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- PDB-4jhk: Crystal structure of Danio rerio SLIP1 in complex with SLBP -

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Basic information

Entry
Database: PDB / ID: 4jhk
TitleCrystal structure of Danio rerio SLIP1 in complex with SLBP
Components
  • MIF4G domain-containing protein B
  • Sb:cb157 protein
KeywordsTRANSLATION / MRNA EXPORT / MRNA TRANSPORT / RNA BINDING / HISTONE MRNA PROCESSING / 3'-UTR / 3'-PROCESSING / SLBP / U7 snRNP / stem loop RNA
Function / homology
Function and homology information


histone mRNA stem-loop binding complex / photoreceptor cell differentiation / histone pre-mRNA stem-loop binding / mRNA 3'-end processing by stem-loop binding and cleavage / cap-dependent translational initiation / translation activator activity / histone pre-mRNA 3'end processing complex / neural retina development / brain morphogenesis / retinal ganglion cell axon guidance ...histone mRNA stem-loop binding complex / photoreceptor cell differentiation / histone pre-mRNA stem-loop binding / mRNA 3'-end processing by stem-loop binding and cleavage / cap-dependent translational initiation / translation activator activity / histone pre-mRNA 3'end processing complex / neural retina development / brain morphogenesis / retinal ganglion cell axon guidance / regulation of translational initiation / mRNA transport / neuron differentiation / mRNA binding / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
MIF4G domain-containing protein B / Sb:cb157 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.507 Å
Authorsvon Moeller, H. / Conti, E.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural and biochemical studies of SLIP1-SLBP identify DBP5 and eIF3g as SLIP1-binding proteins.
Authors: von Moeller, H. / Lerner, R. / Ricciardi, A. / Basquin, C. / Marzluff, W.F. / Conti, E.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Structure summary
Revision 1.2Sep 18, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: MIF4G domain-containing protein B
C: Sb:cb157 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5834
Polymers28,3902
Non-polymers1922
Water1,09961
1
A: MIF4G domain-containing protein B
C: Sb:cb157 protein
hetero molecules

A: MIF4G domain-containing protein B
C: Sb:cb157 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1658
Polymers56,7814
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area4770 Å2
ΔGint-49 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.650, 70.650, 242.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein MIF4G domain-containing protein B


Mass: 25794.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish)
Gene: MIF4G domain-containing protein B, mif4gdb, zgc:110826
Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q5EAQ1
#2: Protein/peptide Sb:cb157 protein


Mass: 2595.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: sb:cb157, si:dkey-102m7.2, slbp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7SXI8
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M K/Na-tartrate, 0.085 M Na-citrate pH 5.6, 1.7 M ammonium sulfate and 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→43.07 Å / Num. all: 13200 / Num. obs: 13244 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.507→43.069 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 540 4.78 %random
Rwork0.1924 ---
obs0.1948 11303 86.1 %-
all-13244 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.507→43.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 10 61 1979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081984
X-RAY DIFFRACTIONf_angle_d1.1112674
X-RAY DIFFRACTIONf_dihedral_angle_d17.587761
X-RAY DIFFRACTIONf_chiral_restr0.073297
X-RAY DIFFRACTIONf_plane_restr0.004345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5074-2.75970.3552560.25481323X-RAY DIFFRACTION44
2.7597-3.15890.30241370.23593058X-RAY DIFFRACTION100
3.1589-3.97950.22941700.18253085X-RAY DIFFRACTION100
3.9795-43.07570.20551770.15933297X-RAY DIFFRACTION99

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