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- PDB-6le1: Structure of RRM2 domain of DND1 protein -

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Basic information

Entry
Database: PDB / ID: 6le1
TitleStructure of RRM2 domain of DND1 protein
ComponentsDead end protein homolog 1
KeywordsTRANSCRIPTION / Domain swapped dimerisation
Function / homology
Function and homology information


negative regulation of miRNA-mediated gene silencing / 3'-UTR-mediated mRNA destabilization / mRNA stabilization / germ cell development / mRNA 3'-UTR binding / focal adhesion / mRNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Dead end protein 1, RNA recognition motif 1 / DND1, double-stranded RNA binding domain / double strand RNA binding domain from DEAD END PROTEIN 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily ...Dead end protein 1, RNA recognition motif 1 / DND1, double-stranded RNA binding domain / double strand RNA binding domain from DEAD END PROTEIN 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dead end protein homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKumari, P. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
International Centre for Genetic Engineering and Biotechnology, New Delhi and Department of Biotechnology (India) India
CitationJournal: Protein Sci. / Year: 2021
Title: Human DND1-RRM2 forms a non-canonical domain swapped dimer.
Authors: Kumari, P. / Bhavesh, N.S.
History
DepositionNov 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dead end protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8993
Polymers10,7111
Non-polymers1882
Water54030
1
A: Dead end protein homolog 1
hetero molecules

A: Dead end protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7986
Polymers21,4222
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area4330 Å2
ΔGint-55 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.615, 44.615, 111.332
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21A-330-

HOH

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Components

#1: Protein Dead end protein homolog 1 / RNA-binding motif / single-stranded-interacting protein 4


Mass: 10710.891 Da / Num. of mol.: 1 / Fragment: RRM2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DND1, RBMS4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYX4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.64 Å3/Da / Density % sol: 53 % / Description: Tetragonal bipyramids, plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M MES Monohydrate pH- 6.5, 30% PEG MME 5000, 0.2M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.3→31.6 Å / Num. obs: 4233 / % possible obs: 92.4 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Net I/σ(I): 15.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.53 / Num. unique obs: 237 / CC1/2: 0.921 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→31.57 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 0.008 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.236
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 235 5.3 %RANDOM
Rwork0.2099 ---
obs0.2116 4233 92.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.58 Å2 / Biso mean: 34.518 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.76 Å20 Å2
3----1.53 Å2
Refinement stepCycle: final / Resolution: 2.3→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms651 0 11 30 692
Biso mean--49.95 34.84 -
Num. residues----89
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 28 -
Rwork0.217 330 -
all-358 -
obs--100 %

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