[English] 日本語
Yorodumi
- PDB-1jjj: SOLUTION STRUCTURE OF RECOMBINANT HUMAN EPIDERMAL-TYPE FATTY ACID... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jjj
TitleSOLUTION STRUCTURE OF RECOMBINANT HUMAN EPIDERMAL-TYPE FATTY ACID BINDING PROTEIN
ComponentsEPIDERMAL-TYPE FATTY ACID BINDING PROTEIN (E-FABP)
KeywordsLIPID BINDING PROTEIN / BETA BARREL / FATTY ACID CARRIER / HOLO FORM / NMR SPECTROSCOPY / 15N ISOTOPE ENRICHMENT
Function / homology
Function and homology information


regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / retrograde trans-synaptic signaling by endocannabinoid / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / retrograde trans-synaptic signaling by endocannabinoid / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / long-chain fatty acid transmembrane transporter activity / Signaling by Retinoic Acid / Triglyceride catabolism / postsynaptic cytosol / epidermis development / postsynaptic density, intracellular component / long-chain fatty acid transport / fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / lipid binding / Neutrophil degranulation / glutamatergic synapse / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, ENERGY MINIMIZATION
AuthorsGutierrez-Gonzalez, L.H. / Ludwig, C. / Hohoff, C. / Rademacher, M. / Hanhoff, T. / Rueterjans, H. / Spener, F. / Luecke, C.
Citation
Journal: BIOCHEM.J. / Year: 2002
Title: Solution structure and backbone dynamics of human epidermal-type fatty acid-binding protein (E-FABP)
Authors: Gutierrez-Gonzalez, L.H. / Ludwig, C. / Hohoff, C. / Rademacher, M. / Hanhoff, T. / Rueterjans, H. / Spener, F. / Luecke, C.
#1: Journal: Biochemistry / Year: 1999
Title: Expression, Purification, and Crystal Structure Determination of Recombinant Human Epidermal-Type Fatty Acid Binding Protein
Authors: Hohoff, C. / Boerchers, T. / Ruestow, B. / Spener, F. / Van Tilbeurgh, H.
History
DepositionJul 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPIDERMAL-TYPE FATTY ACID BINDING PROTEIN (E-FABP)


Theoretical massNumber of molelcules
Total (without water)15,1851
Polymers15,1851
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 / 300target function
Representative

-
Components

#1: Protein EPIDERMAL-TYPE FATTY ACID BINDING PROTEIN (E-FABP)


Mass: 15185.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01469
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1312D 15N-HSQC
1412D 15N-HTQC
1513D 15N-TOCSY-HSQC
1613D 15N-NOESY-HSQC

-
Sample preparation

DetailsContents: 1.5-2 MM E-FABP PHOSPHATE BUFFER; 0.05% SODIUM AZIDE
Sample conditionsIonic strength: 20 mM POTASSIUM PHOSPHATE / pH: 5.6 / Pressure: AMBIENT / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Discover97MSIrefinement
XwinNMR1.3structure solution
AURELIA2.5.9structure solution
DYANA1.5structure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, ENERGY MINIMIZATION
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2008 NOE-DERIVED DISTANCE RESTRAINTS
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / 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