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- PDB-4jhj: Crystal structure of Danio rerio Slip1 in complex with Dbp5 -

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Basic information

Entry
Database: PDB / ID: 4jhj
TitleCrystal structure of Danio rerio Slip1 in complex with Dbp5
Components
  • DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)
  • MIF4G domain-containing protein B
KeywordsTRANSLATION / DEAD-BOX HELICASE / MRNA EXPORT / RECA-LIKE / RNA-DEPENDENT ATPASE / DDX19 / DEAD-BOX PROTEIN 19B / MRNA TRANSPORT / ATP BINDING / HELICASE / HYDROLASE / NUCLEOTIDE BINDING / RNA BINDING / TRANSPORT HISTONE MRNA PROCESSING / 3'-UTR / 3'-PROCESSING / NUP214
Function / homology
Function and homology information


histone mRNA stem-loop binding complex / translation activator activity / cap-dependent translational initiation / regulation of translational initiation / poly(A)+ mRNA export from nucleus / cytoplasmic stress granule / RNA helicase activity / hydrolase activity / RNA helicase / mRNA binding ...histone mRNA stem-loop binding complex / translation activator activity / cap-dependent translational initiation / regulation of translational initiation / poly(A)+ mRNA export from nucleus / cytoplasmic stress granule / RNA helicase activity / hydrolase activity / RNA helicase / mRNA binding / RNA binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain ...: / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
MIF4G domain-containing protein B / RNA helicase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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 1.1Sep 18, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: MIF4G domain-containing protein B
C: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)
D: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)


Theoretical massNumber of molelcules
Total (without water)58,5804
Polymers58,5804
Non-polymers00
Water19811
1
A: MIF4G domain-containing protein B
C: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)

B: MIF4G domain-containing protein B
D: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)


Theoretical massNumber of molelcules
Total (without water)58,5804
Polymers58,5804
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454y-1,-x+y,z-1/61
Buried area4290 Å2
ΔGint-20 kcal/mol
Surface area22490 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-25 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.185, 85.185, 258.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUTYRTYRAA7 - 2177 - 217
21GLUGLUTYRTYRBB7 - 2177 - 217
12ALAALAILEILECC2 - 202 - 20
22ALAALAILEILEDD2 - 202 - 20

NCS ensembles :
ID
1
2

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Components

#1: Protein MIF4G domain-containing protein B / STEM-LOOP INTERACTING PROTEIN 1 / SLIP1


Mass: 25794.500 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mif4gdb, zgc:110826 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5EAQ1
#2: Protein/peptide DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)


Mass: 3495.730 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ddx19 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q7ZU28, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.73 Å3/Da / Density % sol: 73.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.05 M MES pH 6.0, 18% (w/v) PEG 8000, 0.2 M Ca-Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.25→86.13 Å / Num. obs: 16724 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rsym value: 0.083 / Net I/σ(I): 16.34
Reflection shellResolution: 3.25→3.45 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.68 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I2O

2i2o


Resolution: 3.25→73.77 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.36 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 836 5 %RANDOM
Rwork0.244 ---
obs0.245 15869 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 102.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.92 Å22.96 Å20 Å2
2--5.92 Å20 Å2
3----8.88 Å2
Refinement stepCycle: LAST / Resolution: 3.25→73.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3761 0 0 11 3772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223813
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.9675139
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9475461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79225.152198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.58915724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1761526
X-RAY DIFFRACTIONr_chiral_restr0.070.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022846
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3821.52311
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70623716
X-RAY DIFFRACTIONr_scbond_it0.56431502
X-RAY DIFFRACTIONr_scangle_it1.0474.51423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1723loose positional0.55
2C139loose positional0.655
1A1723loose thermal1.7910
2C139loose thermal0.8910
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 62 -
Rwork0.388 1165 -
obs--100 %

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