PDB-5apt: Sequence IENKADKAD inserted between GCN4 adaptors - Structure A9

ID or keywords:

Entry

Database: PDB / ID: 5apt

Title

Sequence IENKADKAD inserted between GCN4 adaptors - Structure A9

Components

GENERAL CONTROL PROTEIN GCN4

Keywords

STRUCTURAL PROTEIN / ALPHA/BETA COILED COIL / BETA LAYER / TRIMER

Function / homology

Function and homology information

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

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5apt.cif.gz	103.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5apt.ent.gz	81.6 KB	Display	PDB format
PDBx/mmJSON format	5apt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5apt_validation.pdf.gz	451.7 KB	Display	wwPDB validaton report
Full document	5apt_full_validation.pdf.gz	452.3 KB	Display
Data in XML	5apt_validation.xml.gz	11.4 KB	Display
Data in CIF	5apt_validation.cif.gz	16.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ap/5apt ftp://data.pdbj.org/pub/pdb/validation_reports/ap/5apt	HTTPS FTP

-
Related structure data

Related structure data	5appC 5apqC 5apsC 5apuC 5apvC 5apwC 5apxC 5apyC 5apzC 2wpqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5apu-d 3h6p-d 6wjk-d 6ual-d 6yf5-2 6xor-d 4e40-d 6yf5-1 3i57-1 2ztb-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

34.2 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)	65.180, 34.590, 67.510
Angle α, β, γ (deg.)	90.00, 117.66, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	A	-11 - 30
2	1	1	6	B	-11 - 30
3	1	1	6	C	-11 - 30
1	1	2	6	A	35 - 66
2	1	2	6	B	35 - 66
3	1	2	6	C	35 - 66

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.354436, 0.670964, -0.651293), (-0.628572, -0.344708, -0.69719), (-0.692295, 0.656494, 0.299572)	17.19999, 15.89318, 18.05606
3	given	(0.237051, -0.576306, -0.782099), (0.564856, -0.573221, 0.593595), (-0.790408, -0.582486, 0.189647)	19.64044, -15.15699, 20.58216

#1: Protein	GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN Mass: 11394.077 Da / Num. of mol.: 3 / 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.: 197 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56 % / Description: NONE
Crystal grow	Details: 1.6 M TRI-SODIUM CITRATE PH 6.5

-
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	Resolution: 1.8→33.7 Å / Num. obs: 24951 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / R_merge(I) obs: 0.05 / Net I/σ(I): 14.3
Reflection shell	Resolution: 1.8→1.91 Å / Redundancy: 3.67 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 2.07 / % possible all: 97.4

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPQ

2wpq

Resolution: 1.8→32.58 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.938 / SU B: 7.767 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.134 / 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	0.25635	1252	5 %	RANDOM
R_work	0.20558	-	-	-
obs	0.20812	23695	99.09 %	-

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: 46.867 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.55 Å²	0 Å²	2.9 Å²
2-	-	-0.59 Å²	0 Å²
3-	-	-	-1.93 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→32.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1681	0	0	197	1878

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.019	1737
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1794
X-RAY DIFFRACTION	r_angle_refined_deg	0.877	2.009	2332
X-RAY DIFFRACTION	r_angle_other_deg	0.67	3	4154
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.511	5	219
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.812	26.463	82
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.415	15	390
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.999	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.043	0.2	275
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	1893
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	328
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	2.963	8.402	843
X-RAY DIFFRACTION	r_mcbond_other	2.952	8.389	842
X-RAY DIFFRACTION	r_mcangle_it	3.892	14.055	1052
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	5.209	10.266	894
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

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	458	loose positional	1.01	5
1	2	B	458	loose positional	1.11	5
1	3	C	458	loose positional	1.1	5
2	1	A	468	loose positional	1.19	5
2	2	B	468	loose positional	1.11	5
2	3	C	468	loose positional	1.01	5
1	1	A	458	loose thermal	4.3	10
1	2	B	458	loose thermal	5.78	10
1	3	C	458	loose thermal	4.99	10
2	1	A	468	loose thermal	3.23	10
2	2	B	468	loose thermal	3.4	10
2	3	C	468	loose thermal	4.03	10

LS refinement shell

Resolution: 1.799→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	89	-
R_work	0.371	1631	-
obs	-	-	94.66 %

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	2.9719	1.2395	-4.4905	2.9491	-1.4138	7.0231	-0.271	0.2917	-0.1306	-0.0905	0.1377	-0.3714	0.1652	-0.3831	0.1333	0.3487	-0.1016	-0.0127	0.066	0.0016	0.0891	35.8378	4.7037	-14.7822
2	3.5011	0.0632	-1.7863	0.0399	0.1114	1.4538	-0.0444	-0.0594	0.144	-0.0106	-0	0.0304	0.0122	0.0417	0.0444	0.1137	-0.0054	-0.0064	0.0351	0.0045	0.1193	22.9587	4.9545	3.5265
3	4.2012	3.8551	-4.6862	3.9634	-3.5577	6.5338	0.0569	-0.4796	-0.1085	-0.0046	-0.3127	-0.0205	-0.1071	0.6867	0.2558	0.0365	0.0035	-0.0359	0.2109	0.0822	0.0761	8.1209	-0.325	21.7059
4	2.8347	0.5406	-1.8483	0.27	-0.255	1.3295	0.0794	-0.1366	-0.0197	0.0563	-0.1197	0.023	0.0542	0.096	0.0404	0.1365	0.0169	-0.0419	0.1542	0.0276	0.0775	-10.8847	-4.886	34.009
5	1.6711	-3.5121	-0.8044	8.2106	3.3365	3.6585	-0.0746	0.046	-0.186	0.2271	-0.1716	0.4601	0.1783	-0.1824	0.2462	0.0682	-0.0485	0.0079	0.1231	-0.0584	0.1023	-30.0115	-3.3974	44.9405
6	7.1655	5.6057	-0.3641	4.4402	-0.2181	0.1049	-0.0746	0.5423	0.0134	0.0781	0.2492	-0.0631	0.1105	-0.1546	-0.1746	0.2387	-0.1254	-0.0942	0.3148	0.1268	0.2069	36.4376	-5.1183	-14.3783
7	3.4916	-0.0608	-2.1013	0.8856	-0.0898	1.2854	0.0078	0.0187	-0.2468	-0.0393	-0.1209	0.0464	-0.0113	-0.002	0.113	0.0829	0.0232	-0.0483	0.1177	-0.038	0.1195	18.5894	-1.9963	-0.2963
8	5.5478	1.7371	-2.7416	0.5494	-0.8577	1.355	0.1102	-0.2318	0.0108	0.0046	-0.0922	0.0048	-0.0644	0.1103	-0.0181	0.2087	0.0403	-0.0096	0.0907	0.0229	0.0097	4.4059	3.9232	17.6126
9	0.9118	-0.3923	-1.8906	0.3364	0.7232	3.9879	0.1053	-0.1847	0.0828	0.0118	0.0855	-0.0246	-0.217	0.3352	-0.1908	0.1153	-0.0534	-0.0439	0.1773	-0.0184	0.0519	-8.9243	3.7721	37.2072
10	3.8943	0.1294	-0.9108	1.3371	-0.3207	0.2882	-0.0813	-0.1178	-0.288	0.0667	0.0543	-0.0688	-0.0193	-0.0247	0.027	0.1453	-0.0039	-0.0126	0.1463	0.0839	0.0954	-23.9019	-1.8122	54.2043
11	8.3014	-3.9889	5.4736	2.4211	-4.0802	7.7804	-0.1001	0.2345	0.5351	0.0816	-0.205	-0.2327	-0.1527	0.4298	0.3052	0.0669	-0.0137	0.0347	0.0365	0.052	0.2272	43.2192	-0.1137	-7.1872
12	3.4854	-1.854	-0.8279	1.3353	0.0835	0.5621	-0.3633	-0.1047	-0.2373	0.2543	0.1492	-0.0404	0.0158	-0.0819	0.2141	0.1032	0.0536	-0.0115	0.0641	0.0004	0.1846	25.7756	-3.6289	6.1945
13	6.024	1.0467	-3.8135	0.322	-0.3799	2.99	-0.3083	-0.4145	-0.3566	-0.0615	-0.1011	0.0073	0.2485	0.0688	0.4094	0.1436	0.0203	0.0426	0.1379	0.0377	0.119	4.261	-2.4657	17.3063
14	1.9104	-0.689	-1.5792	0.5899	0.7474	1.4136	0.0738	0.0257	-0.056	-0.0454	-0.1298	0.0311	-0.1109	-0.0454	0.056	0.1319	-0.0022	-0.0651	0.1574	0.0114	0.0427	-15.2061	2.8652	29.4666
15	2.0087	0.4464	1.4306	3.1581	-1.2038	1.8906	-0.2166	-0.2113	0.0686	0.3488	0.2537	0.0331	-0.4795	-0.3494	-0.0371	0.2334	0.1276	0.0614	0.0838	0.0077	0.0779	-26.6918	6.0706	50.1474

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-6 - 6
2	X-RAY DIFFRACTION	2	A	7 - 29
3	X-RAY DIFFRACTION	3	A	30 - 37
4	X-RAY DIFFRACTION	4	A	38 - 59
5	X-RAY DIFFRACTION	5	A	60 - 80
6	X-RAY DIFFRACTION	6	B	-6 - 6
7	X-RAY DIFFRACTION	7	B	7 - 29
8	X-RAY DIFFRACTION	8	B	30 - 37
9	X-RAY DIFFRACTION	9	B	38 - 59
10	X-RAY DIFFRACTION	10	B	60 - 80
11	X-RAY DIFFRACTION	11	C	-6 - 6
12	X-RAY DIFFRACTION	12	C	7 - 29
13	X-RAY DIFFRACTION	13	C	30 - 37
14	X-RAY DIFFRACTION	14	C	38 - 59
15	X-RAY DIFFRACTION	15	C	60 - 80

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi