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Basic information

Entry
Database: PDB / ID: 2c1n
TitleMolecular basis for the recognition of phosphorylated and phosphoacetylated histone H3 by 14-3-3
Components
  • 14-3-3 PROTEIN ZETA/DELTA
  • HISTONE H3 ACETYLPHOSPHOPEPTIDE
KeywordsSIGNALING PROTEIN / SIGNALING PROTEIN-COMPLEX / HISTONE H3 / NUCLEOSOME
Function / homology
Function and homology information


Golgi reassembly / synaptic target recognition / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / regulation of synapse maturation / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA ...Golgi reassembly / synaptic target recognition / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / regulation of synapse maturation / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / 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 / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Chromatin modifying enzymes / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / protein sequestering activity / telomere organization / negative regulation of innate immune response / ERK1 and ERK2 cascade / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / hippocampal mossy fiber to CA3 synapse / Assembly of the ORC complex at the origin of replication / regulation of ERK1 and ERK2 cascade / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Translocation of SLC2A4 (GLUT4) to the plasma membrane / HDACs deacetylate histones / TP53 Regulates Metabolic Genes / RNA Polymerase I Promoter Escape / Deactivation of the beta-catenin transactivating complex / Transcriptional regulation by small RNAs / lung development / Negative regulation of NOTCH4 signaling / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / regulation of protein stability / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / protein localization / melanosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / DNA-binding transcription factor binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / vesicle / blood microparticle / transmembrane transporter binding / cadherin binding / protein heterodimerization activity / protein phosphorylation / Amyloid fiber formation / protein domain specific binding / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / DNA binding / RNA binding / extracellular space
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein zeta/delta / Histone H3.1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWelburn, J.P.I. / Macdonald, N. / Noble, M.E.M. / Nguyen, A. / Yaffe, M.B. / Clynes, D. / Moggs, J.G. / Orphanides, G. / Thomson, S. / Edmunds, J.W. ...Welburn, J.P.I. / Macdonald, N. / Noble, M.E.M. / Nguyen, A. / Yaffe, M.B. / Clynes, D. / Moggs, J.G. / Orphanides, G. / Thomson, S. / Edmunds, J.W. / Clayton, A.L. / Endicott, J.A. / Mahadevan, L.C.
CitationJournal: Mol.Cell / Year: 2005
Title: Molecular Basis for the Recognition of Phosphorylated and Phosphoacetylated Histone H3 by 14-3-3.
Authors: Macdonald, N. / Welburn, J.P.I. / Noble, M.E.M. / Nguyen, A. / Yaffe, M.B. / Clynes, D. / Moggs, J.G. / Orphanides, G. / Thomson, S. / Edmunds, J.W. / Clayton, A.L. / Endicott, J.A. / Mahadevan, L.C.
History
DepositionSep 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / struct_conn
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 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 1.4Oct 23, 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 ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
C: HISTONE H3 ACETYLPHOSPHOPEPTIDE
E: HISTONE H3 ACETYLPHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)60,3714
Polymers60,3714
Non-polymers00
Water4,324240
1
A: 14-3-3 PROTEIN ZETA/DELTA
C: HISTONE H3 ACETYLPHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)30,1862
Polymers30,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-2.7 kcal/mol
Surface area12410 Å2
MethodPISA
2
B: 14-3-3 PROTEIN ZETA/DELTA
E: HISTONE H3 ACETYLPHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)30,1862
Polymers30,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-3.1 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.135, 72.375, 71.171
Angle α, β, γ (deg.)90.00, 103.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29298.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACYC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 PLYS/S / References: UniProt: P63104
#2: Protein/peptide HISTONE H3 ACETYLPHOSPHOPEPTIDE


Mass: 886.911 Da / Num. of mol.: 2
Fragment: 14-3-3, HISTONE H3 ACETYLPHOSPHOPEPTIDE RESIDUES 7-14
Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 61.2 %
Crystal growpH: 7 / Details: 100MM HEPES PH 7.0, 23% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→72.5 Å / Num. obs: 37201 / % possible obs: 77.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 77.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJA

1qja


Resolution: 2→69.34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.956 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1890 5.1 %RANDOM
Rwork0.255 ---
obs0.258 35082 77.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å25.05 Å2
2---0.83 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 0 240 3972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9785072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05825.217184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19215.04744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3031524
X-RAY DIFFRACTIONr_chiral_restr0.090.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2910.22237
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22586
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.320.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.52393
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23123702
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75631586
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.694.51370
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
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.368 150
Rwork0.333 2695
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)
10.11970.1174-0.00280.9463-0.22520.36910.1541-0.06210.14030.0220.0322-0.0049-0.16730.056-0.1864-0.06780.0034-0.02340.0368-0.02870.024419.9311012.0791
20.39810.36320.2041.00680.10090.1153-0.1874-0.1354-0.2817-0.0996-0.02990.02110.02130.0320.2173-0.07070.0393-0.03170.05650.02020.05247.1916-33.995922.1406
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 230
2X-RAY DIFFRACTION1C7 - 14
3X-RAY DIFFRACTION2B1 - 230
4X-RAY DIFFRACTION2E7 - 14

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