[English] 日本語
Yorodumi
- PDB-7vpr: Crystal structure of the ligand-binding domain of C. glabrata Upc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vpr
TitleCrystal structure of the ligand-binding domain of C. glabrata Upc2 in complex with ergosterol
ComponentsSterol uptake control protein 2 (Upc2)
KeywordsTRANSCRIPTION / ergosterol / transcription factor / ligand-binding / zinc finger
Function / homology
Function and homology information


positive regulation of sterol import / positive regulation of ergosterol biosynthetic process / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / ergosterol biosynthetic process / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / zinc ion binding / membrane
Similarity search - Function
Fungal transcription factor / : / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain
Similarity search - Domain/homology
ERGOSTEROL / Candida glabrata strain CBS138 chromosome C complete sequence
Similarity search - Component
Biological species[Candida] glabrata CBS 138 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsTan, L. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1085530 Korea, Republic Of
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Structural basis for activation of fungal sterol receptor Upc2 and azole resistance.
Authors: Tan, L. / Chen, L. / Yang, H. / Jin, B. / Kim, G. / Im, Y.J.
History
DepositionOct 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sterol uptake control protein 2 (Upc2)
B: Sterol uptake control protein 2 (Upc2)
C: Sterol uptake control protein 2 (Upc2)
D: Sterol uptake control protein 2 (Upc2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5558
Polymers136,9694
Non-polymers1,5874
Water1,15364
1
A: Sterol uptake control protein 2 (Upc2)
B: Sterol uptake control protein 2 (Upc2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2784
Polymers68,4842
Non-polymers7932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-11 kcal/mol
Surface area24840 Å2
MethodPISA
2
C: Sterol uptake control protein 2 (Upc2)
D: Sterol uptake control protein 2 (Upc2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2784
Polymers68,4842
Non-polymers7932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-11 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.423, 105.626, 98.872
Angle α, β, γ (deg.)90.000, 93.282, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Sterol uptake control protein 2 (Upc2)


Mass: 34242.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] glabrata CBS 138 (fungus) / Strain: CBS 138 / Gene: UPC2A / Plasmid: pHIS2-Thr
Details (production host): N-terminal thrombin-cleavable hexa-histidine tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6FX18
#2: Chemical
ChemComp-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H44O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M Na-Acetate pH 4.0, 10% PEG 4000, 0.1 M Sodium Citrate

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 34631 / % possible obs: 97.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 44.46 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.391 / Num. unique obs: 1404 / % possible all: 79.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N9N

4n9n


Resolution: 2.59→27.6 Å / SU ML: 0.3441 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2498 1722 4.98 %
Rwork0.2305 32855 -
obs0.2315 34577 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.66 Å2
Refinement stepCycle: LAST / Resolution: 2.59→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8658 0 116 64 8838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01988992
X-RAY DIFFRACTIONf_angle_d1.914112275
X-RAY DIFFRACTIONf_chiral_restr0.18981449
X-RAY DIFFRACTIONf_plane_restr0.01041505
X-RAY DIFFRACTIONf_dihedral_angle_d25.32533259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.670.31991200.31232434X-RAY DIFFRACTION87.47
2.67-2.760.35581310.29492760X-RAY DIFFRACTION98.94
2.76-2.850.32281490.28342767X-RAY DIFFRACTION100
2.85-2.970.33641400.29052769X-RAY DIFFRACTION99.97
2.97-3.10.32161580.2852796X-RAY DIFFRACTION99.97
3.1-3.270.31211620.27532778X-RAY DIFFRACTION99.97
3.27-3.470.28891410.2532750X-RAY DIFFRACTION98.7
3.47-3.740.2541350.23432788X-RAY DIFFRACTION98.95
3.74-4.110.21131550.20522713X-RAY DIFFRACTION97.85
4.11-4.70.18461420.18692786X-RAY DIFFRACTION99.49
4.71-5.920.23681350.20162787X-RAY DIFFRACTION98.92
5.92-27.60.19991540.19892727X-RAY DIFFRACTION95.4

+
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