PDB-2b05: Crystal Structure of 14-3-3 gamma in complex with a phosphoserine...

ID or keywords:

Entry

Database: PDB / ID: 2b05

Title

Crystal Structure of 14-3-3 gamma in complex with a phosphoserine peptide

Components

14-3-3 protein gamma
peptide

Keywords

CELL CYCLE

Function / homology

Function and homology information

positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Papagrigoriou, E. / Elkins, J. / Arrowsmith, C. / Zhao, Y. / Debreczeni, E.J. / Edwards, A. / Weigelt, J. / Doyle, D. / von Delft, F. / Turnbull, A. / Yang, X.

Citation

Journal: TO BE PUBLISHED
Title: Crystal Structure of 14-3-3 gamma in complex with a phosphoserine peptide
Authors: Papagrigoriou, E. / Elkins, J. / Arrowsmith, C. / Zhao, Y. / Debreczeni, E.J. / Edwards, A. / Weigelt, J. / Doyle, D. / von Delft, F. / Turnbull, A. / Yang, X.

History

Deposition	Sep 13, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Aug 23, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2b05.cif.gz	275.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2b05_validation.pdf.gz	462.7 KB	Display	wwPDB validaton report
Full document	2b05_full_validation.pdf.gz	471.7 KB	Display
Data in XML	2b05_validation.xml.gz	27.6 KB	Display
Data in CIF	2b05_validation.cif.gz	42.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/2b05 ftp://data.pdbj.org/pub/pdb/validation_reports/b0/2b05	HTTPS FTP

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Related structure data

Related structure data	2bq0S S: Starting model for refinement
Similar structure data	2c1j-d 6gkf-2 7d8p-d 5m35-d 6ymo-d 6gkf-3 6t80-1 6yo8-2 6hep-2 4n7y-d 3nkx-d 5iqp-d 5xy9-d 6ef5-1 6gkg-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

2bq0S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#222 - Jun 2018 Proteins and Nanoparticles similarity (13) #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 gamma

G: peptide

B: 14-3-3 protein gamma

H: peptide

C: 14-3-3 protein gamma

I: peptide

D: 14-3-3 protein gamma

J: peptide

E: 14-3-3 protein gamma

K: peptide

F: 14-3-3 protein gamma

L: peptide

174 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 14-3-3 protein gamma

G: peptide

D: 14-3-3 protein gamma

J: peptide

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

2

B: 14-3-3 protein gamma

H: peptide

C: 14-3-3 protein gamma

I: peptide

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

3

E: 14-3-3 protein gamma

K: peptide

F: 14-3-3 protein gamma

L: peptide

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

4

A: 14-3-3 protein gamma

G: peptide

D: 14-3-3 protein gamma

J: peptide

A: 14-3-3 protein gamma

G: peptide

D: 14-3-3 protein gamma

J: peptide

E: 14-3-3 protein gamma

K: peptide

F: 14-3-3 protein gamma

L: peptide

E: 14-3-3 protein gamma

K: peptide

F: 14-3-3 protein gamma

L: peptide

B: 14-3-3 protein gamma

H: peptide

C: 14-3-3 protein gamma

I: peptide

B: 14-3-3 protein gamma

H: peptide

C: 14-3-3 protein gamma

I: peptide

defined by software
347 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	8_444	-y-1,-x-1,-z-1/2	1
crystal symmetry operation	1_455	x-1,y,z	1
crystal symmetry operation	8_454	-y-1,-x,-z-1/2	1
crystal symmetry operation	4_444	y-1/2,-x-1/2,z-1/4	1
crystal symmetry operation	6_444	x-1/2,-y-1/2,-z-1/4	1

Unit cell

Length a, b, c (Å)	121.571, 121.571, 313.164
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	VAL	VAL	ASP	ASP	6	A	A	2 - 3	1 - 2
2	1	1	VAL	VAL	ASP	ASP	6	B	C	2 - 3	1 - 2
3	1	1	VAL	VAL	ASP	ASP	6	C	E	2 - 3	1 - 2
4	1	1	VAL	VAL	ASP	ASP	6	D	G	2 - 3	1 - 2
5	2	1	ARG	ARG	ALA	ALA	3	A	A	4 - 72	3 - 71
6	2	1	ARG	ARG	ALA	ALA	3	B	C	4 - 72	3 - 71
7	2	1	ARG	ARG	ALA	ALA	3	C	E	4 - 72	3 - 71
8	2	1	ARG	ARG	ALA	ALA	3	D	G	4 - 72	3 - 71
9	2	1	ARG	ARG	ALA	ALA	3	E	I	4 - 72	3 - 71
10	3	1	GLU	GLU	THR	THR	3	A	A	76 - 210	75 - 209
11	3	1	GLU	GLU	THR	THR	3	B	C	76 - 210	75 - 209
12	3	1	GLU	GLU	THR	THR	3	C	E	76 - 210	75 - 209
13	3	1	GLU	GLU	THR	THR	3	D	G	76 - 210	75 - 209
14	3	1	GLU	GLU	THR	THR	3	E	I	76 - 210	75 - 209
15	4	1	LEU	LEU	LEU	LEU	6	A	A	211 - 221	210 - 220
16	4	1	LEU	LEU	LEU	LEU	6	B	C	211 - 221	210 - 220
17	4	1	LEU	LEU	LEU	LEU	6	C	E	211 - 221	210 - 220
18	4	1	LEU	LEU	LEU	LEU	6	D	G	211 - 221	210 - 220
19	4	1	LEU	LEU	LEU	LEU	6	E	I	211 - 221	210 - 220
20	5	1	ILE	ILE	THR	THR	3	A	A	222 - 234	221 - 233
21	5	1	ILE	ILE	THR	THR	3	B	C	222 - 234	221 - 233
22	5	1	ILE	ILE	THR	THR	3	C	E	222 - 234	221 - 233
23	5	1	ILE	ILE	THR	THR	3	D	G	222 - 234	221 - 233
24	5	1	ILE	ILE	THR	THR	3	E	I	222 - 234	221 - 233
1	1	2	ARG	ARG	PRO	PRO	1	G	B	502 - 507	1 - 6
2	1	2	ARG	ARG	PRO	PRO	1	L	L	502 - 507	1 - 6
1	1	3	ASP	ASP	ASN	ASN	2	A	A	73 - 75	72 - 74
2	1	3	ASP	ASP	ASN	ASN	2	B	C	73 - 75	72 - 74
3	1	3	ASP	ASP	ASN	ASN	2	C	E	73 - 75	72 - 74
4	1	3	ASP	ASP	ASN	ASN	2	D	G	73 - 75	72 - 74
1	1	4	VAL	VAL	ASP	ASP	1	A	A	2 - 3	1 - 2
2	1	4	VAL	VAL	ASP	ASP	1	C	E	2 - 3	1 - 2
1	1	5	VAL	VAL	ASP	ASP	1	B	C	2 - 3	1 - 2
2	1	5	VAL	VAL	ASP	ASP	1	D	G	2 - 3	1 - 2

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	14-3-3 protein gamma / Protein kinase C inhibitor protein 1 / KCIP-1 Mass: 28205.391 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Plasmid: pTvHR21- SGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)R3 / References: UniProt: P61981
#2: Protein/peptide	peptide Mass: 736.774 Da / Num. of mol.: 6 / Source method: obtained synthetically
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 61.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 3350, magnesium chloride, Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9919 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jul 2, 2005
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9919 Å / Relative weight: 1
Reflection	Resolution: 2.55→48.2 Å / Num. all: 77674 / Num. obs: 77602 / % possible obs: 99.9 % / R_merge(I) obs: 0.079
Reflection shell	Resolution: 2.55→2.64 Å / R_merge(I) obs: 0.931 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2BQ0

2bq0

Resolution: 2.55→48.2 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.899 / SU B: 21.776 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Electron density for the chain F molecule clearly varyfies its presence. However, the density is of very low quality. Hence, chain F has ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30175	2301	3 %	RANDOM
R_work	0.258	-	-	-
all	0.2655	77403	-	-
obs	0.25933	74805	99.62 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 54.465 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.94 Å²	0 Å²	0 Å²
2-	-	0.94 Å²	0 Å²
3-	-	-	-1.89 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→48.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10960	0	0	128	11088

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	11146
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.222	1.962	15136
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.378	5	1418
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.225	24.487	497
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.427	15.048	1877
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.383	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1762
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	8339
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	5123
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	7860
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	347
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	0.368	0.2	139
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.265	0.2	20
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	0.551	1.5	7317
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.923	2	11415
X-RAY DIFFRACTION	r_scbond_it	1.51	3	4356
X-RAY DIFFRACTION	r_scangle_it	2.384	4.5	3721
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	888	tight positional	0.06	0.05
1	2	B	888	tight positional	0.07	0.05
1	3	C	888	tight positional	0.06	0.05
1	4	D	888	tight positional	0.05	0.05
1	9	E	888	tight positional	0.07	0.05
2	1	G	1828	tight positional	0.04	0.05
3	1	A	12	tight positional	0.03	0.05
3	2	B	12	tight positional	0.05	0.05
3	3	C	12	tight positional	0.02	0.05
3	4	D	12	tight positional	0.04	0.05
4	1	A	15	tight positional	0.03	0.05
5	1	B	15	tight positional	0.03	0.05
3	1	A	5	medium positional	0.34	0.5
3	2	B	5	medium positional	1	0.5
3	3	C	5	medium positional	0.42	0.5
3	4	D	5	medium positional	0.35	0.5
1	1	A	783	loose positional	0.39	5
1	2	B	783	loose positional	0.45	5
1	3	C	783	loose positional	0.36	5
1	4	D	783	loose positional	0.38	5
1	9	E	783	loose positional	0.43	5
1	1	A	888	tight thermal	2.46	10
1	2	B	888	tight thermal	1.78	10
1	3	C	888	tight thermal	2.48	10
1	4	D	888	tight thermal	2.35	10
1	9	E	888	tight thermal	3.37	10
2	2	L	1828	tight thermal	2.43	10
3	1	A	12	tight thermal	2.8	10
3	2	B	12	tight thermal	0.39	10
3	3	C	12	tight thermal	2.23	10
3	4	D	12	tight thermal	5.06	10
4	1	A	15	tight thermal	2.75	10
5	1	B	15	tight thermal	1.33	10
3	1	A	5	medium thermal	2.28	10
3	2	B	5	medium thermal	1.49	10
3	3	C	5	medium thermal	2.5	10
3	4	D	5	medium thermal	5.83	10
1	1	A	783	loose thermal	2.71	10
1	2	B	783	loose thermal	2.19	10
1	3	C	783	loose thermal	2.68	10
1	4	D	783	loose thermal	2.43	10
1	9	E	783	loose thermal	3.22	10

LS refinement shell

Resolution: 2.55→2.616 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.439	157	-
R_work	0.357	5467	-
obs	-	-	99.98 %

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