PDB-6rrc: Crystal structure of the N-terminal region of human cohesin subun...

ID or keywords:

Entry

Database: PDB / ID: 6rrc

Title

Crystal structure of the N-terminal region of human cohesin subunit STAG1 in complex with RAD21 peptide

Components

Cohesin subunit SA-1
Double-strand-break repair protein rad21 homolog

Keywords

GENE REGULATION / Cohesin / SA-1 / chromosome segregation

Function / homology

Function and homology information

negative regulation of mitotic metaphase/anaphase transition / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.37 Å

Authors

Newman, J.A. / Katis, V.L. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.

Funding support

United Kingdom, 1items

Citation

Journal: Life Sci Alliance / Year: 2020
Title: STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers.
Authors: van der Lelij, P. / Newman, J.A. / Lieb, S. / Jude, J. / Katis, V. / Hoffmann, T. / Hinterndorfer, M. / Bader, G. / Kraut, N. / Pearson, M.A. / Peters, J.M. / Zuber, J. / Gileadi, O. / Petronczki, M.

History

Deposition	May 17, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 19, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Jul 1, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Aug 19, 2020	Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6rrc.cif.gz	294.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6rrc.ent.gz	242.2 KB	Display	PDB format
PDBx/mmJSON format	6rrc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6rrc_validation.pdf.gz	467.3 KB	Display	wwPDB validaton report
Full document	6rrc_full_validation.pdf.gz	474.3 KB	Display
Data in XML	6rrc_validation.xml.gz	24.9 KB	Display
Data in CIF	6rrc_validation.cif.gz	33.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rr/6rrc ftp://data.pdbj.org/pub/pdb/validation_reports/rr/6rrc	HTTPS FTP

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Related structure data

Related structure data	6qb5C 6r7oC 6rrkC 4pk7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ky8-d 1uxu-d 1uxq-d 6ht5-d 1uxn-d 3fdd-d 3vlc-d 1uxp-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#205 - Jan 2017 Nuclear Pore Complex similarity (2) #55 - Jul 2004 DNA Ligase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

C: Cohesin subunit SA-1

B: Double-strand-break repair protein rad21 homolog

A: Cohesin subunit SA-1

D: Double-strand-break repair protein rad21 homolog

hetero molecules

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

1

C: Cohesin subunit SA-1

B: Double-strand-break repair protein rad21 homolog

hetero molecules

defined by author&software
Evidence: gel filtration
42.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Cohesin subunit SA-1

D: Double-strand-break repair protein rad21 homolog

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

Unit cell

Length a, b, c (Å)	117.077, 151.662, 126.656
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	21
Space group name H-M	C222

#1: Protein	Cohesin subunit SA-1 / SCC3 homolog 1 / Stromal antigen 1 Mass: 39629.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STAG1, SA1, SCC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WVM7
#2: Protein/peptide	Double-strand-break repair protein rad21 homolog / hHR21 / Nuclear matrix protein 1 / NXP-1 / SCC1 homolog Mass: 2899.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60216
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.3 Å³/Da / Density % sol: 62.78 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 2.1 M Ammonium Sulfate, 0.1 M MES pH 6.3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 2.37→75.83 Å / Num. obs: 46073 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.024 / Net I/σ(I): 14
Reflection shell	Resolution: 2.37→2.41 Å / Redundancy: 6.9 % / R_merge(I) obs: 1.325 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2213 / CC_1/2: 0.705 / R_pim(I) all: 0.543 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4pk7

4pk7

Resolution: 2.37→74.792 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9

	R_factor	Num. reflection	% reflection
R_free	0.2483	2295	4.99 %
R_work	0.2136	-	-
obs	0.2154	46007	99.75 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.37→74.792 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5574	0	20	65	5659

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5674
X-RAY DIFFRACTION	f_angle_d	0.386	7646
X-RAY DIFFRACTION	f_dihedral_angle_d	20.607	3450
X-RAY DIFFRACTION	f_chiral_restr	0.033	863
X-RAY DIFFRACTION	f_plane_restr	0.002	976

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 (%)
2.3688-2.4203	0.3527	142	0.3352	2639	X-RAY DIFFRACTION	98
2.4203-2.4766	0.3209	140	0.3118	2687	X-RAY DIFFRACTION	100
2.4766-2.5385	0.3359	127	0.3019	2728	X-RAY DIFFRACTION	100
2.5385-2.6072	0.3286	160	0.2947	2693	X-RAY DIFFRACTION	100
2.6072-2.6839	0.2816	129	0.2806	2719	X-RAY DIFFRACTION	100
2.6839-2.7705	0.2912	148	0.2621	2679	X-RAY DIFFRACTION	100
2.7705-2.8695	0.2922	143	0.2543	2714	X-RAY DIFFRACTION	100
2.8695-2.9844	0.3021	142	0.2674	2734	X-RAY DIFFRACTION	100
2.9844-3.1203	0.3129	125	0.2723	2721	X-RAY DIFFRACTION	100
3.1203-3.2848	0.3054	131	0.259	2758	X-RAY DIFFRACTION	100
3.2848-3.4906	0.2946	133	0.2411	2734	X-RAY DIFFRACTION	100
3.4906-3.7601	0.2836	145	0.2168	2738	X-RAY DIFFRACTION	100
3.7601-4.1385	0.2026	153	0.1819	2732	X-RAY DIFFRACTION	100
4.1385-4.7372	0.2075	144	0.1724	2779	X-RAY DIFFRACTION	100
4.7372-5.968	0.2574	166	0.2042	2771	X-RAY DIFFRACTION	100
5.968-74.8292	0.2067	167	0.1841	2886	X-RAY DIFFRACTION	100

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	3.1385	0.7296	0.5335	4.9608	0.3711	4.9481	-0.0213	0.2551	-0.5144	-0.1558	0.1123	-0.2306	0.7948	0.1663	-0.0824	0.8588	0.066	0.0224	0.6696	-0.194	0.6828	27.0595	4.2096	12.8874
2	0.844	0.3312	0.5558	5.5554	-2.5678	3.5561	0.0581	0.3145	-0.087	-0.1505	0.0524	0.3318	-0.0057	-0.0927	-0.147	0.5469	0.0722	-0.0049	0.6588	-0.1124	0.545	22.8572	23.8046	19.2403
3	5.1258	-2.196	3.8647	3.0124	-0.9916	7.3319	0.0519	0.0475	0.1046	0.1803	-0.1548	-0.1124	0.0587	0.0392	0.1164	0.55	-0.006	0.0215	0.4921	-0.0362	0.5048	31.3087	21.5549	41.6737
4	7.7933	-0.4881	1.6745	8.7366	-1.8503	9.3674	0.4304	-0.3074	-1.904	1.7408	-0.1311	0.2341	0.3664	0.5142	-0.2754	0.8708	0.1378	-0.1334	1.0355	0.0352	1.1978	40.4193	47.4552	47.749
5	9.1354	1.9317	4.191	9.8384	-2.8104	6.364	0.2497	-0.0393	-1.042	0.5776	0.0405	0.0794	2.1067	-0.6493	-0.2625	1.3615	-0.1758	-0.0482	0.9833	-0.0226	0.7907	21.8129	-4.5961	32.3253
6	5.3163	-4.5088	2.8728	4.8133	-3.4322	3.2383	0.4118	0.6656	-0.3388	-0.6911	-1.1455	-0.925	1.1221	-0.7138	0.5369	2.1113	0.1459	0.4241	1.703	0.3657	1.2783	18.5561	7.1322	46.4699
7	4.0642	1.2806	0.6486	3.7011	-0.4425	2.4371	-0.2781	0.8383	0.9058	-0.5335	-0.0376	0.0683	-0.2741	0.2398	0.3575	0.88	0.0453	-0.1075	0.8897	0.2066	0.7555	58.6123	32.8147	39.579
8	0.3517	1.3388	-0.6602	7.3738	-2.0818	1.9022	-0.2968	0.1632	-0.0467	-1.3366	0.2277	0.9688	0.247	-0.4657	-0.0564	1.2121	0.0365	-0.1274	1.0491	-0.0862	0.8866	55.0587	7.2402	38.347
9	6.78	4.1405	0.0605	7.5349	0.2153	4.3004	-0.1877	0.2979	0.5291	-0.2698	-0.008	-0.3337	-0.5974	0.4662	0.2085	0.7955	0.002	-0.0229	0.6902	0.1369	0.7133	71.6743	27.8826	50.1951
10	4.3374	-0.4726	2.6816	1.0638	1.2896	5.9172	-0.1249	0.1689	0.1902	0.0595	-0.1254	-0.1571	0.0969	0.1081	0.3104	0.643	0.0157	-0.0229	0.5136	0.0372	0.6506	73.6726	19.9599	63.1793
11	5.0225	1.4472	0.2086	4.8838	0.5923	6.3893	-0.401	1.0099	0.6574	0.3603	-0.3566	-1.7693	-1.004	0.4545	0.7359	1.2474	-0.2035	-0.0985	1.2147	0.3772	1.4889	79.8011	41.6659	42.5848
12	6.0263	-1.895	-1.1755	6.7228	6.5756	6.5244	0.032	-0.8544	-0.6154	-0.2347	0.6173	-0.3431	-0.0942	0.5939	-0.8169	1.7158	-0.1892	-0.1005	1.4374	0.1796	1.6486	89.0965	25.2265	52.4639

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 84 through 215 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 216 through 321 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 322 through 402 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 403 through 419 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 322 through 333 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 334 through 339 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 85 through 255 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 256 through 294 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 295 through 321 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 322 through 408 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 322 through 333 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 334 through 345 )

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