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- PDB-3gvo: Structure and RNA binding of the mouse Pumilio-2 Puf Domain -

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Basic information

Entry
Database: PDB / ID: 3gvo
TitleStructure and RNA binding of the mouse Pumilio-2 Puf Domain
ComponentsPumilio homolog 2
KeywordsRNA BINDING PROTEIN / RNA-binding / Pumilio / Puf domain
Function / homology
Function and homology information


positive regulation of sprouting of injured axon / pumilio-response element binding / regulation of intracellular mRNA localization / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / miRNA processing / lncRNA binding / miRNA binding / post-transcriptional regulation of gene expression ...positive regulation of sprouting of injured axon / pumilio-response element binding / regulation of intracellular mRNA localization / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / miRNA processing / lncRNA binding / miRNA binding / post-transcriptional regulation of gene expression / hair follicle development / chromosome organization / adipose tissue development / stress granule assembly / regulation of mRNA stability / respiratory electron transport chain / mitochondrion organization / skeletal system development / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / nuclear membrane / negative regulation of gene expression / neuronal cell body / perinuclear region of cytoplasm / RNA binding / cytoplasm / cytosol
Similarity search - Function
Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DITHIANE DIOL / Pumilio homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsJenkins, H.T. / Edwards, T.A.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Structure and RNA binding of the mouse Pumilio-2 Puf domain
Authors: Jenkins, H.T. / Baker-Wilding, R. / Edwards, T.A.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pumilio homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9736
Polymers40,4531
Non-polymers5215
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.393, 142.393, 112.233
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2-

HOH

21A-29-

HOH

31A-311-

HOH

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Components

#1: Protein Pumilio homolog 2 / Pumilio 2


Mass: 40452.551 Da / Num. of mol.: 1 / Fragment: Puf domain, UNP residues 706-1056
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pum2 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q80U58
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS ENTITY BASED ON THE ISOFORM 2 OF UNIPROTKB/SUISS-PROT Q80U58 (PUM2_MOUSE). ...THE SEQUENCE OF THIS ENTITY BASED ON THE ISOFORM 2 OF UNIPROTKB/SUISS-PROT Q80U58 (PUM2_MOUSE). RESIDUES 829 VAL AND 830 ILE WERE MISSING IN ISOFORM 2.

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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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 277 K / pH: 7
Details: 0.2M ammonium citrate, 20%(w/v) PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.05 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2008
RadiationMonochromator: double crystal Si(111) monochromator with sagittal focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.6→83.045 Å / Num. all: 57386 / Num. obs: 56410 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.7 / Redundancy: 5.4 % / Biso Wilson estimate: 19.609 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 1.7 / Num. measured all: 15337 / Num. unique all: 7642 / % possible all: 92.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å14.97 Å
Translation2.5 Å14.97 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ib2

1ib2


Resolution: 1.6→32.72 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.174 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Isotropic with TLS (5 TLS groups per monomer)
Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2866 5.1 %RANDOM
Rwork0.167 ---
obs0.168 56219 97.9 %-
all-57413 --
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 32 423 3231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9644054
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65224.156154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6315568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4551523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022260
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21588
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22087
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2354
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.51823
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37122884
X-RAY DIFFRACTIONr_scbond_it2.43231289
X-RAY DIFFRACTIONr_scangle_it3.8834.51153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 200 -
Rwork0.246 3676 -
obs--91.78 %
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)
12.2164-0.29170.18071.30941.4626.0440.05270.0946-0.0420.10170.0333-0.01480.4050.1278-0.086-0.00380.06690.0007-0.06840.0057-0.054244.6593-53.030732.5909
20.6105-0.5498-0.71141.2270.57891.7898-0.04180.0136-0.03970.04940.03740.02560.1335-0.00470.0044-0.05360.0050.0179-0.03070.0079-0.01835.6617-39.722844.8163
30.5174-0.39620.0561.5708-0.38840.55640.01840.02140.0558-0.0633-0.0396-0.0131-0.14410.01190.02120.02560.00340.0043-0.0814-0.0109-0.029627.3375-9.090942.767
44.3611-0.4101-0.64683.05280.69796.45980.21941.01430.427-0.8447-0.22210.0266-0.5847-0.66810.00270.28950.1268-0.03770.13590.102-0.128621.53215.427620.7697
54.6495-1.67390.14880.8062-2.176722.1440.30050.8380.0101-0.5139-0.2035-0.0218-0.2433-0.2482-0.0970.28620.0216-0.00810.18660.0095-0.049721.67852.57019.2476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A706 - 730
2X-RAY DIFFRACTION2A731 - 828
3X-RAY DIFFRACTION3A831 - 968
4X-RAY DIFFRACTION4A969 - 1015
5X-RAY DIFFRACTION5A1016 - 1049

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