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- PDB-7ruq: Structure of the human GIGYF1-TNRC6C complex -

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Basic information

Entry
Database: PDB / ID: 7ruq
TitleStructure of the human GIGYF1-TNRC6C complex
Components
  • GRB10-interacting GYF protein 1
  • Trinucleotide repeat-containing gene 6C protein
KeywordsGENE REGULATION / miRNA / 4EHP / translation repression
Function / homology
Function and homology information


Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Transcriptional Regulation by MECP2 / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / Regulation of RUNX1 Expression and Activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Transcriptional Regulation by MECP2 / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / Regulation of RUNX1 Expression and Activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / insulin-like growth factor receptor signaling pathway / P-body / TP53 Regulates Metabolic Genes / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein-containing complex / RNA binding / nucleoplasm / cytosol
Similarity search - Function
TNRC6C, RNA recognition motif / Trinucleotide repeat-containing gene 6C protein, UBA domain / GW182, middle domain / M domain of GW182 / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / Argonaute hook / GYF domain / GYF-like domain superfamily ...TNRC6C, RNA recognition motif / Trinucleotide repeat-containing gene 6C protein, UBA domain / GW182, middle domain / M domain of GW182 / 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 / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / RNA recognition motif / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
GRB10-interacting GYF protein 1 / Trinucleotide repeat-containing gene 6C protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSobti, M. / Mead, B.J. / Igreja, C. / Stewart, A.G. / Christie, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE160100608 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRB10-interacting GYF protein 1
C: GRB10-interacting GYF protein 1
D: Trinucleotide repeat-containing gene 6C protein
B: Trinucleotide repeat-containing gene 6C protein


Theoretical massNumber of molelcules
Total (without water)19,6004
Polymers19,6004
Non-polymers00
Water1,26170
1
A: GRB10-interacting GYF protein 1
B: Trinucleotide repeat-containing gene 6C protein


Theoretical massNumber of molelcules
Total (without water)9,8002
Polymers9,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-5 kcal/mol
Surface area4320 Å2
MethodPISA
2
C: GRB10-interacting GYF protein 1
D: Trinucleotide repeat-containing gene 6C protein


Theoretical massNumber of molelcules
Total (without water)9,8002
Polymers9,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-4 kcal/mol
Surface area4480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.918, 32.503, 69.578
Angle α, β, γ (deg.)90.000, 133.836, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein GRB10-interacting GYF protein 1 / PERQ amino acid-rich with GYF domain-containing protein 1


Mass: 8267.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIGYF1, CDS2, PERQ1, PP3360 / Production host: Escherichia coli (E. coli) / References: UniProt: O75420
#2: Protein/peptide Trinucleotide repeat-containing gene 6C protein


Mass: 1532.720 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNRC6C, KIAA1582 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HCJ0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Hepes 7.0, 1 M sodium malonate

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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: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.79→29.63 Å / Num. obs: 15377 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.2
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 5.9 % / Num. unique obs: 861 / CC1/2: 0.747 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RUP

7rup


Resolution: 1.79→29.63 Å / SU ML: 0.1161 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5374 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1893 649 4.22 %
Rwork0.1655 14725 -
obs0.1665 15374 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.74 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 0 70 1189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051186
X-RAY DIFFRACTIONf_angle_d1.23781619
X-RAY DIFFRACTIONf_chiral_restr0.0609154
X-RAY DIFFRACTIONf_plane_restr0.0082209
X-RAY DIFFRACTIONf_dihedral_angle_d4.9932917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.930.21241410.17922854X-RAY DIFFRACTION98.07
1.93-2.120.16151170.1622949X-RAY DIFFRACTION99.87
2.12-2.430.204970.16192947X-RAY DIFFRACTION99.84
2.43-3.060.21941360.17512952X-RAY DIFFRACTION99.9
3.06-29.630.17581580.16033023X-RAY DIFFRACTION99.66
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)
11.822951852620.2200106801220.4196760695860.908501318159-0.2156840250730.5537569711020.0604024675617-0.0332624142467-0.002035817080450.0659594471847-0.07809875513140.100888268544-0.0504834242643-0.195516235823-2.54282032637E-50.1275428095520.005317460216320.002647927475180.120238213241-0.001112593302540.12551709176416.112215134-3.954061326050.833183682784
21.3215463994-0.165407110078-0.7141504629930.994639067408-0.1209406288621.080754868420.03542524926820.1313321514070.00424046465661-0.0872867835403-0.008397748225770.1258050024560.0987657140899-0.1145972136583.86190414266E-50.125913755997-0.00883630216956-0.00512226989880.126992416802-0.00789905788330.113177937807-0.463572359707-4.6597961623816.2748213534
31.059552862280.2297504819430.3290418737140.04991231478840.07115486793250.10233019005-0.096666858411-0.470074054720.4230933740250.0611890394576-0.373064891486-0.3131436537570.1999756615070.398254663474-0.04439444921830.209091372927-0.00469252608868-0.008740806038240.3363220910730.04870803951470.2599776463110.9168773623-2.1050615048323.1652970681
40.00907586654950.0083281871166-0.001879818746230.0210320131243-0.02150911728590.0291560588701-0.01255075218020.3308863430930.422471492246-0.2726313356130.09472589640270.0750582566662-0.3248178377360.4390057995880.000476222830830.247250368623-0.0448737226466-0.01267188871040.2639322958980.04195792774210.20525887884823.77641991740.808322000041-9.54146188573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 474 through 536)
2X-RAY DIFFRACTION2(chain 'C' and resid 474 through 535)
3X-RAY DIFFRACTION3(chain 'D' and resid 1472 through 1480)
4X-RAY DIFFRACTION4(chain 'B' and resid 1473 through 1480)

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