[English] 日本語
Yorodumi
- PDB-8jq1: Solution NMR Structure of zinc fingers 1-2 (fragment 257-320) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jq1
TitleSolution NMR Structure of zinc fingers 1-2 (fragment 257-320) from human insulinoma-associated protein 1(INSM1)
ComponentsInsulinoma-associated protein 1
KeywordsDNA BINDING PROTEIN / Zinc fingers / Long flexible linker / C3H/C2H2-type Zinc-fingers
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 / regulation of protein-containing complex assembly / transcription repressor complex / cyclin binding / negative regulation of protein phosphorylation / positive regulation of cell differentiation / neuron differentiation / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell migration / regulation of gene expression / cell population proliferation / molecular adaptor activity / regulation of cell cycle / positive regulation of cell migration / cell cycle / 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 / nucleoplasm / nucleus / metal ion binding
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: To Be Published
Title: Solution NMR Structure of zinc fingers 1-2 (fragment 257-320) from human insulinoma-associated protein 1(INSM1)
Authors: He, X.L. / Yang, Y.H.
History
DepositionJun 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100all calculated structures submitted
RepresentativeModel #1lowest energy

-
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: Homo sapiens (human) / 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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-13C HSQC
121isotropic22D 1H-15N HSQC
131isotropic23D 1H-15N NOESY
141isotropic23D 1H-13C NOESY aliphatic
151isotropic23D 1H-13C NOESY aromatic
161isotropic23D HN(CA)CB
171isotropic23D HNCO
181isotropic23D HBHA(CO)NH
191isotropic23D CBCA(CO)NH

-
Sample preparation

DetailsType: solution
Contents: 2.0 % [U-13C; U-15N] ribonuclease, 90% H2O/10% D2O
Label: 13C-15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.0 % / Component: ribonuclease / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 Pa / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE8502

-
Processing

NMR software
NameDeveloperClassification
FMCGUILemak A., Sunnergagen M., Gutmanas A., Doherty R., Wu B.refinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more