PDB-4c46: ANDREI-N-LVPAS fused to GCN4 adaptors

ID or keywords:

Entry

Database: PDB / ID: 4c46

Title

ANDREI-N-LVPAS fused to GCN4 adaptors

Components

GENERAL CONTROL PROTEIN GCN4, GENERAL CONTROL PROTEIN GCN4

Keywords

TRANSCRIPTION / ION COORDINATION / POLAR CORE RESIDUES / FUSION PROTEIN / CHIMERA / COILED COIL / PROLINE

Function / homology

Function and homology information

Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding / amino acid biosynthetic process / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Albrecht, R. / Alva, V. / Ammelburg, M. / Baer, K. / Basina, E. / Boichenko, I. / Bonhoeffer, F. / Braun, V. / Chaubey, M. / Chauhan, N. ...

Citation

Journal: J.Struct.Biol. / Year: 2014
Title: Your Personalized Protein Structure: Andrei N. Lupas Fused to GCN4 Adaptors.
Authors: Deiss, S. / Hernandez Alvarez, B. / Bar, K. / Ewers, C.P. / Coles, M. / Albrecht, R. / Hartmann, M.D.

History

Deposition	Aug 30, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2014	Group: Database references / Structure summary
Revision 1.2	Mar 19, 2014	Group: Database references
Revision 1.3	Jun 11, 2014	Group: Database references
Revision 1.4	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.5	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4c46.cif.gz	104.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4c46.ent.gz	82.3 KB	Display	PDB format
PDBx/mmJSON format	4c46.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c4/4c46 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c46	HTTPS FTP

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Related structure data

Related structure data	1gcmS S: Starting model for refinement
Similar structure data	2odu-d 4yv3-d 4atm-d 6ual-d 6wjk-d 2ztb-2 2ztb-1 2pnv-3 6wsm-1 2spc-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (7) #122 - Feb 2010 Enhanceosome similarity (5) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: GENERAL CONTROL PROTEIN GCN4, GENERAL CONTROL PROTEIN GCN4

B: GENERAL CONTROL PROTEIN GCN4, GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4, GENERAL CONTROL PROTEIN GCN4

hetero molecules

26.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	42.000, 41.600, 64.140
Angle α, β, γ (deg.)	90.00, 95.48, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	GENERAL CONTROL PROTEIN GCN4, GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN Mass: 8869.462 Da / Num. of mol.: 3 / Fragment: RESIDUES 250-278,250-278 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ANDREI-N-LVPAS FUSED TO GCN4 ADAPTORS Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069
#2: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.2 Å³/Da / Density % sol: 43.5 % / Description: NONE
Crystal grow	Method: vapor diffusion, sitting drop / pH: 4 Details: SITTING DROP, PROTEIN SOLUTION 50 MM NACL AND 50 MM SODIUM ACETATE PH 4.0, RESERVOUR SOLUTION 0.1 M HEPES PH 7.5 1.75 M SODIUM BROMIDE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.95→36.6 Å / Num. obs: 16104 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.28 % / R_merge(I) obs: 0.06 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.95→2.07 Å / Redundancy: 3.33 % / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 1.94 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm

Resolution: 1.95→36.64 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.945 / SU B: 12.125 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27543	803	5 %	RANDOM
R_work	0.2376	-	-	-
obs	0.23962	15294	98.59 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 42.801 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.75 Å²	0 Å²	3.68 Å²
2-	-	1.46 Å²	0 Å²
3-	-	-	0.92 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→36.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1745	0	1	73	1819

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	1777
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1838
X-RAY DIFFRACTION	r_angle_refined_deg	1.717	1.979	2392
X-RAY DIFFRACTION	r_angle_other_deg	0.854	3	4238
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.153	5	218
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.02	26.812	69
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.329	15	381
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.733	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	288
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1907
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	332
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.448	46	-
R_work	0.345	1091	-
obs	-	-	94.75 %

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	23.3684	-4.4279	-9.378	5.8971	0.5107	14.3173	0.0102	0.2774	0.5287	-0.0064	0.1119	0.5471	0.1354	-0.6153	-0.1221	0.1956	0.0174	-0.0639	0.0358	0.0083	0.1242	-2.2118	4.1432	18.3069
2	23.4212	6.4701	-16.7091	9.6915	-0.9535	20.3867	0.4559	-1.5511	0.6407	0.7833	-0.1184	0.3157	0.1758	0.471	-0.3375	0.2722	-0.0252	-0.1077	0.3178	-0.0131	0.1165	4.0845	1.6048	27.7594
3	26.6634	-1.4909	-8.37	5.1098	0.9858	5.3415	-0.3313	0.18	-0.4648	0.1356	0.1741	0.5416	0.1803	-0.4728	0.1572	0.2184	-0.029	-0.0514	0.0972	-0.0024	0.1462	-1.0814	-6.4993	20.7721
4	21.5984	2.1599	-15.7047	0.5455	0.444	23.7629	-0.1059	0.6344	0.1962	-0.066	0.0729	0.0563	-0.2364	-0.2085	0.033	0.1928	0.0621	-0.0944	0.1137	-0.0113	0.0501	9.8124	1.0665	8.7398
5	22.2606	2.7782	-11.4934	13.3088	-0.5428	6.6788	0.0482	-0.6913	0.1076	-0.0918	0.0496	-0.0653	-0.2211	0.6122	-0.0979	0.2016	-0.0519	-0.0549	0.132	-0.0344	0.0364	15.614	4.5253	16.7967
6	25.3671	0.3417	-11.6597	11.8455	-4.3173	6.9308	-0.277	-0.0426	-0.5814	-0.0759	0.0375	0.187	0.2929	0.1267	0.2394	0.2273	0.1042	-0.0329	0.1244	0.0394	0.0646	14.3211	-5.8027	15.0054
7	24.0336	1.7077	-14.9486	1.0962	-1.5826	11.3749	-0.2317	0.4994	-0.4863	-0.0976	-0.0659	0.0078	-0.0029	-0.1924	0.2976	0.1392	0.014	-0.0604	0.2139	-0.0295	0.0444	22.2075	-1.6081	0.652
8	21.9278	1.1477	-16.1345	6.8481	5.5345	17.8883	0.6018	-0.3789	0.9421	-0.1105	0.2273	-0.1655	-0.5128	0.5319	-0.8292	0.2729	0.0058	0.0104	0.252	0.0536	0.1242	26.0162	5.6101	5.8139
9	26.9752	-0.8946	-8.0841	5.746	-0.935	8.251	-0.3391	-0.4019	-0.747	0.1226	0.0231	0.0045	0.5677	0.6027	0.316	0.1934	0.0079	-0.0506	0.1937	0.0349	0.061	27.7598	-4.5737	8.2078
10	23.3736	-8.1963	-8.5874	5.6335	3.1207	3.1641	-0.1643	0.8375	-0.9297	0.0064	-0.1452	-0.0086	0.0919	-0.3168	0.3095	0.3207	-0.0165	-0.0956	0.3694	-0.0792	0.1598	35.1619	-4.2362	-7.9475
11	14.1226	2.5236	-7.741	0.4566	-1.3841	4.2433	0.7944	0.9244	1.1455	0.1588	-0.0235	0.1993	-0.5191	-0.4983	-0.7709	0.5619	0.0863	0.1309	0.4819	0.0785	0.2535	37.1878	5.5726	-5.8698
12	34.7891	6.8367	-9.7881	1.3502	-1.8752	3.8976	0.0978	-0.5856	-0.7944	0.041	-0.1501	-0.1834	-0.2699	0.4373	0.0523	0.3078	-0.0686	-0.1045	0.4588	0.0646	0.1473	41.3042	-1.4895	-0.237
13	23.7173	3.2748	-11.0421	9.7861	-1.3629	12.6602	0.0676	-0.6266	-0.4061	0.3794	-0.2789	0.5609	0.0681	-0.3077	0.2114	0.1619	0.0057	-0.0664	0.0752	-0.02	0.1057	49.4014	-6.3615	-15.1378
14	24.315	-5.4707	-2.4461	2.4251	-1.1846	2.7702	0.0124	-0.1412	0.1044	0.037	0.2363	0.1466	-0.0772	-0.3072	-0.2487	0.2827	0.0443	0.0124	0.097	-0.0077	0.1625	48.3431	4.5683	-17.3637
15	9.6346	3.2379	-12.5975	4.7547	1.4006	25.3681	-0.0585	-0.5746	-0.192	0.2255	-0.2663	0.0193	0.4122	0.3393	0.3248	0.2281	0.0255	-0.0725	0.4146	0.0843	0.0719	54.9147	1.0923	-9.3239
16	29.2614	3.0652	-12.1763	5.9053	-4.7258	7.7603	-0.559	0.3498	-0.8932	-0.1631	0.0922	0.1577	0.6326	-0.4523	0.4668	0.3031	-0.149	0.0869	0.1463	-0.1456	0.1974	63.2744	-6.2303	-22.2333
17	24.646	-0.4182	-13.7421	2.2602	4.7147	16.5774	0.636	0.8874	1.4037	-0.1303	-0.1789	0.1444	-0.6082	-0.8097	-0.4571	0.2731	0.0734	-0.0422	0.1175	0.047	0.1179	59.6378	2.1486	-27.5833
18	25.6905	5.8987	-24.6037	3.5072	-3.7159	25.4441	0.0991	-1.2787	0.195	0.366	0.1198	-0.1145	0.1496	1.5262	-0.2189	0.2509	0.0055	-0.0945	0.2168	-0.078	0.0936	66.0401	3.7999	-19.1707
19	22.7629	-1.7224	-8.2734	3.2615	-1.6929	11.033	-0.3169	-0.0752	-0.7364	-0.0865	-0.0743	-0.8014	0.5101	0.5965	0.3912	0.2423	0.0167	-0.0396	0.2317	0.046	0.3327	77.8144	-4.8103	-28.4041
20	23.255	-0.6471	-11.911	9.6991	0.5179	13.3603	0.025	0.8121	-0.4706	-0.2948	-0.2017	-0.2468	-0.0347	0.0494	0.1767	0.1944	0.0058	-0.0574	0.1953	-0.0372	0.0432	71.912	-1.5664	-36.5471
21	10.7281	0.2994	-11.363	12.3265	-1.6889	18.084	0.4767	-0.2167	0.8497	-0.1147	-0.0153	-0.5249	-0.2636	0.8111	-0.4614	0.2637	-0.0673	-0.019	0.1659	0.0081	0.1602	75.8928	5.6538	-30.4363

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 10
2	X-RAY DIFFRACTION	2	B	-1 - 10
3	X-RAY DIFFRACTION	3	C	-2 - 10
4	X-RAY DIFFRACTION	4	A	11 - 20
5	X-RAY DIFFRACTION	5	B	11 - 20
6	X-RAY DIFFRACTION	6	C	11 - 20
7	X-RAY DIFFRACTION	7	A	21 - 30
8	X-RAY DIFFRACTION	8	B	21 - 30
9	X-RAY DIFFRACTION	9	C	21 - 30
10	X-RAY DIFFRACTION	10	A	31 - 40
11	X-RAY DIFFRACTION	11	B	31 - 40
12	X-RAY DIFFRACTION	12	C	31 - 40
13	X-RAY DIFFRACTION	13	A	41 - 50
14	X-RAY DIFFRACTION	14	B	41 - 50
15	X-RAY DIFFRACTION	15	C	41 - 50
16	X-RAY DIFFRACTION	16	A	51 - 60
17	X-RAY DIFFRACTION	17	B	51 - 60
18	X-RAY DIFFRACTION	18	C	51 - 60
19	X-RAY DIFFRACTION	19	A	61 - 71
20	X-RAY DIFFRACTION	20	B	61 - 71
21	X-RAY DIFFRACTION	21	C	61 - 71

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