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- PDB-5jiu: The crystal structure of RanBPM/9 IUS-SPRY domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 5jiu
TitleThe crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide
Components
  • Probable ATP-dependent RNA helicase DDX4
  • Ran-binding protein 9
KeywordsRAN BINDING PROTEIN/PEPTIDE / beta sandwich / Ran binding protein / TRANSPORT PROTEIN / RAN BINDING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


piP-body / transposable element silencing by piRNA-mediated DNA methylation / pi-body / secondary piRNA processing / L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / chromatoid body / male meiotic nuclear division ...piP-body / transposable element silencing by piRNA-mediated DNA methylation / pi-body / secondary piRNA processing / L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / chromatoid body / male meiotic nuclear division / gamete generation / microtubule nucleation / P granule / microtubule associated complex / male meiosis I / germ cell development / MET activates RAS signaling / ubiquitin ligase complex / cytoskeleton organization / Regulation of pyruvate metabolism / negative regulation of ERK1 and ERK2 cascade / small GTPase binding / regulation of protein localization / RAF/MAP kinase cascade / spermatogenesis / protein-containing complex assembly / RNA helicase activity / cell differentiation / nuclear body / RNA helicase / ribonucleoprotein complex / mRNA binding / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ran binding protein 9/10, SPRY domain / CRA domain / : / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / LisH / SPRY domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif ...Ran binding protein 9/10, SPRY domain / CRA domain / : / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / LisH / SPRY domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Helicase superfamily 1/2, ATP-binding domain / Jelly Rolls / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX4 / Ran-binding protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsHong, S.K. / Kim, K.-H. / Kim, E.E.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of ScienceNRF 20110021713 Korea, Republic Of
Korea Institute of Science and Technology Korea, Republic Of
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development.
Authors: Hong, S.K. / Kim, K.H. / Song, E.J. / Kim, E.E.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ran-binding protein 9
B: Ran-binding protein 9
C: Probable ATP-dependent RNA helicase DDX4
D: Probable ATP-dependent RNA helicase DDX4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9626
Polymers56,8914
Non-polymers712
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.318, 123.318, 91.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Ran-binding protein 9 / RanBP9 / BPM-L / BPM90 / Ran-binding protein M / RanBPM / RanBP7


Mass: 26344.484 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 108-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP9, RANBPM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q96S59
#2: Protein/peptide Probable ATP-dependent RNA helicase DDX4 / DEAD box protein 4 / Mvh / Vasa homolog


Mass: 2101.184 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 201-220 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q61496, RNA helicase
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20~25% (w/v) PEG 3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 42894 / % possible obs: 97.3 % / Redundancy: 2.5 % / Net I/σ(I): 22.2658
Reflection shellResolution: 2.05→2.12 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JI7

5ji7


Resolution: 2.054→32.058 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.54 / Phase error: 20.2
RfactorNum. reflection% reflection
Rfree0.2025 2011 4.82 %
Rwork0.1661 --
obs0.1678 41717 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.054→32.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 2 276 3662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083480
X-RAY DIFFRACTIONf_angle_d1.0684720
X-RAY DIFFRACTIONf_dihedral_angle_d14.1751276
X-RAY DIFFRACTIONf_chiral_restr0.043480
X-RAY DIFFRACTIONf_plane_restr0.006628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0541-2.10550.27791370.26812633X-RAY DIFFRACTION92
2.1055-2.16240.26721350.24282749X-RAY DIFFRACTION94
2.1624-2.2260.25461500.21762799X-RAY DIFFRACTION96
2.226-2.29780.26351470.20152820X-RAY DIFFRACTION96
2.2978-2.37990.25811370.19962769X-RAY DIFFRACTION96
2.3799-2.47520.22631400.1962835X-RAY DIFFRACTION97
2.4752-2.58780.29121420.19392845X-RAY DIFFRACTION98
2.5878-2.72420.23331470.18732861X-RAY DIFFRACTION99
2.7242-2.89470.2581450.19082909X-RAY DIFFRACTION99
2.8947-3.11810.19931460.18022884X-RAY DIFFRACTION99
3.1181-3.43150.21831400.17192898X-RAY DIFFRACTION99
3.4315-3.92730.18691500.14882921X-RAY DIFFRACTION99
3.9273-4.94510.13551440.12152851X-RAY DIFFRACTION97
4.9451-32.06190.16541510.13462932X-RAY DIFFRACTION98

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