PDB-5apy: Sequence MATKDDIAN inserted between GCN4 adaptors - Structure T9(9)

ID or keywords:

Entry

Database: PDB / ID: 5apy

Title

Sequence MATKDDIAN inserted between GCN4 adaptors - Structure T9(9)

Components

GENERAL CONTROL PROTEIN GCN4

Keywords

DNA BINDING PROTEIN / ALPHA/BETA COILED COIL / BETA LAYER / TRIMER

Function / homology

Function and homology information

protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Hartmann, M.D. / Mendler, C.T. / Lupas, A.N. / Hernandez Alvarez, B.

Citation

Journal: Elife / Year: 2016
Title: alpha / beta coiled coils.
Authors: Hartmann, M.D. / Mendler, C.T. / Bassler, J. / Karamichali, I. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B.

History

Deposition	Sep 17, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 22, 2017	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5apy.cif.gz	89.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5apy.ent.gz	69.9 KB	Display	PDB format
PDBx/mmJSON format	5apy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5apy_validation.pdf.gz	427.8 KB	Display	wwPDB validaton report
Full document	5apy_full_validation.pdf.gz	428.1 KB	Display
Data in XML	5apy_validation.xml.gz	5.3 KB	Display
Data in CIF	5apy_validation.cif.gz	7.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ap/5apy ftp://data.pdbj.org/pub/pdb/validation_reports/ap/5apy	HTTPS FTP

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Related structure data

Related structure data	5appC 5apqC 5apsC 5aptC 5apuC 5apvC 5apwC 5apxC 5apzC 2wpqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5aps-1 3m06-2 5apq-d 3b5n-3 3m06-1 5da6-1 5apx-d 4whe-d 1495 5wj8-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 (9) #122 - Feb 2010 Enhanceosome similarity (4)

Deposited unit

A: GENERAL CONTROL PROTEIN GCN4

B: GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4

34.1 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)	60.770, 35.090, 112.190
Angle α, β, γ (deg.)	90.00, 100.39, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-2027- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ASP	ASP	GLY	GLY	A	A	6 - 67	32 - 93
2	GLU	GLU	VAL	VAL	B	B	5 - 66	31 - 92
3	ASP	ASP	VAL	VAL	C	C	6 - 66	32 - 92

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.477132, 0.878806, 0.00669), (-0.878827, -0.47714, -0.000528), (0.002728, -0.006131, 0.999977)	14.69743, 8.81476, 0.01112
3	given	(-0.520773, -0.853694, 0.001229), (0.853695, -0.520773, 0.000759), (-8.0E-6, 0.001444, 0.999999)	15.25803, -8.79435, 0.01175

#1: Protein	GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN Mass: 11368.084 Da / Num. of mol.: 3 / Fragment: 250-277,250-281 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.5 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	Details: 0.1 M CITRIC ACID PH 5.0, 20 %(V/V) ISOPROPANOL

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1

Detector

Type: MARRESEARCH / Detector: CCD / Date: Sep 20, 2009

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.291
1	1	1/2H+3/2K, 1/2H-1/2K, -1/2H-1/2K-L	2	0.35
1	1	1/2H-3/2K, -1/2H-1/2K, -1/2H+1/2K-L	3	0.359

Reflection

Resolution: 2→19.5 Å / Num. obs: 15902 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.73 % / R_merge(I) obs: 0.04 / Net I/σ(I): 19.5

Reflection shell

Resolution: 2→2.12 Å / Redundancy: 3.73 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 2.25 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPQ

2wpq

Resolution: 2→19.52 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.927 / SU B: 7.667 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.036 / 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	0.25467	793	5 %	RANDOM
R_work	0.2113	-	-	-
obs	0.21347	15106	98.81 %	-

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: 42.616 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.62 Å²	0 Å²	0.66 Å²
2-	-	13.14 Å²	0 Å²
3-	-	-	-18.76 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1460	0	0	113	1573

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.019	1482
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1522
X-RAY DIFFRACTION	r_angle_refined_deg	0.789	2.008	1992
X-RAY DIFFRACTION	r_angle_other_deg	0.666	3	3505
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.922	5	186
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.895	26.508	63
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.934	15	316
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.769	15	5
X-RAY DIFFRACTION	r_chiral_restr	0.037	0.2	246
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	1603
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	274
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	1.804	6.369	741
X-RAY DIFFRACTION	r_mcbond_other	1.779	6.363	740
X-RAY DIFFRACTION	r_mcangle_it	2.589	9.493	922
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.163	6.831	741
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

Refine LS restraints NCS

Ens-ID: 1 / Number: 891 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	loose positional	0.51	5
2	B	loose positional	0.53	5
3	C	loose positional	0.48	5
1	A	loose thermal	2.18	10
2	B	loose thermal	2.59	10
3	C	loose thermal	2.17	10

LS refinement shell

Resolution: 1.999→2.051 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	76	-
R_work	0.224	1085	-
obs	-	-	95.95 %

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	2.1286	1.6781	-1.7696	4.6381	-3.9354	12.7023	-0.0039	0.0902	0.2163	-0.13	0.2254	-0.0614	0.3606	0.0696	-0.2215	0.0295	0.0527	0.0028	0.1716	-0.0115	0.0786	14.7491	-2.9685	6.7525
2	1.6033	2.1943	0.8213	13.7002	-3.7257	2.6202	-0.0119	0.116	-0.1077	0.1519	0.0113	-0.2557	-0.0787	0.1273	0.0006	0.1031	0.0106	-0.0123	0.0987	-0.008	0.0811	11.8615	-5.9723	24.4881
3	9.9053	-7.3794	-6.6165	6.341	3.0752	8.4989	-0.1737	-0.2057	-0.1799	0.0964	0.0712	0.1451	0.1878	0.3006	0.1025	0.0591	-0.0055	-0.007	0.0978	-0.0237	0.0663	10.7305	-3.8017	31.1967
4	7.754	-4.3453	5.1967	2.471	-2.5501	7.1619	-0.057	0.1231	0.0615	0.0248	-0.0536	-0.0311	-0.0721	0.2593	0.1106	0.0695	0.0043	0.0296	0.1145	-0.0129	0.0873	4.2645	0.064	37.3228
5	1.0637	0.4445	1.3915	1.2922	1.4201	9.3502	0.0335	-0.0848	0.0623	0.1175	-0.0349	-0.0253	0.0125	-0.0552	0.0014	0.0211	0.0136	0.0122	0.0557	-0.0074	0.094	6.2258	3.5976	61.5762
6	2.9084	0.0826	1.1573	2.4201	-2.2432	12.5763	0.0165	0.0805	0.0857	-0.1497	0.0279	0.0481	-0.3696	-0.0319	-0.0444	0.041	-0.0182	0.01	0.1041	-0.0023	0.081	11.0793	5.7404	6.9571
7	6.0072	1.7877	-1.9709	0.5949	-1.1451	5.6444	0.0921	-0.2827	0.6969	0.0002	-0.1013	0.1866	0.1998	0.1845	0.0093	0.0997	-0.053	-0.0364	0.2416	-0.0097	0.2363	14.572	5.1747	24.0848
8	1.556	1.3635	0.3653	9.9226	1.9094	3.4213	-0.2905	-0.1221	0.2025	-0.3537	0.2495	-0.3011	-0.0174	-0.0461	0.0409	0.0696	0.0002	-0.0181	0.1092	-0.007	0.1031	13.1531	1.7841	31.342
9	1.378	2.4104	-2.1266	11.734	1.2997	6.6344	0.0504	0.0184	-0.0538	-0.5918	-0.1903	-0.0212	-0.5302	-0.1807	0.1399	0.0675	0.0087	0.0019	0.1442	-0.0056	0.0828	12.8116	-5.2998	37.2305
10	1.1242	0.1721	-1.4034	1.1999	-0.0705	9.3618	-0.0131	-0.1019	-0.0064	0.0967	0.026	0.0652	0.1127	0.1177	-0.0129	0.0138	-0.0092	0.0007	0.0536	0.0169	0.0879	9.0506	-5.5845	60.6592
11	3.7561	-0.4776	-3.0139	2.584	1.6913	12.2118	-0.0806	0.1301	-0.1641	-0.1057	-0.1799	0.1002	0.6187	-0.2803	0.2606	0.0506	0.0078	-0.004	0.2127	0.0187	0.0898	5.2202	-2.5665	6.7671
12	2.0348	-4.0135	-1.0367	8.7014	2.7476	1.1575	-0.0044	0.0826	-0.103	-0.0304	-0.0663	0.2194	-0.033	0.0489	0.0707	0.0614	-0.0006	0.0152	0.1493	0.0061	0.0688	4.7828	1.4975	24.5687
13	4.8087	3.5728	2.9093	3.5456	4.1233	6.0932	-0.042	0.0166	0.3149	-0.0321	-0.0543	0.1972	-0.046	-0.1119	0.0963	0.0587	-0.0001	0.0008	0.1128	0.0114	0.0989	7.07	1.7822	31.3057
14	8.8878	2.0397	0.6489	0.9798	-1.6518	6.3911	-0.2612	0.2987	-0.1095	-0.1204	0.1133	-0.0665	0.1966	-0.1607	0.1479	0.0653	-0.0053	0.0117	0.114	-0.0233	0.0824	13.1325	4.8101	37.1904
15	0.3937	-0.2592	0.576	0.8822	-0.9258	5.9632	0.0115	-0.0361	-0.0725	0.1198	0.0112	0.0001	-0.0628	0.0029	-0.0227	0.0232	-0.0021	-0.011	0.0908	-0.0026	0.0868	15.1611	1.3148	61.4824

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-6 - 26
2	X-RAY DIFFRACTION	2	A	27 - 30
3	X-RAY DIFFRACTION	3	A	31 - 34
4	X-RAY DIFFRACTION	4	A	35 - 38
5	X-RAY DIFFRACTION	5	A	39 - 80
6	X-RAY DIFFRACTION	6	B	-6 - 26
7	X-RAY DIFFRACTION	7	B	27 - 30
8	X-RAY DIFFRACTION	8	B	31 - 34
9	X-RAY DIFFRACTION	9	B	35 - 38
10	X-RAY DIFFRACTION	10	B	39 - 80
11	X-RAY DIFFRACTION	11	C	-6 - 26
12	X-RAY DIFFRACTION	12	C	27 - 30
13	X-RAY DIFFRACTION	13	C	31 - 34
14	X-RAY DIFFRACTION	14	C	35 - 38
15	X-RAY DIFFRACTION	15	C	39 - 80

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