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- PDB-8a3p: Structure of human Fy-5. -

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Basic information

Entry
Database: PDB / ID: 8a3p
TitleStructure of human Fy-5.
ComponentsGlutamine amidotransferase-like class 1 domain-containing protein 1
KeywordsRNA BINDING PROTEIN / FERRY complex / RNA binding / RNA transport / early endosome
Function / homologyglyoxalase III activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / Class I glutamine amidotransferase-like / extracellular exosome / cytoplasm / Glutamine amidotransferase-like class 1 domain-containing protein 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsSchuhmacher, J.S. / Zerial, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)112927078 Germany
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2023
Title: Structural basis of mRNA binding by the human FERRY Rab5 effector complex.
Authors: Dennis Quentin / Jan S Schuhmacher / Björn U Klink / Jeni Lauer / Tanvir R Shaikh / Pim J Huis In 't Veld / Luisa M Welp / Henning Urlaub / Marino Zerial / Stefan Raunser /
Abstract: The pentameric FERRY Rab5 effector complex is a molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of human FERRY. It reveals ...The pentameric FERRY Rab5 effector complex is a molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of human FERRY. It reveals a unique clamp-like architecture that bears no resemblance to any known structure of Rab effectors. A combination of functional and mutational studies reveals that while the Fy-2 C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils and Fy-5 concur to bind mRNA. Mutations causing truncations of Fy-2 in patients with neurological disorders impair Rab5 binding or FERRY complex assembly. Thus, Fy-2 serves as a binding hub connecting all five complex subunits and mediating the binding to mRNA and early endosomes via Rab5. Our study provides mechanistic insights into long-distance mRNA transport and demonstrates that the particular architecture of FERRY is closely linked to a previously undescribed mode of RNA binding, involving coiled-coil domains.
History
DepositionJun 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 14, 2023Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine amidotransferase-like class 1 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)23,3221
Polymers23,3221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, cryoEM structure 7ND2
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.619, 99.573, 62.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glutamine amidotransferase-like class 1 domain-containing protein 1 / Parkinson disease 7 domain-containing protein 1


Mass: 23321.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATD1, PDDC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NB37

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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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 5.0, 0.8 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.7→47.31 Å / Num. all: 8339 / Num. obs: 8339 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 62.16 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.094 / Rsym value: 0.088 / Net I/av σ(I): 5.5 / Net I/σ(I): 13.4 / Num. measured all: 79865
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.8510.10.6031.21211812050.2010.6360.6033.299.9
2.85-3.029.90.4531.61125911330.1530.4790.4534.199.9
3.02-3.239.90.2662.71051810630.0910.2810.2666.2100
3.23-3.499.70.1464.6973710020.0510.1550.14610.1100
3.49-3.829.50.101687799280.0360.1080.10114.6100
3.82-4.279.10.0866.775448320.0310.0910.08619100
4.27-4.938.50.0629.361607210.0230.0660.06224.196.1
4.93-6.049.90.0659.863076390.0220.0680.06524.3100
6.04-8.549.60.05810.449175130.020.0610.05828.1100
8.54-47.318.30.04710.125263030.0170.050.04733.699.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
XDSdata reduction
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u9c

1u9c


Resolution: 2.7→47.309 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 837 10.09 %
Rwork0.2198 7456 -
obs0.2247 8293 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.97 Å2 / Biso mean: 85.7001 Å2 / Biso min: 48.3 Å2
Refinement stepCycle: final / Resolution: 2.7→47.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 0 0 1426
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061455
X-RAY DIFFRACTIONf_angle_d0.8941980
X-RAY DIFFRACTIONf_chiral_restr0.047233
X-RAY DIFFRACTIONf_plane_restr0.006256
X-RAY DIFFRACTIONf_dihedral_angle_d17.958863
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7003-2.86940.34551330.2949122399
2.8694-3.09090.32021410.2756121499
3.0909-3.40190.27731300.23991233100
3.4019-3.8940.28881470.22781239100
3.894-4.90520.21541350.18123097
4.9052-47.3090.271510.2181317100

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