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- PDB-5om0: CH2 chimera of human 14-3-3 sigma with the Gli1 phosphopeptide ar... -

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Basic information

Entry
Database: PDB / ID: 5om0
TitleCH2 chimera of human 14-3-3 sigma with the Gli1 phosphopeptide around Ser640
Components14-3-3 protein sigma,Zinc finger protein GLI1
KeywordsSIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding
Function / homology
Function and homology information


notochord regression / regulation of hepatocyte proliferation / GLI proteins bind promoters of Hh responsive genes to promote transcription / GLI-SUFU complex / ventral midline development / pituitary gland development / epidermal cell differentiation / proximal/distal pattern formation / prostate gland development / ciliary tip ...notochord regression / regulation of hepatocyte proliferation / GLI proteins bind promoters of Hh responsive genes to promote transcription / GLI-SUFU complex / ventral midline development / pituitary gland development / epidermal cell differentiation / proximal/distal pattern formation / prostate gland development / ciliary tip / positive regulation of cell cycle G1/S phase transition / cerebellar cortex morphogenesis / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / digestive tract morphogenesis / smoothened signaling pathway / regulation of osteoblast differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / ciliary base / keratinocyte development / keratinization / spermatid development / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / axoneme / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / Hedgehog 'off' state / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of cardiac muscle cell proliferation / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / liver regeneration / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / positive regulation of DNA replication / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / lung development / Degradation of GLI1 by the proteasome / negative regulation of canonical Wnt signaling pathway / Hedgehog 'on' state / response to wounding / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / intracellular protein localization / regulation of protein localization / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of cell growth / microtubule binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / ciliary basal body / positive regulation of cell migration / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
C2H2-type zinc-finger protein GLI-like / : / C2H2 zinc finger / 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 ...C2H2-type zinc-finger protein GLI-like / : / C2H2 zinc finger / 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 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Zinc finger protein GLI1 / 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 Trust101528 United Kingdom
Wellcome Trust098230 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 28, 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 1.2Jan 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 1.3Nov 13, 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,Zinc finger protein GLI1
B: 14-3-3 protein sigma,Zinc finger protein GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2498
Polymers55,6202
Non-polymers6296
Water1267
1
A: 14-3-3 protein sigma,Zinc finger protein GLI1
hetero molecules

B: 14-3-3 protein sigma,Zinc finger protein GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2498
Polymers55,6202
Non-polymers6296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
MethodPISA
2
B: 14-3-3 protein sigma,Zinc finger protein GLI1
hetero molecules

A: 14-3-3 protein sigma,Zinc finger protein GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2498
Polymers55,6202
Non-polymers6296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)110.426, 110.426, 174.114
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein 14-3-3 protein sigma,Zinc finger protein GLI1 / Epithelial cell marker protein 1 / Stratifin / Glioma-associated oncogene / Oncogene GLI


Mass: 27810.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 75-77 were mutated to Alanines to reduce surface entropy and improve crystallization.
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1, GLI1, GLI / Production host: Escherichia coli (E. coli) / References: UniProt: P31947, UniProt: P08151
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M bis-Tris (pH 6.5), 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→47 Å / Num. obs: 10910 / % possible obs: 99.6 % / Redundancy: 23 % / Biso Wilson estimate: 92.51 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 14.3
Reflection shellResolution: 3.19→3.38 Å / Redundancy: 22.3 % / Rmerge(I) obs: 4.3 / Mean I/σ(I) obs: 0.91 / CC1/2: 0.5 / % possible all: 98.2

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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→47 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.497
RfactorNum. reflection% reflectionSelection details
Rfree0.267 977 8.96 %RANDOM
Rwork0.215 ---
obs0.22 10910 99.8 %-
Displacement parametersBiso max: 240.94 Å2 / Biso mean: 141.58 Å2 / Biso min: 80.54 Å2
Baniso -1Baniso -2Baniso -3
1--14.2391 Å20 Å20 Å2
2---14.2391 Å20 Å2
3---28.4783 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: final / Resolution: 3.2→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 60 7 3679
Biso mean--169.4 90.73 -
Num. residues----457
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1655SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1029HARMONIC5
X-RAY DIFFRACTIONt_it7250HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion472SEMIHARMONIC5
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_contact7917SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7250HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13070HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion18.08
LS refinement shellResolution: 3.2→3.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2853 226 8.94 %
Rwork0.2519 2303 -
all0.2549 2529 -
obs--99.96 %
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)
12.392-0.6503-0.48221.45880.03114.1596-0.07570.0704-0.1670.07230.38560.11210.3101-0.4494-0.3099-0.0863-0.16630.0275-0.1180.1752-0.194938.4437-29.37097.7685
25.93893.3765-2.30943.2379-1.77661.8628-0.22480.0956-0.67620.30720.33190.0827-0.1762-0.5936-0.1071-0.25630.11190.1006-0.03450.1297-0.248819.64759.126117.3333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* B|234 - B|244 }A1 - 233
2X-RAY DIFFRACTION1{ A|* B|234 - B|244 }B234 - 244
3X-RAY DIFFRACTION2{ B|2 - B|231 }B2 - 231

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