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- PDB-8q1s: Pathogenic mutations of human phosphorylation sites affect protei... -

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Basic information

Entry
Database: PDB / ID: 8q1s
TitlePathogenic mutations of human phosphorylation sites affect protein-protein interactions
Components
  • 14-3-3 protein epsilon
  • GATA zinc finger domain-containing protein 1
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / GATAD1 / protein-protein interaction
Function / homology
Function and homology information


: / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / positive regulation of hippo signaling / cytoplasmic sequestering of protein / membrane repolarization during cardiac muscle cell action potential / negative regulation of toll-like receptor signaling pathway / protein localization to endoplasmic reticulum / regulation of membrane repolarization / NADE modulates death signalling ...: / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / positive regulation of hippo signaling / cytoplasmic sequestering of protein / membrane repolarization during cardiac muscle cell action potential / negative regulation of toll-like receptor signaling pathway / protein localization to endoplasmic reticulum / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / cytoplasmic pattern recognition receptor signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of calcium ion export across plasma membrane / regulation of heart rate by cardiac conduction / phosphoserine residue binding / protein localization to nucleus / calcium channel regulator activity / Activation of BAD and translocation to mitochondria / HSF1 activation / Regulation of HSF1-mediated heat shock response / protein targeting / calcium channel inhibitor activity / potassium channel regulator activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / signaling adaptor activity / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / regulation of cytosolic calcium ion concentration / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / protein sequestering activity / substantia nigra development / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / hippocampus development / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / mitochondrial membrane / neuron migration / cerebral cortex development / histone deacetylase binding / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / protein localization / melanosome / MHC class II protein complex binding / chromatin organization / cellular response to heat / scaffold protein binding / protein phosphatase binding / sequence-specific DNA binding / transmembrane transporter binding / intracellular signal transduction / cadherin binding / chromatin remodeling / protein heterodimerization activity / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / endoplasmic reticulum / signal transduction / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
GATA zinc finger domain-containing protein 1 / GATA-type zinc finger domain profile. / Zinc finger, GATA-type / 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 ...GATA zinc finger domain-containing protein 1 / GATA-type zinc finger domain profile. / Zinc finger, GATA-type / 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, NHR/GATA-type
Similarity search - Domain/homology
BROMIDE ION / 14-3-3 protein epsilon / GATA zinc finger domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsRoske, Y. / Daumke, O. / Rrustemi, T. / Selbach, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2024
Title: Pathogenic mutations of human phosphorylation sites affect protein-protein interactions.
Authors: Rrustemi, T. / Meyer, K. / Roske, Y. / Uyar, B. / Akalin, A. / Imami, K. / Ishihama, Y. / Daumke, O. / Selbach, M.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein epsilon
B: 14-3-3 protein epsilon
C: GATA zinc finger domain-containing protein 1
P: GATA zinc finger domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2258
Polymers61,9984
Non-polymers2274
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-36 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.780, 123.780, 250.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCP

#1: Protein 14-3-3 protein epsilon / 14-3-3E


Mass: 29208.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P62258
#2: Protein/peptide GATA zinc finger domain-containing protein 1 / Ocular development-associated gene protein


Mass: 1789.985 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATAD1, ODAG / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUU5

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Non-polymers , 4 types, 16 molecules

#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 19% PEG 3350, 0.35 M NaBr, 0.1 M BisTris-Propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.23→49.7 Å / Num. obs: 22972 / % possible obs: 99.9 % / Redundancy: 10.39 % / CC1/2: 0.995 / Rrim(I) all: 0.035 / Net I/σ(I): 6.91
Reflection shellResolution: 3.23→3.42 Å / Num. unique obs: 3708 / CC1/2: 0.368 / Rrim(I) all: 0.296

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→49.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 40.186 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27937 608 5 %RANDOM
Rwork0.23036 ---
obs0.23286 11549 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 122.895 Å2
Baniso -1Baniso -2Baniso -3
1-15.92 Å20 Å20 Å2
2--15.92 Å20 Å2
3----31.83 Å2
Refinement stepCycle: 1 / Resolution: 3.23→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 10 12 3930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133978
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153806
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.6475361
X-RAY DIFFRACTIONr_angle_other_deg1.0451.5888788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.485487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.47522.903217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19115747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0371527
X-RAY DIFFRACTIONr_chiral_restr0.0350.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.76611.2031954
X-RAY DIFFRACTIONr_mcbond_other1.75811.2011953
X-RAY DIFFRACTIONr_mcangle_it3.09716.7912436
X-RAY DIFFRACTIONr_mcangle_other3.09816.7942437
X-RAY DIFFRACTIONr_scbond_it1.35811.2632023
X-RAY DIFFRACTIONr_scbond_other1.35411.2582021
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.44416.8292924
X-RAY DIFFRACTIONr_long_range_B_refined5.0624409
X-RAY DIFFRACTIONr_long_range_B_other5.0654410
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
11A3642medium positional0.470.5
22A152medium positional0.260.5
11B3642medium thermal10.082
22B152medium thermal11.232
LS refinement shellResolution: 3.23→3.312 Å
RfactorNum. reflection% reflection
Rfree0.425 43 -
Rwork0.376 823 -
obs--99.43 %
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)
11.5846-0.7998-0.34420.48990.44281.0467-0.177-0.20240.2073-0.00270.1474-0.1068-0.20660.14280.02960.3381-0.0741-0.04340.0967-0.04280.088122.165-37.613722.0959
200000000000000-00.0434000.043400.0434000
31.91990.06730.76290.3923-0.24690.575-0.038-0.35390.29090.0062-0.01790.21090.0794-0.18120.05590.24330.02930.07470.1415-0.1180.2351-14.5224-36.697223.4485
400000000000000-00.0434000.043400.0434000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 302
2X-RAY DIFFRACTION2P34 - 43
3X-RAY DIFFRACTION3A3 - 234
4X-RAY DIFFRACTION4C34 - 45

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