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- PDB-2yjy: A specific and modular binding code for cytosine recognition in P... -

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Basic information

Entry
Database: PDB / ID: 2yjy
TitleA specific and modular binding code for cytosine recognition in PUF domains
Components
  • 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'
  • PUMILIO HOMOLOG 1
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / NANOS RESPONSE ELEMENT
Function / homology
Function and homology information


regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / post-transcriptional gene silencing / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / Golgi Associated Vesicle Biogenesis ...regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / post-transcriptional gene silencing / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / Golgi Associated Vesicle Biogenesis / mRNA destabilization / regulation of mRNA stability / adult locomotory behavior / mRNA 3'-UTR binding / stem cell differentiation / P-body / cytoplasmic stress granule / regulation of translation / spermatogenesis / regulation of cell cycle / axon / RNA binding / nucleoplasm / 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
RNA / Pumilio homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsDong, S. / Wang, Y. / Cassidy-Amstutz, C. / Lu, G. / Qiu, C. / Bigler, R. / Jezyk, M. / Li, C. / Hall, T.M.T. / Wang, Z.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Specific and Modular Binding Code for Cytosine Recognition in Pumilio/Fbf (Puf) RNA-Binding Domains.
Authors: Dong, S. / Wang, Y. / Cassidy-Amstutz, C. / Lu, G. / Bigler, R. / Jezyk, M.R. / Li, C. / Hall, T.M. / Wang, Z.
History
DepositionMay 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Version format compliance
Revision 1.2Oct 28, 2015Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUMILIO HOMOLOG 1
B: PUMILIO HOMOLOG 1
C: 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'
D: 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)87,2894
Polymers87,2894
Non-polymers00
Water1,802100
1
B: PUMILIO HOMOLOG 1
D: 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)43,6452
Polymers43,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint1.7 kcal/mol
Surface area21000 Å2
MethodPISA
2
A: PUMILIO HOMOLOG 1
C: 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)43,6452
Polymers43,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint1.4 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.796, 59.340, 344.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PUMILIO HOMOLOG 1 / HSPUM / PUMILIO-1


Mass: 40497.762 Da / Num. of mol.: 2 / Fragment: HOMOLOGY DOMAIN, RESIDUES 828-1176 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14671
#2: RNA chain 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3' / HPUM1 R6C RNA


Mass: 3146.917 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 1043 TO SER ENGINEERED RESIDUE IN CHAIN A, GLN 1047 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, ASN 1043 TO SER ENGINEERED RESIDUE IN CHAIN A, GLN 1047 TO ARG ENGINEERED RESIDUE IN CHAIN B, ASN 1043 TO SER ENGINEERED RESIDUE IN CHAIN B, GLN 1047 TO ARG

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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: 2.29 Å3/Da / Density % sol: 46.28 % / Description: NONE
Crystal growpH: 6
Details: 30% PEG 3350, 0.2M SODIUM TARTRATE, 0.1M BIS-TRIS PH 6.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Mar 12, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→24.98 Å / Num. obs: 20661 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37.97 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.4 / % possible all: 79.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M8Y

1m8y


Resolution: 2.598→24.977 Å / SU ML: 2.43 / σ(F): 0.07 / Phase error: 30.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3056 1063 5.1 %
Rwork0.2104 --
obs0.2153 20661 86.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.003 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 42.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.7898 Å20 Å20 Å2
2---8.4101 Å20 Å2
3---11.1999 Å2
Refinement stepCycle: LAST / Resolution: 2.598→24.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 422 0 100 6012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066060
X-RAY DIFFRACTIONf_angle_d1.0928267
X-RAY DIFFRACTIONf_dihedral_angle_d20.9842365
X-RAY DIFFRACTIONf_chiral_restr0.074936
X-RAY DIFFRACTIONf_plane_restr0.0031003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5975-2.71560.36521160.23211927X-RAY DIFFRACTION70
2.7156-2.85860.31831230.22912333X-RAY DIFFRACTION85
2.8586-3.03740.35241310.222439X-RAY DIFFRACTION88
3.0374-3.27140.37971190.23042597X-RAY DIFFRACTION92
3.2714-3.59980.31221470.22382597X-RAY DIFFRACTION93
3.5998-4.11870.24951420.1942580X-RAY DIFFRACTION92
4.1187-5.18140.27871430.1832611X-RAY DIFFRACTION90
5.1814-24.97790.30141420.20382514X-RAY DIFFRACTION83

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