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

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Basic information

Entry
Database: PDB / ID: 2b05
TitleCrystal Structure of 14-3-3 gamma in complex with a phosphoserine peptide
Components
  • 14-3-3 protein gamma
  • peptide
KeywordsCELL 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity ...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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / protein targeting / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / insulin-like growth factor receptor binding / negative regulation of TORC1 signaling / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / protein kinase C binding / AURKA Activation by TPX2 / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of synaptic plasticity / receptor tyrosine kinase binding / cellular response to insulin stimulus / positive regulation of T cell activation / intracellular protein localization / Regulation of PLK1 Activity at G2/M Transition / regulation of protein localization / presynapse / mitochondrial matrix / protein domain specific binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein ...14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPapagrigoriou, E. / Elkins, J. / Arrowsmith, C. / Zhao, Y. / Debreczeni, E.J. / Edwards, A. / Weigelt, J. / Doyle, D. / von Delft, F. / Turnbull, A. / Yang, X.
CitationJournal: 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
DepositionSep 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)173,65312
Polymers173,65312
Non-polymers00
Water2,252125
1
A: 14-3-3 protein gamma
G: peptide
D: 14-3-3 protein gamma
J: peptide


Theoretical massNumber of molelcules
Total (without water)57,8844
Polymers57,8844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-29 kcal/mol
Surface area22410 Å2
MethodPISA
2
B: 14-3-3 protein gamma
H: peptide
C: 14-3-3 protein gamma
I: peptide


Theoretical massNumber of molelcules
Total (without water)57,8844
Polymers57,8844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-29 kcal/mol
Surface area22710 Å2
MethodPISA
3
E: 14-3-3 protein gamma
K: peptide
F: 14-3-3 protein gamma
L: peptide


Theoretical massNumber of molelcules
Total (without water)57,8844
Polymers57,8844
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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


Theoretical massNumber of molelcules
Total (without water)347,30624
Polymers347,30624
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444-y-1,-x-1,-z-1/21
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation8_454-y-1,-x,-z-1/21
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/41
crystal symmetry operation6_444x-1/2,-y-1/2,-z-1/41
Buried area29560 Å2
ΔGint-219 kcal/mol
Surface area125790 Å2
MethodPISA
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 number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91E
101A
111B
121C
131D
141E
151A
161B
171C
181D
191E
201A
211B
221C
231D
241E
12G
22L
13A
23B
33C
43D
14A
24C
15B
25D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALASPASP6AA2 - 31 - 2
211VALVALASPASP6BC2 - 31 - 2
311VALVALASPASP6CE2 - 31 - 2
411VALVALASPASP6DG2 - 31 - 2
521ARGARGALAALA3AA4 - 723 - 71
621ARGARGALAALA3BC4 - 723 - 71
721ARGARGALAALA3CE4 - 723 - 71
821ARGARGALAALA3DG4 - 723 - 71
921ARGARGALAALA3EI4 - 723 - 71
1031GLUGLUTHRTHR3AA76 - 21075 - 209
1131GLUGLUTHRTHR3BC76 - 21075 - 209
1231GLUGLUTHRTHR3CE76 - 21075 - 209
1331GLUGLUTHRTHR3DG76 - 21075 - 209
1431GLUGLUTHRTHR3EI76 - 21075 - 209
1541LEULEULEULEU6AA211 - 221210 - 220
1641LEULEULEULEU6BC211 - 221210 - 220
1741LEULEULEULEU6CE211 - 221210 - 220
1841LEULEULEULEU6DG211 - 221210 - 220
1941LEULEULEULEU6EI211 - 221210 - 220
2051ILEILETHRTHR3AA222 - 234221 - 233
2151ILEILETHRTHR3BC222 - 234221 - 233
2251ILEILETHRTHR3CE222 - 234221 - 233
2351ILEILETHRTHR3DG222 - 234221 - 233
2451ILEILETHRTHR3EI222 - 234221 - 233
112ARGARGPROPRO1GB502 - 5071 - 6
212ARGARGPROPRO1LL502 - 5071 - 6
113ASPASPASNASN2AA73 - 7572 - 74
213ASPASPASNASN2BC73 - 7572 - 74
313ASPASPASNASN2CE73 - 7572 - 74
413ASPASPASNASN2DG73 - 7572 - 74
114VALVALASPASP1AA2 - 31 - 2
214VALVALASPASP1CE2 - 31 - 2
115VALVALASPASP1BC2 - 31 - 2
215VALVALASPASP1DG2 - 31 - 2

NCS ensembles :
ID
1
2
3
4
5

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Components

#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 modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9919 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 2, 2005
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.55→48.2 Å / Num. all: 77674 / Num. obs: 77602 / % possible obs: 99.9 % / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BQ0

2bq0


Resolution: 2.55→48.2 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc 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 ...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 been tightly ncs restrained with chain A molecule.
RfactorNum. reflection% reflectionSelection details
Rfree0.30175 2301 3 %RANDOM
Rwork0.258 ---
all0.2655 77403 --
obs0.25933 74805 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10960 0 0 128 11088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211146
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.96215136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37851418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22524.487497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42715.0481877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3831571
X-RAY DIFFRACTIONr_chiral_restr0.090.21762
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028339
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.25123
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.27860
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2347
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3680.2139
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5511.57317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.923211415
X-RAY DIFFRACTIONr_scbond_it1.5134356
X-RAY DIFFRACTIONr_scangle_it2.3844.53721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A888tight positional0.060.05
12B888tight positional0.070.05
13C888tight positional0.060.05
14D888tight positional0.050.05
19E888tight positional0.070.05
21G1828tight positional0.040.05
31A12tight positional0.030.05
32B12tight positional0.050.05
33C12tight positional0.020.05
34D12tight positional0.040.05
41A15tight positional0.030.05
51B15tight positional0.030.05
31A5medium positional0.340.5
32B5medium positional10.5
33C5medium positional0.420.5
34D5medium positional0.350.5
11A783loose positional0.395
12B783loose positional0.455
13C783loose positional0.365
14D783loose positional0.385
19E783loose positional0.435
11A888tight thermal2.4610
12B888tight thermal1.7810
13C888tight thermal2.4810
14D888tight thermal2.3510
19E888tight thermal3.3710
22L1828tight thermal2.4310
31A12tight thermal2.810
32B12tight thermal0.3910
33C12tight thermal2.2310
34D12tight thermal5.0610
41A15tight thermal2.7510
51B15tight thermal1.3310
31A5medium thermal2.2810
32B5medium thermal1.4910
33C5medium thermal2.510
34D5medium thermal5.8310
11A783loose thermal2.7110
12B783loose thermal2.1910
13C783loose thermal2.6810
14D783loose thermal2.4310
19E783loose thermal3.2210
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 157 -
Rwork0.357 5467 -
obs--99.98 %

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