[English] 日本語
Yorodumi
- PDB-2jtn: NMR Solution Structure of a ldb1-LID:Lhx3-LIM complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jtn
TitleNMR Solution Structure of a ldb1-LID:Lhx3-LIM complex
ComponentsLIM domain-binding protein 1, LIM/homeobox protein Lhx3
KeywordsPROTEIN BINDING/TRANSCRIPTION / intramolecular (fusion) protein-protein complex / PROTEIN BINDING-TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


prolactin secreting cell differentiation / somatotropin secreting cell differentiation / medial motor column neuron differentiation / ventral spinal cord interneuron specification / spinal cord motor neuron cell fate specification / regulation of kinase activity / spinal cord association neuron differentiation / cellular component assembly / negative regulation of erythrocyte differentiation / thyroid-stimulating hormone-secreting cell differentiation ...prolactin secreting cell differentiation / somatotropin secreting cell differentiation / medial motor column neuron differentiation / ventral spinal cord interneuron specification / spinal cord motor neuron cell fate specification / regulation of kinase activity / spinal cord association neuron differentiation / cellular component assembly / negative regulation of erythrocyte differentiation / thyroid-stimulating hormone-secreting cell differentiation / cerebellar Purkinje cell differentiation / positive regulation of hemoglobin biosynthetic process / primitive erythrocyte differentiation / head development / pituitary gland development / beta-catenin-TCF complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / epithelial structure maintenance / LIM domain binding / gastrulation with mouth forming second / dorsal/ventral pattern formation / motor neuron axon guidance / anterior/posterior axis specification / regulation of focal adhesion assembly / cell leading edge / inner ear development / somatic stem cell population maintenance / hair follicle development / positive regulation of cell adhesion / cerebellum development / regulation of cell migration / transcription coregulator binding / positive regulation of transcription elongation by RNA polymerase II / placenta development / lung development / transcription coactivator binding / Wnt signaling pathway / RNA polymerase II transcription regulator complex / neuron differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / transcription cis-regulatory region binding / cell adhesion / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / : / : / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / LIM zinc-binding domain signature. / LIM domain ...: / : / : / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
LIM/homeobox protein Lhx3 / LIM domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, cartesian dynamics
AuthorsLee, C. / Nancarrow, A.L. / Mackay, J.P. / Matthews, J.M.
CitationJournal: Embo J. / Year: 2008
Title: Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes
Authors: Bhati, M. / Lee, C. / Nancarrow, A.L. / Lee, M. / Craig, V.J. / Bach, I. / Guss, J.M. / Mackay, J.P. / Matthews, J.M.
History
DepositionAug 3, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999 SEQUENCE The sequence is composed of LIM domain-binding protein 1 and LIM/homeobox protein Lhx3 ... SEQUENCE The sequence is composed of LIM domain-binding protein 1 and LIM/homeobox protein Lhx3 with a linker, GGSGGHMGSGG.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIM domain-binding protein 1, LIM/homeobox protein Lhx3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5255
Polymers20,2631
Non-polymers2624
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein LIM domain-binding protein 1, LIM/homeobox protein Lhx3 / Nuclear LIM interactor / LIM homeobox protein 3 / Homeobox protein LIM-3 / Homeobox protein P-LIM


Mass: 20263.014 Da / Num. of mol.: 1
Fragment: Fusion of Ldb1 residues 295-340 and Lhx3 LIM zinc-binding domains 1 and 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ldb1, Nli, Lhx3, Lim-3, Lim3, Plim / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P70662, UniProt: P50481
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HNCA
131HN(CA)CO
141HN(CO)CA
151(H)CCH-TOCSY
161(H)CCH-COSY
171HNHA
18115N-HSQC
19113C-CT-HSQC
11022D-homonuclear TOCSY
11122D-homonuclear NOESY
1121HN(CA)CB
1131CBCA(CO)NH
11453D 15N-separated NOESY
11553D 13C-separated NOESY
116415N-HSQC (optimised for histidine sidechain J-coupling)
117313C-CT-HSQC (10% 13C sample)

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM [U-99% 13C; U-99% 15N] FLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains, 3 mM ZINC ION, 15-30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 40 mM sodium chloride, 10 % [U-99% 2H] D2O, 90 % H2O10 % [U-99% 2H] D2O, 90 % H2O
21.2 mM FLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains, 4.8 mM ZINC ION, 15-30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 40 mM sodium chloride, 90 % H2O, 10 % [U-99% 2H] D2O90 % H2O, 10 % [U-99% 2H] D2O
30.6 mM [U-10% 13C; U-99% 15N] FLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains, 2.4 mM ZINC ION, 15-30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 40 mM sodium chloride, 90 % [U-99% 2H] D2O, 10 % H2O90 % [U-99% 2H] D2O, 10 % H2O
40.3 mM [U-99% 15N] FLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains, 1.2 mM ZINC ION, 15-30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 40 mM sodium chloride, 90 % [U-99% 2H] D2O, 10 % H2O90 % [U-99% 2H] D2O, 10 % H2O
50.6 mM [U-99% 13C; U-99% 15N] FLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains, 2.4 mM ZINC ION, 15-30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 40 mM sodium chloride, 99 % [U-99% 2H] D2O, 1 % H2O99 % [U-99% 2H] D2O, 1 % H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMFLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains[U-99% 13C; U-99% 15N]1
3 mMZINC ION1
15 uMDSS1
1 mMDTT1
20 mMsodium phosphate1
40 mMsodium chloride1
10 %D2O[U-99% 2H]1
90 %H2O1
1.2 mMFLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains2
4.8 mMZINC ION2
15 uMDSS2
1 mMDTT2
20 mMsodium phosphate2
40 mMsodium chloride2
90 %H2O2
10 %D2O[U-99% 2H]2
0.6 mMFLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains[U-10% 13C; U-99% 15N]3
2.4 mMZINC ION3
15 uMDSS3
1 mMDTT3
20 mMsodium phosphate3
40 mMsodium chloride3
90 %D2O[U-99% 2H]3
10 %H2O3
0.3 mMFLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains[U-99% 15N]4
1.2 mMZINC ION4
15 uMDSS4
1 mMDTT4
20 mMsodium phosphate4
40 mMsodium chloride4
90 %D2O[U-99% 2H]4
10 %H2O4
0.6 mMFLIX3 - Fusion of ldb1-LID and Lhx3 LIM domains[U-99% 13C; U-99% 15N]5
2.4 mMZINC ION5
15 uMDSS5
1 mMDTT5
20 mMsodium phosphate5
40 mMsodium chloride5
99 %D2O[U-99% 2H]5
1 %H2O5
Sample conditionsIonic strength: 20 mM phosphate, 40 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE8002
Bruker DRXBrukerDRX6003

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA1.2Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TopSpin1.2Bruker Biospinprocessing
TopSpin1.2Bruker Biospincollection
CNSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing, torsion angle dynamics, cartesian dynamics
Software ordinal: 1
Details: Total of 2679 NOE distance restraints (9 ambiguous) and 204 TALOS dihedral restraints
NMR constraintsNOE constraints total: 2679 / NOE intraresidue total count: 1342 / NOE long range total count: 742 / NOE medium range total count: 136 / NOE sequential total count: 450 / Protein phi angle constraints total count: 102 / Protein psi angle constraints total count: 102
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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://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