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- PDB-8dio: Crystal structure of LARP1-DM15 from Danio rerio bound to m7GpppC -

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Basic information

Entry
Database: PDB / ID: 8dio
TitleCrystal structure of LARP1-DM15 from Danio rerio bound to m7GpppC
ComponentsLa ribonucleoprotein 1, translational regulator
KeywordsRNA BINDING PROTEIN / LARP1 / DM15
Function / homologyChem-91P / 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one / :
Function and homology information
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNguyen, E. / Berman, A.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
American Cancer Society United States
CitationJournal: Plos One / Year: 2024
Title: Comparative analysis of the LARP1 C-terminal DM15 region through Coelomate evolution.
Authors: Nguyen, E. / Sosa, J.A. / Cassidy, K.C. / Berman, A.J.
History
DepositionJun 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: La ribonucleoprotein 1, translational regulator
B: La ribonucleoprotein 1, translational regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6154
Polymers37,6872
Non-polymers9292
Water1,44180
1
A: La ribonucleoprotein 1, translational regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6072
Polymers18,8431
Non-polymers7631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: La ribonucleoprotein 1, translational regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0092
Polymers18,8431
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.950, 59.702, 60.381
Angle α, β, γ (deg.)90.000, 100.307, 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 ribonucleoprotein 1, translational regulator


Mass: 18843.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: larp1 / Production host: Escherichia coli (E. coli) / References: UniProt: F1R0U5
#2: Chemical ChemComp-91P / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate / dinucleotide triphosphate cap analog m7GpppC


Mass: 763.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N8O18P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MY6 / 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one


Mass: 165.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES, pH 7, 0 or 100 mM NaCl, 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.3→47.18 Å / Num. obs: 13814 / % possible obs: 91.78 % / Redundancy: 2 % / Biso Wilson estimate: 19.43 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0145 / Net I/σ(I): 28.43
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2 % / Num. unique obs: 1391 / CC1/2: 0.998 / CC star: 1 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
AutoProcessdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V87

5v87


Resolution: 2.3→47.18 Å / SU ML: 0.2395 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 1375 9.96 %
Rwork0.2068 12435 -
obs0.2123 13810 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 61 80 2639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242659
X-RAY DIFFRACTIONf_angle_d1.29223586
X-RAY DIFFRACTIONf_chiral_restr0.0487342
X-RAY DIFFRACTIONf_plane_restr0.0105457
X-RAY DIFFRACTIONf_dihedral_angle_d8.0762348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.32261410.22891250X-RAY DIFFRACTION93.8
2.38-2.480.28221340.22541250X-RAY DIFFRACTION92.82
2.48-2.590.29021350.22081231X-RAY DIFFRACTION92.17
2.59-2.730.27131320.22851221X-RAY DIFFRACTION89.6
2.73-2.90.29991330.23841168X-RAY DIFFRACTION87.55
2.9-3.120.30311430.23081273X-RAY DIFFRACTION94.53
3.12-3.440.29111420.21071273X-RAY DIFFRACTION93.34
3.44-3.930.21271400.18361241X-RAY DIFFRACTION91.64
3.93-4.950.21261400.17241237X-RAY DIFFRACTION90.59
4.96-47.180.2521350.20871291X-RAY DIFFRACTION91.94
Refinement TLS params.Method: refined / Origin x: -3.13743205247 Å / Origin y: 16.1561648962 Å / Origin z: -15.2470063745 Å
111213212223313233
T0.148864278925 Å20.0219108961262 Å20.0531662158618 Å2-0.16752512186 Å2-0.0451218625778 Å2--0.107989263328 Å2
L2.1853079048 °2-0.848246864199 °21.67422070514 °2-2.56689831002 °2-1.39578220638 °2--2.32654394412 °2
S0.0193434930881 Å °0.36630350096 Å °0.0733889572394 Å °-0.14362994033 Å °-0.121947917986 Å °-0.0969737518353 Å °0.0292666252577 Å °0.253569097302 Å °0.0656620719558 Å °
Refinement TLS groupSelection details: all

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