[English] 日本語
Yorodumi
- PDB-7z0i: human PEX13 SH3 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z0i
Titlehuman PEX13 SH3 domain
ComponentsPeroxisomal membrane protein PEX13
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


microtubule-based peroxisome localization / protein import into peroxisome matrix, translocation / peroxisomal importomer complex / protein import into peroxisome matrix, docking / Class I peroxisomal membrane protein import / fatty acid alpha-oxidation / peroxisomal membrane / suckling behavior / cerebral cortex cell migration / protein transmembrane transporter activity ...microtubule-based peroxisome localization / protein import into peroxisome matrix, translocation / peroxisomal importomer complex / protein import into peroxisome matrix, docking / Class I peroxisomal membrane protein import / fatty acid alpha-oxidation / peroxisomal membrane / suckling behavior / cerebral cortex cell migration / protein transmembrane transporter activity / locomotory behavior / Peroxisomal protein import / neuron migration / cellular response to reactive oxygen species / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / membrane / cytosol
Similarity search - Function
Peroxin 13, N-terminal / Peroxin 13 / Peroxin 13, N-terminal region / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Peroxisomal membrane protein PEX13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGaussmann, S. / Zak, K. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR1905 Germany
CitationJournal: Biorxiv / Year: 2022
Title: Intramolecular autoinhibition of human PEX13 modulates peroxisomal import
Authors: Gaussmann, S. / Ott, J. / Zak, K.M. / Delhommel, F. / Popowicz, G.M. / Schliebs, W. / Erdmann, R. / Sattler, M.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: Peroxisomal membrane protein PEX13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5893
Polymers9,4621
Non-polymers1272
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-22 kcal/mol
Surface area5300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.949, 43.949, 86.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

-
Components

#1: Protein Peroxisomal membrane protein PEX13 / Peroxin-13


Mass: 9461.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEX13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92968
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.01M Zinc chloride, 0.1M Sodium acetate, 20% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.8→43.39 Å / Num. obs: 7660 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9-43.39130.0316410.0130.03399.1
1.8-1.8413.41.4434620.7380.5881.55999.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wxu

1wxu


Resolution: 1.8→39.238 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.172 / SU B: 3.501 / SU ML: 0.105 / Average fsc free: 0.8961 / Average fsc work: 0.9082 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 387 5.059 %RANDOM
Rwork0.1817 7262 --
all0.184 ---
obs-7649 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.564 Å2
Baniso -1Baniso -2Baniso -3
1-1.568 Å20 Å2-0 Å2
2--1.568 Å2-0 Å2
3----3.137 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 5 51 664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013633
X-RAY DIFFRACTIONr_bond_other_d0.0010.015619
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.638851
X-RAY DIFFRACTIONr_angle_other_deg1.2821.5951420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.882579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.7221.38936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49815114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.799156
X-RAY DIFFRACTIONr_chiral_restr0.0620.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02151
X-RAY DIFFRACTIONr_nbd_refined0.180.2100
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.2538
X-RAY DIFFRACTIONr_nbtor_refined0.1580.2282
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.226
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.213
X-RAY DIFFRACTIONr_nbd_other0.2540.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0740.22
X-RAY DIFFRACTIONr_mcbond_it2.6813.261316
X-RAY DIFFRACTIONr_mcbond_other2.6763.254315
X-RAY DIFFRACTIONr_mcangle_it3.8514.858395
X-RAY DIFFRACTIONr_mcangle_other3.8484.868396
X-RAY DIFFRACTIONr_scbond_it3.5613.78315
X-RAY DIFFRACTIONr_scbond_other3.5563.782316
X-RAY DIFFRACTIONr_scangle_it5.5255.431456
X-RAY DIFFRACTIONr_scangle_other5.5195.434457
X-RAY DIFFRACTIONr_lrange_it7.48837.495661
X-RAY DIFFRACTIONr_lrange_other7.48237.542662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.279200.306555X-RAY DIFFRACTION99.1379
1.847-1.8970.298320.252510X-RAY DIFFRACTION99.8158
1.897-1.9520.314210.23511X-RAY DIFFRACTION99.8124
1.952-2.0120.291190.213494X-RAY DIFFRACTION99.8055
2.012-2.0780.203330.187470X-RAY DIFFRACTION99.8016
2.078-2.1510.189270.186461X-RAY DIFFRACTION99.7955
2.151-2.2320.336330.176445X-RAY DIFFRACTION99.7912
2.232-2.3220.271260.181415X-RAY DIFFRACTION100
2.322-2.4250.247170.176423X-RAY DIFFRACTION99.7732
2.425-2.5430.225170.169393X-RAY DIFFRACTION100
2.543-2.680.266220.173374X-RAY DIFFRACTION100
2.68-2.8420.137170.176350X-RAY DIFFRACTION100
2.842-3.0380.227150.179338X-RAY DIFFRACTION100
3.038-3.280.275180.174314X-RAY DIFFRACTION100
3.28-3.5910.251200.175281X-RAY DIFFRACTION100
3.591-4.0110.20280.17263X-RAY DIFFRACTION100
4.011-4.6250.19680.162236X-RAY DIFFRACTION100
4.625-5.6480.215200.166184X-RAY DIFFRACTION100
5.648-7.9210.16760.196159X-RAY DIFFRACTION100
7.921-39.2380.20380.1786X-RAY DIFFRACTION98.9474

+
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