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Basic information

Entry
Database: PDB / ID: 2c1j
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 / NUCLEOSOME
Function / homology
Function and homology information


Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA ...Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / 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 / cellular response to glucose starvation / Chromatin modifying enzymes / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / epigenetic regulation of gene expression / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / protein sequestering activity / telomere organization / ERK1 and ERK2 cascade / negative regulation of innate immune response / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / hippocampal mossy fiber to CA3 synapse / Assembly of the ORC complex at the origin of replication / DNA methylation / regulation of ERK1 and ERK2 cascade / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / HDACs deacetylate histones / Deactivation of the beta-catenin transactivating complex / RNA Polymerase I Promoter Escape / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / Negative regulation of NOTCH4 signaling / Formation of the beta-catenin:TCF transactivating complex / lung development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / regulation of protein stability / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / melanosome / 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 / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / Estrogen-dependent gene expression / vesicle / transmembrane transporter binding / blood microparticle / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein domain specific binding / protein phosphorylation / 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 / extracellular exosome / extracellular region / nucleoplasm / identical protein binding
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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations / Structure summary
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Source and taxonomy
Category: pdbx_database_status / pdbx_entity_src_syn / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: HISTONE H3 ACETYLPHOSPHOPEPTIDE
D: HISTONE H3 ACETYLPHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)60,4534
Polymers60,4534
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-16.3 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.191, 72.413, 71.160
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSERAA1 - 23014 - 243
21METMETSERSERBB1 - 23014 - 243
12ALAALALYSLYSCC7 - 141 - 8
22ALAALALYSLYSDD7 - 141 - 8

NCS ensembles :
ID
1
2

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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: 927.940 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.: 86 / 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: 3.2 Å3/Da / Density % sol: 61.2 %
Crystal growpH: 7 / Details: 0.1 M HEPES PH7.0, 23% ETHYLENE GLYCOL, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.6→21.2 Å / Num. obs: 21834 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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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: 2.6→69.34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.89 / SU B: 30.333 / SU ML: 0.296 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.525 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1113 5.1 %RANDOM
Rwork0.227 ---
obs0.23 20689 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: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å27.76 Å2
2---3.11 Å20 Å2
3---2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 0 86 3892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223852
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9825164
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.96325.319188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.6815.04748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3781524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022834
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.21988
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22651
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4791.52420
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85923768
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3831615
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2614.51396
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A920tight positional0.040.05
12B920tight positional0.040.05
21C32tight positional0.120.05
22D32tight positional0.120.05
11A921medium positional0.260.5
12B921medium positional0.260.5
21C30medium positional0.450.5
22D30medium positional0.450.5
11A920tight thermal0.060.5
12B920tight thermal0.060.5
21C32tight thermal0.060.5
22D32tight thermal0.060.5
11A921medium thermal0.472
12B921medium thermal0.472
21C30medium thermal0.552
22D30medium thermal0.552
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.405 87
Rwork0.352 1492
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)
11.45290.9249-0.96652.4902-1.7621.970.4054-0.27520.2820.24360.023-0.0329-0.49590.1852-0.4284-0.0944-0.0099-0.05440.0299-0.0938-0.0519.791-0.08412.352
22.26741.6453-0.70892.1352-0.26761.0948-0.4607-0.2623-0.66930.03080.0667-0.28470.21970.22460.394-0.07930.0862-0.01420.02310.04340.01347.655-34.25322.132
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 DIFFRACTION2D7 - 14

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