95→67.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	3735	21	0	3756

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.01	4225
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.255	1.13	6544
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	525
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	2006
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.175	8.283	4221
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	15.722	78.435	21451
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	540	0.2
1	2	B	540	0.2
2	1	A	584	0.18
2	2	C	584	0.18
3	1	A	504	0.22
3	2	D	504	0.22
4	1	A	568	0.19
4	2	E	568	0.19
5	1	A	584	0.14
5	2	F	584	0.14
6	1	A	476	0.22
6	2	Z	476	0.22
7	1	B	538	0.19
7	2	C	538	0.19
8	1	B	482	0.19
8	2	D	482	0.19
9	1	B	526	0.19
9	2	E	526	0.19
10	1	B	546	0.18
10	2	F	546	0.18
11	1	B	444	0.22
11	2	Z	444	0.22
12	1	C	502	0.2
12	2	D	502	0.2
13	1	C	560	0.2
13	2	E	560	0.2
14	1	C	584	0.16
14	2	F	584	0.16
15	1	C	474	0.22
15	2	Z	474	0.22
16	1	D	492	0.22
16	2	E	492	0.22
17	1	D	508	0.21
17	2	F	508	0.21
18	1	D	434	0.23
18	2	Z	434	0.23
19	1	E	572	0.16
19	2	F	572	0.16
20	1	E	484	0.21
20	2	Z	484	0.21
21	1	F	488	0.22
21	2	Z	488	0.22

LS refinement shell

Resolution: 2.95→3.027 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.616	78	-
Rwork	0.611	737	-
obs	-	-	100 %