[English] 日本語
Yorodumi
- PDB-6wf2: Crystal structure of mouse SCD1 with a diiron center -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wf2
TitleCrystal structure of mouse SCD1 with a diiron center
ComponentsAcyl-CoA desaturase 1
KeywordsOXIDOREDUCTASE / SCD1 / membrane enzyme / diiron center / electron transfer / double bond formation / MEMBRANE PROTEIN
Function / homology
Function and homology information


stearoyl-CoA 9-desaturase / palmitoyl-CoA 9-desaturase activity / Fatty acyl-CoA biosynthesis / stearoyl-CoA 9-desaturase activity / tarsal gland development / unsaturated fatty acid biosynthetic process / sebaceous gland development / monounsaturated fatty acid biosynthetic process / sterol homeostasis / response to fatty acid ...stearoyl-CoA 9-desaturase / palmitoyl-CoA 9-desaturase activity / Fatty acyl-CoA biosynthesis / stearoyl-CoA 9-desaturase activity / tarsal gland development / unsaturated fatty acid biosynthetic process / sebaceous gland development / monounsaturated fatty acid biosynthetic process / sterol homeostasis / response to fatty acid / lipid biosynthetic process / triglyceride metabolic process / lipid homeostasis / white fat cell differentiation / brown fat cell differentiation / cholesterol homeostasis / response to bacterium / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / oxidoreductase activity / defense response to Gram-positive bacterium / iron ion binding / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / membrane / metal ion binding
Similarity search - Function
Fatty acid desaturase type 1, conserved site / Acyl-CoA desaturase / Fatty acid desaturases family 1 signature. / Fatty acid desaturase domain / Fatty acid desaturase
Similarity search - Domain/homology
Chem-3VV / : / Acyl-CoA desaturase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsShen, J. / Zhou, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122784 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086392 United States
Cancer Prevention and Research Institute of Texas (CPRIT)R1223 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase.
Authors: Shen, J. / Wu, G. / Tsai, A.L. / Zhou, M.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyl-CoA desaturase 1
B: Acyl-CoA desaturase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4298
Polymers79,1412
Non-polymers2,2876
Water00
1
A: Acyl-CoA desaturase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7144
Polymers39,5711
Non-polymers1,1443
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acyl-CoA desaturase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7144
Polymers39,5711
Non-polymers1,1443
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.647, 113.981, 140.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Acyl-CoA desaturase 1 / Delta(9)-desaturase 1 / Delta-9 desaturase 1 / Fatty acid desaturase 1 / Stearoyl-CoA desaturase 1


Mass: 39570.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Scd1 / Production host: Homo sapiens (human) / References: UniProt: P13516, stearoyl-CoA 9-desaturase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3VV / S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name) / oleoyl-CoA


Mass: 1031.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H68N7O17P3S
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.38 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris, pH7.8-8.2, PEG400 37-42%, 20 mM Mg(Ace)2, and 50 mM MgCl2
PH range: 7.8 - 8.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.51→88.63 Å / Num. obs: 16020 / % possible obs: 99.73 % / Redundancy: 13.4 % / Biso Wilson estimate: 75.72 Å2 / CC1/2: 0.997 / Net I/σ(I): 6.5
Reflection shellResolution: 3.51→3.636 Å / Num. unique obs: 1582 / CC1/2: 0.619

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YMK

4ymk


Resolution: 3.51→88.63 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.79
RfactorNum. reflection% reflection
Rfree0.2766 1598 10 %
Rwork0.2187 --
obs0.2244 15985 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.51→88.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 138 0 5360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045530
X-RAY DIFFRACTIONf_angle_d0.687503
X-RAY DIFFRACTIONf_dihedral_angle_d8.696868
X-RAY DIFFRACTIONf_chiral_restr0.04766
X-RAY DIFFRACTIONf_plane_restr0.004924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.51-3.620.36971440.28221288X-RAY DIFFRACTION100
3.62-3.750.28931390.25411268X-RAY DIFFRACTION100
3.75-3.90.28151450.26061293X-RAY DIFFRACTION100
3.9-4.080.31151430.22631297X-RAY DIFFRACTION100
4.08-4.30.28481440.22171297X-RAY DIFFRACTION100
4.3-4.570.35791430.26411286X-RAY DIFFRACTION99
4.57-4.920.26261420.21051291X-RAY DIFFRACTION100
4.92-5.410.251450.19581306X-RAY DIFFRACTION100
5.41-6.20.27551470.20461317X-RAY DIFFRACTION100
6.2-7.80.2371480.19041336X-RAY DIFFRACTION100
7.81-88.630.22131580.18391408X-RAY DIFFRACTION99

+
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