PDB-9i1p: Structure of RecQL- Myc G-quadruplex - ADP complex from Bos taurus

ID or keywords:

Entry

Database: PDB / ID: 9i1p

Title

Structure of RecQL- Myc G-quadruplex - ADP complex from Bos taurus

Components

ATP-dependent DNA helicase
DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

Keywords

HYDROLASE / helicase DNA G-quadruplex

Function / homology

Function and homology information

four-way junction helicase activity / DNA 3'-5' helicase / 3'-5' DNA helicase activity / double-strand break repair via homologous recombination / chromosome / nucleic acid binding / DNA replication / hydrolase activity / ATP binding / metal ion binding ...
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Song, Z.Y. / Liu, N.N. / Ai, X. / Rety, S. / Xi, X.G.

Funding support

China, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2025
Title: Structural mechanism of RECQ1 helicase in unfolding G-quadruplexes compared with duplex DNA.
Authors: Song, Z.Y. / Zhang, X. / Ai, X. / Huang, L.Y. / Hou, X.M. / Fosse, P. / Liu, N.N. / Mauffret, O. / Rety, S. / Xi, X.G.

History

Deposition	Jan 16, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 1, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9i1p.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9i1p.ent.gz	800 KB	Display	PDB format
PDBx/mmJSON format	9i1p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9i1p_validation.pdf.gz	3.7 MB	Display	wwPDB validaton report
Full document	9i1p_full_validation.pdf.gz	3.8 MB	Display
Data in XML	9i1p_validation.xml.gz	85.5 KB	Display
Data in CIF	9i1p_validation.cif.gz	109.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i1/9i1p ftp://data.pdbj.org/pub/pdb/validation_reports/i1/9i1p	HTTPS FTP

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Related structure data

Related structure data	9i0sC 9i16C 9i22C 9i23C 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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RecA and Rad51
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Catabolite Activator Protein
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RNA Polymerase
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similarity (1)
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Zinc Fingers
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Parvoviruses
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Actinomycin
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Deposited unit

A: ATP-dependent DNA helicase

B: ATP-dependent DNA helicase

C: ATP-dependent DNA helicase

D: ATP-dependent DNA helicase

E: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

F: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

G: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

H: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

hetero molecules

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

1

A: ATP-dependent DNA helicase

B: ATP-dependent DNA helicase

E: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

F: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

hetero molecules

defined by author
138 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ATP-dependent DNA helicase

D: ATP-dependent DNA helicase

G: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

H: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*T)-3')

hetero molecules

defined by author
137 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.437, 126.417, 198.198
Angle α, β, γ (deg.)	90.000, 100.897, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	E-103- K
2	1	F-103- K
3	1	F-104- PO4

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 62 through 87 or resid 89...
d_2	ens_1	(chain "B" and (resid 62 through 87 or resid 89...
d_3	ens_1	(chain "C" and (resid 62 through 87 or resid 89...
d_4	ens_1	(chain "D" and (resid 62 through 87 or resid 89...
d_1	ens_2	(chain "E" and (resid 2 through 8 or resid 11 through 12 or resid 14 through 19))
d_2	ens_2	(chain "F" and (resid 2 through 8 or resid 11 through 12 or resid 14 through 19))
d_3	ens_2	(chain "G" and (resid 2 through 8 or resid 11 through 12 or resid 14 through 19))

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
d_1	1	ens_1	MET	MET	PHE	PHE	A	A	62 - 87	1 - 26
d_1	2	ens_1	LEU	LEU	GLN	GLN	A	A	89 - 90	28 - 29
d_1	3	ens_1	PHE	PHE	GLY	GLY	A	A	92 - 106	31 - 45
d_1	4	ens_1	GLU	GLU	LEU	LEU	A	A	108 - 148	47 - 87
d_1	5	ens_1	VAL	VAL	LEU	LEU	A	A	150 - 151	89 - 90
d_1	6	ens_1	LEU	LEU	PRO	PRO	A	A	154 - 166	93 - 105
d_1	7	ens_1	GLU	GLU	LYS	LYS	A	A	168 - 171	107 - 110
d_1	8	ens_1	VAL	VAL	TYR	TYR	A	A	173 - 208	112 - 147
d_1	9	ens_1	ALA	ALA	ALA	ALA	A	A	210	149
d_1	10	ens_1	ARG	ARG	GLY	GLY	A	A	212 - 228	151 - 167
d_1	11	ens_1	ASP	ASP	LEU	LEU	A	A	230 - 241	169 - 180
d_1	12	ens_1	ARG	ARG	GLN	GLN	A	A	243 - 266	182 - 205
d_1	13	ens_1	ILE	ILE	VAL	VAL	A	A	268 - 271	207 - 210
d_1	14	ens_1	CYS	CYS	THR	THR	A	A	274 - 297	213 - 236
d_1	15	ens_1	ASP	ASP	VAL	VAL	A	A	299 - 305	238 - 244
d_1	16	ens_1	LEU	LEU	GLY	GLY	A	A	307 - 310	246 - 249
d_1	17	ens_1	TYR	TYR	GLN	GLN	A	A	312 - 324	251 - 263
d_1	18	ens_1	ASP	ASP	GLU	GLU	A	A	326 - 328	265 - 267
d_1	19	ens_1	VAL	VAL	TYR	TYR	A	A	330 - 344	269 - 283
d_1	20	ens_1	ALA	ALA	ASP	ASP	A	A	346 - 352	285 - 291
d_1	21	ens_1	THR	THR	ALA	ALA	A	A	354 - 373	293 - 312
d_1	22	ens_1	GLY	GLY	GLY	GLY	A	A	375	314
d_1	23	ens_1	GLY	GLY	GLY	GLY	A	A	377	316
d_1	24	ens_1	LYS	LYS	VAL	VAL	A	A	380 - 383	319 - 322
d_1	25	ens_1	PHE	PHE	MET	MET	A	A	385 - 395	324 - 334
d_1	26	ens_1	ASN	ASN	GLY	GLY	A	A	397 - 403	336 - 342
d_1	27	ens_1	ALA	ALA	MET	MET	A	A	405 - 410	344 - 349
d_1	28	ens_1	ALA	ALA	PHE	PHE	A	A	412 - 424	351 - 363
d_1	29	ens_1	ILE	ILE	SER	SER	A	A	426 - 428	365 - 367
d_1	30	ens_1	VAL	VAL	MET	MET	A	A	430 - 432	369 - 371
d_1	31	ens_1	ASN	ASN	CYS	CYS	A	A	434 - 479	373 - 418
d_1	32	ens_1	SER	SER	SER	SER	A	A	483	422
d_1	33	ens_1	GLU	GLU	GLU	GLU	A	A	485	424
d_1	34	ens_1	ASN	ASN	CYS	CYS	A	A	488 - 493	427 - 432
d_1	35	ens_1	ASP	ASP	LEU	LEU	A	A	495 - 500	434 - 439
d_1	36	ens_1	GLN	GLN	GLU	GLU	A	A	502 - 508	441 - 447
d_1	37	ens_1	LEU	LEU	GLY	GLY	A	A	510 - 521	449 - 460
d_1	38	ens_1	GLY	GLY	PRO	PRO	A	A	523 - 538	462 - 477
d_1	39	ens_1	GLU	GLU	GLU	GLU	A	A	540 - 543	479 - 482
d_1	40	ens_1	ILE	ILE	ASN	ASN	A	A	545 - 581	484 - 520
d_1	41	ens_1	ALA	ALA	VAL	VAL	A	A	583 - 585	522 - 524
d_1	42	ens_1	THR	THR	MET	MET	A	A	587 - 588	526 - 527
d_1	43	ens_1	VAL	VAL	LYS	LYS	A	A	590 - 592	529 - 531
d_1	44	ens_1	ZN	ZN	ZN	ZN	A	I	1001
d_1	45	ens_1	ADP	ADP	ADP	ADP	A	J	1002
d_2	1	ens_1	MET	MET	PHE	PHE	B	B	62 - 87	1 - 26
d_2	2	ens_1	LEU	LEU	GLN	GLN	B	B	89 - 90	28 - 29
d_2	3	ens_1	PHE	PHE	GLY	GLY	B	B	92 - 106	31 - 45
d_2	4	ens_1	GLU	GLU	LEU	LEU	B	B	108 - 148	47 - 87
d_2	5	ens_1	VAL	VAL	LEU	LEU	B	B	150 - 151	89 - 90
d_2	6	ens_1	LEU	LEU	PRO	PRO	B	B	154 - 166	93 - 105
d_2	7	ens_1	GLU	GLU	LYS	LYS	B	B	168 - 171	107 - 110
d_2	8	ens_1	VAL	VAL	TYR	TYR	B	B	173 - 208	112 - 147
d_2	9	ens_1	ALA	ALA	ALA	ALA	B	B	210	149
d_2	10	ens_1	ARG	ARG	GLY	GLY	B	B	212 - 228	151 - 167
d_2	11	ens_1	ASP	ASP	LEU	LEU	B	B	230 - 241	169 - 180
d_2	12	ens_1	ARG	ARG	GLN	GLN	B	B	243 - 266	182 - 205
d_2	13	ens_1	ILE	ILE	VAL	VAL	B	B	268 - 271	207 - 210
d_2	14	ens_1	CYS	CYS	THR	THR	B	B	274 - 297	213 - 236
d_2	15	ens_1	ASP	ASP	VAL	VAL	B	B	299 - 305	238 - 244
d_2	16	ens_1	LEU	LEU	GLY	GLY	B	B	307 - 310	246 - 249
d_2	17	ens_1	TYR	TYR	GLN	GLN	B	B	312 - 324	251 - 263
d_2	18	ens_1	ASP	ASP	GLU	GLU	B	B	326 - 328	265 - 267
d_2	19	ens_1	VAL	VAL	TYR	TYR	B	B	330 - 344	269 - 283
d_2	20	ens_1	ALA	ALA	ASP	ASP	B	B	346 - 352	285 - 291
d_2	21	ens_1	THR	THR	ALA	ALA	B	B	354 - 373	293 - 312
d_2	22	ens_1	GLY	GLY	GLY	GLY	B	B	375	314
d_2	23	ens_1	GLY	GLY	GLY	GLY	B	B	377	316
d_2	24	ens_1	LYS	LYS	VAL	VAL	B	B	380 - 383	319 - 322
d_2	25	ens_1	PHE	PHE	MET	MET	B	B	385 - 395	324 - 334
d_2	26	ens_1	ASN	ASN	GLY	GLY	B	B	397 - 403	336 - 342
d_2	27	ens_1	ALA	ALA	MET	MET	B	B	405 - 410	344 - 349
d_2	28	ens_1	ALA	ALA	PHE	PHE	B	B	412 - 424	351 - 363
d_2	29	ens_1	ILE	ILE	SER	SER	B	B	426 - 428	365 - 367
d_2	30	ens_1	VAL	VAL	MET	MET	B	B	430 - 432	369 - 371
d_2	31	ens_1	ASN	ASN	CYS	CYS	B	B	434 - 479	373 - 418
d_2	32	ens_1	SER	SER	SER	SER	B	B	483	422
d_2	33	ens_1	GLU	GLU	GLU	GLU	B	B	485	424
d_2	34	ens_1	ASN	ASN	CYS	CYS	B	B	488 - 493	427 - 432
d_2	35	ens_1	ASP	ASP	LEU	LEU	B	B	495 - 500	434 - 439
d_2	36	ens_1	GLN	GLN	GLU	GLU	B	B	502 - 508	441 - 447
d_2	37	ens_1	LEU	LEU	GLY	GLY	B	B	510 - 521	449 - 460
d_2	38	ens_1	GLY	GLY	PRO	PRO	B	B	523 - 538	462 - 477
d_2	39	ens_1	GLU	GLU	GLU	GLU	B	B	540 - 543	479 - 482
d_2	40	ens_1	ILE	ILE	ASN	ASN	B	B	545 - 581	484 - 520
d_2	41	ens_1	ALA	ALA	VAL	VAL	B	B	583 - 585	522 - 524
d_2	42	ens_1	THR	THR	MET	MET	B	B	587 - 588	526 - 527
d_2	43	ens_1	VAL	VAL	LYS	LYS	B	B	590 - 592	529 - 531
d_2	44	ens_1	ZN	ZN	ZN	ZN	B	L	1001
d_2	45	ens_1	ADP	ADP	ADP	ADP	B	M	1002
d_3	1	ens_1	MET	MET	PHE	PHE	C	C	62 - 87	1 - 26
d_3	2	ens_1	LEU	LEU	GLN	GLN	C	C	89 - 90	28 - 29
d_3	3	ens_1	PHE	PHE	GLY	GLY	C	C	92 - 106	31 - 45
d_3	4	ens_1	GLU	GLU	LEU	LEU	C	C	108 - 148	47 - 87
d_3	5	ens_1	VAL	VAL	LEU	LEU	C	C	150 - 151	89 - 90
d_3	6	ens_1	LEU	LEU	PRO	PRO	C	C	154 - 166	93 - 105
d_3	7	ens_1	GLU	GLU	LYS	LYS	C	C	168 - 171	107 - 110
d_3	8	ens_1	VAL	VAL	TYR	TYR	C	C	173 - 208	112 - 147
d_3	9	ens_1	ALA	ALA	ALA	ALA	C	C	210	149
d_3	10	ens_1	ARG	ARG	GLY	GLY	C	C	212 - 228	151 - 167
d_3	11	ens_1	ASP	ASP	LEU	LEU	C	C	230 - 241	169 - 180
d_3	12	ens_1	ARG	ARG	GLN	GLN	C	C	243 - 266	182 - 205
d_3	13	ens_1	ILE	ILE	VAL	VAL	C	C	268 - 271	207 - 210
d_3	14	ens_1	CYS	CYS	THR	THR	C	C	274 - 297	213 - 236
d_3	15	ens_1	ASP	ASP	VAL	VAL	C	C	299 - 305	238 - 244
d_3	16	ens_1	LEU	LEU	GLY	GLY	C	C	307 - 310	246 - 249
d_3	17	ens_1	TYR	TYR	GLN	GLN	C	C	312 - 324	251 - 263
d_3	18	ens_1	ASP	ASP	GLU	GLU	C	C	326 - 328	265 - 267
d_3	19	ens_1	VAL	VAL	TYR	TYR	C	C	330 - 344	269 - 283
d_3	20	ens_1	ALA	ALA	ASP	ASP	C	C	346 - 352	285 - 291
d_3	21	ens_1	THR	THR	ALA	ALA	C	C	354 - 373	293 - 312
d_3	22	ens_1	GLY	GLY	GLY	GLY	C	C	375	314
d_3	23	ens_1	GLY	GLY	GLY	GLY	C	C	377	316
d_3	24	ens_1	LYS	LYS	VAL	VAL	C	C	380 - 383	319 - 322
d_3	25	ens_1	PHE	PHE	MET	MET	C	C	385 - 395	324 - 334
d_3	26	ens_1	ASN	ASN	GLY	GLY	C	C	397 - 403	336 - 342
d_3	27	ens_1	ALA	ALA	MET	MET	C	C	405 - 410	344 - 349
d_3	28	ens_1	ALA	ALA	PHE	PHE	C	C	412 - 424	351 - 363
d_3	29	ens_1	ILE	ILE	SER	SER	C	C	426 - 428	365 - 367
d_3	30	ens_1	VAL	VAL	MET	MET	C	C	430 - 432	369 - 371
d_3	31	ens_1	ASN	ASN	CYS	CYS	C	C	434 - 479	373 - 418
d_3	32	ens_1	SER	SER	SER	SER	C	C	483	422
d_3	33	ens_1	GLU	GLU	GLU	GLU	C	C	485	424
d_3	34	ens_1	ASN	ASN	CYS	CYS	C	C	488 - 493	427 - 432
d_3	35	ens_1	ASP	ASP	LEU	LEU	C	C	495 - 500	434 - 439
d_3	36	ens_1	GLN	GLN	GLU	GLU	C	C	502 - 508	441 - 447
d_3	37	ens_1	LEU	LEU	GLY	GLY	C	C	510 - 521	449 - 460
d_3	38	ens_1	GLY	GLY	PRO	PRO	C	C	523 - 538	462 - 477
d_3	39	ens_1	GLU	GLU	GLU	GLU	C	C	540 - 543	479 - 482
d_3	40	ens_1	ILE	ILE	ASN	ASN	C	C	545 - 581	484 - 520
d_3	41	ens_1	ALA	ALA	VAL	VAL	C	C	583 - 585	522 - 524
d_3	42	ens_1	THR	THR	MET	MET	C	C	587 - 588	526 - 527
d_3	43	ens_1	VAL	VAL	LYS	LYS	C	C	590 - 592	529 - 531
d_3	44	ens_1	ZN	ZN	ZN	ZN	C	P	1001
d_3	45	ens_1	ADP	ADP	ADP	ADP	C	Q	1002
d_4	1	ens_1	MET	MET	PHE	PHE	D	D	62 - 87	1 - 26
d_4	2	ens_1	LEU	LEU	GLN	GLN	D	D	89 - 90	28 - 29
d_4	3	ens_1	PHE	PHE	GLY	GLY	D	D	92 - 106	31 - 45
d_4	4	ens_1	GLU	GLU	LEU	LEU	D	D	108 - 148	47 - 87
d_4	5	ens_1	VAL	VAL	LEU	LEU	D	D	150 - 151	89 - 90
d_4	6	ens_1	LEU	LEU	PRO	PRO	D	D	154 - 166	93 - 105
d_4	7	ens_1	GLU	GLU	LYS	LYS	D	D	168 - 171	107 - 110
d_4	8	ens_1	VAL	VAL	TYR	TYR	D	D	173 - 208	112 - 147
d_4	9	ens_1	ALA	ALA	ALA	ALA	D	D	210	149
d_4	10	ens_1	ARG	ARG	GLY	GLY	D	D	212 - 228	151 - 167
d_4	11	ens_1	ASP	ASP	LEU	LEU	D	D	230 - 241	169 - 180
d_4	12	ens_1	ARG	ARG	GLN	GLN	D	D	243 - 266	182 - 205
d_4	13	ens_1	ILE	ILE	VAL	VAL	D	D	268 - 271	207 - 210
d_4	14	ens_1	CYS	CYS	THR	THR	D	D	274 - 297	213 - 236
d_4	15	ens_1	ASP	ASP	VAL	VAL	D	D	299 - 305	238 - 244
d_4	16	ens_1	LEU	LEU	GLY	GLY	D	D	307 - 310	246 - 249
d_4	17	ens_1	TYR	TYR	GLN	GLN	D	D	312 - 324	251 - 263
d_4	18	ens_1	ASP	ASP	GLU	GLU	D	D	326 - 328	265 - 267
d_4	19	ens_1	VAL	VAL	TYR	TYR	D	D	330 - 344	269 - 283
d_4	20	ens_1	ALA	ALA	ASP	ASP	D	D	346 - 352	285 - 291
d_4	21	ens_1	THR	THR	ALA	ALA	D	D	354 - 373	293 - 312
d_4	22	ens_1	GLY	GLY	GLY	GLY	D	D	375	314
d_4	23	ens_1	GLY	GLY	GLY	GLY	D	D	377	316
d_4	24	ens_1	LYS	LYS	VAL	VAL	D	D	380 - 383	319 - 322
d_4	25	ens_1	PHE	PHE	MET	MET	D	D	385 - 395	324 - 334
d_4	26	ens_1	ASN	ASN	GLY	GLY	D	D	397 - 403	336 - 342
d_4	27	ens_1	ALA	ALA	MET	MET	D	D	405 - 410	344 - 349
d_4	28	ens_1	ALA	ALA	PHE	PHE	D	D	412 - 424	351 - 363
d_4	29	ens_1	ILE	ILE	SER	SER	D	D	426 - 428	365 - 367
d_4	30	ens_1	VAL	VAL	MET	MET	D	D	430 - 432	369 - 371
d_4	31	ens_1	ASN	ASN	CYS	CYS	D	D	434 - 479	373 - 418
d_4	32	ens_1	SER	SER	SER	SER	D	D	483	422
d_4	33	ens_1	GLU	GLU	GLU	GLU	D	D	485	424
d_4	34	ens_1	ASN	ASN	CYS	CYS	D	D	488 - 493	427 - 432
d_4	35	ens_1	ASP	ASP	LEU	LEU	D	D	495 - 500	434 - 439
d_4	36	ens_1	GLN	GLN	GLU	GLU	D	D	502 - 508	441 - 447
d_4	37	ens_1	LEU	LEU	GLY	GLY	D	D	510 - 521	449 - 460
d_4	38	ens_1	GLY	GLY	PRO	PRO	D	D	523 - 538	462 - 477
d_4	39	ens_1	GLU	GLU	GLU	GLU	D	D	540 - 543	479 - 482
d_4	40	ens_1	ILE	ILE	ASN	ASN	D	D	545 - 581	484 - 520
d_4	41	ens_1	ALA	ALA	VAL	VAL	D	D	583 - 585	522 - 524
d_4	42	ens_1	THR	THR	MET	MET	D	D	587 - 588	526 - 527
d_4	43	ens_1	VAL	VAL	LYS	LYS	D	D	590 - 592	529 - 531
d_4	44	ens_1	ZN	ZN	ZN	ZN	D	S	1001
d_4	45	ens_1	ADP	ADP	ADP	ADP	D	T	1002
d_1	1	ens_2	DG	DG	DT	DT	E	E	2 - 5	2 - 5
d_2	1	ens_2	DG	DG	DT	DT	F	F	2 - 5	2 - 5
d_3	1	ens_2	DG	DG	DT	DT	G	G	2 - 5	2 - 5

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.999952991672, 0.00457394162981, 0.00854947386152), (-0.00456888987323, -0.999989376319, 0.000610322978362), (0.00855217461632, 0.000571232683552, 0.999963266327)	-101.183000093, 106.579825733, 0.481609962344
2	given	(0.00445081490019, 0.999974291722, -0.00562193392587), (0.999952644251, -0.0044992335848, -0.00862937725349), (-0.008654449801, -0.00558325993412, -0.999946962447)	-84.2351465972, 60.3022528957, 97.0482581975
3	given	(-0.00242164387543, -0.999996860024, 0.000644656597402), (-0.99999603679, 0.00242256659653, 0.00143442536944), (-0.00143598258891, -0.000641180375082, -0.99999876342)	21.8655314833, -41.1733975131, 97.2014789359
4	given	(-0.999942956879, -0.00552162970659, -0.00914300786123), (0.00564453633586, -0.999893317841, -0.0134719020867), (-0.00906764561065, -0.0135227416475, 0.999867447846)	-99.1541043274, 108.182527286, 0.393509196281
5	given	(0.0109906294605, 0.999892002953, 0.00975645914127), (0.999723474873, -0.0111905818051, 0.0206819889355), (0.0207889357959, 0.00952645315827, -0.999738499228)	-85.4022765118, 57.9960635348, 97.2406196405

-
Protein / DNA chain , 2 types, 8 molecules ABCDEFGH

#1: Protein	ATP-dependent DNA helicase Mass: 60555.328 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RECQL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): K-12 / References: UniProt: A0JN36, DNA helicase
#2: DNA chain	DNA (5'-D(PAPGPGPGPTPGPGPGPTPAPGPGPGPTPGPGPGPTPTPTPT)-3') Mass: 7573.854 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Bos taurus* (domestic cattle)

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Non-polymers , 5 types, 25 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#7: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.56 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Sodium Nitrate 0.3M Sodium Phosphate dibasique 0.3M Ammonium Sulfate 0.3M 0.1M Tris Bicine ph 8.5 12% Ethylene Glycol 6% PEG 8000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97847 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97847 Å / Relative weight: 1
Reflection	Resolution: 3.2→76.55 Å / Num. obs: 37700 / % possible obs: 86.9 % / Redundancy: 6.6 % / B_iso Wilson estimate: 89.26 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.193 / Net I/σ(I): 8
Reflection shell	Resolution: 3.2→3.49 Å / Redundancy: 6 % / R_merge(I) obs: 1.196 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1186 / CC_1/2: 0.536 / % possible all: 34.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
autoPROC		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→76.55 Å / SU ML: 0.4351 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.0424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2876	1847	4.9 %
R_work	0.2443	35810	-
obs	0.2464	37657	74.68 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 103.32 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→76.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16948	1740	134	0	18822

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0034	19376
X-RAY DIFFRACTION	f_angle_d	0.8614	26532
X-RAY DIFFRACTION	f_chiral_restr	0.0597	2919
X-RAY DIFFRACTION	f_plane_restr	0.0042	3042
X-RAY DIFFRACTION	f_dihedral_angle_d	17.876	7434

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	0.847119564964
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	0.854090803362
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	0.859865583232
ens_2	d_2	E	E	X-RAY DIFFRACTION	Torsion NCS	0.442816562745
ens_2	d_3	E	E	X-RAY DIFFRACTION	Torsion NCS	0.519457366048

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 (%)
3.2-3.28	0.2784	13	0.3322	266	X-RAY DIFFRACTION	7.24
3.28-3.38	0.4026	33	0.3289	717	X-RAY DIFFRACTION	19.61
3.38-3.49	0.3493	47	0.3178	809	X-RAY DIFFRACTION	22.13
3.49-3.61	0.3493	94	0.3212	2184	X-RAY DIFFRACTION	58.92
3.61-3.76	0.4045	131	0.3203	2332	X-RAY DIFFRACTION	63.66
3.76-3.93	0.312	185	0.2992	3626	X-RAY DIFFRACTION	99.04
3.93-4.14	0.312	205	0.2671	3653	X-RAY DIFFRACTION	99.97
4.14-4.4	0.2829	190	0.2503	3678	X-RAY DIFFRACTION	99.92
4.4-4.73	0.3062	192	0.2338	3673	X-RAY DIFFRACTION	99.79
4.73-5.21	0.29	186	0.2331	3714	X-RAY DIFFRACTION	99.92
5.21-5.96	0.2889	183	0.2483	3698	X-RAY DIFFRACTION	100
5.97-7.51	0.306	189	0.2588	3713	X-RAY DIFFRACTION	99.95
7.51-76.55	0.221	199	0.1889	3747	X-RAY DIFFRACTION	99.22

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.93610817043	-0.299896322594	-0.57083117134	0.586609011905	0.455635660304	1.59682130827	0.351064446508	-0.297172586782	0.711746928661	0.431341045975	-0.329241472486	0.0665778597804	-0.0624580778816	-0.0231123426492	-0.00963144554576	1.22210895565	-0.631628019262	0.199157449461	0.662034719628	-0.221675169394	0.843621530801	-54.1444823045	76.6921630796	73.2086633898
2	1.4143391611	-0.428825410696	-0.162039134504	3.847482661	0.680870508567	1.24162069663	0.323020898466	-0.246151197621	0.175083662361	0.260771173941	-0.14405917959	-0.252210098913	-0.163060042583	0.288680377101	-0.182200174209	1.00271163831	-0.757868964699	-0.164680675232	0.744244432143	0.0568303301504	0.784339802599	-19.7427501456	59.0138918797	70.8691926154
3	4.28932799394	0.915356457515	0.478347410946	2.40567253538	0.472470855763	1.12967628438	0.304459239033	-0.229207452659	-0.654224240389	0.296058739187	-0.258104093881	-0.140550623005	0.253532693645	0.00682751150193	-0.0571586272679	0.966209128626	-0.664202961025	-0.276532742325	0.613513073109	0.0831265049495	0.569715861448	-45.9169458608	30.0203893642	73.4318930926
4	1.96480625838	-0.674112557596	0.332307845228	4.27982581285	-0.191190849251	1.06219640411	0.128611663255	0.0437330916485	-0.141069400889	0.164819791772	-0.134849138032	0.200773587538	-0.147732232232	-0.152296138786	-0.0588566893895	1.01348046842	-0.706824173182	0.140304013606	0.656210558231	-0.0794485858881	0.671476397171	-80.6154806495	47.8120756521	71.1389455587

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 62 through 285 )	A	A	62 - 285	1 - 224
2	2	chain 'A' and (resid 286 through 592 )	A	A	286 - 592	225 - 531
3	3	chain 'B' and (resid 63 through 285 )	B	E	63 - 285	2 - 224
4	4	chain 'B' and (resid 286 through 592 )	B	E	286 - 592	225 - 531

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