[English] 日本語
Yorodumi
- PDB-1ocu: Crystal structure of the yeast PX-domain protein Grd19p (sorting ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ocu
TitleCrystal structure of the yeast PX-domain protein Grd19p (sorting nexin 3) complexed to phosphatidylinosytol-3-phosphate.
ComponentsSORTING NEXIN
KeywordsSORTING PROTEIN / YEAST PROTEIN / SORTING NEXIN / COMPLEX WITH PHOSPHATIDYLINOSITOL PHOSPHATE
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / protein-lipid complex / late endosome to Golgi transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / fungal-type vacuole membrane / Ub-specific processing proteases / intracellular protein localization / protein transport ...WNT ligand biogenesis and trafficking / protein-lipid complex / late endosome to Golgi transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / fungal-type vacuole membrane / Ub-specific processing proteases / intracellular protein localization / protein transport / early endosome membrane / endosome / Golgi membrane / cytosol
Similarity search - Function
Fungal SNX3, PX domain / : / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PIB / Sorting nexin-3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhou, C.Z. / Li de La Sierra-Gallay, I. / Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henkes, G. / Aufrere, R. / Leulliot, N. / Graille, M. ...Zhou, C.Z. / Li de La Sierra-Gallay, I. / Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henkes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. / de la Torre, F. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
CitationJournal: J. Biol. Chem. / Year: 2003
Title: Crystal structure of the yeast Phox homology (PX) domain protein Grd19p complexed to phosphatidylinositol-3-phosphate.
Authors: Zhou, C.Z. / Li de La Sierra-Gallay, I. / Quevillon-Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henckes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. ...Authors: Zhou, C.Z. / Li de La Sierra-Gallay, I. / Quevillon-Cheruel, S. / Collinet, B. / Minard, P. / Blondeau, K. / Henckes, G. / Aufrere, R. / Leulliot, N. / Graille, M. / Sorel, I. / Savarin, P. / de la Torre, F. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
History
DepositionFeb 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen / struct
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SORTING NEXIN
B: SORTING NEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8624
Polymers37,7542
Non-polymers1,1092
Water1,40578
1
A: SORTING NEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4312
Polymers18,8771
Non-polymers5541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SORTING NEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4312
Polymers18,8771
Non-polymers5541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.430, 55.760, 64.750
Angle α, β, γ (deg.)110.75, 97.35, 99.49
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein SORTING NEXIN


Mass: 18876.814 Da / Num. of mol.: 2 / Fragment: PX-DOMAIN
Source method: isolated from a genetically manipulated source
Details: CHEMICALLY MODIFIED CYSTEINE. D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATE
Source: (gene. exp.) Saccharomyces cerevisiae S288C / Description: CLONED GENE / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08826
#2: Chemical ChemComp-PIB / 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE / D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATED (+)-SN-1,2-DI-O-BUTANOYLGLYCERYL,3-O-PHOSPHO


Mass: 554.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.8
Details: 10% PEG8000, 8% ETHYLENE GLYCOL, 0.1M NA-HEPES PH 7,5
Crystal grow
*PLUS
Temperature: 293 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17 mg/mlprotein1drop
22 mMdiC4PtdIns(3)P1drop
30.1 M1dropNaCl
410 mMbeta-mercaptoethanol1reservoir
520 mMTris-HCl1reservoirpH7
610 %PEG80001reservoir
78 %ethlene glycol1reservoir
80.1 MHEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.984
DetectorDate: Jul 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.28→25 Å / Num. obs: 17289 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 25.1
Reflection shellResolution: 2.28→2.33 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 3.2 / % possible all: 77.3
Reflection
*PLUS
Highest resolution: 2.28 Å / Lowest resolution: 25.08 Å / Num. all: 65105 / Num. obs: 11970 / % possible obs: 95.97 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 77.31 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.2

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OCS

1ocs


Resolution: 2.3→20 Å / Data cutoff high absF: 1000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1 A TO 27 A AND 162 A, 1B TO 30 B ARE ABSENT FROM THE FINAL MODEL BECAUSE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1699 9.6 %RANDOM
Rwork0.221 ---
obs0.221 17072 96.8 %-
Displacement parametersBiso mean: 41.2 Å2
Baniso -1Baniso -2Baniso -3
1--15.893 Å2-1.446 Å27.882 Å2
2--9.085 Å2-0.079 Å2
3---6.808 Å2
Refine analyze
ObsFree
Luzzati coordinate error0.29 Å-
Luzzati d res low20 Å-
Luzzati sigma a-0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 44 78 2319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 33 /
RfactorNum. reflection
Rfree0.2562 44
Rwork0.2758 392
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PIB.PARMAPIB.TOP
X-RAY DIFFRACTION3CME.PARAMCME.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 4.8 % / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

+
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