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- PDB-3e6y: Structure of 14-3-3 in complex with the differentiation-inducing ... -

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Basic information

Entry
Database: PDB / ID: 3e6y
TitleStructure of 14-3-3 in complex with the differentiation-inducing agent Cotylenin A
Components
  • 14-3-3-like protein C
  • H+-ATPase phosphopeptide QSYpTV
KeywordsSIGNALING PROTEIN / ADAPTER PROTEIN
Function / homology
Function and homology information


P-type proton-exporting transporter activity / regulation of intracellular pH / protein localization / signal transduction / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
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 / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cotylenin A / 14-3-3-like protein C / Plasma membrane H+ ATPase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOttmann, C. / Weyand, M. / Wittinghofer, A. / Oecking, C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: A structural rationale for selective stabilization of anti-tumor interactions of 14-3-3 proteins by cotylenin A
Authors: Ottmann, C. / Weyand, M. / Sassa, T. / Inoue, T. / Kato, N. / Wittinghofer, A. / Oecking, C.
History
DepositionAug 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3-like protein C
B: 14-3-3-like protein C
C: H+-ATPase phosphopeptide QSYpTV
D: H+-ATPase phosphopeptide QSYpTV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4947
Polymers60,1534
Non-polymers1,3413
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-36 kcal/mol
Surface area23230 Å2
MethodPISA
2
A: 14-3-3-like protein C
C: H+-ATPase phosphopeptide QSYpTV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7654
Polymers30,0772
Non-polymers6882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-18 kcal/mol
Surface area12590 Å2
MethodPISA
3
B: 14-3-3-like protein C
D: H+-ATPase phosphopeptide QSYpTV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7293
Polymers30,0772
Non-polymers6531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-6 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.800, 141.900, 51.400
Angle α, β, γ (deg.)90.00, 114.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 14-3-3-like protein C / 14-3-3-like protein B


Mass: 29399.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: P93343
#2: Protein/peptide H+-ATPase phosphopeptide QSYpTV


Mass: 676.610 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. It is found naturally in Arabidopsis thaliana
References: UniProt: Q40409*PLUS
#3: Chemical ChemComp-CW1 / Cotylenin A


Mass: 652.769 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H52O12
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1M Na citrate, 24% PEG 4000, 6% isopropanol, 5 mM MgCl2, 2 mM DTT, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2004
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 18639 / Num. obs: 18639 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.038 / Net I/σ(I): 28.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2077 / Rsym value: 0.233 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9C

1o9c


Resolution: 2.5→14.95 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.873 / SU B: 30.977 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.705 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28544 930 5 %RANDOM
Rwork0.19516 ---
obs0.19965 17657 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.184 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.31 Å2
2---0.25 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 93 100 3926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0742.0115287
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92824.444180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.71815662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.61527
X-RAY DIFFRACTIONr_chiral_restr0.170.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022869
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.52371
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15423784
X-RAY DIFFRACTIONr_scbond_it2.07131520
X-RAY DIFFRACTIONr_scangle_it3.2034.51503
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 68 -
Rwork0.291 1285 -
obs--100 %
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)
12.3401-0.40860.46172.5359-0.8112.4507-0.0810.24440.51810.06670.03390.0546-0.14350.17080.04710.0463-0.06590.02620.13040.00080.1679-8.6761-12.8679-12.8394
22.60490.37460.21952.6354-0.86572.49530.17080.0858-0.8006-0.0647-0.0150.11920.34830.1039-0.15580.15610.1036-0.07330.1464-0.09520.3151-7.7418-49.2434-10.0365
315.11462.193614.112811.11046.708215.18990.3584-1.0261-0.3970.6049-0.50781.20580.5908-1.10270.14940.1641-0.00150.0980.2850.00540.3864-16.9255-14.9443-9.434
412.46694.1957-5.51125.63951.99355.9565-0.04690.87260.9043-0.61280.36950.4809-0.4992-0.2817-0.32270.38360.0146-0.07830.23320.02250.4556-16.5687-47.7669-13.9489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2385 - 238
2X-RAY DIFFRACTION2BB4 - 2404 - 240
3X-RAY DIFFRACTION3CC1 - 51 - 5
4X-RAY DIFFRACTION4DD1 - 51 - 5

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