[English] 日本語
Yorodumi
- PDB-2wr6: Structure of the complex of RBP4 with linoleic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wr6
TitleStructure of the complex of RBP4 with linoleic acid
ComponentsRETINOL-BINDING PROTEIN 4
KeywordsSIGNALING PROTEIN / SENSORY TRANSDUCTION / FATTY ACID / VISION
Function / homology
Function and homology information


Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation ...Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / eye development / heart trabecula formation / cardiac muscle tissue development / retinal binding / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / response to retinoic acid / Retinoid metabolism and transport / visual perception / gluconeogenesis / lung development / positive regulation of insulin secretion / glucose homeostasis / heart development / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(11E,13E,15Z)-OCTADECA-11,13,15-TRIENOIC ACID / Retinol-binding protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuang, H.-J. / Nanao, M. / Stout, T. / Rosen, J.
CitationJournal: To be Published
Title: Identification of a Non-Retinoid Compound and Fatty Acids as Ligands for Retinol Binding Protein 4 and Their Implications in Diabetes
Authors: Huang, H.-J. / Nanao, M. / Stout, T. / Rosen, J.
History
DepositionAug 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RETINOL-BINDING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4253
Polymers20,1121
Non-polymers3142
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.558, 102.558, 73.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein RETINOL-BINDING PROTEIN 4 / RBP4 / PLASMA RETINOL-BINDING PROTEIN / PRBP / RBP


Mass: 20111.520 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P02753
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ODT / (11E,13E,15Z)-OCTADECA-11,13,15-TRIENOIC ACID / 11-TRANS-13-TRANS-15-CIS-OCTADECATRIENOIC ACID


Mass: 278.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H30O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 40.2 % / Description: NONE
Crystal growDetails: 3.5-4.2M NACL, 0.1M HEPES, PH 7.2

-
Data collection

DiffractionMean temperature: 155 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 26657 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 27.05 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.21
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.29 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAB

1qab


Resolution: 1.8→56.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.528 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22676 1345 5 %RANDOM
Rwork0.18682 ---
obs0.18887 25312 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.875 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.15 Å20 Å2
2--0.29 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→56.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 21 239 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221491
X-RAY DIFFRACTIONr_bond_other_d0.0020.021053
X-RAY DIFFRACTIONr_angle_refined_deg2.3051.9422016
X-RAY DIFFRACTIONr_angle_other_deg1.2383.0052527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8175181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31823.5881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49215250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6381514
X-RAY DIFFRACTIONr_chiral_restr0.1530.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_nbd_refined0.2230.2279
X-RAY DIFFRACTIONr_nbd_other0.2190.21172
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2680
X-RAY DIFFRACTIONr_nbtor_other0.0930.2819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3410.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0391.51108
X-RAY DIFFRACTIONr_mcbond_other0.4511.5357
X-RAY DIFFRACTIONr_mcangle_it2.36221412
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6973729
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9744.5600
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 89 -
Rwork0.287 1885 -
obs--99.85 %

+
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