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- PDB-4l8r: Structure of mrna stem-loop, human stem-loop binding protein and ... -

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Basic information

Entry
Database: PDB / ID: 4l8r
TitleStructure of mrna stem-loop, human stem-loop binding protein and 3'hexo ternary complex
Components
  • 3'-5' exoribonuclease 1
  • HISTONE MRNA STEM-LOOP
  • Histone RNA hairpin-binding protein
KeywordsRNA/RNA BINDING PROTEIN/HYDROLASE / RNA-RNA BINDING PROTEIN-HYDROLASE COMPLEX / HISTONE MRNA 3'-END PROCESSING / HISTONE MRNA TRANSLATION / MICRORNA HOMEOSTASIS / 5.8S RRNA 3 -END MATURATION / ZFP100 / LSM11 / NUCLEUS
Function / homology
Function and homology information


histone mRNA stem-loop binding complex / histone pre-mRNA stem-loop binding / rRNA 3'-end processing / mRNA 3'-end processing by stem-loop binding and cleavage / cap-dependent translational initiation / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone pre-mRNA DCP binding / histone pre-mRNA 3'end processing complex / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of the SLBP Dependant Mature mRNA ...histone mRNA stem-loop binding complex / histone pre-mRNA stem-loop binding / rRNA 3'-end processing / mRNA 3'-end processing by stem-loop binding and cleavage / cap-dependent translational initiation / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone pre-mRNA DCP binding / histone pre-mRNA 3'end processing complex / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of the SLBP Dependant Mature mRNA / regulatory ncRNA-mediated gene silencing / RNA Polymerase II Transcription Termination / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA transport / 3'-5' exonuclease activity / ribosome binding / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / rRNA binding / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone RNA hairpin-binding protein RNA-binding domain / Histone RNA stem-loop-binding protein SLBP1/SLBP2 / Histone RNA hairpin-binding protein, RNA-binding domain / SLBP, RNA-binding domain superfamily / Histone RNA hairpin-binding protein RNA-binding domain / : / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Exonuclease ...Histone RNA hairpin-binding protein RNA-binding domain / Histone RNA stem-loop-binding protein SLBP1/SLBP2 / Histone RNA hairpin-binding protein, RNA-binding domain / SLBP, RNA-binding domain superfamily / Histone RNA hairpin-binding protein RNA-binding domain / : / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Exonuclease / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Exonuclease, RNase T/DNA polymerase III / EXOIII / Helicase, Ruva Protein; domain 3 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Histone RNA hairpin-binding protein / 3'-5' exoribonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsTan, D. / Tong, L.
CitationJournal: Science / Year: 2013
Title: Structure of Histone Mrna Stem-Loop, Human Stem-Loop Binding Protein, and 3'Hexo Ternary Complex.
Authors: Tan, D. / Marzluff, W.F. / Dominski, Z. / Tong, L.
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJul 10, 2013ID: 4HXH
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE MRNA STEM-LOOP
B: 3'-5' exoribonuclease 1
C: Histone RNA hairpin-binding protein
D: HISTONE MRNA STEM-LOOP
E: 3'-5' exoribonuclease 1


Theoretical massNumber of molelcules
Total (without water)102,1505
Polymers102,1505
Non-polymers00
Water2,432135
1
A: HISTONE MRNA STEM-LOOP
B: 3'-5' exoribonuclease 1
C: Histone RNA hairpin-binding protein


Theoretical massNumber of molelcules
Total (without water)58,1113
Polymers58,1113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-28 kcal/mol
Surface area20110 Å2
MethodPISA
2
D: HISTONE MRNA STEM-LOOP
E: 3'-5' exoribonuclease 1


Theoretical massNumber of molelcules
Total (without water)44,0392
Polymers44,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-17 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.758, 90.802, 128.636
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: RNA chain HISTONE MRNA STEM-LOOP


Mass: 8222.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by IDT
#2: Protein 3'-5' exoribonuclease 1 / 3'-5' exonuclease ERI1 / Eri-1 homolog / Histone mRNA 3'-end-specific exoribonuclease / Histone ...3'-5' exonuclease ERI1 / Eri-1 homolog / Histone mRNA 3'-end-specific exoribonuclease / Histone mRNA 3'-exonuclease 1 / Protein 3'hExo / HEXO


Mass: 35815.645 Da / Num. of mol.: 2
Fragment: SAP DOMAIN AND NUCLEASE DOMAIN, UNP residues 55-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 3'EXO, ERI1, THEX1 / Plasmid: PET-24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) STAR
References: UniProt: Q8IV48, Hydrolases; Acting on ester bonds
#3: Protein Histone RNA hairpin-binding protein / Histone stem-loop-binding protein


Mass: 14072.773 Da / Num. of mol.: 1 / Fragment: RNA-BINDING DOMAIN, UNP residues 125-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBP, SLBP / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) STAR / References: UniProt: Q14493
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% (W/V) TACSIMATE (PH 6.0), 18% (W/V) PEG3350, MACROSEEDING, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 55893 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.1 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CBASSdata collection
SnBTHEN SOLVE/RESOLVEphasing
CNS1.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→37.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 542066.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2634 4.9 %RANDOM
Rwork0.199 ---
obs0.199 53219 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.7262 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-20.1 Å20 Å20 Å2
2---7.57 Å20 Å2
3----12.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→37.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5083 918 0 135 6136
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it3.72
X-RAY DIFFRACTIONc_scangle_it5.382.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.371 223 5.1 %
Rwork0.316 4142 -
obs--77 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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