PDB-5yrq: Crystal structure of Rad5 and Rev1

ID or keywords:

Entry

Database: PDB / ID: 5yrq

Title

Crystal structure of Rad5 and Rev1

Components

DNA repair protein RAD5,DNA repair protein REV1

Keywords

DNA BINDING PROTEIN / Rad5 / DNA damage tolerance / E3 ligase / TLS polymerase / Rev1

Function / homology

Function and homology information

error-free postreplication DNA repair / deoxycytidyl transferase activity / free ubiquitin chain polymerization / Y-form DNA binding / four-way junction helicase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.999 Å

Authors

Chen, Z.C. / Zhou, C.Y.

Citation

Journal: Nucleic Acids Res. / Year: 2016
Title: Involvement of budding yeast Rad5 in translesion DNA synthesis through physical interaction with Rev1.
Authors: Xu, X. / Lin, A.Y. / Zhou, C.Y. / Blackwell, S.R. / Zhang, Y.R. / Wang, Z.H. / Feng, Q.Q. / Guan, R.F. / Hanna, M.D. / Chen, Z.C. / Xiao, W.

History

Deposition	Nov 9, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5yrq.cif.gz	219 KB	Display	PDBx/mmCIF format
PDB format	pdb5yrq.ent.gz	178.1 KB	Display	PDB format
PDBx/mmJSON format	5yrq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5yrq_validation.pdf.gz	458 KB	Display	wwPDB validaton report
Full document	5yrq_full_validation.pdf.gz	464.4 KB	Display
Data in XML	5yrq_validation.xml.gz	20.5 KB	Display
Data in CIF	5yrq_validation.cif.gz	28.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yr/5yrq ftp://data.pdbj.org/pub/pdb/validation_reports/yr/5yrq	HTTPS FTP

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Related structure data

Related structure data	2abc
Similar structure data	6axf-5 6axf-2 6o35-d 5wfn-2 6t5e-d 6sy6-d 1yvp-1 6b2y-d 4rwt-2 1nbs-1 Search similar-shape structures by Omokage search (details) 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	#255 - Mar 2021 Cisplatin and DNA similarity (7) #91 - Jul 2007 Thymine Dimers similarity (5) #161 - May 2013 Ricin similarity (3) #55 - Jul 2004 DNA Ligase similarity (4) #150 - Jun 2012 Sliding Clamps similarity (4) #163 - Jul 2013 HIV Capsid similarity (2) #241 - Jan 2020 Twenty Years of Molecules similarity (4) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: DNA repair protein RAD5,DNA repair protein REV1

B: DNA repair protein RAD5,DNA repair protein REV1

D: DNA repair protein RAD5,DNA repair protein REV1

E: DNA repair protein RAD5,DNA repair protein REV1

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

1

Idetical with deposited unit
defined by author&software
Evidence: immunoprecipitation

Unit cell

Length a, b, c (Å)	58.589, 49.280, 103.074
Angle α, β, γ (deg.)	90.00, 92.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DNA repair protein RAD5,DNA repair protein REV1 / Radiation sensitivity protein 5 / Revertibility protein 2 / Reversionless protein 1 Mass: 16953.314 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The Rad5 (5-20) and Rev1 (876-985) coding sequences linked with the flexible linker sequence GGSSSSLVPRGSGGSGGSP Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RAD5, REV2, SNM2, YLR032W, REV1, YOR346W, O6339 / Production host: Escherichia coli 042 (bacteria) / Strain (production host): 042 References: UniProt: P32849, UniProt: P12689, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; Transferring phosphorus- ...References: UniProt: P32849, UniProt: P12689, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

DNA repair protein RAD5,DNA repair protein REV1 / Radiation sensitivity protein 5 / Revertibility protein 2 / Reversionless protein 1

Mass: 16953.314 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The Rad5 (5-20) and Rev1 (876-985) coding sequences linked with the flexible linker sequence GGSSSSLVPRGSGGSGGSP
Source: (gene. exp.)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD5, REV2, SNM2, YLR032W, REV1, YOR346W, O6339 / Production host:

Escherichia coli 042 (bacteria) / Strain (production host): 042
References: UniProt: P32849, UniProt: P12689, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; Transferring phosphorus- ...

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.9 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18-20% PEG 3350, 100mM potassium citrate, 100mM HEPES, 5mM DTT, pH 7.0 PH range: 7.0-7.5 / Temp details: Homoiothermy

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97911 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97911 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 38367 / % possible obs: 95.7 % / Redundancy: 3 % / R_merge(I) obs: 0.184 / R_sym value: 0.086 / Net I/σ(I): 16
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.184 / Mean I/σ(I) obs: 6.2 / % possible all: 89.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000	v705a	data reduction
HKL-2000	v705a	data scaling
PHASER	v7.0	phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 1.999→29.133 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2463	1911	4.98 %
R_work	0.205	-	-
obs	0.2071	38367	95.49 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.999→29.133 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4075	0	0	154	4229

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4151
X-RAY DIFFRACTION	f_angle_d	0.815	5579
X-RAY DIFFRACTION	f_dihedral_angle_d	15.436	2511
X-RAY DIFFRACTION	f_chiral_restr	0.045	620
X-RAY DIFFRACTION	f_plane_restr	0.006	710

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 (%)
1.9991-2.0491	0.2749	122	0.212	2303	X-RAY DIFFRACTION	84
2.0491-2.1045	0.2862	146	0.2099	2536	X-RAY DIFFRACTION	95
2.1045-2.1664	0.2932	131	0.2094	2572	X-RAY DIFFRACTION	95
2.1664-2.2363	0.2561	144	0.1986	2548	X-RAY DIFFRACTION	94
2.2363-2.3162	0.2691	116	0.2145	2588	X-RAY DIFFRACTION	95
2.3162-2.4089	0.237	136	0.2029	2529	X-RAY DIFFRACTION	94
2.4089-2.5184	0.3108	106	0.2106	2566	X-RAY DIFFRACTION	94
2.5184-2.6511	0.2321	130	0.2146	2601	X-RAY DIFFRACTION	94
2.6511-2.8171	0.2763	152	0.2336	2665	X-RAY DIFFRACTION	99
2.8171-3.0344	0.2471	158	0.2308	2696	X-RAY DIFFRACTION	99
3.0344-3.3394	0.281	146	0.2307	2702	X-RAY DIFFRACTION	99
3.3394-3.8217	0.2313	144	0.193	2714	X-RAY DIFFRACTION	99
3.8217-4.8114	0.2014	143	0.1747	2700	X-RAY DIFFRACTION	98
4.8114-29.1357	0.2321	137	0.1976	2736	X-RAY DIFFRACTION	96

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	3.0966	0.5795	0.8385	6.9962	1.1339	3.8038	-0.1323	0.1479	0.2556	-0.3138	0.0927	-0.4501	-0.0058	0.1687	0.0414	0.0724	-0.024	0.0073	0.1742	-0.023	0.1378	40.5583	-7.5949	3.7537
2	1.756	-0.7168	-0.1111	3.0908	1.7624	2.3779	-0.1582	-0.3235	0.1395	0.2216	0.1097	-0.1479	0.1147	0.0894	0.0398	0.1466	0.0245	-0.0124	0.1362	-0.0015	0.09	36.4657	-10.8905	10.5267
3	1.7506	1.8926	0.3516	2.0855	-0.5483	2.0679	0.0728	-0.3999	-0.8239	-0.5318	0.2341	-0.3586	1.5955	0.8715	0.0063	0.5281	0.1633	0.0201	0.1998	-0.0279	0.2888	37.4073	-25.8287	5.6656
4	3.4401	0.4408	-0.4863	8.7836	5.572	8.739	-0.2901	-0.4987	0.0801	0.9792	0.2569	0.305	0.4957	0.0711	-0.0384	0.1949	0.0689	0.0354	0.2618	0.018	0.1359	34.1389	-13.2988	19.4157
5	0.8658	1.0256	0.9248	2.354	0.5913	7.6485	0.175	0.1288	-0.2941	-0.1276	-0.1805	-0.6136	0.3966	0.3947	-0.034	0.2357	0.0616	0.0856	0.1131	-0.0505	0.1619	28.794	-2.3016	39.7073
6	2.5874	1.0866	0.0804	2.2251	2.5837	3.9933	0.129	-0.2296	-0.0321	0.3412	-0.4038	0.8155	0.2728	-0.6281	0.2702	0.1578	0.0116	-0.0457	0.5575	-0.0505	0.4944	-1.6285	1.3667	23.6484
7	8.009	-1.6355	-0.1339	8.6652	2.1208	9.0434	-0.566	0.2811	0.4919	-0.481	0.4427	1.5381	-1.4122	-1.7344	0.113	0.4398	0.1697	-0.009	0.6307	0.0143	0.7726	1.6188	14.5973	33.7448
8	2.7402	0.6397	-0.7376	6.614	2.32	3.716	-0.1693	0.6476	-0.4042	-0.684	-0.2458	0.9788	0.2378	-0.7544	0.311	0.2214	-0.0842	-0.0581	0.3282	-0.0828	0.2782	10.6241	-8.8917	9.5756
9	5.0474	-4.582	-1.3649	7.6625	2.6786	1.9574	-0.3089	-0.213	-0.4345	0.8338	-0.2739	1.1659	0.5664	-0.8405	0.4154	0.2393	-0.1016	0.1177	0.3046	-0.0355	0.2934	9.2537	-8.7696	20.3566
10	2.1338	0.2586	-1.0205	3.7655	-0.5495	3.4762	-0.1659	-0.0557	-0.1279	0.0068	0.1369	0.0129	0.2998	-0.3169	0.0079	0.1116	-0.0315	-0.0041	0.1087	-0.0067	0.1038	20.1682	-4.6148	14.9587
11	0.1608	0.8733	1.1752	4.2806	5.8737	8.0166	0.0437	-0.3937	-0.6138	0.6476	0.0329	-0.7583	1.7934	0.0608	-0.0555	0.5874	0.0549	0.1631	0.4478	0.1012	0.518	25.3167	-20.2562	17.5121
12	2.4942	0.639	1.4698	5.8196	3.9275	7.0799	-0.2327	-0.2287	0.2348	-0.12	0.0935	-0.6074	0.3593	-0.3807	0.1832	0.6423	0.0857	-0.043	0.4162	0.1186	0.4741	29.846	-31.4243	5.5013
13	9.88	0.3975	0.5183	8.3982	2.4581	6.2835	-0.0705	-0.3847	-1.0436	0.1457	-0.0068	-0.1941	0.2752	0.1585	0.0857	0.1253	0.034	0.0291	0.1612	-0.001	0.2224	38.9124	6.9163	47.6982
14	5.1102	-0.2154	-2.0621	3.8132	1.2552	4.5697	0.1057	-0.0855	0.1501	-0.049	0.1042	-0.5612	-0.7148	0.4251	-0.166	0.1833	-0.0387	-0.0125	0.1914	-0.0433	0.1734	41.6237	21.4801	45.5915
15	2.0943	-1.1178	-1.045	3.837	2.4393	4.5906	0.0162	0.1355	0.0603	-0.3753	0.0584	-0.2494	-0.4165	0.1657	-0.0297	0.1752	-0.0411	0.0226	0.1398	0.011	0.1011	32.8395	17.1261	42.8806
16	1.8838	0.2666	0.6215	3.7488	4.0828	7.9677	-0.3795	0.5692	0.2388	-0.5673	0.3617	0.1382	-0.6685	0.4078	-0.0567	0.3386	-0.1481	-0.0037	0.261	0.0376	0.1157	34.0422	22.747	36.9191
17	2.4735	-0.0634	-1.9296	2.7211	-2.2025	8.4425	0.2083	-0.2061	0.164	0.4071	-0.0708	-0.4158	-0.4321	0.4685	-0.1518	0.1693	-0.0296	-0.035	0.0881	-0.0268	0.1711	29.9297	7.6539	12.4723
18	2.0085	-4.7887	4.5293	8.1556	2.0554	7.3762	0.3396	0.4296	-0.777	-0.2848	0.2601	-0.2499	1.3723	0.2658	-0.5589	0.3344	-0.0116	0.0193	0.2635	-0.085	0.3933	49.1932	-17.5368	4.9128
19	1.7437	2.9242	2.4912	5.7461	4.0952	3.5432	0.1069	-0.9589	0.7357	0.7883	-0.4201	-0.5624	0.0316	0.7349	0.2633	0.2576	-0.0939	-0.0454	0.4518	-0.0411	0.3857	51.1208	-5.8058	10.2156
20	7.0745	-1.4859	-3.276	4.7334	1.0403	5.8436	-0.0202	-0.0333	0.3353	0.067	-0.0135	-0.0159	-0.6957	-0.0345	0.0571	0.2937	-0.0362	-0.028	0.2588	-0.0521	0.3987	48.8211	24.6882	47.5484
21	2.013	-3.2538	-1.6512	2.0193	0.4974	2.0125	-0.2157	0.1822	-0.7918	-0.0399	0.076	-1.1711	0.2096	1.093	0.1802	0.346	-0.0227	0.0562	0.3696	-0.0174	0.5601	49.272	13.8346	45.9993
22	0.7363	-0.2914	1.7621	2.2127	2.8167	2.0057	-0.2201	0.1412	-0.3763	0.101	-0.0308	0.605	0.0314	-0.2955	0.1836	0.1635	-0.0097	0.0271	0.7904	-0.0618	0.4132	-3.4935	6.0202	31.0194
23	2.1342	-3.4295	-2.0284	5.7513	2.3671	6.6674	-0.3283	0.5922	-0.2755	0.0073	-0.1326	1.0091	0.464	-0.9172	0.3338	0.1914	-0.0438	-0.0214	0.516	-0.0851	0.5046	1.5357	-4.6087	17.0085
24	2.4241	-0.0886	0.3284	4.896	2.1601	4.3676	-0.3443	-0.5916	0.2722	0.4188	-0.0828	0.8603	-0.3913	-0.9674	0.3016	0.238	0.1196	0.0178	0.3272	-0.0845	0.2586	8.8175	13.1531	38.749
25	3.5138	1.3412	-0.242	6.4521	-0.121	4.3051	-0.3847	0.0722	0.6333	-0.3504	0.0672	0.3312	-1.0694	-0.592	0.2258	0.4843	0.1345	-0.083	0.1836	0.0542	0.2332	14.0416	21.8303	31.7124
26	1.8136	-0.8476	-0.0775	7.0144	-1.8269	2.5583	0.0174	0.0756	-0.0108	0.1942	0.0059	0.1293	-0.1826	-0.2617	-0.0083	0.1727	0.0169	-0.013	0.1333	-0.0135	0.0909	20.1155	8.3732	40.6663
27	2.6125	-0.9458	-0.7219	4.0536	-0.4023	3.421	-0.1003	0.0169	0.143	-0.6431	-0.0271	-0.1756	-0.2017	0.0424	0.1446	0.2715	0.0179	0.008	0.1546	-0.0129	0.1248	20.224	9.2497	31.1882
28	2.1552	1.9107	0.5459	2.0103	3.7041	1.3658	0.1694	0.0715	-0.0437	-0.1867	0.376	0.0778	-0.6635	-0.3602	-0.4783	0.8572	-0.0603	0.0363	0.5617	0.1803	0.4657	27.9152	35.6409	45.6505

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 873:901)
2	X-RAY DIFFRACTION	2	(chain A and resid 902:944)
3	X-RAY DIFFRACTION	3	(chain A and resid 945:955)
4	X-RAY DIFFRACTION	4	(chain A and resid 956:970)
5	X-RAY DIFFRACTION	5	(chain A and resid 971:985)
6	X-RAY DIFFRACTION	6	(chain B and resid 2:11)
7	X-RAY DIFFRACTION	7	(chain B and resid 12:16)
8	X-RAY DIFFRACTION	8	(chain D and resid 873:903)
9	X-RAY DIFFRACTION	9	(chain D and resid 904:914)
10	X-RAY DIFFRACTION	10	(chain D and resid 915:964)
11	X-RAY DIFFRACTION	11	(chain D and resid 965:977)
12	X-RAY DIFFRACTION	12	(chain D and resid 978:985)
13	X-RAY DIFFRACTION	13	(chain E and resid 874:889)
14	X-RAY DIFFRACTION	14	(chain E and resid 890:912)
15	X-RAY DIFFRACTION	15	(chain E and resid 913:948)
16	X-RAY DIFFRACTION	16	(chain E and resid 949:969)
17	X-RAY DIFFRACTION	17	(chain E and resid 970:985)
18	X-RAY DIFFRACTION	18	(chain A and resid 9:12)
19	X-RAY DIFFRACTION	19	(chain A and resid 13:20)
20	X-RAY DIFFRACTION	20	(chain E and resid 9:11)
21	X-RAY DIFFRACTION	21	(chain E and resid 12:17)
22	X-RAY DIFFRACTION	22	(chain D and resid 2:7)
23	X-RAY DIFFRACTION	23	(chain D and resid 8:16)
24	X-RAY DIFFRACTION	24	(chain B and resid 874:908)
25	X-RAY DIFFRACTION	25	(chain B and resid 909:922)
26	X-RAY DIFFRACTION	26	(chain B and resid 923:947)
27	X-RAY DIFFRACTION	27	(chain B and resid 948:976)
28	X-RAY DIFFRACTION	28	(chain B and resid 977:985)

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Yorodumi