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- PDB-8jpy: Solution NMR Structure of Zinc-fingers 1 and 2 (fragment 257-320)... -

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Basic information

Entry
Database: PDB / ID: 8jpy
TitleSolution NMR Structure of Zinc-fingers 1 and 2 (fragment 257-320) from human Insulinoma-associated protein 1(INSM1)
ComponentsInsulinoma-associated protein 1
KeywordsDNA BINDING PROTEIN / Transcription / Repressor
Function / homology
Function and homology information


adrenal chromaffin cell differentiation / Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells / pancreatic A cell differentiation / noradrenergic neuron development / type B pancreatic cell differentiation / transdifferentiation / norepinephrine biosynthetic process / regulation of cell cycle process / sympathetic ganglion development / type B pancreatic cell development ...adrenal chromaffin cell differentiation / Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells / pancreatic A cell differentiation / noradrenergic neuron development / type B pancreatic cell differentiation / transdifferentiation / norepinephrine biosynthetic process / regulation of cell cycle process / sympathetic ganglion development / type B pancreatic cell development / positive regulation of neural precursor cell proliferation / negative regulation of protein phosphorylation / regulation of protein-containing complex assembly / transcription repressor complex / cyclin binding / positive regulation of cell differentiation / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / neuron differentiation / cell migration / regulation of gene expression / molecular adaptor activity / cell population proliferation / regulation of cell cycle / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Insulinoma-associated protein 1/2 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Insulinoma-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHe, X.L. / Yang, Y.H.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22074152 China
National Natural Science Foundation of China (NSFC)21921004 China
National Natural Science Foundation of China (NSFC)21991080 China
National Natural Science Foundation of China (NSFC)21735007 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into a highly flexible zinc finger module unravel INSM1 function in transcription regulation.
Authors: Zhou, H. / He, X. / Xiong, Y. / Gong, Y. / Zhang, Y. / Li, S. / Hu, R. / Li, Y. / Zhang, X. / Zhou, X. / Zhu, J. / Yang, Y. / Liu, M.
History
DepositionJun 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: 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_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: Insulinoma-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4183
Polymers7,2871
Non-polymers1312
Water00
1


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

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Components

#1: Protein Insulinoma-associated protein 1 / Zinc finger protein IA-1


Mass: 7287.485 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSM1, IA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01101
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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
111isotropic22D 1H-13C HSQC
1101isotropic22D 1H-15N HSQC
131isotropic22D 1H-13C HSQC aliphatic
121isotropic13D 1H-13C NOESY aliphatic
161isotropic13D 1H-13C NOESY aromatic
141anisotropic13D HN(CA)CB
171anisotropic13D HNCO
1141anisotropic13D HNCA
1131anisotropic13D HN(CO)CA
181isotropic13D HBHA(CO)NH
191isotropic13D CBCA(CO)NH
1151isotropic23D Nnoesy

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Sample preparation

DetailsType: solution
Contents: 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 0.69 ...Contents: 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 0.69 mM [U-100% 13C; U-100% 15N] ZF3 protein, 90% H2O/10% D2O
Label: 13C-15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.69 mM / Component: ZF3 protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.5 / Pressure: ambient Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8501
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 20

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