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- PDB-5ok9: CH1 chimera of human 14-3-3 sigma with the HSPB6 phosphopeptide i... -

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Basic information

Entry
Database: PDB / ID: 5ok9
TitleCH1 chimera of human 14-3-3 sigma with the HSPB6 phosphopeptide in a conformation with swapped phosphopeptides
Components14-3-3 protein sigma,Heat shock protein beta-6
KeywordsSIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding
Function / homology
Function and homology information


structural constituent of eye lens / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / regulation of cell-cell adhesion / establishment of skin barrier / Regulation of localization of FOXO transcription factors / negative regulation of cardiac muscle cell apoptotic process / Regulation of GBP-mediated host defense / phosphoserine residue binding ...structural constituent of eye lens / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / regulation of cell-cell adhesion / establishment of skin barrier / Regulation of localization of FOXO transcription factors / negative regulation of cardiac muscle cell apoptotic process / Regulation of GBP-mediated host defense / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cAMP/PKA signal transduction / protein export from nucleus / release of cytochrome c from mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of protein export from nucleus / protein folding chaperone / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein sequestering activity / protein refolding / intracellular protein localization / positive regulation of angiogenesis / : / regulation of protein localization / positive regulation of cell growth / response to heat / protein-folding chaperone binding / protein folding / nuclear speck / cadherin binding / negative regulation of apoptotic process / protein kinase binding / signal transduction / protein homodimerization activity / : / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma ...Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Heat shock protein beta-6 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSluchanko, N.N. / Tugaeva, K.V. / Greive, S.J. / Antson, A.A.
Funding support Russian Federation, United Kingdom, 3items
OrganizationGrant numberCountry
Russian Science Foundation17-74-10053 Russian Federation
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: Chimeric 14-3-3 proteins for unraveling interactions with intrinsically disordered partners.
Authors: Sluchanko, N.N. / Tugaeva, K.V. / Greive, S.J. / Antson, A.A.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Mar 13, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_seq_map_depositor_info ...diffrn_source / pdbx_seq_map_depositor_info / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jan 17, 2024Group: 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 1.5Oct 9, 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 sigma,Heat shock protein beta-6
B: 14-3-3 protein sigma,Heat shock protein beta-6
E: 14-3-3 protein sigma,Heat shock protein beta-6
F: 14-3-3 protein sigma,Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5029
Polymers109,9724
Non-polymers5315
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-17 kcal/mol
Surface area43570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.631, 140.635, 68.663
Angle α, β, γ (deg.)90.000, 114.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
14-3-3 protein sigma,Heat shock protein beta-6 / Epithelial cell marker protein 1 / Stratifin / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 27492.893 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1, HSPB6 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947, UniProt: O14558
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MMT (malateMES-Tris) buffer (pH 4) and 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.21→46.65 Å / Num. obs: 48345 / % possible obs: 88.3 % / Observed criterion σ(I): -3 / Redundancy: 3.85 % / Biso Wilson estimate: 42.88 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.229 / Rrim(I) all: 0.266 / Χ2: 0.963 / Net I/σ(I): 5.51 / Num. measured all: 186114
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.21-2.353.6451.7950.7345360.2852.09551.5
2.35-2.513.7711.2281.269620.5151.43284.3
2.51-2.713.9740.8871.975310.6751.02597.5
2.71-2.973.7910.5413.0969250.8560.6397.4
2.97-3.323.9370.3395.2663100.9270.39298.2
3.32-3.833.8520.1948.955790.970.22398
3.83-4.683.9080.12212.2347260.9850.14198.1
4.68-6.583.9250.12111.6837050.9870.1498.5
6.58-46.653.7650.07316.8420710.9940.08597

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LU1

5lu1


Resolution: 2.35→46.65 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.389 / SU Rfree Blow DPI: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1385 3.16 %RANDOM
Rwork0.191 ---
obs0.193 43838 96.2 %-
Displacement parametersBiso max: 129.07 Å2 / Biso mean: 42.14 Å2 / Biso min: 11.18 Å2
Baniso -1Baniso -2Baniso -3
1--5.1051 Å20 Å28.34 Å2
2--4.0122 Å20 Å2
3---1.0929 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.35→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7543 0 35 493 8071
Biso mean--47.48 40.05 -
Num. residues----959
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3434SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes214HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2179HARMONIC5
X-RAY DIFFRACTIONt_it15115HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion986SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16508SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d15115HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg27278HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion16.89
LS refinement shellResolution: 2.35→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 89 3.69 %
Rwork0.2303 2321 -
all0.232 2410 -
obs--72.36 %
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)
10.6434-0.31020.33321.5638-0.22350.32430.05630.0609-0.0345-0.1263-0.04710.1019-0.01020.0136-0.0091-0.02640.00050.03380.0888-0.0086-0.0334-24.0663-70.9525-20.846
20.55290.09750.02630.98180.34590.87050.0887-0.0657-0.04020.221-0.0286-0.0664-0.03630.063-0.060.0644-0.0563-0.00740.09820.0132-0.0351.5896-67.2536.5572
31.0315-0.27870.20960.647-0.14050.8723-0.0056-0.0039-0.12160.08430.0181-0.0772-0.0105-0.0717-0.01250-0.01710.00030.0941-0.0033-0.0125-39.576-35.5709-11.8053
40.6961-0.28950.11450.55880.16741.15330.0530.0611-0.0515-0.0365-0.040.02440.0031-0.1068-0.013-0.0506-0.01670.00890.06550.0101-0.0568-16.5413-31.052915.7001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 243
2X-RAY DIFFRACTION2{ B|* }B-2 - 243
3X-RAY DIFFRACTION3{ E|* }E-1 - 243
4X-RAY DIFFRACTION4{ F|* }F-1 - 242

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