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- PDB-1m8w: CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMIL... -

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Basic information

Entry
Database: PDB / ID: 1m8w
TitleCRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE1-19 RNA
Components
  • 5'-R(P*UP*GP*UP*AP*UP*AP*U)-3'
  • 5'-R(P*UP*GP*UP*CP*CP*AP*G)-3'
  • 5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3'
  • 5'-R(P*UP*UP*GP*UP*CP*CP*AP*G)-3'
  • Pumilio 1
KeywordsRNA Binding Protein/RNA / Pumilio-homology domain / Puf domain / Nanos response element / RNA Binding Protein-RNA COMPLEX
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 / cytosol / cytoplasm
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, X. / McLachlan, J. / Zamore, P.D. / Hall, T.M.T.
Citation
Journal: CELL(CAMBRIDGE,MASS.) / Year: 2002
Title: MODULAR RECOGNITION OF RNA BY A HUMAN PUMILIO-HOMOLOGY DOMAIN
Authors: Wang, X. / McLachlan, J. / Zamore, P.D. / Hall, T.M.T.
#1: Journal: Mol.Cell / Year: 2001
Title: Crystal structure of a Pumilio Homology Domain
Authors: Wang, X. / Zamore, P.D. / Hall, T.M.T.
History
DepositionJul 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND CHAIN C AND E ARE ALTERNATE CONFORMATIONS OF EACH OTHER. CHAIN D AND F ARE ALTERNATE ...COMPOUND CHAIN C AND E ARE ALTERNATE CONFORMATIONS OF EACH OTHER. CHAIN D AND F ARE ALTERNATE CONFORMATIONS OF EACH OTHER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3'
D: 5'-R(P*UP*GP*UP*AP*UP*AP*U)-3'
E: 5'-R(P*UP*UP*GP*UP*CP*CP*AP*G)-3'
F: 5'-R(P*UP*GP*UP*CP*CP*AP*G)-3'
A: Pumilio 1
B: Pumilio 1


Theoretical massNumber of molelcules
Total (without water)90,1036
Polymers90,1036
Non-polymers00
Water5,531307
1
C: 5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3'
E: 5'-R(P*UP*UP*GP*UP*CP*CP*AP*G)-3'
A: Pumilio 1


Theoretical massNumber of molelcules
Total (without water)45,3583
Polymers45,3583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-R(P*UP*GP*UP*AP*UP*AP*U)-3'
F: 5'-R(P*UP*GP*UP*CP*CP*AP*G)-3'
B: Pumilio 1


Theoretical massNumber of molelcules
Total (without water)44,7453
Polymers44,7453
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)262.730, 37.730, 82.520
Angle α, β, γ (deg.)90.00, 102.95, 90.00
Int Tables number5
Space group name H-MC121
DetailsTwo biological units are contained within an asymmetric unit

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Components

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RNA chain , 4 types, 4 molecules CDEF

#1: RNA chain 5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3'


Mass: 2489.489 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Drosophila melanogaster
#2: RNA chain 5'-R(P*UP*GP*UP*AP*UP*AP*U)-3'


Mass: 2183.323 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Drosophila melanogaster
#3: RNA chain 5'-R(P*UP*UP*GP*UP*CP*CP*AP*G)-3'


Mass: 2503.521 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Drosophila melanogaster
#4: RNA chain 5'-R(P*UP*GP*UP*CP*CP*AP*G)-3'


Mass: 2197.355 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Drosophila melanogaster

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Protein / Non-polymers , 2 types, 309 molecules AB

#5: Protein Pumilio 1


Mass: 40364.523 Da / Num. of mol.: 2 / Fragment: Pumilio-homology domain, Residues 828-1176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTYB3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14671
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 3350, lithium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.5 mg/mlprotein1drop
210 mMTris1droppH7.4
3150 mM1dropNaCl
42 mMdithiothreitol1drop
514 %(w/v)PEG33501reservoir
6100 mM1reservoirLi2SO4
7100 mMsodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.0093 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.2→42.68 Å / Num. all: 40790 / Num. obs: 40790 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.042 / Net I/σ(I): 25.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3 / Num. unique all: 3936 / Rsym value: 0.359 / % possible all: 97.8
Reflection
*PLUS
Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 97.8 % / Num. unique obs: 3936 / Rmerge(I) obs: 0.359

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IB3

1ib3
PDB Unreleased entry


Resolution: 2.2→42.68 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2378 6.1 %RANDOM
Rwork0.224 ---
all0.2279 40790 --
obs0.224 39279 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8275 Å2 / ksol: 0.320912 e/Å3
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.42 Å20 Å21.36 Å2
2--7.37 Å20 Å2
3---3.05 Å2
Refine analyzeLuzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5538 630 0 307 6475
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 362 6 %
Rwork0.278 5668 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3BME.PARAMWATER.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.2 Å / % reflection Rfree: 6 % / Rfactor all: 0.2279 / Rfactor obs: 0.225 / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_deg1.06
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.323 / Rfactor Rwork: 0.278

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