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- PDB-8a3o: Structure of human Fy-4 -

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Basic information

Entry
Database: PDB / ID: 8a3o
TitleStructure of human Fy-4
ComponentsQuinone oxidoreductase-like protein 1
KeywordsSTRUCTURAL PROTEIN / FERRY complex / mRNA transport / Early endosome
Function / homology
Function and homology information


quinone metabolic process / NADPH:quinone reductase activity / Oxidoreductases / NADP binding / early endosome / cytosol
Similarity search - Function
Quinone oxidoreductase-like protein 1 / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Quinone oxidoreductase-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 1.1Jun 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 1.2Feb 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

Downloads & links

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Assembly

Deposited unit
A: Quinone oxidoreductase-like protein 1
B: Quinone oxidoreductase-like protein 1


Theoretical massNumber of molelcules
Total (without water)79,3232
Polymers79,3232
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Cryo-EM structure of the human FERRY complex (7ND2)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.421, 45.273, 93.956
Angle α, β, γ (deg.)90.000, 109.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Quinone oxidoreductase-like protein 1 / Protein 4P11 / Quinone oxidoreductase homolog 1 / QOH-1 / Zeta-crystallin homolog


Mass: 39661.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYZL1, 4P11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95825, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 5 % (w/v) PEG 3000 and 30 % (w/v) PEG 200

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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: 2.9→45.273 Å / Num. all: 15389 / Num. obs: 15389 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 75.76 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.064 / Rsym value: 0.056 / Net I/av σ(I): 3.6 / Net I/σ(I): 17.9 / Num. measured all: 74872
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
2.9-3.0650.2093.61131722470.1030.2340.2096.299.7
3.06-3.2450.1335.41050221140.0660.1490.1339.199.6
3.24-3.474.90.0957.3977719780.0470.1070.09512.599.3
3.47-3.744.80.0719880918330.0360.080.07116.699.2
3.74-4.14.50.069.6758016800.0310.0680.062098.2
4.1-4.594.50.04911.2670115010.0250.0550.04924.596.3
4.59-5.295.20.04612711613760.0230.0520.04628.4100
5.29-6.485.10.04711.9606811970.0230.0530.04726.9100
6.48-9.1750.0473.745939230.0250.0540.04730.5100
9.17-45.2734.50.0526.624095400.0280.0590.05231.499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.21data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yb5

1yb5


Resolution: 2.9→44.165 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 31.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 1537 10 %
Rwork0.2369 13834 -
obs0.2418 15371 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.33 Å2 / Biso mean: 82.0474 Å2 / Biso min: 22.84 Å2
Refinement stepCycle: final / Resolution: 2.9→44.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4933 0 0 21 4954
Biso mean---30 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045029
X-RAY DIFFRACTIONf_angle_d0.7096813
X-RAY DIFFRACTIONf_chiral_restr0.048789
X-RAY DIFFRACTIONf_plane_restr0.005876
X-RAY DIFFRACTIONf_dihedral_angle_d21.2623034
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9001-2.99370.36151400.299126299
2.9937-3.10060.37081360.2889122799
3.1006-3.22470.30881420.279127299
3.2247-3.37140.3991370.278122999
3.3714-3.54910.31741370.2705123599
3.5491-3.77140.29911410.2498127599
3.7714-4.06240.27771370.2368123698
4.0624-4.47080.26041340.2231120395
4.4708-5.1170.2651420.20351275100
5.117-6.44360.2861440.24781289100
6.4436-44.1650.24581470.2121133199

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