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- PDB-8s6o: Structure of MLLE3 domain of Rrm4 in complex with PAM2L2 of Upa1 -

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Basic information

Entry
Database: PDB / ID: 8s6o
TitleStructure of MLLE3 domain of Rrm4 in complex with PAM2L2 of Upa1
Components
  • PAMPL2
  • RNA-binding protein RRM4
KeywordsRNA / RNA transport Ustilago maydis
Function / homology
Function and homology information


poly(A) binding / poly(U) RNA binding / mRNA transport / mRNA 3'-UTR binding / cytoplasmic stress granule / cytoskeleton / endosome / ribonucleoprotein complex / nucleus / cytosol
Similarity search - Function
Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE 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
Similarity search - Domain/homology
RNA-binding protein RRM4
Similarity search - Component
Biological speciesUstilago maydis (corn smut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDevan, S. / Shanmugasundaram, S. / Muentjes, K. / Smits, S.H. / Altegoer, F. / Feldbruegge, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)417919780 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Deciphering the RNA-binding protein network during endosomal mRNA transport.
Authors: Devan, S.K. / Shanmugasundaram, S. / Muntjes, K. / Postma, J. / Smits, S.H.J. / Altegoer, F. / Feldbrugge, M.
History
DepositionFeb 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: RNA-binding protein RRM4
H: PAMPL2
A: RNA-binding protein RRM4
B: PAMPL2
C: RNA-binding protein RRM4
E: PAMPL2
F: RNA-binding protein RRM4
G: PAMPL2
I: RNA-binding protein RRM4
J: PAMPL2
K: RNA-binding protein RRM4
L: PAMPL2
M: RNA-binding protein RRM4
N: PAMPL2
O: RNA-binding protein RRM4
P: PAMPL2


Theoretical massNumber of molelcules
Total (without water)121,61216
Polymers121,61216
Non-polymers00
Water59433
1
D: RNA-binding protein RRM4
H: PAMPL2


Theoretical massNumber of molelcules
Total (without water)15,2012
Polymers15,2012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-5 kcal/mol
Surface area6640 Å2
MethodPISA
2
A: RNA-binding protein RRM4
B: PAMPL2


Theoretical massNumber of molelcules
Total (without water)15,2012
Polymers15,2012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area6570 Å2
MethodPISA
3
C: RNA-binding protein RRM4
E: PAMPL2


Theoretical massNumber of molelcules
Total (without water)15,2012
Polymers15,2012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area6830 Å2
MethodPISA
4
F: RNA-binding protein RRM4
G: PAMPL2


Theoretical massNumber of molelcules
Total (without water)15,2012
Polymers15,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-6 kcal/mol
Surface area6770 Å2
MethodPISA
5
I: RNA-binding protein RRM4
J: PAMPL2


Theoretical massNumber of molelcules
Total (without water)15,2012
Polymers15,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-6 kcal/mol
Surface area6640 Å2
MethodPISA
6
K: RNA-binding protein RRM4
L: PAMPL2


Theoretical massNumber of molelcules
Total (without water)15,2012
Polymers15,2012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area6670 Å2
MethodPISA
7
M: RNA-binding protein RRM4
N: PAMPL2


Theoretical massNumber of molelcules
Total (without water)15,2012
Polymers15,2012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-6 kcal/mol
Surface area6700 Å2
MethodPISA
8
O: RNA-binding protein RRM4
P: PAMPL2


Theoretical massNumber of molelcules
Total (without water)15,2012
Polymers15,2012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-6 kcal/mol
Surface area6680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.881, 74.633, 168.511
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
RNA-binding protein RRM4


Mass: 14418.616 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ustilago maydis (corn smut) / Gene: RRM4, UMAG_10836 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1DWZ5
#2: Protein/peptide
PAMPL2


Mass: 782.837 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Ustilago maydis (corn smut)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: HEPES pH 7.5, 25% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→56.17 Å / Num. obs: 39386 / % possible obs: 97.17 % / Redundancy: 3 % / CC1/2: 0.997 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 3912 / CC1/2: 0.581

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→56.17 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.276 --
Rwork0.2399 --
obs-39281 98 %
Displacement parametersBiso mean: 65.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→56.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7424 0 0 33 7457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02487544
X-RAY DIFFRACTIONf_angle_d2.341110176
X-RAY DIFFRACTIONf_chiral_restr0.08581192
X-RAY DIFFRACTIONf_plane_restr0.01311304
X-RAY DIFFRACTIONf_dihedral_angle_d19.0052832

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