PDB-6f63: Crystal structure of the SYCP1 C-terminal back-to-back assembly

ID or keywords:

Entry

Database: PDB / ID: 6f63

Title

Crystal structure of the SYCP1 C-terminal back-to-back assembly

Components

Synaptonemal complex protein 1

Keywords

STRUCTURAL PROTEIN / Meiosis / Chromosome structure / Coiled-coil / Self-assembly

Function / homology

Function and homology information

transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.154 Å

Authors

Dunce, J.M. / Millan, C. / Uson, I. / Davies, O.R.

Funding support

United Kingdom, 1items

Citation

Journal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis of meiotic chromosome synapsis through SYCP1 self-assembly.
Authors: Dunce, J.M. / Dunne, O.M. / Ratcliff, M. / Millan, C. / Madgwick, S. / Uson, I. / Davies, O.R.

History

Deposition	Dec 4, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 6, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 4, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Aug 1, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Apr 22, 2020	Group: Database references / Category: pdbx_related_exp_data_set

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6f63.cif.gz	168.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6f63.ent.gz	143.7 KB	Display	PDB format
PDBx/mmJSON format	6f63.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6f63_validation.pdf.gz	450.6 KB	Display	wwPDB validaton report
Full document	6f63_full_validation.pdf.gz	456.1 KB	Display
Data in XML	6f63_validation.xml.gz	17 KB	Display
Data in CIF	6f63_validation.cif.gz	23.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f6/6f63 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/6f63	HTTPS FTP

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Related structure data

Related structure data	6f5xC 6f62C 6f64C C: citing same article (ref.)
Similar structure data	6f64-1 6mfo-d 6yqf-d 5vvm-2 4ll7-1 4zpp-1 4zpq-2 5c22-3 4zpp-2 5k9l-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18430/m36f63 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Synaptonemal complex protein 1

B: Synaptonemal complex protein 1

C: Synaptonemal complex protein 1

D: Synaptonemal complex protein 1

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS, The structure undergoes pH-induced assembly from a dimeric parallel coiled-coil at pH 8.0 to the tetrameric assembly observed in the crystal structure at pH 5.5. This has been validated by MALS and SAXS.

Unit cell

Length a, b, c (Å)	233.420, 42.850, 43.690
Angle α, β, γ (deg.)	90.00, 93.61, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Synaptonemal complex protein 1 / SCP-1 / Cancer/testis antigen 8 / CT8 Mass: 11384.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYCP1, SCP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15431
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.39 Å³/Da / Density % sol: 48.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.5 M sodium formate pH 7.0; soaked in 6 M sodium formate pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.15→116.48 Å / Num. obs: 23092 / % possible obs: 97.4 % / Redundancy: 3.6 % / B_iso Wilson estimate: 24.94 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.052 / R_pim(I) all: 0.032 / R_rim(I) all: 0.061 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2.15→2.27 Å / R_merge(I) obs: 0.695 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3024 / CC_1/2: 0.872 / R_pim(I) all: 0.429 / R_rim(I) all: 0.821 / % possible all: 88

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Processing

Software

Name	Version	Classification
PHENIX	(1.12rc1_2807: ???)	refinement
XDS		data reduction
Aimless		data scaling
Arcimboldo		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.154→58.239 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.3

	R_factor	Num. reflection	% reflection
R_free	0.2526	1041	4.86 %
R_work	0.2186	-	-
obs	0.2203	21416	90.34 %

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å

Refinement step

Cycle: LAST / Resolution: 2.154→58.239 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3099	0	0	175	3274

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3165
X-RAY DIFFRACTION	f_angle_d	0.511	4211
X-RAY DIFFRACTION	f_dihedral_angle_d	16.629	1308
X-RAY DIFFRACTION	f_chiral_restr	0.035	478
X-RAY DIFFRACTION	f_plane_restr	0.004	538

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 (%)
2.1542-2.2678	0.3325	67	0.3169	1410	X-RAY DIFFRACTION	44
2.2678-2.4099	0.335	170	0.2848	2980	X-RAY DIFFRACTION	94
2.4099-2.596	0.3075	149	0.2532	3204	X-RAY DIFFRACTION	100
2.596-2.8572	0.2891	154	0.2447	3205	X-RAY DIFFRACTION	100
2.8572-3.2706	0.2351	167	0.2249	3191	X-RAY DIFFRACTION	100
3.2706-4.1205	0.2423	165	0.1859	3171	X-RAY DIFFRACTION	98
4.1205-58.2605	0.2005	169	0.1842	3214	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	4.476	5.0296	-3.3373	6.8382	-1.9826	5.1212	-1.2165	-0.2566	-1.5064	-0.4229	0.4908	-1.042	0.8709	0.4571	0.7037	0.5764	0.1753	0.2413	1.5421	0.0965	0.6843	230.4916	9.18	-11.6504
2	4.709	-0.5144	-3.6581	2.4072	0.3319	3.9054	-0.0859	0.1371	-0.352	-0.2933	-0.0561	-0.3565	0.2174	0.0958	0.3284	0.1781	0.072	0.0973	0.7975	-0.0725	0.2381	215.704	9.9707	3.389
3	6.8592	-2.7118	-5.2002	3.8936	2.707	4.1112	-0.0593	0.2937	0.0279	-0.1025	0.1091	-0.0766	-0.031	0.2542	0.0358	0.1829	0.034	-0.0379	0.3378	-0.0176	0.1162	192.9195	17.1863	27.3924
4	4.8864	-1.1506	-2.2823	0.4649	1.0131	2.2332	0.0282	0.4493	-0.1794	-0.3902	-0.031	-0.2096	0.1922	-0.0123	0.1085	0.4467	0.0119	0.096	0.1229	-0.0101	0.1792	171.6953	24.8912	51.1325
5	6.0234	-5.5784	-4.0392	8.3487	1.5803	4.6453	-0.1538	-0.4199	0.6028	0.6757	0.2814	-0.8934	-0.2483	0.1837	-0.0771	0.2645	0.0888	-0.0427	0.049	0.0082	0.2059	163.7571	25.6633	69.0331
6	8.7383	-1.7885	0.8546	3.0605	2.309	5.4406	-0.2181	0.0512	-0.1035	0.4692	-0.0073	0.7163	-1.0341	-1.3796	0.2226	0.4732	0.0959	0.0151	0.3558	-0.0268	0.2285	157.1584	24.8881	79.6786
7	4.4967	2.6344	-3.2658	8.365	0.1038	5.8246	-0.728	-1.4688	0.1051	1.8296	0.058	0.9349	0.6092	-0.4291	0.6455	1.235	0.411	0.4176	0.7199	0.0286	0.8497	151.556	24.4108	91.3422
8	3.0946	2.8352	0.6515	3.9158	-2.2138	6.127	0.1988	-1.8343	-0.6196	1.9314	0.1069	0.655	0.3382	0.0689	-0.253	0.6105	0.0718	0.0916	0.8438	0.1516	0.4092	161.5649	17.96	87.2681
9	2.4435	-1.7413	-1.0339	5.853	4.1933	4.8359	-0.0023	-0.1734	0.0876	0.4368	-0.0832	0.0791	-0.0289	-0.08	0.0775	0.2802	-0.0506	0.0142	0.0735	-0.072	0.2363	169.0808	20.9646	78.0529
10	2.8742	-0.0021	-1.1369	3.5423	-2.0246	2.6778	0.1761	0.1237	0.2752	0.1212	0.0413	0.0101	-0.3209	-0.0838	0.0071	0.4221	-0.0636	-0.0294	0.1545	0.1074	0.1951	178.9487	22.3619	65.7902
11	3.3303	0.5884	-2.8009	1.9011	-0.8804	2.4406	0.2057	0.1837	0.1829	-0.011	0.1389	-0.0379	-0.2877	0.1097	-0.1049	0.2195	-0.0646	0.0863	0.396	-0.0329	0.126	190.3446	25.0391	40.4253
12	9.289	4.5297	-0.3109	8.9879	-2.8639	8.8494	0.1129	-0.7818	-0.3668	0.6186	0.1793	0.1197	0.8766	-0.0158	-0.2608	1.049	-0.0307	0.1198	1.4039	0.3623	0.6846	199.3596	27.6055	17.9971
13	3.6354	-0.7419	-3.0601	2.3768	1.0583	3.743	0.0967	0.0357	0.1262	0.2007	0.0432	0.217	-0.158	-0.1128	-0.1523	0.1832	-0.0229	0.0764	0.9697	0.0544	0.2012	211.2073	20.6464	-0.8299
14	5.1819	2.5974	2.8395	5.3419	-1.3146	3.411	0.148	1.3849	-0.3196	-0.3775	-0.2637	-0.5049	0.0611	0.1279	0.1261	0.2982	0.0059	-0.0071	1.2455	0.0666	0.4297	226.4571	13.1461	-19.5457
15	3.9725	-0.7603	-4.1623	3.5668	3.1784	6.2046	0.5318	0.3471	0.6192	-0.5413	0.1528	-0.3645	-0.7907	-0.1458	-0.7056	0.3144	-0.0295	0.0984	1.1442	0.1168	0.3471	223.7397	24.5345	-6.9966
16	5.344	-2.377	-5.2793	4.0092	3.189	5.4791	0.287	-0.1717	0.1958	-0.1888	-0.3182	-0.3858	-0.5387	0.7039	-0.0761	0.4222	-0.1696	0.0967	0.8653	0.0313	0.2336	215.1128	23.8224	9.4216
17	6.1381	0.051	-1.1978	8.8366	-4.207	2.3306	-0.0781	0.0244	0.0817	-0.0648	-0.1959	0.0994	-0.3871	0.0972	0.2723	0.4657	-0.0047	-0.0231	0.9784	-0.1644	0.2862	209.4824	22.9137	18.9969
18	3.4558	0.3624	-3.3004	0.7527	-0.2931	5.1937	0.2099	-0.3656	-0.0502	0.108	0.0161	0.0456	-0.1057	0.328	0.0414	0.1542	-0.026	0.055	0.6365	0.0422	0.1851	199.3728	17.7	40.9237
19	0.8793	-0.0977	-0.5988	0.344	0.274	0.9214	0.0634	-0.0082	-0.0275	0.1207	0.0094	0.1226	-0.0609	0.0429	0.0587	0.1667	-0.0323	-0.0388	0.0197	-0.0111	0.2898	180.3621	12.8425	66.1119
20	3.6244	-3.0036	-2.5482	3.3467	0.4739	5.7017	-0.0769	0.0574	0.0546	-0.0743	0.381	-0.7734	0.1017	0.2969	-0.2285	0.3561	-0.0013	0.1028	0.1322	-0.0604	0.3819	163.7663	11.9989	76.8641
21	3.9688	-2.0045	-1.4618	4.5609	0.2551	2.7049	-0.0695	-0.1251	-0.0794	0.2785	0.1109	0.181	0.002	-0.0612	-0.0191	0.3219	0.1877	0.1198	0.1834	0.1063	0.2672	150.9607	11.2677	85.9441
22	2.9426	-3.8827	-3.1185	5.6787	3.9404	3.6824	0.0409	0.0109	0.4373	0.5394	0.5722	2.3257	-1.3283	-3.3416	-0.6043	0.569	0.1837	0.0609	0.8693	0.1157	0.5651	148.5726	18.2322	78.8591
23	2.7477	1.4464	-1.1911	3.3049	-2.9576	2.7441	0.1264	-0.1659	-0.1207	0.486	0.0076	0.395	-0.0437	-0.1702	-0.0388	0.3193	-0.1036	0.0795	0.1016	0.017	0.3352	158.0944	16.8028	70.0487
24	2.0996	0.2532	-1.4798	6.396	-0.3939	4.4221	0.0136	0.0349	-0.2326	-0.1124	-0.0166	0.1736	0.4122	-0.2057	-0.0541	0.179	-0.0628	0.0106	0.0606	-0.0226	0.3017	167.5986	15.8346	61.3338
25	7.7783	-1.4083	-6.0239	2.8611	1.5293	6.6576	-0.3661	0.4203	-0.3241	-0.062	0.0924	-0.1963	0.475	0.1814	0.2321	0.1773	0.0177	0.0128	0.3253	0.0417	0.1782	189.4471	12.7051	42.7578
26	4.3946	2.9519	-3.6363	6.4204	-0.6423	3.7391	-0.2253	-0.4042	0.791	0.0582	0.2794	1.2353	-0.0499	-0.5938	-0.1436	0.3269	0.1424	-0.0354	1.281	-0.003	0.5091	212.0563	8.9824	24.9905
27	6.662	2.1752	-7.0432	2.8447	-3.0256	8.0396	-0.1501	0.9995	-0.4511	-0.3955	-0.0904	-0.0463	0.1799	-0.7146	0.2453	0.3095	0.0571	0.0772	1.1302	-0.1357	0.413	217.42	10.0174	16.4676
28	1.1055	0.1423	-0.2481	0.2929	-0.2385	0.9245	-0.0279	0.148	0.1003	-0.045	-0.0277	-0.0141	0.0002	0.08	-0.1208	0.1831	0.062	-0.012	1.2076	-0.0369	0.3142	228.9861	16.8665	-2.1794

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 673:679)
2	X-RAY DIFFRACTION	2	(chain A and resid 680:699)
3	X-RAY DIFFRACTION	3	(chain A and resid 700:726)
4	X-RAY DIFFRACTION	4	(chain A and resid 727:744)
5	X-RAY DIFFRACTION	5	(chain A and resid 745:751)
6	X-RAY DIFFRACTION	6	(chain A and resid 752:761)
7	X-RAY DIFFRACTION	7	(chain A and resid 762:768)
8	X-RAY DIFFRACTION	8	(chain B and resid 673:682)
9	X-RAY DIFFRACTION	9	(chain B and resid 683:689)
10	X-RAY DIFFRACTION	10	(chain B and resid 690:702)
11	X-RAY DIFFRACTION	11	(chain B and resid 703:726)
12	X-RAY DIFFRACTION	12	(chain B and resid 727:735)
13	X-RAY DIFFRACTION	13	(chain B and resid 736:758)
14	X-RAY DIFFRACTION	14	(chain B and resid 759:768)
15	X-RAY DIFFRACTION	15	(chain C and resid 674:690)
16	X-RAY DIFFRACTION	16	(chain C and resid 691:697)
17	X-RAY DIFFRACTION	17	(chain C and resid 698:705)
18	X-RAY DIFFRACTION	18	(chain C and resid 706:729)
19	X-RAY DIFFRACTION	19	(chain C and resid 730:749)
20	X-RAY DIFFRACTION	20	(chain C and resid 750:756)
21	X-RAY DIFFRACTION	21	(chain C and resid 757:769)
22	X-RAY DIFFRACTION	22	(chain D and resid 673:680)
23	X-RAY DIFFRACTION	23	(chain D and resid 681:690)
24	X-RAY DIFFRACTION	24	(chain D and resid 691:697)
25	X-RAY DIFFRACTION	25	(chain D and resid 698:728)
26	X-RAY DIFFRACTION	26	(chain D and resid 729:736)
27	X-RAY DIFFRACTION	27	(chain D and resid 737:741)
28	X-RAY DIFFRACTION	28	(chain D and resid 742:767)

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