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- PDB-7rup: Structure of the human GIGYF2-TNRC6A complex -

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Basic information

Entry
Database: PDB / ID: 7rup
TitleStructure of the human GIGYF2-TNRC6A complex
Components
  • GRB10-interacting GYF protein 2
  • Trinucleotide repeat-containing gene 6A protein
KeywordsGENE REGULATION / miRNA / 4EHP / translational repression
Function / homology
Function and homology information


musculoskeletal movement / Regulation of NPAS4 mRNA translation / post-transcriptional gene silencing / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / spinal cord motor neuron differentiation / Transcriptional Regulation by MECP2 / proximal dendrite / miRNA-mediated post-transcriptional gene silencing ...musculoskeletal movement / Regulation of NPAS4 mRNA translation / post-transcriptional gene silencing / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / spinal cord motor neuron differentiation / Transcriptional Regulation by MECP2 / proximal dendrite / miRNA-mediated post-transcriptional gene silencing / endoderm development / miRNA-mediated gene silencing by inhibition of translation / feeding behavior / RISC complex / proline-rich region binding / Regulation of RUNX1 Expression and Activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / neuromuscular process controlling balance / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / rescue of stalled ribosome / homeostasis of number of cells within a tissue / negative regulation of translational initiation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / mitotic G1 DNA damage checkpoint signaling / cellular response to starvation / adult locomotory behavior / post-embryonic development / insulin-like growth factor receptor signaling pathway / P-body / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / multicellular organism growth / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic stress granule / Ca2+ pathway / perikaryon / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / vesicle / negative regulation of translation / molecular adaptor activity / endosome / cadherin binding / intracellular membrane-bounded organelle / Golgi apparatus / endoplasmic reticulum / protein-containing complex / RNA binding / nucleoplasm / membrane / cytosol
Similarity search - Function
TNRC6A, RNA recognition motif / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / Argonaute hook / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues ...TNRC6A, RNA recognition motif / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / Argonaute hook / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
GRB10-interacting GYF protein 2 / Trinucleotide repeat-containing gene 6A protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsSobti, M. / Mead, B.J. / Igreja, C. / Stewart, A.G. / Christie, M.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE160100608 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1159347 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1146403 Australia
CitationJournal: Rna / Year: 2023
Title: Molecular basis for GIGYF-TNRC6 complex assembly.
Authors: Sobti, M. / Mead, B.J. / Stewart, A.G. / Igreja, C. / Christie, M.
History
DepositionAug 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRB10-interacting GYF protein 2
B: Trinucleotide repeat-containing gene 6A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0263
Polymers9,9302
Non-polymers961
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-15 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.779, 38.319, 62.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GRB10-interacting GYF protein 2 / PERQ amino acid-rich with GYF domain-containing protein 2 / Trinucleotide repeat-containing gene 15 protein


Mass: 8468.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIGYF2, KIAA0642, PERQ2, TNRC15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6Y7W6
#2: Protein/peptide Trinucleotide repeat-containing gene 6A protein / CAG repeat protein 26 / EMSY interactor protein / GW182 autoantigen / Protein GW1 / Glycine- ...CAG repeat protein 26 / EMSY interactor protein / GW182 autoantigen / Protein GW1 / Glycine-tryptophan protein of 182 kDa


Mass: 1461.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNRC6A, CAGH26, KIAA1460, TNRC6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NDV7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.0-1.4 M Na/K phosphate / PH range: 7.4-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.23→19.43 Å / Num. obs: 23420 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 13.6
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1130 / CC1/2: 0.778 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FMA

3fma


Resolution: 1.23→19.425 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 1111 4.75 %
Rwork0.1521 --
obs0.1533 23369 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.23→19.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms572 0 5 96 673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015625
X-RAY DIFFRACTIONf_angle_d1.389854
X-RAY DIFFRACTIONf_dihedral_angle_d3.707464
X-RAY DIFFRACTIONf_chiral_restr0.178
X-RAY DIFFRACTIONf_plane_restr0.013115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.2860.21491290.17852731X-RAY DIFFRACTION100
1.286-1.35380.17541140.15872763X-RAY DIFFRACTION100
1.3538-1.43860.19891560.13852728X-RAY DIFFRACTION100
1.4386-1.54960.16671440.12772738X-RAY DIFFRACTION100
1.5496-1.70540.16651330.12332762X-RAY DIFFRACTION100
1.7054-1.9520.16771410.13012787X-RAY DIFFRACTION100
1.952-2.45860.17311550.14752791X-RAY DIFFRACTION100
2.4586-19.4250.17971390.1712958X-RAY DIFFRACTION100

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