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- PDB-7lga: PEG10 CA-like C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7lga
TitlePEG10 CA-like C-terminal domain
ComponentsRetrotransposon-derived protein PEG10
KeywordsONCOPROTEIN / imprinted gene / domesticated Gag
Function / homology
Function and homology information


negative regulation of transforming growth factor beta receptor signaling pathway / cell differentiation / apoptotic process / DNA binding / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Domain of unknown function DUF4939 / LDOC1-related / Domain of unknown function (DUF4939) / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Retrotransposon-derived protein PEG10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZurowska, K. / Pornillos, O. / Ganser-Pornillos, B.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI129678 United States
CitationJournal: Proteins / Year: 2022
Title: Structural evidence that MOAP1 and PEG10 are derived from retrovirus/retrotransposon Gag proteins.
Authors: Zurowska, K. / Alam, A. / Ganser-Pornillos, B.K. / Pornillos, O.
History
DepositionJan 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retrotransposon-derived protein PEG10
B: Retrotransposon-derived protein PEG10
D: Retrotransposon-derived protein PEG10
E: Retrotransposon-derived protein PEG10


Theoretical massNumber of molelcules
Total (without water)46,8084
Polymers46,8084
Non-polymers00
Water4,053225
1
A: Retrotransposon-derived protein PEG10
B: Retrotransposon-derived protein PEG10


Theoretical massNumber of molelcules
Total (without water)23,4042
Polymers23,4042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Retrotransposon-derived protein PEG10
E: Retrotransposon-derived protein PEG10


Theoretical massNumber of molelcules
Total (without water)23,4042
Polymers23,4042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.598, 70.289, 52.689
Angle α, β, γ (deg.)90.000, 98.102, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Retrotransposon-derived protein PEG10 / Embryonal carcinoma differentiation-regulated protein / Mammalian retrotransposon-derived protein 2 ...Embryonal carcinoma differentiation-regulated protein / Mammalian retrotransposon-derived protein 2 / Myelin expression factor 3-like protein 1 / MEF3-like protein 1 / Paternally expressed gene 10 protein / Retrotransposon gag domain-containing protein 3 / Retrotransposon-derived gag-like polyprotein / Ty3/Gypsy-like protein


Mass: 11701.937 Da / Num. of mol.: 4 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Details: The first 9 amino acids (GHHHHHHGS) is a purification tag derived from the expression vector.
Source: (gene. exp.) Homo sapiens (human) / Gene: PEG10, EDR, KIAA1051, MAR2, MART2, MEF3L1, RGAG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86TG7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5 25% (w/v) PEG 3,350 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 58024 / % possible obs: 98.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 17.19 Å2 / CC1/2: 0.992 / Net I/σ(I): 19.625
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1166 / CC1/2: 0.644

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18_3845phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→41.89 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.4287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2093 3441 7.12 %
Rwork0.1822 44867 -
obs0.1842 48308 83.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 0 225 2952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612774
X-RAY DIFFRACTIONf_angle_d0.7633735
X-RAY DIFFRACTIONf_chiral_restr0.041412
X-RAY DIFFRACTIONf_plane_restr0.0057494
X-RAY DIFFRACTIONf_dihedral_angle_d16.62831053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.34330.2964404X-RAY DIFFRACTION19.36
1.93-1.950.3108510.2564629X-RAY DIFFRACTION28.72
1.95-1.980.271670.2401848X-RAY DIFFRACTION40.03
1.98-2.010.2505850.21561077X-RAY DIFFRACTION50.79
2.01-2.050.3038980.22061289X-RAY DIFFRACTION59.66
2.05-2.080.23921040.1911446X-RAY DIFFRACTION66.67
2.08-2.120.19571330.18631574X-RAY DIFFRACTION74.57
2.12-2.160.20681240.18161699X-RAY DIFFRACTION80.03
2.16-2.20.24121460.18581867X-RAY DIFFRACTION85.12
2.2-2.250.27171550.19661930X-RAY DIFFRACTION91.13
2.25-2.30.23161660.19282054X-RAY DIFFRACTION95.69
2.3-2.360.25881540.18392147X-RAY DIFFRACTION98.97
2.36-2.430.23821630.19142105X-RAY DIFFRACTION99.82
2.43-2.50.22591570.18442190X-RAY DIFFRACTION100
2.5-2.580.24361610.17122162X-RAY DIFFRACTION99.96
2.58-2.670.18191600.16682104X-RAY DIFFRACTION100
2.67-2.780.20821620.1822169X-RAY DIFFRACTION100
2.78-2.90.22341650.1872164X-RAY DIFFRACTION100
2.9-3.060.22941690.19912127X-RAY DIFFRACTION100
3.06-3.250.23231700.19162166X-RAY DIFFRACTION100
3.25-3.50.21441660.18022138X-RAY DIFFRACTION100
3.5-3.850.17151600.16472119X-RAY DIFFRACTION100
3.85-4.410.16981700.15252179X-RAY DIFFRACTION100
4.41-5.550.16251620.16372132X-RAY DIFFRACTION100
5.55-41.890.19071600.20232148X-RAY DIFFRACTION99.53

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