[English] 日本語
Yorodumi
- PDB-5wvr: Crystal structure of Osh1 ORD domain in complex with cholesterol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wvr
TitleCrystal structure of Osh1 ORD domain in complex with cholesterol
ComponentsKLLA0C04147p
KeywordsLIPID BINDING PROTEIN / oxysterol binding / lipid transfer / cholesterol
Function / homology
Function and homology information


sterol transfer activity / sterol binding / perinuclear endoplasmic reticulum / maintenance of cell polarity / piecemeal microautophagy of the nucleus / exocytosis / endocytosis / nuclear envelope / plasma membrane / cytosol
Similarity search - Function
Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PH domain / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain ...Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PH domain / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
CHOLESTEROL / KLLA0C04147p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIm, Y.J. / Manik, M.K. / Yang, H.S. / Tong, J.S.
CitationJournal: Structure / Year: 2017
Title: Structure of Yeast OSBP-Related Protein Osh1 Reveals Key Determinants for Lipid Transport and Protein Targeting at the Nucleus-Vacuole Junction
Authors: Manik, M.K. / Yang, H. / Tong, J. / Im, Y.J.
History
DepositionDec 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: KLLA0C04147p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3436
Polymers50,5721
Non-polymers7715
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-18 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.174, 46.602, 73.103
Angle α, β, γ (deg.)90.00, 96.35, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein KLLA0C04147p


Mass: 50571.898 Da / Num. of mol.: 1 / Fragment: UNP residues 808-1240 / Mutation: 1109-1111 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_C04147g / Plasmid: modified pHIS-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CUK7
#2: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Bicine-HCl pH 9.0, 20% PEG 3350, 0.2M MgSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2016
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20511 / % possible obs: 97.2 % / Redundancy: 3 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 5.24 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H2D

5h2d


Resolution: 2.2→22.19 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.85
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1014 4.95 %Random selection
Rwork0.191 ---
obs0.193 20491 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→22.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 48 162 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093573
X-RAY DIFFRACTIONf_angle_d1.0384834
X-RAY DIFFRACTIONf_dihedral_angle_d19.0862134
X-RAY DIFFRACTIONf_chiral_restr0.067497
X-RAY DIFFRACTIONf_plane_restr0.006617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1983-2.31410.25241480.21472712X-RAY DIFFRACTION96
2.3141-2.45890.30641220.22442794X-RAY DIFFRACTION97
2.4589-2.64840.27781430.22472770X-RAY DIFFRACTION98
2.6484-2.91440.27481440.23142795X-RAY DIFFRACTION98
2.9144-3.33490.22991550.19832797X-RAY DIFFRACTION98
3.3349-4.1970.20991460.15642794X-RAY DIFFRACTION98
4.197-22.1890.1931560.17572815X-RAY DIFFRACTION95

+
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