PDB-8ir2: Crystal structure of the SLF1 BRCT domain in complex with a Rad18...

ID or keywords:

Entry

Database: PDB / ID: 8ir2

Title

Crystal structure of the SLF1 BRCT domain in complex with a Rad18 peptide containing pS442 and pS444

Components

SER-ASP-SER-CYS-ASN-SER-SEP-SER-SEP-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU
SMC5-SMC6 complex localization factor protein 1

Keywords

GENE REGULATION / SLF1 / BRCT

Function / homology

ISOPROPYL ALCOHOL / Uncharacterized protein

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Xiang, S. / Huang, W. / Qiu, F.

Funding support

China, 2items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Structural insights into Rad18 targeting by the SLF1 BRCT domains.
Authors: Huang, W. / Qiu, F. / Zheng, L. / Shi, M. / Shen, M. / Zhao, X. / Xiang, S.

History

Deposition	Mar 17, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 15, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ir2.cif.gz	204.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ir2.ent.gz	160.5 KB	Display	PDB format
PDBx/mmJSON format	8ir2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ir2_validation.pdf.gz	473.5 KB	Display	wwPDB validaton report
Full document	8ir2_full_validation.pdf.gz	478.6 KB	Display
Data in XML	8ir2_validation.xml.gz	24.2 KB	Display
Data in CIF	8ir2_validation.cif.gz	36.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ir/8ir2 ftp://data.pdbj.org/pub/pdb/validation_reports/ir/8ir2	HTTPS FTP

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Related structure data

Related structure data	8ir4C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: SMC5-SMC6 complex localization factor protein 1

B: SMC5-SMC6 complex localization factor protein 1

C: SER-ASP-SER-CYS-ASN-SER-SEP-SER-SEP-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU

D: SER-ASP-SER-CYS-ASN-SER-SEP-SER-SEP-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU

hetero molecules

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

1

A: SMC5-SMC6 complex localization factor protein 1

C: SER-ASP-SER-CYS-ASN-SER-SEP-SER-SEP-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU

hetero molecules

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

2

B: SMC5-SMC6 complex localization factor protein 1

D: SER-ASP-SER-CYS-ASN-SER-SEP-SER-SEP-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU

hetero molecules

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

Unit cell

Length a, b, c (Å)	40.352, 76.203, 141.614
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein	SMC5-SMC6 complex localization factor protein 1 / Ankyrin repeat domain-containing protein 32 / BRCT domain-containing protein 1 / Smc5/6 localization factor 1 Mass: 24034.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLF1, ANKRD32, BRCTD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQI6
#2: Protein/peptide	SER-ASP-SER-CYS-ASN-SER-SEP-SER-SEP-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU Mass: 2001.888 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

#1: Protein

SMC5-SMC6 complex localization factor protein 1 / Ankyrin repeat domain-containing protein 32 / BRCT domain-containing protein 1 / Smc5/6 localization factor 1

Mass: 24034.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: SLF1, ANKRD32, BRCTD1 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9BQI6

#2: Protein/peptide

SER-ASP-SER-CYS-ASN-SER-SEP-SER-SEP-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU

Mass: 2001.888 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.)

Homo sapiens (human)

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Non-polymers , 4 types, 575 molecules

#3: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.09 Å³/Da / Density % sol: 41.16 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.19M MgCl2, 0.1M BIS-TRIS pH6.5, 25% PEG3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.9785 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 4, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9785 Å / Relative weight: 1

Reflection

Resolution: 1.75→50 Å / Num. obs: 44776 / % possible obs: 100 % / Redundancy: 11.6 % / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.17 / R_pim(I) all: 0.051 / R_rim(I) all: 0.178 / Χ²: 0.646 / Net I/σ(I): 3.7 / Num. measured all: 520523

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.75-1.78	7.9	1.126	2159	0.715	0.913	0.428	1.206	0.445	99.5
1.78-1.81	8.7	1.008	2201	0.817	0.948	0.362	1.072	0.463	100
1.81-1.85	9.7	0.904	2200	0.863	0.963	0.3	0.953	0.473	100
1.85-1.89	10.7	0.783	2211	0.893	0.971	0.246	0.821	0.488	100
1.89-1.93	10.8	0.696	2197	0.904	0.974	0.218	0.73	0.504	100
1.93-1.97	10.6	0.647	2199	0.924	0.98	0.207	0.68	0.571	100
1.97-2.02	11.5	0.603	2238	0.944	0.986	0.182	0.63	0.61	100
2.02-2.07	11.7	0.521	2171	0.953	0.988	0.157	0.544	0.624	100
2.07-2.14	11.5	0.435	2256	0.973	0.993	0.132	0.455	0.621	100
2.14-2.2	12.1	0.4	2222	0.981	0.995	0.118	0.417	0.642	100
2.2-2.28	12.6	0.375	2202	0.981	0.995	0.109	0.391	0.648	100
2.28-2.38	12.3	0.324	2245	0.986	0.996	0.095	0.338	0.693	100
2.38-2.48	13.1	0.283	2203	0.99	0.997	0.08	0.294	0.691	100
2.48-2.61	12.8	0.238	2246	0.992	0.998	0.068	0.248	0.669	100
2.61-2.78	12.8	0.207	2241	0.994	0.998	0.06	0.215	0.69	100
2.78-2.99	12.8	0.167	2249	0.995	0.999	0.048	0.174	0.754	100
2.99-3.29	13.3	0.127	2280	0.996	0.999	0.036	0.132	0.793	100
3.29-3.77	12.8	0.088	2279	0.998	0.999	0.025	0.091	0.845	100
3.77-4.75	12.8	0.068	2325	0.998	0.999	0.02	0.071	0.783	100
4.75-50	11.8	0.057	2452	0.999	1	0.017	0.06	0.613	99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→38.1 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2023	2255	5.07 %
R_work	0.1639	-	-
obs	0.1658	44475	99.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.75→38.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3458	0	15	566	4039

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007
X-RAY DIFFRACTION	f_angle_d	0.89
X-RAY DIFFRACTION	f_dihedral_angle_d	7.397	480
X-RAY DIFFRACTION	f_chiral_restr	0.055	521
X-RAY DIFFRACTION	f_plane_restr	0.008	590

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 (%)
1.75-1.79	0.2585	134	0.2311	2448	X-RAY DIFFRACTION	95
1.79-1.83	0.2411	139	0.2019	2598	X-RAY DIFFRACTION	99
1.83-1.88	0.267	141	0.1882	2587	X-RAY DIFFRACTION	99
1.88-1.93	0.2386	131	0.1862	2605	X-RAY DIFFRACTION	99
1.93-1.99	0.2478	144	0.1901	2592	X-RAY DIFFRACTION	100
1.99-2.05	0.2148	161	0.1759	2615	X-RAY DIFFRACTION	100
2.05-2.12	0.2145	130	0.1579	2647	X-RAY DIFFRACTION	100
2.12-2.21	0.1995	140	0.1541	2611	X-RAY DIFFRACTION	100
2.21-2.31	0.187	132	0.1606	2642	X-RAY DIFFRACTION	100
2.31-2.43	0.1891	119	0.1526	2645	X-RAY DIFFRACTION	100
2.43-2.58	0.1689	150	0.1552	2652	X-RAY DIFFRACTION	100
2.58-2.78	0.2291	147	0.167	2652	X-RAY DIFFRACTION	100
2.78-3.06	0.1988	157	0.1723	2655	X-RAY DIFFRACTION	100
3.06-3.5	0.1943	118	0.1535	2716	X-RAY DIFFRACTION	100
3.5-4.41	0.1541	155	0.1359	2725	X-RAY DIFFRACTION	100
4.42-38.1	0.2292	157	0.1764	2830	X-RAY DIFFRACTION	99

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	1.8836	0.1848	0.5835	3.27	0.271	2.8909	0.034	-0.0404	0.2182	-0.0564	0.1222	-0.1415	0.0086	-0.1934	-0.0751	0.1444	0.0094	0.019	0.1194	0.0331	0.1134	11.1827	-1.732	-25.4141
2	5.1919	-2.2865	-1.211	5.2585	1.4894	3.3882	-0.1815	0.0972	-0.0475	-0.2996	0.3306	-0.3101	-0.1371	0.2353	-0.1087	0.161	-0.0269	0.0391	0.1774	-0.01	0.1546	15.3207	2.4792	-34.1957
3	0.8024	0.1204	0.2106	1.0824	-0.534	0.9107	0.046	0.0369	-0.0084	-0.0784	-0.0133	-0.0405	0.1055	0.0794	-0.0294	0.1236	0.0021	0.0095	0.1169	-0.0142	0.1081	11.137	-6.2323	-22.5921
4	1.1421	-0.0643	-0.1788	2.6525	-0.4536	0.53	0.0248	0.1653	-0.0405	-0.294	-0.0406	0.1393	0.1467	0.0673	0.0102	0.1775	-0.0023	-0.0292	0.1662	-0.0113	0.1279	1.6228	-7.2439	-32.0458
5	1.5223	-0.2542	-0.811	1.5739	1.1193	3.4736	-0.062	0.0139	-0.1257	0.0853	-0.0012	0.1335	0.1564	-0.1866	0.0138	0.1366	-0.0231	-0.0172	0.1547	0.0232	0.1406	-0.7043	-15.4619	-19.4704
6	1.5527	-0.7202	0.5582	1.4046	-0.1206	0.9845	-0.0033	0.1083	0.0546	-0.029	0.0228	-0.1181	0.0176	0.3016	-0.0338	0.1864	0.0203	0.0074	0.2314	0.0227	0.1361	16.1006	-18.0148	-8.4493
7	0.8718	-0.0035	1.0291	0.951	-0.9046	2.2273	-0.0133	-0.2728	0.0532	0.084	-0.0568	-0.2145	-0.314	0.0557	0.0509	0.1622	-0.0154	-0.0152	0.209	0.005	0.1681	17.3152	-13.4874	-6.7155
8	1.832	0.0187	-0.4867	1.7684	0.1063	3.0797	-0.0517	0.0266	-0.2504	-0.0316	0.1077	-0.2568	0.5458	-0.0696	-0.0486	0.2459	-0.0057	0.0107	0.1965	0.0069	0.2136	18.2798	-29.2286	-2.7801
9	1.6226	-1.5695	1.5716	1.7864	-1.5639	2.8249	0.1453	-0.0584	-0.2782	-0.0521	-0.0278	0.1753	0.3499	-0.0289	-0.1136	0.2163	-0.0053	-0.0129	0.1624	0.0041	0.1823	9.5434	-24.7846	-14.8506
10	1.8046	-0.0809	-0.3942	2.4392	-0.6597	1.7568	-0.0472	-0.0853	-0.0297	0.2405	0.1468	-0.0089	-0.0425	0.0097	-0.0778	0.1431	0.022	0.0157	0.1526	0.0033	0.1362	19.697	-26.8865	-43.0626
11	1.048	-0.1692	-0.1408	1.1956	-0.4185	0.8845	-0.0021	-0.0136	-0.0233	0.0877	0.0213	0.0714	-0.0435	-0.0332	-0.014	0.112	0.0102	0.0135	0.1224	-0.0134	0.1253	17.3381	-22.6006	-49.7532
12	0.802	-0.4361	-0.2128	3.7985	0.1428	0.8938	0.0332	-0.5227	0.2587	0.4341	-0.1421	0.4758	-0.4683	-0.3078	0.0511	0.295	0.0405	0.0192	0.2716	-0.0587	0.2827	9.8302	-7.5351	-47.8167
13	1.1894	-0.1697	-0.0991	1.4099	1.1611	3.6328	0.005	0.0102	0.1996	-0.0288	-0.0476	0.0425	-0.2041	-0.2543	0.0611	0.1304	0.0229	0.0046	0.1526	0.0196	0.1673	12.7836	-11.7559	-60.2086
14	1.5128	0.2851	-1.284	2.4236	-0.5007	1.1106	-0.206	0.3369	0.0653	-0.0101	0.1607	-0.3152	-0.0404	0.3416	0.0409	0.1493	-0.0035	0.0141	0.2668	0.0096	0.1772	31.3904	-10.9749	-65.6315
15	1.3769	-0.1571	-0.8043	0.8787	-0.3092	1.1713	0.0741	0.0438	0.0864	0.0181	0.0325	-0.1956	-0.136	0.1648	-0.1224	0.1348	-0.0244	0.0428	0.1817	-0.0111	0.2069	35.0435	-11.8622	-64.3315
16	2.0011	0.4612	-0.0922	1.516	-0.3341	0.4895	0.3017	0.4652	1.1708	0.1221	0.3442	-1.1943	-0.6958	0.5539	-0.3871	0.5176	-0.1157	0.0716	0.4227	-0.0067	0.9411	38.2025	2.68	-67.325
17	2.3445	-0.3529	-1.2572	4.0306	-0.0752	2.9684	0.201	0.196	0.5432	-0.1782	-0.0431	0.1156	-0.5026	-0.0775	-0.1094	0.2251	0.0229	0.0228	0.1414	0.0173	0.2477	21.2808	-3.4625	-60.4896
18	2.8724	0.4698	0.4311	2.6266	0.5318	2.8937	-0.2066	0.4917	0.1558	-0.6201	0.0957	-1.1695	-0.0215	0.5173	0.1876	0.2108	0.0092	0.0694	0.2866	0.0371	0.3343	22.9066	-10.2518	-27.8191
19	4.2563	1.2843	3.9396	4.1186	-1.6107	5.7473	-0.1097	0.1664	-0.0034	-0.0364	-0.4026	-0.961	0.6186	0.6844	0.3273	0.3194	0.0974	0.062	0.1852	0.0416	0.2878	22.3545	-22.3345	-21.1511
20	1.1247	-0.2426	-0.3473	0.3232	-0.454	1.1543	-0.0004	-0.6639	0.0325	1.0779	0.1096	-0.7205	-0.4891	0.0483	0.2795	0.3283	-0.0213	-0.115	0.2523	0.001	0.2938	29.9936	-15.7155	-41.3747
21	2.3109	0.3438	0.3601	1.87	0.7175	2.9466	-0.1064	-0.3737	0.1957	0.3256	-0.3105	-0.8322	-0.903	0.3273	0.3304	0.3659	-0.0899	-0.0828	0.2184	0.0304	0.397	31.9747	-5.2325	-49.9289

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 29 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 30 through 69 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 101 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 102 through 118 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 119 through 139 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 140 through 158 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 159 through 185 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 186 through 201 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 5 through 29 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 30 through 88 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 89 through 101 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 102 through 118 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 119 through 136 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 137 through 169 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 170 through 188 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 189 through 202 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 437 through 445 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 446 through 452 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 436 through 445 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 446 through 451 )

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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Non-polymers , 4 types, 575 molecules

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-Protein / Protein/peptide , 2 types, 4 molecules ABCD

-Non-polymers , 4 types, 575 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

-
Non-polymers , 4 types, 575 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi