[English] 日本語
Yorodumi
- PDB-2c0m: apo form of the TPR domain of the pex5p receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c0m
Titleapo form of the TPR domain of the pex5p receptor
ComponentsPEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
KeywordsTRANSPORT PROTEIN / TPR REPEAT / TRANSPORT / IMPORT RECEPTOR COMPLEX / PEROXISOME / DISEASE MUTATION / PROTEIN TRANSPORT / ZELLWEGER SYNDROME
Function / homology
Function and homology information


protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome matrix targeting signal-1 binding / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / protein targeting to peroxisome / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix, docking / protein import into peroxisome matrix ...protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome matrix targeting signal-1 binding / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / protein targeting to peroxisome / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix, docking / protein import into peroxisome matrix / protein carrier chaperone / very long-chain fatty acid metabolic process / cerebral cortex neuron differentiation / cell development / pexophagy / positive regulation of multicellular organism growth / mitochondrial membrane organization / endoplasmic reticulum organization / peroxisomal membrane / neuromuscular process / fatty acid beta-oxidation / cerebral cortex cell migration / peroxisomal matrix / negative regulation of protein-containing complex assembly / Pexophagy / Peroxisomal protein import / protein tetramerization / neuron migration / small GTPase binding / cellular response to reactive oxygen species / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / Golgi apparatus / enzyme binding / protein-containing complex / mitochondrion / membrane / cytosol / cytoplasm
Similarity search - Function
PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / 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 / Mainly Alpha
Similarity search - Domain/homology
Peroxisomal targeting signal 1 receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStanley, W.A. / Kursula, P. / Wilmanns, M.
CitationJournal: Mol.Cell / Year: 2006
Title: Recognition of a Functional Peroxisome Type 1 Target by the Dynamic Import Receptor Pex5P.
Authors: Stanley, W.A. / Filipp, F.V. / Kursula, P. / Schuller, N. / Erdmann, R. / Schliebs, W. / Sattler, M. / Wilmanns, M.
History
DepositionSep 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
C: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
F: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)140,9874
Polymers140,9874
Non-polymers00
Water2,630146
1
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)35,2471
Polymers35,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)35,2471
Polymers35,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)35,2471
Polymers35,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
F: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)35,2471
Polymers35,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.470, 85.550, 88.890
Angle α, β, γ (deg.)71.17, 89.99, 73.43
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41F
12A
22B
32C
42F
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A285 - 403
2114B285 - 403
3114C285 - 403
4114F285 - 403
1124A429 - 550
2124B429 - 550
3124C429 - 550
4124F429 - 550
1224A560 - 602
2224B560 - 602
3224C560 - 602
4224F560 - 602
1134C420 - 428
2134F420 - 428

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR / PEX5P / PEROXISMORE RECEPTOR 1 / PEROXIN-5 / PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT ...PEX5P / PEROXISMORE RECEPTOR 1 / PEROXIN-5 / PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR / PTS1-BP / PTS1 RECEPTOR


Mass: 35246.699 Da / Num. of mol.: 4 / Fragment: TPR REPEAT DOMAIN, RESIDUES 284-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P50542
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.46 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 47257 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.31
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 85.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.54 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.84 / SU B: 38.188 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R: 0.832 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.309 2363 5 %RANDOM
Rwork0.263 ---
obs0.265 44893 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å2-1.4 Å2-0.37 Å2
2--6.45 Å2-0.8 Å2
3----3.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9406 0 0 146 9552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229669
X-RAY DIFFRACTIONr_bond_other_d0.0030.028787
X-RAY DIFFRACTIONr_angle_refined_deg1.391.97413123
X-RAY DIFFRACTIONr_angle_other_deg0.83320371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19351206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2824.122490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54151625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6441586
X-RAY DIFFRACTIONr_chiral_restr0.0720.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210976
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021974
X-RAY DIFFRACTIONr_nbd_refined0.2380.22749
X-RAY DIFFRACTIONr_nbd_other0.1890.29623
X-RAY DIFFRACTIONr_nbtor_refined0.1870.24741
X-RAY DIFFRACTIONr_nbtor_other0.0890.25745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.2147
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.53326454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73739577
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.08243984
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.45553546
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1810medium positional0.340.3
12B1810medium positional0.340.3
13C1810medium positional0.260.3
14F1810medium positional0.230.3
21A2378medium positional0.220.3
22B2378medium positional0.230.3
23C2378medium positional0.210.3
24F2378medium positional0.220.3
31C139medium positional0.810.3
11A1810medium thermal1.5325
12B1810medium thermal1.2625
13C1810medium thermal1.125
14F1810medium thermal1.0125
21A2378medium thermal1.7325
22B2378medium thermal1.1625
23C2378medium thermal1.1325
24F2378medium thermal1.0525
31C139medium thermal0.4925
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.44 151
Rwork0.383 2875

+
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