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- PDB-6nty: 2.1 A resolution structure of the Musashi-2 (Msi2) RNA recognitio... -

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Basic information

Entry
Database: PDB / ID: 6nty
Title2.1 A resolution structure of the Musashi-2 (Msi2) RNA recognition motif 1 (RRM1) domain
ComponentsRNA-binding protein Musashi homolog 2
KeywordsRNA BINDING PROTEIN / RNA binding / RRM1 domain / Musashi-2
Function / homology
Function and homology information


stem cell development / poly(U) RNA binding / RHOBTB2 GTPase cycle / central nervous system development / regulation of translation / intracellular membrane-bounded organelle / mRNA binding / RNA binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
RNA-binding protein Musashi homologue, RNA recognition motif 2 / 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
PHOSPHATE ION / RNA-binding protein Musashi homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Lan, L. / Xiaoqing, W. / Cooper, A. / Gao, F.P. / Xu, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA191785 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: Proteins / Year: 2020
Title: Crystal and solution structures of human oncoprotein Musashi-2 N-terminal RNA recognition motif 1.
Authors: Lan, L. / Xing, M. / Kashipathy, M. / Douglas, J. / Gao, P. / Battaile, K. / Hanzlik, R. / Lovell, S. / Xu, L.
History
DepositionJan 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 6, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein Musashi homolog 2
B: RNA-binding protein Musashi homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3733
Polymers21,2782
Non-polymers951
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, This protein construct is dimeric in solution but is a functional monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-21 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.795, 57.370, 41.315
Angle α, β, γ (deg.)90.000, 101.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA-binding protein Musashi homolog 2 / Musashi-2


Mass: 10639.242 Da / Num. of mol.: 2
Fragment: RNA recognition motif 1 (RRM1) Domain (UNP residues 21-111)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSI2 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96DH6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.6 Å3/Da / Density % sol: 25 % / Description: needle cluster
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.4 M ammonium phosphate dibasic, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40.51 Å / Num. obs: 8271 / % possible obs: 99.4 % / Redundancy: 3.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.112 / Net I/σ(I): 6.5 / Num. measured all: 27686 / Scaling rejects: 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.1-2.163.20.8016750.559199.3
8.91-40.513.20.0731210.996198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.15 Å32.57 Å
Translation2.15 Å32.57 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.3data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5C8U

5c8u


Resolution: 2.1→33.092 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 33.68
RfactorNum. reflection% reflection
Rfree0.2797 440 5.33 %
Rwork0.2054 --
obs0.2096 8254 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.59 Å2 / Biso mean: 36.8584 Å2 / Biso min: 18.76 Å2
Refinement stepCycle: final / Resolution: 2.1→33.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 5 37 1243
Biso mean--60.59 37.5 -
Num. residues----162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.40380.28451340.21952587272199
2.4038-3.02820.31891520.25225962748100
3.0282-33.09620.2641540.18432631278599

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