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- PDB-4qoz: Crystal structure of the histone mRNA stem-loop, stem-loop bindin... -

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Basic information

Entry
Database: PDB / ID: 4qoz
TitleCrystal structure of the histone mRNA stem-loop, stem-loop binding protein (phosphorylated), and 3'hExo ternary complex
Components
  • 3'-5' exoribonuclease 1
  • Histone RNA hairpin-binding protein
  • histone mRNA stem-loop
KeywordsRNA/HYDROLASE/RNA BINDING PROTEIN / histone mRNA 3'-end processing / histone mRNA translation / microRNA homeostasis / 5.8S rRNA 3'-end maturation / ZFP100 / Lsm11 / phosphorylation / nucleus / RNA-HYDROLASE-RNA BINDING PROTEIN complex
Function / homology
Function and homology information


histone mRNA stem-loop binding complex / histone pre-mRNA stem-loop binding / rRNA 3'-end processing / exoribonuclease II / 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 ...histone mRNA stem-loop binding complex / histone pre-mRNA stem-loop binding / rRNA 3'-end processing / exoribonuclease II / 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 / maturation of 5.8S rRNA / mRNA transport / Major pathway of rRNA processing in the nucleolus and cytosol / 3'-5' exonuclease activity / ribosome binding / 3'-5'-RNA exonuclease activity / rRNA binding / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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 / 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 / Exonuclease / SAP domain superfamily / Exonuclease, RNase T/DNA polymerase III / EXOIII / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsTan, D. / Tong, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation.
Authors: Zhang, J. / Tan, D. / DeRose, E.F. / Perera, L. / Dominski, Z. / Marzluff, W.F. / Tong, L. / Hall, T.M.
History
DepositionJun 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)101,2925
Polymers101,2925
Non-polymers00
Water5,350297
1
A: histone mRNA stem-loop
B: 3'-5' exoribonuclease 1
C: Histone RNA hairpin-binding protein


Theoretical massNumber of molelcules
Total (without water)57,7223
Polymers57,7223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-32 kcal/mol
Surface area20990 Å2
MethodPISA
2
D: histone mRNA stem-loop
E: 3'-5' exoribonuclease 1


Theoretical massNumber of molelcules
Total (without water)43,5702
Polymers43,5702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-21 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.107, 91.505, 128.722
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
#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: 35346.699 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: ERI1, 3'EXO, THEX1 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 14152.753 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: SLBP, HBP / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q14493
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% w/v Tacsimate, pH 6.0, 18% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2013
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.304→38.169 Å / Num. all: 43593 / Num. obs: 40611 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.5
Reflection shellResolution: 2.304→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 84.5

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Processing

Software
NameVersionClassification
CBASSdata collection
COMOphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.304→38.169 Å / SU ML: 0.31 / σ(F): 1.33 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1997 4.92 %RANDOM
Rwork0.1931 ---
obs0.1957 40611 93.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.304→38.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 917 0 297 6414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086337
X-RAY DIFFRACTIONf_angle_d1.128742
X-RAY DIFFRACTIONf_dihedral_angle_d14.3222588
X-RAY DIFFRACTIONf_chiral_restr0.044989
X-RAY DIFFRACTIONf_plane_restr0.006950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.304-2.38590.32861780.27053432X-RAY DIFFRACTION84
2.3859-2.48150.3151950.25823766X-RAY DIFFRACTION92
2.4815-2.59440.31182010.2483909X-RAY DIFFRACTION96
2.5944-2.73110.30592040.25293943X-RAY DIFFRACTION96
2.7311-2.90220.27242020.22193927X-RAY DIFFRACTION96
2.9022-3.12610.28392040.21623940X-RAY DIFFRACTION95
3.1261-3.44060.24632030.18723926X-RAY DIFFRACTION95
3.4406-3.9380.22232040.16913928X-RAY DIFFRACTION94
3.938-4.95970.20712040.14713934X-RAY DIFFRACTION94
4.9597-38.17420.20252020.17633909X-RAY DIFFRACTION90

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