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- PDB-4bg6: 14-3-3 interaction with Rnd3 prenyl-phosphorylation motif -

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Basic information

Entry
Database: PDB / ID: 4bg6
Title14-3-3 interaction with Rnd3 prenyl-phosphorylation motif
Components
  • 14-3-3 PROTEIN ZETA/DELTA
  • RHO-RELATED GTP-BINDING PROTEIN RHOE
KeywordsSIGNALING PROTEIN / PRENYLATION / ACTIN CYTOSKELETON
Function / homology
Function and homology information


Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / RND3 GTPase cycle / KSRP (KHSRP) binds and destabilizes mRNA / small GTPase-mediated signal transduction / GP1b-IX-V activation signalling ...Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / RND3 GTPase cycle / KSRP (KHSRP) binds and destabilizes mRNA / small GTPase-mediated signal transduction / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / negative regulation of innate immune response / regulation of ERK1 and ERK2 cascade / protein sequestering activity / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / cell migration / melanosome / actin cytoskeleton organization / blood microparticle / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / cell adhesion / cadherin binding / Golgi membrane / protein phosphorylation / focal adhesion / GTPase activity / glutamatergic synapse / ubiquitin protein ligase binding / GTP binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho-related GTP-binding protein RhoE / 14-3-3 domain / Delta-Endotoxin; domain 1 / Small GTPase Rho / small GTPase Rho family profile. / 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 ...Rho-related GTP-binding protein RhoE / 14-3-3 domain / Delta-Endotoxin; domain 1 / Small GTPase Rho / small GTPase Rho family profile. / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
FARNESYL / Rho-related GTP-binding protein RhoE / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRiou, P. / Kjaer, S. / Purkiss, A. / O'Reilly, N. / McDonald, N.Q.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: 14-3-3 Proteins Interact with a Hybrid Prenyl-Phosphorylation Motif to Inhibit G Proteins.
Authors: Riou, P. / Kjaer, S. / Garg, R. / Purkiss, A. / George, R. / Cain, R.J. / Bineva, G. / Reymond, N. / Mccoll, B. / Thompson, A.J. / O'Reilly, N. / Mcdonald, N.Q. / Parker, P.J. / Ridley, A.J.
History
DepositionMar 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: diffrn_source / exptl_crystal_grow ...diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_biol / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method ..._diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: 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 / struct_site
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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 PROTEIN ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
Q: RHO-RELATED GTP-BINDING PROTEIN RHOE
R: RHO-RELATED GTP-BINDING PROTEIN RHOE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5259
Polymers58,0494
Non-polymers1,4765
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint1 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.783, 81.313, 111.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99735, -0.07218, -0.00942), (-0.06981, 0.98509, -0.15721), (0.02063, -0.15614, -0.98752)
Vector: -0.01764, -0.00277, 0.02935)

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Components

#1: Protein 14-3-3 PROTEIN ZETA/DELTA / PROTEIN KINASE C INHIBITOR PROTEIN 1 / KCIP-1


Mass: 27777.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P63104
#2: Protein/peptide RHO-RELATED GTP-BINDING PROTEIN RHOE / PROTEIN MEMB / RHO FAMILY GTPASE 3 / RHO-RELATED GTP-BINDING PROTEIN RHO8 / RND3


Mass: 1247.359 Da / Num. of mol.: 2 / Fragment: C-TERMINUS, RESIDUES 232-241 / Source method: obtained synthetically / Details: FARNESYLATION ON CYS 347 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61587
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 3.08 Å3/Da / Density % sol: 60.02 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17 M SODIUM ACETATE; 0.085 M TRIS, PH 8.5; 25.5% (W/V) PEG4000, 15% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2011 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→38.51 Å / Num. obs: 28918 / % possible obs: 99.1 % / Observed criterion σ(I): 5 / Redundancy: 3.21 % / Biso Wilson estimate: 56.28 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WH0

1wh0


Resolution: 2.3→38.508 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 35.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2728 1468 5.1 %
Rwork0.2436 --
obs0.2451 28863 98.91 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.018 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 48 80 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013724
X-RAY DIFFRACTIONf_angle_d0.4955020
X-RAY DIFFRACTIONf_dihedral_angle_d14.3541379
X-RAY DIFFRACTIONf_chiral_restr0.019569
X-RAY DIFFRACTIONf_plane_restr0.001646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.42251370.3672698X-RAY DIFFRACTION99
2.3822-2.47760.40791570.33992680X-RAY DIFFRACTION99
2.4776-2.59030.35751440.33312721X-RAY DIFFRACTION99
2.5903-2.72680.42631400.33662744X-RAY DIFFRACTION100
2.7268-2.89760.42141500.31912676X-RAY DIFFRACTION98
2.8976-3.12130.31471610.30862745X-RAY DIFFRACTION100
3.1213-3.43520.30791490.27482728X-RAY DIFFRACTION99
3.4352-3.93180.26151320.2232769X-RAY DIFFRACTION99
3.9318-4.9520.22791690.18552767X-RAY DIFFRACTION99
4.952-38.5130.18711290.21182867X-RAY DIFFRACTION97
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)
13.09410.7815-1.43862.2211-0.02082.99610.00030.7433-0.0072-0.0136-0.01620.166-0.0606-0.34780.03580.2926-0.0288-0.04040.6776-0.00580.5315-9.745-7.84298.9665
22.71370.74241.36114.15070.42473.19710.21860.6374-0.25540.4007-0.23790.85410.3135-1.2007-0.01780.3627-0.09780.08490.9599-0.05590.8678-24.9913-4.291411.9143
31.1556-0.4523-1.62895.47081.20525.08170.36840.43891.0660.2681-0.25090.344-0.4351-0.3555-0.07390.4019-0.0410.18260.89790.05641.1216-23.615910.711812.3001
45.6337-4.0238-0.04398.98480.36410.03380.21690.86850.4289-0.3915-0.7988-0.7826-0.05080.2330.5970.4660.04220.09060.66160.15380.8606-17.71346.46194.1127
52.7516-0.566-3.22431.72730.64323.77890.00320.4012-0.2375-0.13220.01040.0240.0805-0.52920.00570.2973-0.0105-0.02790.45680.01880.43599.7421-7.5005-2.2955
62.76781.6093-1.60364.446-3.25972.4747-0.048-0.0279-0.1652-0.1945-0.1734-0.47990.31750.61360.25070.27650.02240.01410.6031-0.04740.494724.1123-3.6373-7.7138
78.2432-3.32174.34778.3097-4.8675.5482-0.04940.1060.5881-0.2113-0.0606-0.3347-0.0742-0.27480.14680.2660.01890.08620.4928-0.06660.453321.830711.23-10.2934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:111)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 112:159)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 160:229)
4X-RAY DIFFRACTION4CHAIN Q
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 4:111)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 112:159)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 160:229)

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