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- PDB-2c74: 14-3-3 Protein Eta (Human) Complexed to Peptide -

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Basic information

Entry
Database: PDB / ID: 2c74
Title14-3-3 Protein Eta (Human) Complexed to Peptide
Components
  • 14-3-3 PROTEIN ETA
  • CONSENSUS PEPTIDE MODE 1 FOR 14-3-3 PROTEINS
KeywordsSIGNALING PROTEIN/PEPTIDE / SIGNALING PROTEIN-PEPTIDE COMPLEX / 14-3-3 / PHOSPHOSERINE / PHOSPHORYLATION
Function / homology
Function and homology information


glucocorticoid catabolic process / cerebellar granule cell to Purkinje cell synapse / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of dendrite morphogenesis / nuclear glucocorticoid receptor binding / membrane depolarization during action potential / regulation of neuron differentiation / intercalated disc / sodium channel regulator activity / Activation of BAD and translocation to mitochondria ...glucocorticoid catabolic process / cerebellar granule cell to Purkinje cell synapse / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of dendrite morphogenesis / nuclear glucocorticoid receptor binding / membrane depolarization during action potential / regulation of neuron differentiation / intercalated disc / sodium channel regulator activity / Activation of BAD and translocation to mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of sodium ion transport / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / insulin-like growth factor receptor binding / Transcriptional and post-translational regulation of MITF-M expression and activity / presynaptic modulation of chemical synaptic transmission / substantia nigra development / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / regulation of synaptic plasticity / intracellular protein localization / presynapse / actin binding / transmembrane transporter binding / protein heterodimerization activity / protein domain specific binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / mitochondrion / extracellular exosome / identical protein binding / plasma membrane / 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
CITRIC ACID / 14-3-3 protein eta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsElkins, J.M. / Yang, X. / Smee, C.E.A. / Johansson, C. / Sundstrom, M. / Edwards, A. / Weigelt, J. / Arrowsmith, C. / Doyle, D.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / 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
DepositionNov 17, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 31, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Oct 9, 2019Group: Data collection / Derived calculations / Other / Category: pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Derived calculations / Source and taxonomy / Category: pdbx_entity_src_syn / struct_site
Item: _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 PROTEIN ETA
B: 14-3-3 PROTEIN ETA
P: CONSENSUS PEPTIDE MODE 1 FOR 14-3-3 PROTEINS
Q: CONSENSUS PEPTIDE MODE 1 FOR 14-3-3 PROTEINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7765
Polymers58,5844
Non-polymers1921
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-23.04 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.731, 75.360, 113.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12P
22Q

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A3 - 237
2112B3 - 237
1121P1 - 7
2121Q1 - 7

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.17433, -0.05026, 0.9834), (-0.06468, -0.99596, -0.06236), (0.98256, -0.07448, 0.17037)
Vector: -28.01764, -8.79856, 23.09445)
DetailsTHE PROTEIN IS DIMERIC (CHAINS A,B) BUT SINCE EACH COMPONENT OF THIS DIMER IS IN COMPLEX WITH A PEPTIDE (CHAINSP,Q), THE ENTRY IS MARKED AS TETRAMERIC.

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Components

#1: Protein 14-3-3 PROTEIN ETA / PROTEIN AS1


Mass: 28338.797 Da / Num. of mol.: 2
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 CLONEID 3543571
Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q04917
#2: Protein/peptide CONSENSUS PEPTIDE MODE 1 FOR 14-3-3 PROTEINS


Mass: 952.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PHOSPHOSERINE AT RESIDUE P 5, Q 5 / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN THE REGULATION OF SIGNALING PATHWAYS.
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: 3.15 Å3/Da / Density % sol: 60.66 %
Crystal growpH: 5.6 / Details: 0.1M CITRATE PH 5.6, 20% ISOPROPANOL, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→38.9 Å / Num. obs: 18419 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BQ0

2bq0


Resolution: 2.7→62.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.888 / SU B: 26.783 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.7 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 935 5.1 %RANDOM
Rwork0.22 ---
obs0.224 17445 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2---2.19 Å20 Å2
3---4.17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→62.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3659 0 10 3 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223720
X-RAY DIFFRACTIONr_bond_other_d0.0010.023372
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9725041
X-RAY DIFFRACTIONr_angle_other_deg0.85537762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7775475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27124.819166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33915.048629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0681522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024187
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02735
X-RAY DIFFRACTIONr_nbd_refined0.2280.2910
X-RAY DIFFRACTIONr_nbd_other0.1670.23088
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21909
X-RAY DIFFRACTIONr_nbtor_other0.0860.22290
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.52454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98723791
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.44331447
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3464.51250
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1389tight positional0.050.05
2P59tight positional0.030.05
1A1974medium positional0.30.5
1A1389tight thermal0.090.5
2P59tight thermal0.160.5
1A1974medium thermal0.412
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.4 75
Rwork0.334 1246
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.0082-0.8482-0.80921.25820.34651.78850.1435-0.104-0.30610.0304-0.115-0.08450.16370.1126-0.02860.0733-0.05740.0046-0.06850.0078-0.0761-11.181-22.8918.113
21.2214-0.09970.23122.3750.1461.62270.0479-0.15110.1999-0.1307-0.0967-0.3324-0.2412-0.0050.04890.01770.00640.1097-0.0510.0118-0.0142-17.19314.04815.192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 236
2X-RAY DIFFRACTION2B2 - 235

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