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- PDB-8xe8: Solution structure of ubiquitin-like domain (UBL) of human ZFAND1 -

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Basic information

Entry
Database: PDB / ID: 8xe8
TitleSolution structure of ubiquitin-like domain (UBL) of human ZFAND1
ComponentsAN1-type zinc finger protein 1
KeywordsPROTEIN BINDING / ubiquitin-like domain / UBL / human 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 / na
AuthorsLai, C.H. / Ko, K.T. / Fan, P.J. / Yu, T.A. / 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)110-2113-M-001-050-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
DepositionDec 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AN1-type zinc finger protein 1


Theoretical massNumber of molelcules
Total (without water)15,6801
Polymers15,6801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 15679.980 Da / Num. of mol.: 1
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
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 HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
191isotropic13D HBHA(CO)NH
181isotropic13D CCH-TOCSY
171isotropic13D (H)CCH-TOCSY
161isotropic13D C(CO)NH
1181isotropic13D 1H-13C NOESY aromatic
1121isotropic13D H(CCO)NH
1111isotropic13D 1H-13C NOESY aromatic
1101isotropic13D 13C/15N simultaneous NOESY
2151isotropic13D HN(CA)CB
2141isotropic13D CBCA(CO)NH
2131isotropic13D 13C/15N simultaneous NOESY
2171isotropic13D 13C/15N simultaneous NOESY
2161isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-13C; U-15N] UBL prtoein, 90% H2O/10% D2O
Details: 50 mM Tris-HCl (pH 7.1), 150 mM NaCl, 0.5 mM TCEP / Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.4 mM / Component: UBL prtoein / Isotopic labeling: [U-13C; U-15N]
Sample conditions

Ionic strength: 150 mM / Ionic strength err: 0.2 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 300 K

Conditions-IDDetailsLabelpH
150 mM Tris-HCl (pH 7.1), 150 mM NaCl, 0.5 mM TCEPcondiction_17.1
250 mM Tris-HCl (pH 6.5), 150 mM NaCl, 0.5 mM TCEPcondiction_26.5

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYWoonghee Leepeak picking
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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