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

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Basic information

Entry
Database: PDB / ID: 5okf
TitleCH1 chimera of human 14-3-3 sigma with the HSPB6 phosphopeptide in a conformation with self-bound 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 / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria ...structural constituent of eye lens / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / chaperone-mediated protein folding / protein folding chaperone / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / positive regulation of cell growth / regulation of cell cycle / nuclear speck / cadherin binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / mitochondrion / extracellular space / 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
: / Heat shock protein beta-6 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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 sigma,Heat shock protein beta-6
B: 14-3-3 protein sigma,Heat shock protein beta-6
C: 14-3-3 protein sigma,Heat shock protein beta-6
D: 14-3-3 protein sigma,Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,94721
Polymers110,0364
Non-polymers1,91117
Water39622
1
A: 14-3-3 protein sigma,Heat shock protein beta-6
B: 14-3-3 protein sigma,Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25413
Polymers55,0182
Non-polymers1,23711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-63 kcal/mol
Surface area22000 Å2
MethodPISA
2
C: 14-3-3 protein sigma,Heat shock protein beta-6
D: 14-3-3 protein sigma,Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6928
Polymers55,0182
Non-polymers6746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-56 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.399, 97.760, 158.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 27508.893 Da / Num. of mol.: 4
Fragment: Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12- ...Fragment: Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19,Phosphopeptide, UNP Residues 12-19
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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES buffer (pH 7.5), 1 M Naacetate, and 50 mM cadmium sulfate

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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: 3.14→48 Å / Num. obs: 21607 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.469 % / Biso Wilson estimate: 46.79 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.464 / Rrim(I) all: 0.505 / Χ2: 1.144 / Net I/σ(I): 4.2 / Num. measured all: 139771
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.14-3.336.4893.3030.6421627343633330.2723.59397
3.33-3.566.3382.091.0920479323632310.5872.2899.8
3.56-3.846.6391.3121.8820104303130280.8331.42599.9
3.84-4.216.670.7633.5718649280227960.9480.82899.8
4.21-4.76.4020.4985.3316261254325400.970.54399.9
4.7-5.426.7340.4255.6415306227422730.9860.461100
5.42-6.616.4160.3855.6312409193619340.9750.4299.9
6.61-9.266.3030.1210.89694154215380.9970.13199.7
9.26-485.6170.05416.6752419439330.9990.0698.9

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Processing

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

5lu1


Resolution: 3.2→48 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.523
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1016 4.95 %RANDOM
Rwork0.247 ---
obs0.249 20522 100 %-
Displacement parametersBiso max: 189.96 Å2 / Biso mean: 67.73 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-9.4853 Å20 Å20 Å2
2---13.9993 Å20 Å2
3---4.514 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: final / Resolution: 3.2→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 16 22 7326
Biso mean--144.43 15.85 -
Num. residues----921
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3278SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes207HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2066HARMONIC5
X-RAY DIFFRACTIONt_it14447HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion947SEMIHARMONIC5
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_contact15412SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14447HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg26025HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion17.36
LS refinement shellResolution: 3.2→3.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2929 140 4.74 %
Rwork0.2565 2813 -
all0.2582 2953 -
obs--99.93 %
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)
11.9508-1.6763-0.28053.49741.31271.8420.2959-0.15360.567-0.1968-0.2443-0.1655-0.57840.0682-0.0516-0.0056-0.12220.16020.2219-0.03890.0159-19.594444.1607-12.9915
22.9392-0.1576-0.07493.308-1.08613.1190.0036-0.1059-0.4479-0.1543-0.1410.25370.5452-0.20180.1374-0.1946-0.06070.02050.13570.0346-0.0923-19.2326.4672-11.9638
30.0707-0.6390.72030-1.73290.40770.00430.03870.05450.0304-0.02830.00680.01850.11180.02390.01660.01430.11250.03610.1657-0.1662-26.190410.0127-2.6902
42.18670.9881-0.49715.75230.64390.65490.05690.3613-0.51750.019-0.1727-0.29520.32010.08480.1158-0.15860.0527-0.03260.0696-0.0854-0.1951-19.00075.0279-45.3521
53.03060.54160.0473.8958-1.78612.107-0.02650.26770.28430.2383-0.10510.1171-0.2825-0.00330.1316-0.20480.06630.0177-0.0280.0452-0.1232-19.513342.2005-46.5474
60.748-0.79361.5111.0877-0.47921.0204-0.01140.00410.0285-0.04350.0352-0.0541-0.07070.0201-0.0238-0.0888-0.035-0.14180.12480.0047-0.0456-12.78198.8357-55.2237
70-0.00910.571901.24360-0.002-0.03810.00830.01370.078-0.00090.04440.0424-0.0759-0.0442-0.016-0.1270.06820.1532-0.1309-25.393138.5856-55.4766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 242
2X-RAY DIFFRACTION2{ B|* }B-1 - 242
3X-RAY DIFFRACTION3{ D|* }D-1 - 243
4X-RAY DIFFRACTION4{ E|* }D0
5X-RAY DIFFRACTION5{ F|* }D0
6X-RAY DIFFRACTION6{ G|* }D0
7X-RAY DIFFRACTION7{ H|* }D0

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