[English] 日本語
Yorodumi
- PDB-5v5z: Structure of CYP51 from the pathogen Candida albicans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v5z
TitleStructure of CYP51 from the pathogen Candida albicans
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE/OXIDOREDUCATSE INHIBITOR / pathogen / Candida albicans / CYP51 / itraconazole / OXIDOREDUCTASE-OXIDOREDUCATSE INHIBITOR complex
Function / homology
Function and homology information


cell growth mode switching, budding to filamentous / membrane raft polarization / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / endosome organization / bile acid biosynthetic process ...cell growth mode switching, budding to filamentous / membrane raft polarization / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / endosome organization / bile acid biosynthetic process / ergosterol biosynthetic process / cholesterol homeostasis / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / membrane / plasma membrane
Similarity search - Function
Cytochrome P450, E-class, group IV / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-1YN / PROTOPORPHYRIN IX CONTAINING FE / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKeniya, M.V. / Sabherwal, M. / Wilson, R.K. / Sagatova, A.A. / Tyndall, J.D.A. / Monk, B.C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
Marsden Fund New Zealand
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2018
Title: Crystal Structures of Full-Length Lanosterol 14 alpha-Demethylases of Prominent Fungal Pathogens Candida albicans and Candida glabrata Provide Tools for Antifungal Discovery.
Authors: Keniya, M.V. / Sabherwal, M. / Wilson, R.K. / Woods, M.A. / Sagatova, A.A. / Tyndall, J.D.A. / Monk, B.C.
#1: Journal: Antimicrob. Agents Chemother. / Year: 2015
Title: Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14alpha-Demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Monk, B.C. / Tyndall, J.D.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer.
Authors: Monk, B.C. / Tomasiak, T.M. / Keniya, M.V. / Huschmann, F.U. / Tyndall, J.D. / O'Connell, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionMar 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Oct 4, 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: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1713
Polymers61,8481
Non-polymers1,3222
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.940, 92.510, 101.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Lanosterol 14-alpha demethylase / CYPLI / Cytochrome P450 51 / Cytochrome P450-14DM / Cytochrome P450-LIA1 / Sterol 14-alpha demethylase


Mass: 61848.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ERG11, CYP51, ERG16, CAALFM_C500660CA, CaO19.922 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ADDELTA / References: UniProt: P10613, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-1YN / 2-[(2R)-butan-2-yl]-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one / Itraconazole


Mass: 705.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H38Cl2N8O4 / References: sterol 14alpha-demethylase / Comment: medication, antifungal*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 0.5 M GLYCINE-NAOH, 35% PEG400,

-
Data collection

DiffractionMean temperature: 91 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.9→91.94 Å / Num. obs: 19796 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3130 / CC1/2: 0.799 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.9→44.505 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 968 4.91 %
Rwork0.219 --
obs0.2214 19726 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→44.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 92 0 4083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114221
X-RAY DIFFRACTIONf_angle_d1.2285740
X-RAY DIFFRACTIONf_dihedral_angle_d16.2562499
X-RAY DIFFRACTIONf_chiral_restr0.061597
X-RAY DIFFRACTIONf_plane_restr0.007760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.0530.39651410.35172618X-RAY DIFFRACTION100
3.053-3.24430.33191430.29822613X-RAY DIFFRACTION100
3.2443-3.49470.32741420.23362648X-RAY DIFFRACTION100
3.4947-3.84620.31281130.20422684X-RAY DIFFRACTION100
3.8462-4.40230.23331450.18922669X-RAY DIFFRACTION100
4.4023-5.54480.22061390.18642686X-RAY DIFFRACTION100
5.5448-44.50980.23931450.20982840X-RAY DIFFRACTION100

+
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