[English] 日本語
Yorodumi
- PDB-2lfh: Solution NMR Structure of the Helix-loop-Helix Domain of Human ID... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lfh
TitleSolution NMR Structure of the Helix-loop-Helix Domain of Human ID3 Protein, Northeast Structural Genomics Consortium Target HR3111A
ComponentsDNA-binding protein inhibitor ID-3
KeywordsDNA binding protein inhibitor / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative / Helix-loop-helix
Function / homology
Function and homology information


cellular response to leptomycin B / leptomycin B binding / : / notochord development / multicellular organism development / negative regulation of myoblast differentiation / NGF-stimulated transcription / metanephros development / transcription regulator inhibitor activity / odontogenesis ...cellular response to leptomycin B / leptomycin B binding / : / notochord development / multicellular organism development / negative regulation of myoblast differentiation / NGF-stimulated transcription / metanephros development / transcription regulator inhibitor activity / odontogenesis / muscle organ development / regulation of DNA replication / transcription factor binding / negative regulation of osteoblast differentiation / epithelial cell differentiation / central nervous system development / circadian regulation of gene expression / neuron differentiation / negative regulation of DNA-binding transcription factor activity / response to wounding / heart development / cell differentiation / protein dimerization activity / regulation of cell cycle / positive regulation of apoptotic process / protein domain specific binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
DNA-binding protein inhibitor / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA-binding protein inhibitor ID-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Wang, D. / Kohan, E. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the Helix-loop-Helix Domain of Human ID3 Protein, Northeast Structural Genomics Consortium Target HR3111A
Authors: Eletsky, A. / Wang, D. / Kohan, E. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding protein inhibitor ID-3
B: DNA-binding protein inhibitor ID-3


Theoretical massNumber of molelcules
Total (without water)15,2792
Polymers15,2792
Non-polymers00
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein DNA-binding protein inhibitor ID-3 / Class B basic helix-loop-helix protein 25 / bHLHb25 / Helix-loop-helix protein HEIR-1 / ID-like ...Class B basic helix-loop-helix protein 25 / bHLHb25 / Helix-loop-helix protein HEIR-1 / ID-like protein inhibitor HLH 1R21 / Inhibitor of DNA binding 3


Mass: 7639.716 Da / Num. of mol.: 2 / Fragment: Helix-loop-helix motif domain residues 27-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 1R21, BHLHB25, HEIR1, ID3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q02535

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C CT-HSQC aliphatic
1313D HNCO
141(4,3)D GFT CABCA(CO)NHN
151(4,3)D GFT HNNCABCA
1612D 1H-13C HSQC aromatic
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HN(CA)CO
1913D (H)CCH-COSY aliphatic
11013D (H)CCH-TOCSY aliphatic
11113D HBHA(CO)NH
11212D 1H-15N LR-HSQC for histidines
11311D 15N T1
11411D 15N T2
11522D 1H-13C CT-HSQC methyl

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] HR3111A, 100 mM sodium chloride, 10 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [5% 13C; U-100% 15N] HR3111A, 100 mM sodium chloride, 10 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMHR3111A-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
10 mMDTT-31
10 mMTRIS-41
0.02 %sodium azide-51
0.5 mMHR3111A-6[5% 13C; U-100% 15N]2
100 mMsodium chloride-72
10 mMDTT-82
10 mMTRIS-92
0.02 %sodium azide-102
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
XEASY1.3.13Bartels et al.data analysis
PROSA6.4Guntertprocessing
VnmrJ2.2DVariancollection
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed using CYANA with NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the lowest target ...Details: Structure determination was performed using CYANA with NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field
NMR constraintsNOE constraints total: 1400 / NOE intraresidue total count: 524 / NOE long range total count: 238 / NOE medium range total count: 278 / NOE sequential total count: 360 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 89 / Protein psi angle constraints total count: 89
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / 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