[English] 日本語
Yorodumi
- PDB-3cvn: Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cvn
TitleStructure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) PTS1 peptide
Components
  • Peroxisome targeting signal 1 receptor
  • T. brucei GAPDH PTS1 peptide Ac-DRDAAKL
KeywordsTRANSPORT PROTEIN / TPR motifs / TPR protein / Peroxin 5 / PEX5 / PTS1 binding domain / Protein-peptide complex / Receptor / TPR repeat
Function / homology
Function and homology information


peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glycosome / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / peroxisomal membrane / glycolytic process / glucose metabolic process / NAD binding / NADP binding ...peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glycosome / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / peroxisomal membrane / glycolytic process / glucose metabolic process / NAD binding / NADP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
PEX5/PEX5L / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain ...PEX5/PEX5L / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / NAD(P)-binding domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase, glycosomal / Peroxisome targeting signal 1 receptor / Peroxisome targeting signal 1 receptor PEX5
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSampathkumar, P. / Roach, C. / Michels, P.A.M. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Insights into the recognition of peroxisomal targeting signal 1 by Trypanosoma brucei peroxin 5.
Authors: Sampathkumar, P. / Roach, C. / Michels, P.A. / Hol, W.G.
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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: Peroxisome targeting signal 1 receptor
B: T. brucei GAPDH PTS1 peptide Ac-DRDAAKL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,74324
Polymers37,3782
Non-polymers1,36522
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.619, 66.178, 51.979
Angle α, β, γ (deg.)90.00, 104.55, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL UNIT OF PROTEIN PEX5 IS MONOMER

-
Components

#1: Protein Peroxisome targeting signal 1 receptor


Mass: 36545.844 Da / Num. of mol.: 1 / Fragment: Binding domain,UNP residues 332-655 / Mutation: K378A/E379A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PEX5 / Plasmid details: Derivative pET28 / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57W55, UniProt: Q9U7C3*PLUS
#2: Protein/peptide T. brucei GAPDH PTS1 peptide Ac-DRDAAKL


Mass: 831.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P22512
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8 - 5.0, vapor diffusion, sitting drop, temperature 298KK
PH range: 4.8 - 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 7, 2006 / Details: Osmic VariMax optics
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→43.19 Å / Num. all: 19925 / Num. obs: 19415 / % possible obs: 97.6 % / Observed criterion σ(I): 5 / Redundancy: 3.48 % / Biso Wilson estimate: 24.79 Å2 / Rsym value: 0.098 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.32 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1538 / Rsym value: 0.316 / % possible all: 81.3

-
Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1FCH

1fch


Resolution: 2→40.06 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.975 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.203
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.265 983 5.1 %RANDOM
Rwork0.192 ---
obs0.196 19411 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.734 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 88 112 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212495
X-RAY DIFFRACTIONr_bond_other_d0.0010.021676
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9643361
X-RAY DIFFRACTIONr_angle_other_deg0.97634053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2255315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44624.344122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71715373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.751518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022801
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined0.2210.2629
X-RAY DIFFRACTIONr_nbd_other0.1960.21802
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21197
X-RAY DIFFRACTIONr_nbtor_other0.0880.21252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.215
X-RAY DIFFRACTIONr_mcbond_it0.9451.51975
X-RAY DIFFRACTIONr_mcbond_other0.1691.5613
X-RAY DIFFRACTIONr_mcangle_it1.09522441
X-RAY DIFFRACTIONr_scbond_it231090
X-RAY DIFFRACTIONr_scangle_it2.9164.5913
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 62 -
Rwork0.249 1112 -
all-1174 -
obs--79.59 %

+
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