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- PDB-2yqm: Solution structure of the FYVE domain in zinc finger FYVE domain-... -

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Basic information

Entry
Database: PDB / ID: 2yqm
TitleSolution structure of the FYVE domain in zinc finger FYVE domain-containing protein 12
ComponentsRUN and FYVE domain-containing protein 1
KeywordsPROTEIN TRANSPORT / FYVE domain / zinc finger FYVE domain-containing protein 12 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


endosomal vesicle fusion / early endosome to Golgi transport / small GTPase-mediated signal transduction / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / SH2 domain binding / SH3 domain binding / endocytosis / protein transport / early endosome membrane ...endosomal vesicle fusion / early endosome to Golgi transport / small GTPase-mediated signal transduction / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / SH2 domain binding / SH3 domain binding / endocytosis / protein transport / early endosome membrane / protein-macromolecule adaptor activity / endosome / nuclear speck / intracellular membrane-bounded organelle / lipid binding / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / : / : / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / FYVE zinc finger / FYVE zinc finger ...: / : / : / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, FYVE/PHD-type / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RUN and FYVE domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHe, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the FYVE domain in zinc finger FYVE domain-containing protein 12
Authors: He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUN and FYVE domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9973
Polymers9,8661
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein RUN and FYVE domain-containing protein 1 / FYVE-finger protein EIP1 / Zinc finger FYVE domain-containing protein 12 / La-binding protein 1 / ...FYVE-finger protein EIP1 / Zinc finger FYVE domain-containing protein 12 / La-binding protein 1 / Rab4-interacting protein


Mass: 9866.173 Da / Num. of mol.: 1 / Fragment: FYVE domain, UNP residues 627-708
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: RUFY1 / Plasmid: P060327-08 / References: UniProt: Q96T51
#2: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.0mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.1Guntert, P.structure solution
CYANA2.1Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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