[English] 日本語
Yorodumi
- PDB-1m3v: FLIN4: Fusion of the LIM binding domain of Ldb1 and the N-termina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m3v
TitleFLIN4: Fusion of the LIM binding domain of Ldb1 and the N-terminal LIM domain of LMO4
Componentsfusion of the LIM interacting domain of ldb1 and the N-terminal LIM domain of LMO4
KeywordsMETAL BINDING PROTEIN / LIM domain / fusion protein / LMO proteins / Ldb1
Function / homology
Function and homology information


regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / cerebellar Purkinje cell differentiation / positive regulation of hemoglobin biosynthetic process / primitive erythrocyte differentiation / head 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 ...regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / cerebellar Purkinje cell differentiation / positive regulation of hemoglobin biosynthetic process / primitive erythrocyte differentiation / head 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 / anterior/posterior axis specification / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / hair follicle development / positive regulation of cell adhesion / regulation of cell migration / cerebellum development / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcription regulator complex / Wnt signaling pathway / neuron differentiation / transcription regulator complex / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / negative regulation of DNA-templated transcription / chromatin binding / chromatin / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / 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. / Cysteine Rich Protein / Cysteine Rich Protein / Ribbon / Mainly Beta
Similarity search - Domain/homology
LIM domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsDeane, J.E. / Mackay, J.P. / Kwan, A.H.Y. / Sum, E.Y. / Visvader, J.E. / Matthews, J.M.
Citation
Journal: EMBO J. / Year: 2003
Title: Structural basis for the recognition of ldb1 by the N-terminal LIM domains of LMO2 and LMO4
Authors: Deane, J.E. / Mackay, J.P. / Kwan, A.H. / Sum, E.Y. / Visvader, J.E. / Matthews, J.M.
#1: Journal: J.Biomol.NMR / Year: 2002
Title: 1H, 15N and 13C assignments of FLIN4, an intramolecular LMO4:ldb1 complex.
Authors: Deane, J.E. / Visvader, J.E. / Mackay, J.P. / Matthews, J.M.
#2: Journal: Protein Eng. / Year: 2001
Title: Design, production and characterization of FLIN2 and FLIN4: the engineering of intramolecular ldb1:LMO complexes
Authors: Deane, J.E. / Sum, E. / Mackay, J.P. / Lindeman, G.J. / Visvader, J.E. / Matthews, J.M.
History
DepositionJun 30, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.6May 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: fusion of the LIM interacting domain of ldb1 and the N-terminal LIM domain of LMO4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1483
Polymers13,0181
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein fusion of the LIM interacting domain of ldb1 and the N-terminal LIM domain of LMO4 / FLIN4


Mass: 13017.508 Da / Num. of mol.: 1 / Mutation: C37S, C49S
Source method: isolated from a genetically manipulated source
Details: Fusion protein comprises LIM domain transcription factor LMO4 (residues 16-86) via glycine-rich linker (GGSGGHMGSGG), LIM domain-binding protein 1 (residues 300-339).
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P70662
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1423D 15N-separated NOESY
153HNHA
163HNCA
173HN(CO)CA
183HN(CA)CB
193CBCA(CO)NH
1103(H)CCH-TOCSY
NMR detailsText: This structure was solved using triple resonance NMR techniques. In addition to the experiments listed above HNCO, HN(CA)CO, CC(CO)NH-TOCSY and HCC(CO)NH-TOCSY were also used for backbone and ...Text: This structure was solved using triple resonance NMR techniques. In addition to the experiments listed above HNCO, HN(CA)CO, CC(CO)NH-TOCSY and HCC(CO)NH-TOCSY were also used for backbone and side chain assignments.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM FLIN4, 20mM NaH2PO4, pH7.0, 50mM NaCl, 1mM DTT, 20uM d4-TSP95% H2O/5% D2O
20.5mM [15N]-FLIN4, 20mM NaH2PO4, pH7.0, 50mM NaCl, 1mM DTT, 20uM d4-TSP95% H2O/5% D2O
31.0mM [13C,15N]-FLIN4, 20mM NaH2PO4, pH7.0, 50mM NaCl, 1mM DTT, 20uM d4-TSP95% H2O/5% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
DYANA1.5Guntert et alrefinement
ARIA1.1.2Linge et alstructure solution
TALOS98.040.21.02Cornilescu et alstructure solution
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: Structure calculations were performed using ARIA 1.1. Final structures are based on 1804 unambiguous and 81 ambiguous NOE-derived distance restraints and 112 angle constraints from coupling ...Details: Structure calculations were performed using ARIA 1.1. Final structures are based on 1804 unambiguous and 81 ambiguous NOE-derived distance restraints and 112 angle constraints from coupling constant data and predictions from chemical shift analysis using TALOS.
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