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- PDB-3h3d: Drosophila Pumilio RNA binding domain (Puf domain) -

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Basic information

Entry
Database: PDB / ID: 3h3d
TitleDrosophila Pumilio RNA binding domain (Puf domain)
ComponentsMaternal protein pumilio
KeywordsRNA BINDING PROTEIN / Pumilio / Puf / RNA binding domain / Alternative splicing / Cytoplasm / Developmental protein / Phosphoprotein / Repressor / RNA-binding / Translation regulation
Function / homology
Function and homology information


type Is terminal bouton / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / type Ib terminal bouton / head involution / : / muscle cell postsynaptic specialization / regulation of synaptic assembly at neuromuscular junction / CCR4-NOT complex binding / post-transcriptional gene silencing / neuronal ribonucleoprotein granule ...type Is terminal bouton / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / type Ib terminal bouton / head involution / : / muscle cell postsynaptic specialization / regulation of synaptic assembly at neuromuscular junction / CCR4-NOT complex binding / post-transcriptional gene silencing / neuronal ribonucleoprotein granule / anterior/posterior axis specification, embryo / behavioral response to ethanol / miRNA processing / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / dendrite morphogenesis / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / post-transcriptional regulation of gene expression / oogenesis / negative regulation of epidermal growth factor receptor signaling pathway / germ cell development / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of cell cycle / long-term memory / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / positive regulation of translation / modulation of chemical synaptic transmission / neuromuscular junction / cell migration / nuclear envelope / mitotic cell cycle / postsynapse / chemical synaptic transmission / negative regulation of translation / negative regulation of DNA-templated transcription / RNA binding / nucleus / 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
Maternal protein pumilio
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsEdwards, T.A. / Aggarwal, A.K. / Wharton, R.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structure of Pumilio reveals similarity between RNA and peptide binding motifs.
Authors: Edwards, T.A. / Pyle, S.E. / Wharton, R.P. / Aggarwal, A.K.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Maternal protein pumilio
Y: Maternal protein pumilio


Theoretical massNumber of molelcules
Total (without water)74,0232
Polymers74,0232
Non-polymers00
Water6,035335
1
X: Maternal protein pumilio


Theoretical massNumber of molelcules
Total (without water)37,0111
Polymers37,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
Y: Maternal protein pumilio


Theoretical massNumber of molelcules
Total (without water)37,0111
Polymers37,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.580, 94.580, 229.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Maternal protein pumilio


Mass: 37011.402 Da / Num. of mol.: 2 / Fragment: Puf domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pumilio / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P25822
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE SEQUENCE IS GENBANK DATABASE, CAA44474. SEE REFERENCE 1 IN UNP DATABASE P25822.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.0269.43
2
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 2.1M Ammonium sulfate, 100mM HEPES, 4% DMSO, 2mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21102
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X2521.009, 1.0084, 0.990
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 1, 2000
ADSC QUANTUM 315r2CCDJun 1, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.0091
31.00841
40.991
ReflectionResolution: 2.3→20 Å / Num. all: 51334 / Num. obs: 49178 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 20.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4917 / Rsym value: 0.311 / % possible all: 73.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 2.3→19.78 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.861 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.394 / SU ML: 0.185 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.298 2440 5 %RANDOM
Rwork0.252 ---
all0.254 49217 --
obs0.254 48553 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.97 Å2 / Biso mean: 44.222 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.41 Å2-0 Å2
2---0.83 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 0 335 5344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0225097
X-RAY DIFFRACTIONr_angle_refined_deg2.611.9436883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3665625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.55925.469256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.70215945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6851521
X-RAY DIFFRACTIONr_chiral_restr0.1760.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023821
X-RAY DIFFRACTIONr_nbd_refined0.2670.22650
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.214
X-RAY DIFFRACTIONr_mcbond_it1.6341.53265
X-RAY DIFFRACTIONr_mcangle_it2.44325054
X-RAY DIFFRACTIONr_scbond_it4.01632084
X-RAY DIFFRACTIONr_scangle_it5.9084.51828
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 114 -
Rwork0.28 2303 -
all-2417 -
obs--100 %

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