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- PDB-6w9n: Solution structure of the FYVE domain of ALFY -

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Basic information

Entry
Database: PDB / ID: 6w9n
TitleSolution structure of the FYVE domain of ALFY
ComponentsWD repeat and FYVE domain-containing protein 3
KeywordsLIPID BINDING PROTEIN / FYVE domain / phosphoinositide binding / zinc binding
Function / homology
Function and homology information


1-phosphatidylinositol binding / aggrephagy / autophagosome membrane / inclusion body / autophagosome / PML body / nuclear envelope / nuclear membrane / perikaryon / axon ...1-phosphatidylinositol binding / aggrephagy / autophagosome membrane / inclusion body / autophagosome / PML body / nuclear envelope / nuclear membrane / perikaryon / axon / nucleolus / nucleoplasm / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / BEACH domain / PH-BEACH domain / BEACH domain superfamily / Beige/BEACH domain / PH domain associated with Beige/BEACH / BEACH domain profile. / BEACH-type PH domain profile. / Beige/BEACH domain / FYVE zinc finger ...: / BEACH domain / PH-BEACH domain / BEACH domain superfamily / Beige/BEACH domain / PH domain associated with Beige/BEACH / BEACH domain profile. / BEACH-type PH domain profile. / Beige/BEACH domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Zinc finger, FYVE/PHD-type / Armadillo-like helical / Concanavalin A-like lectin/glucanase domain superfamily / PH-like domain superfamily / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat and FYVE domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / na
AuthorsReinhart, E.F. / Pellegrini, M. / Ragusa, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P35GM128662 United States
CitationJournal: Traffic / Year: 2021
Title: A highly conserved glutamic acid in ALFY inhibits membrane binding to aid in aggregate clearance.
Authors: Reinhart, E.F. / Litt, N.A. / Katzenell, S. / Pellegrini, M. / Yamamoto, A. / Ragusa, M.J.
History
DepositionMar 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat and FYVE domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0713
Polymers8,9401
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein WD repeat and FYVE domain-containing protein 3 / Autophagy-linked FYVE protein / Alfy


Mass: 8940.072 Da / Num. of mol.: 1 / Fragment: FYVE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDFY3, KIAA0993 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IZQ1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic12D 1H-15N HSQC
124isotropic13D 1H-15N NOESY
232isotropic13D CBCA(CO)NH
272isotropic13D HN(CO)CA
282isotropic13D HNCA
292isotropic13D HN(CA)CB
2102isotropic13D HNCO
2162isotropic13D HN(CA)CO
2182isotropic13D HBHA(CBCACO)NH
2172isotropic13D (H)C(CCO)NH
2192isotropic13D H(CCCO)NH
2132isotropic13D 1H-13C NOESY aliphatic
2122isotropic12D 1H-13C HSQC aliphatic
2142isotropic13D (H)CCH-COSY
2112isotropic13D (H)CCH-TOCSY
345isotropic12D 1H-1H NOESY
355isotropic12D 1H-1H COSY
365isotropic12D 1H-1H TOCSY
2202isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution4583 uM [U-99% 15N] The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 99% H2O/1% D2O15N_sample99% H2O/1% D2O
solution2768 uM [U-99% 13C; U-99% 15N] The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 95% H2O/5% D2O15N13C_sample95% H2O/5% D2O
solution5589 uM The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
583 uMThe FYVE domain of ALFY[U-99% 15N]4
20 mMsodium phosphatenatural abundance4
150 mMsodium chloridenatural abundance4
0.2 mMTCEPnatural abundance4
768 uMThe FYVE domain of ALFY[U-99% 13C; U-99% 15N]2
20 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
0.2 mMTCEPnatural abundance2
589 uMThe FYVE domain of ALFYnatural abundance5
20 mMsodium phosphatenatural abundance5
150 mMsodium chloridenatural abundance5
0.2 mMTCEPnatural abundance5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1150 mM15N_sample6.51 atm298 K
2150 mM15N13C_sample6.51 atm298 K
3150 mMD2O_sample6.51 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: na / Software ordinal: 3
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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