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- PDB-6pw3: LARP1 DM15 FYRE (F844Y, R847E) mutant bound to m7GpppG dinucleoti... -

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Basic information

Entry
Database: PDB / ID: 6pw3
TitleLARP1 DM15 FYRE (F844Y, R847E) mutant bound to m7GpppG dinucleotide (capG)
ComponentsLa-related protein 1
KeywordsRNA BINDING PROTEIN / HEAT-like / cap-binding / TOP mRNA / translation regulation
Function / homology
Function and homology information


cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / TORC1 signaling / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / TOR signaling ...cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / TORC1 signaling / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / TOR signaling / positive regulation of translational initiation / positive regulation of macroautophagy / ribosomal small subunit binding / positive regulation of viral genome replication / translation initiation factor binding / negative regulation of translational initiation / positive regulation of translation / mRNA 3'-UTR binding / translational initiation / mRNA 5'-UTR binding / cytoplasmic stress granule / cell population proliferation / negative regulation of translation / cadherin binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / membrane / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DM15 / LARP1 HEAT repeat region / Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / La-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsLahr, R.M. / Berman, A.J.
Funding support United States, 2items
OrganizationGrant numberCountry
American Cancer Society
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2019
Title: Capturing the Mechanism Underlying TOP mRNA Binding to LARP1.
Authors: Cassidy, K.C. / Lahr, R.M. / Kaminsky, J.C. / Mack, S. / Fonseca, B.D. / Das, S.R. / Berman, A.J. / Durrant, J.D.
History
DepositionJul 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: La-related protein 1
A: La-related protein 1
B: La-related protein 1
D: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0487
Polymers78,4174
Non-polymers1,6313
Water81145
1
C: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4082
Polymers19,6041
Non-polymers8031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6292
Polymers19,6041
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4082
Polymers19,6041
Non-polymers8031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: La-related protein 1


Theoretical massNumber of molelcules
Total (without water)19,6041
Polymers19,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.582, 87.355, 72.890
Angle α, β, γ (deg.)90.000, 93.367, 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
La-related protein 1 / La ribonucleoprotein domain family member 1


Mass: 19604.201 Da / Num. of mol.: 4 / Mutation: F844Y, R847E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PKG0
#2: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N10O18P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 100 mM Hepes 7.5, 0.08 M NaCl, 36% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.34→29.3 Å / Num. obs: 30894 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 54.3315929648 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.6
Reflection shellResolution: 2.34→2.4 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 2210

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZC4

4zc4


Resolution: 2.34→29.24 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.16
RfactorNum. reflection% reflection
Rfree0.2672 1905 6.5 %
Rwork0.2205 --
obs0.2235 29243 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 74.96 Å2
Refinement stepCycle: LAST / Resolution: 2.34→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 105 45 5111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001604374000525299
X-RAY DIFFRACTIONf_angle_d0.5404504692487141
X-RAY DIFFRACTIONf_chiral_restr0.0286194663413669
X-RAY DIFFRACTIONf_plane_restr0.00122497334352893
X-RAY DIFFRACTIONf_dihedral_angle_d13.87317633393013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.40050.37491110.30851644X-RAY DIFFRACTION80.7639208468
2.4005-2.46540.371320.30051731X-RAY DIFFRACTION84.566500227
2.4654-2.53790.31181250.28551784X-RAY DIFFRACTION87.0497036024
2.5379-2.61970.32361230.27261881X-RAY DIFFRACTION91.2568306011
2.6197-2.71330.29131310.26471925X-RAY DIFFRACTION93.7528499772
2.7133-2.82180.30321490.27791964X-RAY DIFFRACTION95.39503386
2.8218-2.95020.42131290.27561996X-RAY DIFFRACTION96.5909090909
2.9502-3.10550.34911490.27682008X-RAY DIFFRACTION97.6018099548
3.1055-3.29990.31071300.26352034X-RAY DIFFRACTION98.6326344576
3.2999-3.55420.28081420.23442050X-RAY DIFFRACTION99.2753623188
3.5542-3.91120.23971520.20492067X-RAY DIFFRACTION99.4621246078
3.9112-4.47540.21461430.18362064X-RAY DIFFRACTION99.5040577096
4.4754-5.63190.21331460.17932076X-RAY DIFFRACTION99.8651685393
5.6319-29.240.25681430.20052114X-RAY DIFFRACTION99.4273127753

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