[English] 日本語
Yorodumi
- PDB-7v62: Crystal structure of human OSBP ORD in complex with cholesterol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v62
TitleCrystal structure of human OSBP ORD in complex with cholesterol
ComponentsOxysterol-binding protein 1
KeywordsLIPID TRANSPORT / Lipid binding protein / Lipid transport protein / Oxysterol binding protein / Oxysterol binding protein-related domain
Function / homology
Function and homology information


positive regulation of secretory granule organization / sterol transfer activity / sphingomyelin biosynthetic process / sterol transport / : / ceramide transport / sterol binding / intracellular cholesterol transport / perinuclear endoplasmic reticulum / Sphingolipid de novo biosynthesis ...positive regulation of secretory granule organization / sterol transfer activity / sphingomyelin biosynthetic process / sterol transport / : / ceramide transport / sterol binding / intracellular cholesterol transport / perinuclear endoplasmic reticulum / Sphingolipid de novo biosynthesis / bile acid biosynthetic process / phospholipid transport / oxysterol binding / phosphatidylinositol-4-phosphate binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis of bile acids and bile salts / positive regulation of tyrosine phosphorylation of STAT protein / trans-Golgi network / cell junction / protein domain specific binding / Golgi membrane / endoplasmic reticulum membrane / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / membrane / plasma membrane / cytoplasm / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / CHOLESTEROL / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Oxysterol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsKobayashi, J. / Kato, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)21am0101083j0005 Japan
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Ligand Recognition by the Lipid Transfer Domain of Human OSBP Is Important for Enterovirus Replication.
Authors: Kobayashi, J. / Arita, M. / Sakai, S. / Kojima, H. / Senda, M. / Senda, T. / Hanada, K. / Kato, R.
History
DepositionAug 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oxysterol-binding protein 1
B: Oxysterol-binding protein 1
C: Oxysterol-binding protein 1
D: Oxysterol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,64219
Polymers187,6654
Non-polymers2,97715
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.880, 111.880, 367.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 405 through 410 or (resid 411...
d_2ens_1(chain "B" and (resid 405 through 413 or (resid 414...
d_3ens_1(chain "C" and (resid 405 through 407 or (resid 408...
d_4ens_1(chain "D" and (resid 405 through 407 or (resid 408...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLNA2 - 253
d_12ens_1SERILEA259 - 389
d_21ens_1PROILEG1 - 383
d_31ens_1PROGLNK1 - 252
d_32ens_1SERILEK259 - 389
d_41ens_1PROILEP1 - 383

NCS oper:
IDCodeMatrixVector
1given(0.791614128892, 0.610716914231, 0.0192852692557), (-0.606866077063, 0.782164390597, 0.14118226019), (0.0711381434123, -0.123465447613, 0.989795760648)-29.2917439445, 33.2613786622, 43.3669587374
2given(-0.994355067085, -0.105957384303, -0.00557075168333), (-0.104777593555, 0.988847812516, -0.105837892886), (0.0167229319064, -0.104656755125, -0.994367792698)117.163220454, 20.9856471553, 276.725120739
3given(-0.721563614359, -0.692040696203, -0.0206306866885), (-0.69231079579, 0.721513790297, 0.011118113344), (0.00719113805, 0.0223052731683, -0.999725343443)140.789223485, 54.6496571296, 230.511126266

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Oxysterol-binding protein 1


Mass: 46916.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSBP, OSBP1 / Production host: Homo sapiens (human) / References: UniProt: P22059

-
Non-polymers , 5 types, 25 molecules

#2: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: citrate, PEG4000, sodium acetate, GSH/GSSG / PH range: 6.0 - 6.25

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 3.25→49.6 Å / Num. obs: 37700 / % possible obs: 99.7 % / Redundancy: 28.4 % / Biso Wilson estimate: 86.34 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.99
Reflection shellResolution: 3.25→3.34 Å / Num. unique obs: 6043 / CC1/2: 0.837

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZM8

5zm8


Resolution: 3.25→49.58 Å / SU ML: 0.3762 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 1884 5 %
Rwork0.2126 35816 -
obs0.2146 37700 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.64 Å2
Refinement stepCycle: LAST / Resolution: 3.25→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12440 0 189 10 12639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002912965
X-RAY DIFFRACTIONf_angle_d0.714317610
X-RAY DIFFRACTIONf_chiral_restr0.04661892
X-RAY DIFFRACTIONf_plane_restr0.0052239
X-RAY DIFFRACTIONf_dihedral_angle_d21.93914826
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.27325669003
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.949061315445
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.05340570879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.340.33641410.31522681X-RAY DIFFRACTION98.77
3.34-3.440.35141420.28262683X-RAY DIFFRACTION98.95
3.44-3.550.28051400.26132670X-RAY DIFFRACTION98.94
3.55-3.670.29541420.24272708X-RAY DIFFRACTION99.2
3.67-3.820.2821410.232693X-RAY DIFFRACTION99.37
3.82-3.990.26951440.22452731X-RAY DIFFRACTION99.41
3.99-4.20.2351430.19812711X-RAY DIFFRACTION99.48
4.21-4.470.23191450.18692760X-RAY DIFFRACTION99.69
4.47-4.810.21091450.18382743X-RAY DIFFRACTION99.93
4.81-5.30.23191460.18352776X-RAY DIFFRACTION99.9
5.3-6.060.25891470.21282800X-RAY DIFFRACTION99.93
6.06-7.630.25821500.212841X-RAY DIFFRACTION99.97
7.63-49.580.22711580.20333019X-RAY DIFFRACTION99.37
Refinement TLS params.Method: refined / Origin x: 57.2721007083 Å / Origin y: 24.7775297438 Å / Origin z: 137.856126801 Å
111213212223313233
T0.395356460431 Å20.0340553700283 Å2-0.0209541254798 Å2-0.289948634548 Å2-0.00726077093612 Å2--0.431113959059 Å2
L0.14552828111 °20.0297546078941 °2-0.300214141938 °2-0.108000372062 °20.0621736826138 °2--1.02403612731 °2
S-0.106982523165 Å °-0.0106411448774 Å °0.0430664620888 Å °-0.00974233624432 Å °-0.0190012837997 Å °0.00791569906886 Å °-0.0192338451271 Å °-0.0141289273473 Å °-2.0320162827E-6 Å °
Refinement TLS groupSelection details: all

+
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