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- PDB-7yab: Solution structure of zinc finger domain 1 of human ZFAND1 -

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Basic information

Entry
Database: PDB / ID: 7yab
TitleSolution structure of zinc finger domain 1 of human ZFAND1
ComponentsAN1-type zinc finger protein 1
KeywordsMETAL BINDING PROTEIN / An1-type zinc finger protein / ZFAND1 / proteasome / stress granule / proteostasis
Function / homology
Function and homology information


positive regulation of intracellular protein transport / cellular response to arsenite ion / stress granule disassembly / proteasome binding / cytoplasmic stress granule / zinc ion binding / cytoplasm
Similarity search - Function
ZFAND1-like ubiquitin-like domain / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger
Similarity search - Domain/homology
AN1-type zinc finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsFang, P.J. / Lai, C.H. / Ko, K.T. / Chang, C.F. / Hsu, S.T.D.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-001-050-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2811-M-001-583- Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2311-B-001-013-MY3 Taiwan
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural insight into the ZFAND1-p97 interaction involved in stress granule clearance.
Authors: Lai, C.H. / Ko, K.T. / Fan, P.J. / Yu, T.A. / Chang, C.F. / Draczkowski, P. / Hsu, S.D.
History
DepositionJun 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Revision 1.2Nov 20, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AN1-type zinc finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1013
Polymers4,9711
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide AN1-type zinc finger protein 1 / Zinc finger AN1-type-containing protein 1


Mass: 4970.525 Da / Num. of mol.: 1 / Fragment: AN1-type 1,zinc finger domain 1 (ZF1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZFAND1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TCF1
#2: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY
171isotropic13D CCH-TOCSY
181isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.34 mM [U-13C; U-15N] ZFAND1 zinc finger domain 1 (ZF1), 90% H2O/10% D2O
Details: 50 mM Sodium phosphate (pH 6.5) at 300K / Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.34 mM / Component: ZFAND1 zinc finger domain 1 (ZF1) / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 mM / Label: condition1 / pH: 6.5 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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