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- PDB-8rrm: tripartite complex between 14-3-3 sigma, Fusicoccin-A, and a phos... -

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Basic information

Entry
Database: PDB / ID: 8rrm
Titletripartite complex between 14-3-3 sigma, Fusicoccin-A, and a phosphopeptide optimized for a Fusicoccin-mediated stabilization of the complex
Components
  • 14-3-3 protein sigma
  • Phosphopeptide designed according to the sequence preferences favouring stabilisation by Fusicoccin-A
KeywordsSIGNALING PROTEIN / PROTEIN-PHOSPHOPEPTIDE COMPLEX / 14-3-3 sigma
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 protein sigma / 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
Similarity search - Domain/homology
BICARBONATE ION / FUSICOCCIN / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCousido-Siah, A. / McEwen, A.G. / Monsellier, E. / Trave, G.
Funding support France, 6items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE92-0017 France
La ligue contre le cancer France
French National Research AgencyANR-10-INSB-05-01 France
French National Research AgencyANR-10-IDEX-0002 France
French National Research AgencyANR 20-SFRI-0012 France
French National Research AgencyANR-17-EURE-0023 France
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Holdup Multiplex Assay for High-Throughput Measurement of Protein-Ligand Affinity Constants Using a Mass Spectrometry Readout.
Authors: Delalande, F. / Ostergaard, S.R. / Gogl, G. / Cousido-Siah, A. / McEwen, A.G. / Men, Y. / Salimova, F. / Rohrbacher, A. / Kostmann, C. / Nomine, Y. / Vincentelli, R. / Eberling, P. / ...Authors: Delalande, F. / Ostergaard, S.R. / Gogl, G. / Cousido-Siah, A. / McEwen, A.G. / Men, Y. / Salimova, F. / Rohrbacher, A. / Kostmann, C. / Nomine, Y. / Vincentelli, R. / Eberling, P. / Carapito, C. / Trave, G. / Monsellier, E.
History
DepositionJan 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: Phosphopeptide designed according to the sequence preferences favouring stabilisation by Fusicoccin-A
D: Phosphopeptide designed according to the sequence preferences favouring stabilisation by Fusicoccin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6368
Polymers59,1784
Non-polymers1,4584
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-60 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.330, 55.910, 82.750
Angle α, β, γ (deg.)90.00, 101.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28137.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31947
#2: Protein/peptide Phosphopeptide designed according to the sequence preferences favouring stabilisation by Fusicoccin-A


Mass: 1451.588 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 210 molecules

#3: Chemical ChemComp-FSC / FUSICOCCIN


Mass: 680.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H56O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CHO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% PEG 6000, 100mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.8→47.44 Å / Num. obs: 111525 / % possible obs: 99.1 % / Redundancy: 3.56 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.085 / Net I/σ(I): 7.81
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.913.282179590.2163.8461
1.91-2.041.665168570.4981.9581
2.04-2.20.705157730.8420.8391
2.2-2.410.347145400.9520.4071
2.41-2.70.197131780.9810.2311
2.7-3.110.099116560.9920.1181
3.11-3.810.05197610.9970.061
3.81-5.370.03676080.9980.0421
5.37-47.440.0341910.9990.0361

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5015: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.44 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 2081 4.99 %
Rwork0.1832 --
obs0.185 41680 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 101 206 4146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114089
X-RAY DIFFRACTIONf_angle_d0.8785540
X-RAY DIFFRACTIONf_dihedral_angle_d13.7891533
X-RAY DIFFRACTIONf_chiral_restr0.051621
X-RAY DIFFRACTIONf_plane_restr0.008708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.42771350.42062570X-RAY DIFFRACTION98
2.05-2.10.35161370.32892609X-RAY DIFFRACTION98
2.1-2.150.30081360.27212584X-RAY DIFFRACTION98
2.15-2.220.27871360.24532610X-RAY DIFFRACTION98
2.22-2.290.25031360.22432612X-RAY DIFFRACTION99
2.29-2.370.26191380.2062623X-RAY DIFFRACTION99
2.37-2.470.25681390.19942624X-RAY DIFFRACTION99
2.47-2.580.2251410.18712671X-RAY DIFFRACTION99
2.58-2.710.24541380.18722611X-RAY DIFFRACTION99
2.71-2.880.25631390.19292650X-RAY DIFFRACTION99
2.88-3.110.25611400.2112679X-RAY DIFFRACTION100
3.11-3.420.25471390.19182640X-RAY DIFFRACTION100
3.42-3.910.20681410.17172683X-RAY DIFFRACTION100
3.91-4.930.15581420.14112690X-RAY DIFFRACTION100
4.93-47.440.19051440.16362743X-RAY DIFFRACTION99
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)
10.72530.4483-0.02631.18990.79220.7034-0.0921-0.4428-1.64490.32-0.077-0.39010.96150.1161-0.00040.73930.02720.07240.71840.08490.9559-11.3455-47.82528.3427
20.63610.9234-0.23021.84320.23470.7179-0.0717-0.9482-0.47380.2827-0.00640.15720.3327-0.2686-0.00020.57540.01430.02660.6490.07420.5677-10.8662-40.064128.9592
32.30781.2754-0.58830.8887-0.22391.23870.3234-0.16810.2131-0.3702-0.0732-0.0918-0.08030.2276-0.00010.5251-0.03940.00460.5044-0.05720.4317-14.3701-25.808823.7571
40.0182-0.01890.00870.0442-0.06070.09660.67141.11971.0982-2.08770.14020.3948-0.7569-0.4053-0.00121.16170.10320.14510.8751-0.02761.1717-31.6837-5.192329.5336
51.14330.574-0.27581.1603-0.60930.80240.0598-1.58820.02840.31580.18840.3764-0.03670.32890.02420.5757-0.07270.02290.7218-0.12780.4095-15.2294-22.435533.8897
61.39721.1674-0.06171.5223-0.98761.5720.0984-0.53780.0116-0.14750.0743-0.62690.10270.5771-0.00010.4369-0.0122-0.05730.645-0.06780.3781-0.3285-27.939726.4133
71.29430.25421.25762.1126-1.1812.1891-0.0927-0.9260.23540.26590.1485-0.1897-0.35380.79490.00030.4898-0.1478-0.0460.7447-0.12950.48132.7532-18.870727.0961
81.09440.6980.490.5853-0.17921.9257-0.0085-0.21410.15830.02070.1785-0.1105-0.27050.458100.479-0.06690.0060.5624-0.06320.38980.4022-20.869216.4675
91.8691-0.10380.3910.1461-0.28941.68830.18870.2870.0834-0.11730.0203-0.4484-0.0260.9392-00.5688-0.08660.0690.83630.01830.50564.6659-21.14376.7234
103.0670.840.52010.39330.27382.99640.11330.0765-0.14110.1656-0.09030.21140.03560.0790.00010.5509-0.0399-0.0070.6924-0.03540.3731-4.1095-22.19456.6253
111.57090.52291.33322.3747-0.30341.6847-0.0275-0.26670.2887-0.06670.13040.2382-0.1626-0.0374-00.5095-0.02470.03320.4182-0.04040.5253-37.6086-20.038931.7388
122.1221.0594-0.11370.9684-0.47232.49060.13120.4973-0.7615-0.7265-0.12250.63770.04720.21630.00020.5031-0.0695-0.01750.4388-0.10340.5438-33.3371-38.190322.2407
133.7837-0.1337-0.02341.7193-0.34781.7603-0.07680.1209-0.6806-0.03710.05580.38560.1363-0.149200.4524-0.07260.00790.427-0.04830.6668-44.4124-40.688225.307
142.05720.511-0.85290.44650.10172.44370.14431.14810.1427-0.4086-0.09870.1611-0.4724-0.12740.00010.8539-0.1467-0.04741.2065-0.0930.8726-50.9129-35.93846.8327
150.38250.31790.07050.4269-0.34530.9925-0.0231-0.18950.18020.11350.36061.2244-0.1899-1.16190.01810.5863-0.0455-0.00410.7812-0.07550.7377-12.7358-19.943814.7923
160.28250.0447-0.02160.13850.05420.26770.46130.9907-0.0551-1.8138-0.4461-1.0154-0.64540.36390.00130.9329-0.06890.1151.09990.02070.9414-37.319-40.024712.0462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 161 )
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 186 )
9X-RAY DIFFRACTION9chain 'A' and (resid 187 through 209 )
10X-RAY DIFFRACTION10chain 'A' and (resid 210 through 234 )
11X-RAY DIFFRACTION11chain 'B' and (resid -3 through 37 )
12X-RAY DIFFRACTION12chain 'B' and (resid 38 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 186 )
14X-RAY DIFFRACTION14chain 'B' and (resid 187 through 233 )
15X-RAY DIFFRACTION15chain 'C'
16X-RAY DIFFRACTION16chain 'D'

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