PDB-3kjl: Sgf11:Sus1 complex

ID or keywords:

Entry

Database: PDB / ID: 3kjl

Title

Sgf11:Sus1 complex

Components

Protein SUS1
SAGA-associated factor 11

Keywords

TRANSCRIPTION / SAGA / Sus1 / Sgf11 / complex / Activator / Chromatin regulator / Metal-binding / Nucleus / Transcription regulation / Zinc / Zinc-finger / mRNA transport / Nuclear pore complex / Protein transport / Translocation / Transport

Function / homology

Function and homology information

DUBm complex / transcription export complex 2 / nuclear mRNA surveillance / SLIK (SAGA-like) complex / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SAGA complex / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / transcription elongation by RNA polymerase II ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Stewart, M. / Ellisdon, A.M.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Structural basis for the interaction between yeast Spt-Ada-Gcn5 acetyltransferase (SAGA) complex components Sgf11 and Sus1.
Authors: Ellisdon, A.M. / Jani, D. / Kohler, A. / Hurt, E. / Stewart, M.

History

Deposition	Nov 3, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	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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Download

PDBx/mmCIF format	3kjl.cif.gz	198.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3kjl.ent.gz	160.3 KB	Display	PDB format
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Validation report

Summary document	3kjl_validation.pdf.gz	481.1 KB	Display	wwPDB validaton report
Full document	3kjl_full_validation.pdf.gz	496.6 KB	Display
Data in XML	3kjl_validation.xml.gz	19.8 KB	Display
Data in CIF	3kjl_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kj/3kjl ftp://data.pdbj.org/pub/pdb/validation_reports/kj/3kjl	HTTPS FTP

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Related structure data

Related structure data	3kikSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4m8a-d 2jmo-d 6k3m-d 1868 2m2a-d 5h8o-d 4dk3-1 3wwq-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

3kikSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (1)

Deposited unit

A: Protein SUS1

E: SAGA-associated factor 11

B: Protein SUS1

F: SAGA-associated factor 11

C: Protein SUS1

G: SAGA-associated factor 11

D: Protein SUS1

H: SAGA-associated factor 11

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

1

A: Protein SUS1

E: SAGA-associated factor 11

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

2

B: Protein SUS1

F: SAGA-associated factor 11

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

3

C: Protein SUS1

G: SAGA-associated factor 11

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

4

D: Protein SUS1

H: SAGA-associated factor 11

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

Unit cell

Length a, b, c (Å)	68.670, 68.670, 232.860
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Details

SAGA Complex

#1: Protein	Protein SUS1 Mass: 11094.497 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: see publication Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SUS1, YBR111W-A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6WNK7
#2: Protein/peptide	SAGA-associated factor 11 / 11 kDa SAGA-associated factor Mass: 3503.884 Da / Num. of mol.: 4 / Fragment: Sus1-binding region Source method: isolated from a genetically manipulated source Details: see publication Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SGF11, YPL047W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q03067
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.71 Å³/Da / Density % sol: 54.68 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0719 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2009 / Details: mirrors
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0719 Å / Relative weight: 1
Reflection	Resolution: 2.7→59.4 Å / Num. all: 17082 / Num. obs: 17082 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.4 % / R_merge(I) obs: 0.112 / Net I/σ(I): 18.1
Reflection shell	Highest resolution: 2.7 Å / Redundancy: 22.6 % / R_merge(I) obs: 0.757 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2485 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.4_129)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KIK

3kik

Resolution: 2.7→19.943 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.96 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2531	1714	10.1 %	random but taking merohedral twinning into account
R_work	0.2129	-	-	-
obs	0.217	16973	99.99 %	-
all	-	17082	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 63.696 Å² / k_sol: 0.349 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.7→19.943 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3593	0	0	54	3647

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3614
X-RAY DIFFRACTION	f_angle_d	0.623	4879
X-RAY DIFFRACTION	f_dihedral_angle_d	13.728	1373
X-RAY DIFFRACTION	f_chiral_restr	0.038	615
X-RAY DIFFRACTION	f_plane_restr	0.001	616

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 (%)
2.7006-2.7734	0.3063	134	0.2644	1165	X-RAY DIFFRACTION	90
2.7734-2.8548	0.3543	128	0.2603	1190	X-RAY DIFFRACTION	90
2.8548-2.9466	0.2879	130	0.255	1152	X-RAY DIFFRACTION	90
2.9466-3.0515	0.2519	133	0.2534	1173	X-RAY DIFFRACTION	90
3.0515-3.1732	0.3195	132	0.2484	1165	X-RAY DIFFRACTION	90
3.1732-3.317	0.3155	133	0.2584	1180	X-RAY DIFFRACTION	90
3.317-3.4909	0.2772	131	0.2391	1169	X-RAY DIFFRACTION	90
3.4909-3.7082	0.2683	132	0.2161	1169	X-RAY DIFFRACTION	90
3.7082-3.9922	0.2584	125	0.2137	1194	X-RAY DIFFRACTION	91
3.9922-4.3898	0.2008	129	0.18	1159	X-RAY DIFFRACTION	90
4.3898-5.0155	0.2293	133	0.1758	1178	X-RAY DIFFRACTION	90
5.0155-6.2834	0.3014	142	0.2548	1180	X-RAY DIFFRACTION	89
6.2834-19.4513	0.2009	132	0.174	1171	X-RAY DIFFRACTION	90

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	5.0619	-2.1358	-1.6243	0.8876	0.6131	0.6932	-1.7488	0.2274	-0.5816	0.1792	1.0418	0.6982	-1.1702	1.0652	-0.0654	1.4968	0.0258	0.0109	1.3544	-0.1663	0.3547	6.6676	-51.4978	-23.7972
2		0.2832	0.2078	-0.1755	0.1285	-0.1204	0.0858	0.6051	0.5853	-1.5835	0.2976	-0.5425	0.9568	-0.4378	0.7802	-0.0017	1.0582	0.1622	0.055	0.7965	-0.2687	0.7041
3		0.5924	0.7908	0.1971	0.8285	0.2505	0.0136	0.1121	-0.2126	0.3731	0.301	-0.8893	-0.0338	0.326	-0.0542	0.0001	0.8747	0.2625	-0.1641	0.832	0.1179	0.5755
4		0.3133	0.2718	0.1648	0.591	-0.2221	0.2915	-0.6362	-0.1974	-0.0782	0.5946	0.9886	-0.3613	0.6614	0.23	0.0048	0.4464	0.4246	0.1021	0.9136	0.0364	0.4967
5		1.4322	-0.6776	-1.0361	0.6053	0.3024	0.8031	0.4506	-0.6584	1.1976	0.3282	0.8422	-0.5737	0.7895	0.5106	0.0411	0.3654	0.366	-0.1244	0.9766	-0.0045	0.5262
6		0.0125	0.0402	0.0314	0.0989	0.0521	0.0159	-0.1216	0.02	1.5531	-0.1926	0.8348	0.4764	0.146	-0.2318	0.0001	0.366	0.0844	-0.2035	0.3197	-0.0783	0.8736
7		0.0765	-0.2855	0.1753	0.7919	-0.3331	0.1438	1.0432	-1.5897	-0.1805	-1.1136	0.025	0.4189	-0.1356	0.233	0.0196	0.5097	0.5809	0.0133	1.1972	-0.1545	0.636
8		1.319	0.0835	0.7379	3.895	0.4586	0.607	-1.5936	0.1548	-0.4285	0.7516	1.3916	0.6779	-0.9551	0.0747	0.1437	0.811	0.5092	-0.024	0.9069	-0.2684	0.2798
9		0.1897	-0.2565	0.0945	0.3394	-0.1665	0.0536	0.3924	1.1278	1.7222	-0.0094	-0.3935	0.0275	1.1186	2.0182	-0.0012	0.9941	-0.359	0.2486	1.8766	-0.1961	0.7786
10		0.3063	0.3413	-0.4778	0.1058	-0.5663	1.4133	0.7209	-0.6528	1.2125	-0.782	-0.5074	0.5765	0.8237	0.4675	0.0003	0.7545	0.2034	-0.1076	0.6915	-0.1601	0.4262
11		2.3772	0.5646	-0.3373	0.3349	-0.0825	0.031	1.7618	-0.6584	-1.5787	-0.7204	-0.6027	-1.5172	0.6413	-0.1315	-0.0065	0.7206	0.0291	-0.0905	0.3575	-0.3878	1.0928
12		-0.012	-0.0034	0.0188	0.0952	-0.0822	0.0848	1.0256	0.0338	0.7915	-0.4392	1.9742	-0.6227	0.5841	-1.1451	0.001	0.6432	-0.2056	0.3051	0.412	0.3	1.9599
13		0.0215	-0.3019	-0.0782	1.0373	0.2327	0.263	0.8184	-0.3162	0.1431	-0.177	-0.3725	-1.533	0.2859	-0.7227	0.0111	0.2781	0.1463	-0.0249	0.5595	0.0496	0.3528
14		1.4614	0.3204	1.0192	0.7187	-0.0226	0.4461	-0.0779	0.1818	0.1162	-0.5186	-0.0542	-0.2411	0.5057	-0.0286	-0.0833	0.366	0.2501	-0.1227	0.5866	-0.3432	0.3082
15		0.0693	0.0657	-0.0609	0.0453	-0.0389	0.0303	-0.0233	-0.8585	0.1468	-0.9693	-1.0946	0.6982	0.4371	1.3225	-0.0031	0.5428	0.2682	-0.2181	0.84	-0.2688	0.8762
16		-0.002	0.0185	0.0025	-0.0126	-0.0055	0.062	1.2099	-0.0717	-0.2819	0.4315	0.5117	-0.9465	0.2588	0.8965	-0.0015	0.5218	0.1891	-0.111	0.7257	-0.0276	0.8231
17		1.2348	0.6658	-0.5365	0.7645	-1.001	1.468	1.9014	-2.5497	0.8511	-1.2677	-0.856	0.2578	-0.4089	2.5481	0.039	0.6547	0.1137	-0.0514	1.1722	-0.0691	0.622
18		9.2414	-3.5517	1.079	3.6987	1.1372	5.2575	0.9416	-0.4696	-2.0268	-1.6098	0.3481	-0.4465	-2.1439	0.55	0.4434	0.5215	0.0525	0.2023	0.5802	0.1338	0.5637
19		0.1029	0.0937	-0.0154	0.0886	0.0036	0.0177	0.233	-0.1236	0.397	-0.3019	0.6652	0.5552	-0.254	0.6943	0.0024	0.6589	-0.1658	-0.1043	1.0968	0.2239	0.5875
20		0.1739	-0.146	0.2668	0.1774	-0.0974	0.0911	-0.2331	0.0547	1.2558	-0.0825	1.0456	-0.3127	0.4445	-0.2771	0.0044	0.5641	-0.0251	0.2194	0.5374	-0.2354	0.9462
21		0.0789	-0.1776	-0.0107	0.1944	-0.0359	-0.1046	0.6375	0.5602	-0.1012	0.2823	0.2186	0.4233	-0.1789	0.4874	0.002	0.3187	0.2008	-0.0313	0.6403	-0.1933	0.4789
22		0.3999	0.3033	0.0972	0.1938	-0.196	0.3665	0.9388	-0.316	1.9289	0.309	0.0373	0.6454	1.2693	-0.0501	0.0061	0.4933	-0.0047	-0.1364	0.7331	-0.2181	0.5589
23		0.0192	-0.0147	0.0417	0.0715	0.0147	0.0617	0.0539	0.0331	0.0344	1.0783	0.3513	0.4803	0.5115	-0.1609	0.0008	0.5765	0.4352	-0.6519	0.3895	-0.6725	2.0332
24		0.0279	0.0325	0.0378	0.0087	0.0531	0.1841	-1.0445	-1.0552	-1.0831	-0.2869	0.9597	-0.6398	-1.2121	-0.5854	0.0015	0.8587	-0.1266	0.1088	0.5215	-0.2245	0.7035
25		2.1258	-0.8032	-3.1133	0.4998	1.2035	4.6206	0.2254	-2.5865	0.2097	-1.2311	0.2574	0.0457	-1.1353	2.5857	0.0449	0.5094	0.3578	0.0814	0.3003	0.011	0.928
26		0.5483	0.0412	-0.0067	0.3187	-0.387	0.4542	0.3471	-1.5797	-0.5524	-1.3052	-0.6282	-0.829	-1.2547	-0.6475	0.0003	0.855	0.2581	0.1536	0.8141	0.1454	0.4886
27		0.326	-0.1696	0.495	0.1363	0.0426	0.76	-0.1227	-0.3757	-0.3806	0.2565	-0.8984	-0.0411	0.0486	-0.2437	-0.0005	0.9679	0.2671	0.3245	0.5279	-0.1075	0.8084
28		0.3494	-0.3636	-0.0696	0.473	0.3462	0.4207	0.3446	-0.2974	0.2974	-0.0298	-0.3265	0.5051	-0.3808	0.5795	-0	1.0592	0.1545	0.2774	0.3942	-0.0039	0.3928
29		0.139	0.1339	0.0206	0.1055	0.1181	0.1018	0.4815	-0.5307	0.7003	0.6194	-0.1652	-0.9147	-0.9104	-0.8048	0.0013	1.0645	0.3247	-0.023	1.0263	-0.2487	0.4713
30		0.2063	0.1911	0.267	0.2449	0.1462	0.416	-0.7169	-0.0897	-0.7842	0.2953	0.2206	0.6488	0.5574	0.2168	-0.0004	0.3592	0.1227	-0.0495	0.4366	-0.0384	0.6608
31		0.0955	0.0367	-0.0587	0.0832	0.1068	0.1615	1.5591	0.1869	0.9614	-0.443	-0.8515	-0.5035	0.6998	0.0447	0.0027	1.1117	-0.0092	-0.0032	0.5926	0.0152	0.587
32		-0.0017	-0.0046	-0.0093	0.0581	0.089	0.0778	-1.3995	0.5931	-0.7802	0.698	1.6304	-0.3681	-1.4167	-0.0909	0.0011	0.5782	-0.1077	0.2701	0.2834	-0.1645	0.5017
33		0.2408	0.0608	0.105	0.1635	0.0205	0.8034	0.687	1.1043	1.9122	0.3622	-0.8587	1.0359	1.692	0.6614	-0.0007	0.8937	-0.1341	0.2018	0.383	0.0743	0.5219
34		0.0668	-0.0804	0.0255	0.0536	-0.0041	-0.0046	0.4375	-0.0928	0.1139	1.7576	0.3406	0.0809	-0.8624	1.1198	0.0004	1.7153	-0.0148	0.2917	1.1513	0.2998	0.7873
35		0.2941	-0.3251	-0.0428	0.3819	-0.1545	0.2694	-1.1797	-1.8547	0.1086	0.5833	-0.4321	2.3407	0.323	1.5721	-0.0026	1.2328	0.4738	0.0612	1.0048	-0.075	1.0342
36		1.0448	-1.0733	-1.4143	1.2627	1.2858	3.0154	-2.0819	0.7583	-0.2104	0.7059	-0.9796	1.4094	-0.0912	0.7298	-0.1845	1.4519	0.3552	-0.1206	0.716	0.3038	0.9547
37		-0.0261	0.0012	0.0497	0.3393	-0.0993	0.1139	0.4005	-0.0634	-0.0506	-1.8785	-0.8307	0.0776	-0.4161	-0.2196	-0.0008	0.8726	0.2118	-0.1165	0.4991	-0.1879	0.2954
38		0.1034	-0.1905	0.1219	0.2397	-0.0131	0.1571	-0.848	0.4999	0.0974	-0.6084	0.1817	-0.3734	0.5551	0.6861	-0.0001	1.0821	-0.0297	-0.0277	0.3655	-0.0324	0.8059
39		2.6541	1.7403	-0.1376	1.5521	0.3193	0.7639	0.8908	0.8342	-0.8612	0.3477	-1.0387	-0.6494	-0.4295	-0.014	0.0513	0.6353	0.2097	-0.0066	0.3829	0.0897	0.3022
40		0.5565	0.2608	-0.2414	0.1046	-0.1314	0.1216	1.114	-0.0247	1.1061	-0.1189	-0.8234	1.2306	0.9469	1.5219	0.0007	1.0672	0.2938	-0.0146	1.0863	0.8233	1.7853
41		0.0802	0.0721	0.0956	0.058	0.0954	0.072	1.3867	-0.3293	1.4459	-1.2037	-0.2229	-0.8216	0.1882	0.8711	0.0029	1.542	-0.136	0.2786	1.2876	0.3214	0.9178
42		0.3275	0.209	-0.5008	1.0248	-1.061	1.1922	-0.2473	0.0144	0.7796	1.1945	1.0839	-0.6636	0.2809	-0.1632	0.0268	1.0674	-0.1592	0.1852	0.5908	-0.3352	0.898
43		0.1471	0.0856	0.0345	0.0118	0.0278	0.0082	0.731	-0.3828	-0.0848	0.1585	-0.435	0.5839	-0.3166	0.7261	-0	0.7441	0.069	0.0368	0.3459	0.0611	0.6019
44		0.9983	0.6089	-0.2521	1.2981	-2.0266	5.5939	-0.5365	-0.1748	0.5395	-0.2834	-1.0018	1.1244	0.1937	0.035	-0.249	0.3853	0.0706	0.1079	0.1826	-0.0982	0.7645

Refinement TLS group

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