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

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Basic information

Entry
Database: PDB / ID: 3gvt
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Pumilio homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Pumilio homolog 2
B: Pumilio homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2445
Polymers80,9052
Non-polymers3383
Water1,54986
1
A: Pumilio homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7914
Polymers40,4531
Non-polymers3383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pumilio homolog 2


Theoretical massNumber of molelcules
Total (without water)40,4531
Polymers40,4531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.540, 150.540, 77.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 706 - 1049 / Label seq-ID: 3 - 344

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Pumilio homolog 2 / Pumilio 2


Mass: 40452.551 Da / Num. of mol.: 2 / 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-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium citrate, 0.2M Li2SO4, 22%(w/v) PEG 4000 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2008
RadiationMonochromator: Si (111) double crystal monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.8→37.88 Å / Num. all: 24770 / Num. obs: 24746 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5.7 / Redundancy: 5.4 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 5.7 / Num. unique all: 3595 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GVO

3gvo


Resolution: 2.8→37.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 27.668 / SU ML: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Isotropic with TLS (5 TLS groups per monomer)
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.551 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25317 1250 5.1 %RANDOM
Rwork0.19151 ---
all0.19457 23492 --
obs0.19457 23335 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.549 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 20 86 5658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225673
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9527640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9045682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.12124.236288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4621540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024250
X-RAY DIFFRACTIONr_nbd_refined0.230.22749
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23953
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.210
X-RAY DIFFRACTIONr_mcbond_it0.531.53493
X-RAY DIFFRACTIONr_mcangle_it0.93525516
X-RAY DIFFRACTIONr_scbond_it1.2932382
X-RAY DIFFRACTIONr_scangle_it2.1684.52124
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1368tight positional0.080.05
1408medium positional0.540.5
1368tight thermal0.080.5
1408medium thermal0.522
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 87 -
Rwork0.259 1677 -
obs--97.78 %
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)
110.93943.6132-3.467518.2741-3.30110.87570.5131.97081.794-1.672-1.0588-0.2408-0.3058-0.63230.5459-0.3491-0.0620.15720.10760.64050.1482-52.458863.4575-37.9151
24.8256-0.40960.4176.1376-3.15162.92330.06580.29940.5970.14130.01360.0499-0.02090.0874-0.0794-0.224-0.04160.0439-0.1009-0.017-0.0611-58.019849.6433-23.9362
33.1186-0.28733.0620.8203-0.27493.68030.12930.0295-0.30120.02480.0520.0330.26040.2871-0.1813-0.11050.00810.0209-0.0696-0.0423-0.176-44.459631.90810.0893
45.0128-1.0688-3.17466.6317-1.140111.09950.1354-0.39720.35060.7801-0.089-0.2792-0.92551.1682-0.0463-0.2169-0.1271-0.13730.089-0.0376-0.3069-25.399538.114718.2444
53.6402-2.9848-1.74283.61175.328313.89240.2282-0.53541.36570.8510.0309-1.4369-1.67411.3531-0.2591-0.0514-0.3641-0.01910.1274-0.0650.0766-18.660247.873220.4629
612.5897-7.4344-2.94148.3519-0.61286.7334-1.2167-2.2027-1.9271.18341.1061.77930.2442-0.49880.1107-0.20270.02360.29430.03680.19140.0497-64.101350.813414.5118
77.7387-4.1364-3.66263.4192.30153.55350.16740.02680.5697-0.32260.0387-0.3146-0.0901-0.0532-0.2061-0.162-0.0859-0.0036-0.1304-0.0935-0.0776-50.842257.27110.292
81.6817-0.0305-0.93732.42951.95455.38930.1982-0.11410.3975-0.11240.2732-0.26380.29320.4153-0.4713-0.15240.0156-0.0092-0.073-0.0235-0.066-32.761644.3802-23.9243
98.06591.4906-2.10249.6327-4.622810.2888-0.02750.5016-0.1989-0.44760.18960.36861.0763-0.5987-0.16210.276-0.1081-0.0826-0.2154-0.1087-0.3902-38.397924.9857-41.8074
103.9539-0.21863.22627.7667-2.15373.13560.26840.8103-1.4408-0.5760.71951.10210.7291-0.4047-0.98790.2997-0.3371-0.249-0.14990.20460.0923-47.899917.8112-43.9243
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
6X-RAY DIFFRACTION6B706 - 730
7X-RAY DIFFRACTION7B731 - 828
8X-RAY DIFFRACTION8B831 - 968
9X-RAY DIFFRACTION9B969 - 1015
10X-RAY DIFFRACTION10B1016 - 1049

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