PDB-2c63: 14-3-3 Protein Eta (Human) Complexed to Peptide

ID or keywords:

Entry

Database: PDB / ID: 2c63

Title

14-3-3 Protein Eta (Human) Complexed to Peptide

Components

14-3-3 PROTEIN ETA
CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

Keywords

SIGNALING PROTEIN/PEPTIDE /

SIGNALING PROTEIN-PEPTIDE COMPLEX /

14-3-3 /

PHOSPHOSERINE /

STRUCTURAL GENOMICS /

STRUCTURAL GENOMICS CONSORTIUM /

PHOSPHORYLATION / YWHAH

Function / homology

Function and homology information

glucocorticoid catabolic process / cerebellar granule cell to Purkinje cell synapse / negative regulation of dendrite morphogenesis / intracellular glucocorticoid receptor signaling pathway / regulation of sodium ion transmembrane transporter activity / nuclear glucocorticoid receptor binding / membrane depolarization during action potential / regulation of neuron differentiation /

intercalated disc / sodium channel regulator activity ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Elkins, J.M. / Yang, X. / Smee, C.E.A. / Johansson, C. / Sundstrom, M. / Edwards, A. / Weigelt, J. / Arrowsmith, C. / Doyle, D.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Basis for Protein-Protein Interactions in the 14-3-3 Protein Family.
Authors: Yang, X. / Lee, W.H. / Sobott, F. / Papagrigoriou, E. / Robinson, C.V. / Grossmann, J.G. / Sundstrom, M. / Doyle, D.A. / Elkins, J.M.

History

Deposition	Nov 7, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 21, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 4, 2013	Group: Derived calculations / Non-polymer description / Source and taxonomy
Revision 1.3	Dec 13, 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_conn 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_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2c63.cif.gz	202.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2c63.ent.gz	162.7 KB	Display	PDB format
PDBx/mmJSON format	2c63.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/c6/2c63 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/2c63	HTTPS FTP

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Related structure data

Related structure data	2bq0SC 2br9C 2btpC 2c23C 2c74C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2b05-3 6sad-d 2c74-d 6fel-2 5j31-d 6byl-3 6byj-3 4n84-d 5d3e-1 5d3e-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) 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	#222 - Jun 2018 Proteins and Nanoparticles similarity (12) #245 - May 2020 Spliceosomes similarity (2) #44 - Aug 2003 Calmodulin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: 14-3-3 PROTEIN ETA

B: 14-3-3 PROTEIN ETA

C: 14-3-3 PROTEIN ETA

D: 14-3-3 PROTEIN ETA

P: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

Q: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

R: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

S: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

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

1

A: 14-3-3 PROTEIN ETA

B: 14-3-3 PROTEIN ETA

P: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

Q: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

defined by author&software
58.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 14-3-3 PROTEIN ETA

D: 14-3-3 PROTEIN ETA

R: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

S: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

defined by author&software
58.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.251, 79.398, 125.109
Angle α, β, γ (deg.)	90.00, 95.15, 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
4	1	D
1	2	P
2	2	Q
3	2	R
4	2	S

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	3 - 235
2	1	1	5	B	3 - 235
3	1	1	5	C	3 - 235
4	1	1	5	D	3 - 235
1	1	2	2	P	1 - 6
2	1	2	2	Q	1 - 6
3	1	2	2	R	1 - 6
4	1	2	2	S	1 - 6

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.99888, -0.04691, -0.00533), (-0.04708, 0.99808, 0.04029), (0.00343, 0.04049, -0.99917)	23.78572, -0.86314, 63.76781
2	given	(-0.94846, -0.03961, -0.3144), (0.05229, -0.99812, -0.032), (-0.31254, -0.04679, 0.94875)	33.4706, 36.80296, 4.10002
3	given	(0.94883, 0.0257, 0.31473), (0.02143, -0.99963, 0.01703), (0.31505, -0.00941, -0.94903)	-8.94187, 35.62172, 57.46293

Details

THE PROTEIN IS DIMERIC (CHAINS A,B OR C,D) BUT SINCE EACHCOMPONENT OF THIS DIMER IS IN COMPLEX WITH A PEPTIDE, THE ENTRY IS MARKED AS TETRAMERIC.

#1: Protein	14-3-3 PROTEIN ETA / PROTEIN AS1 Mass: 28338.797 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: THE MAMMALIAN GENE COLLECTION, I.M.A.G.E. CONSORTIUM CLONE ID 3543571 Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04917
#2: Protein/peptide	CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS Mass: 736.774 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: PHOSPHOSERINE AT RESIDUE P 4, Q 4, R 4, S 4 / Source: (synth.) HOMO SAPIENS (human)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	SEQUENCE SER 0 IS A CLONING ARTEFACT

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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: 51.3 %
Crystal grow	pH: 7.5 / Details: 0.2M MGCL2, 0.1M HEPES PH 7.5, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788
Detector	Type: ADSC CCD / Detector: CCD / Date: Oct 24, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9788 Å / Relative weight: 1
Reflection	Resolution: 2.15→66.96 Å / Num. obs: 61914 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_merge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shell	Resolution: 2.15→2.27 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BQ0

2bq0

Resolution: 2.15→125 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.924 / SU B: 10.923 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.248	1883	3 %	RANDOM
R_work	0.184	-	-	-
obs	0.185	60014	99.9 %	-

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: 38.86 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.35 Å²	0 Å²	0.37 Å²
2-	-	1.28 Å²	0 Å²
3-	-	-	-1.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→125 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7489	0	0	397	7886

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	7597
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6879
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.975	10274
X-RAY DIFFRACTION	r_angle_other_deg	0.903	3	15956
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.61	5	940
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.899	25.014	369
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.63	15.044	1367
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.341	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1164
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	8456
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1492
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	1704
X-RAY DIFFRACTION	r_nbd_other	0.171	0.2	6544
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	3740
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	4229
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.178	0.2	367
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	0.2	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.198	0.2	49
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.187	0.2	5
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	3.274	3	4967
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	4.297	5	7567
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	7.81	7	3140
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	10.103	11	2707
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
2	1	P	22	tight positional	0.04	0.05
2	2	Q	22	tight positional	0.03	0.05
2	3	R	22	tight positional	0.03	0.05
2	4	S	22	tight positional	0.03	0.05
1	1	A	1388	medium positional	0.22	0.5
1	2	B	1388	medium positional	0.21	0.5
1	3	C	1388	medium positional	0.2	0.5
1	4	D	1388	medium positional	0.2	0.5
2	1	P	47	medium positional	0.18	0.5
2	2	Q	47	medium positional	0.15	0.5
2	3	R	47	medium positional	0.1	0.5
2	4	S	47	medium positional	0.16	0.5
1	1	A	2084	loose positional	0.44	5
1	2	B	2084	loose positional	0.51	5
1	3	C	2084	loose positional	0.44	5
1	4	D	2084	loose positional	0.43	5
2	1	P	22	tight thermal	0.15	0.5
2	2	Q	22	tight thermal	0.24	0.5
2	3	R	22	tight thermal	0.21	0.5
2	4	S	22	tight thermal	0.17	0.5
1	1	A	1388	medium thermal	1.23	2
1	2	B	1388	medium thermal	1.12	2
1	3	C	1388	medium thermal	1.27	2
1	4	D	1388	medium thermal	1.25	2
2	1	P	47	medium thermal	0.91	2
2	2	Q	47	medium thermal	1.29	2
2	3	R	47	medium thermal	1.26	2
2	4	S	47	medium thermal	1.1	2
1	1	A	2084	loose thermal	3.12	10
1	2	B	2084	loose thermal	3.03	10
1	3	C	2084	loose thermal	2.96	10
1	4	D	2084	loose thermal	3.13	10

LS refinement shell

Resolution: 2.15→2.21 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.294	138
R_work	0.223	4405

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	1.3915	-0.1445	-0.3061	1.3093	0.4073	4.989	0.1156	-0.303	0.0943	0.0142	-0.1099	0.0067	-0.6467	0.0849	-0.0057	0.0452	-0.0401	0.0012	-0.1448	-0.0219	-0.1568	8.1104	5.8854	21.7813
2	1.2147	0.0243	0.0433	1.6755	1.1224	4.0343	0.1272	0.028	-0.0226	-0.305	-0.1685	0.085	-0.5987	-0.3073	0.0413	-0.002	0.0804	-0.0292	-0.174	-0.0145	-0.1567	2.6401	1.457	5.941
3	2.505	-0.7339	0.1061	2.0394	0.5141	3.0755	0.1305	0.0417	-0.3885	-0.1238	-0.1915	0.1616	0.2898	-0.1886	0.0609	-0.0654	0.0162	-0.0591	-0.1795	-0.0093	-0.0694	4.2179	-13.7874	6.8673
4	2.2026	-0.0194	0.6498	1.9189	0.706	2.4701	-0.1377	0.3797	0.2753	0.1236	0.1096	-0.011	-0.0533	0.3093	0.0281	-0.016	-0.037	-0.0174	-0.0613	0.0308	-0.1483	15.1875	5.3894	42.292
5	2.403	0.7199	0.1937	2.7003	0.1521	3.4558	-0.0243	-0.0417	0.0846	0.7197	0.0757	-0.0896	0.0862	0.3442	-0.0514	0.1708	0.0668	-0.0614	-0.0869	-0.0411	-0.1687	21.0531	0.6918	57.9025
6	2.3927	1.3726	0.4439	3.7755	0.4958	1.6557	0.1185	0.0669	-0.3832	0.8543	0.0655	-0.2325	0.5141	0.2676	-0.1841	0.2966	0.1269	-0.1128	-0.075	-0.0334	-0.0936	20.0542	-14.4732	56.2934
7	1.9593	0.1098	-0.6088	1.3733	-0.0339	1.6791	-0.028	-0.317	-0.2659	-0.0132	-0.0541	0.0113	0.0855	0.1594	0.0821	-0.2166	0.0279	0.0034	-0.1221	0.0604	-0.0726	18.6183	30.8137	21.8995
8	2.0162	0.31	-1.1235	2.0122	-0.6482	2.6486	-0.0726	-0.0655	-0.1791	-0.3955	-0.1224	-0.2137	0.1312	0.2259	0.195	-0.1704	0.0494	0.0326	-0.1452	0.0309	-0.0627	28.9247	35.3694	8.7472
9	3.4183	-0.686	-0.0523	1.7843	-0.224	1.4751	0.1268	-0.0844	0.386	-0.2532	-0.0481	-0.1316	-0.3217	0.1534	-0.0787	-0.0911	0.0023	0.0204	-0.162	0.0024	-0.0269	27.8896	50.3991	9.9682
10	0.5965	-0.1895	0.5905	1.1058	-0.3812	3.302	0.0417	0.0524	0.0383	0.1202	-0.0565	0.0393	0.239	0.0189	0.0148	-0.1707	-0.0318	0.0058	-0.1094	0.0068	-0.1124	5.7957	30.3278	39.269
11	1.2589	0.0431	0.1014	1.6676	0.1422	2.9642	0.0497	-0.0378	0.0212	0.4439	0.0378	0.2638	0.0232	-0.3938	-0.0875	-0.0818	-0.0242	0.0674	-0.0408	-0.0017	-0.0661	-4.4038	34.427	52.6666
12	1.6543	1.2382	0.7229	2.1686	0.2455	3.208	0.0466	-0.0468	0.4273	0.4829	-0.0186	0.303	-0.6072	-0.4628	-0.0281	0.083	0.0971	0.0963	-0.062	-0.0082	0.0374	-3.0564	49.4481	52.341

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 112
2	X-RAY DIFFRACTION	2	A	113 - 167
3	X-RAY DIFFRACTION	3	A	168 - 235
4	X-RAY DIFFRACTION	4	B	3 - 112
5	X-RAY DIFFRACTION	5	B	113 - 167
6	X-RAY DIFFRACTION	6	B	168 - 235
7	X-RAY DIFFRACTION	7	C	3 - 112
8	X-RAY DIFFRACTION	8	C	113 - 167
9	X-RAY DIFFRACTION	9	C	168 - 235
10	X-RAY DIFFRACTION	10	D	3 - 112
11	X-RAY DIFFRACTION	11	D	113 - 167
12	X-RAY DIFFRACTION	12	D	168 - 235

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Yorodumi