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- PDB-8s6u: Structure of MLLE domain of Pab1 in complex with PAM2 of Upa1 -

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Basic information

Entry
Database: PDB / ID: 8s6u
TitleStructure of MLLE domain of Pab1 in complex with PAM2 of Upa1
Components
  • FYVE zinc finger domain protein UPA1
  • Polyadenylate-binding protein 1
KeywordsRNA BINDING PROTEIN / RNA transport
Function / homology
Function and homology information


poly(A) binding / poly(U) RNA binding / mRNA transport / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / transferase activity / cytoskeleton / endosome / ribonucleoprotein complex ...poly(A) binding / poly(U) RNA binding / mRNA transport / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / transferase activity / cytoskeleton / endosome / ribonucleoprotein complex / metal ion binding / nucleus / cytosol
Similarity search - Function
: / Ankyrin repeats (many copies) / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. ...: / Ankyrin repeats (many copies) / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / RNA recognition motif domain, eukaryote / RNA recognition motif / Ring finger domain / Ring finger / RNA recognition motif / RNA recognition motif / Ankyrin repeats (3 copies) / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / RNA-binding domain superfamily / Zinc finger, FYVE/PHD-type / Ankyrin repeat-containing domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
FYVE zinc finger domain protein UPA1 / Polyadenylate-binding protein 1
Similarity search - Component
Biological speciesUstilago maydis (corn smut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 20, 2024Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyadenylate-binding protein 1
Q: Polyadenylate-binding protein 1
C: FYVE zinc finger domain protein UPA1
D: FYVE zinc finger domain protein UPA1


Theoretical massNumber of molelcules
Total (without water)18,2874
Polymers18,2874
Non-polymers00
Water1,53185
1
A: Polyadenylate-binding protein 1
C: FYVE zinc finger domain protein UPA1


Theoretical massNumber of molelcules
Total (without water)9,1432
Polymers9,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-11 kcal/mol
Surface area5390 Å2
MethodPISA
2
Q: Polyadenylate-binding protein 1
D: FYVE zinc finger domain protein UPA1


Theoretical massNumber of molelcules
Total (without water)9,1432
Polymers9,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-10 kcal/mol
Surface area5330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.093, 47.608, 45.452
Angle α, β, γ (deg.)90.000, 117.670, 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 Polyadenylate-binding protein 1 / PABP / RNA-binding protein RRM12


Mass: 7563.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ustilago maydis (corn smut) / Gene: PAB1, RRM12, UMAG_03494 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4P8R9
#2: Protein/peptide FYVE zinc finger domain protein UPA1 / PAM2 domain-containing protein UPA1


Mass: 1579.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Ustilago maydis (corn smut) / References: UniProt: A0A0D1E015
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Sodium HEPES pH 7.5, 25% PEG 3000 / PH range: ^

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 2→40.26 Å / Num. obs: 11069 / % possible obs: 97.13 % / Redundancy: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 27.21
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 953 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
PHENIXv17.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.26 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 --
Rwork0.2 --
obs-11055 99.9 %
Displacement parametersBiso mean: 37.91 Å2
Refinement stepCycle: LAST / Resolution: 2→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 0 85 1339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631271
X-RAY DIFFRACTIONf_angle_d0.80711718
X-RAY DIFFRACTIONf_chiral_restr0.0415203
X-RAY DIFFRACTIONf_plane_restr0.0055223
X-RAY DIFFRACTIONf_dihedral_angle_d19.8203494

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