[English] 日本語
Yorodumi
- PDB-3mk4: X-Ray structure of human PEX3 in complex with a PEX19 derived peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mk4
TitleX-Ray structure of human PEX3 in complex with a PEX19 derived peptide
Components
  • Peroxisomal biogenesis factor 19
  • Peroxisomal biogenesis factor 3
KeywordsPROTEIN TRANSPORT / Membrane / Peroxisome
Function / homology
Function and homology information


peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / protein-lipid complex / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / Class I peroxisomal membrane protein import / protein carrier chaperone ...peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / protein-lipid complex / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / Class I peroxisomal membrane protein import / protein carrier chaperone / peroxisome organization / ABC transporters in lipid homeostasis / peroxisome fission / peroxisomal membrane / : / brush border membrane / peroxisome / ATPase binding / protein-macromolecule adaptor activity / protein stabilization / lipid binding / endoplasmic reticulum / protein-containing complex / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Peroxin-3 / Peroxin-3 / Pex19 protein / Pex19, C-terminal domain superfamily / Pex19 protein family
Similarity search - Domain/homology
Peroxisomal biogenesis factor 19 / Peroxisomal biogenesis factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsSchmidt, F. / Treiber, N. / Dodt, G. / Stehle, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Insights into peroxisome function from the structure of PEX3 in complex with a soluble fragment of PEX19
Authors: Schmidt, F. / Treiber, N. / Zocher, G. / Bjelic, S. / Steinmetz, M.O. / Kalbacher, H. / Stehle, T. / Dodt, G.
History
DepositionApr 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Feb 19, 2014Group: Database references
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisomal biogenesis factor 3
B: Peroxisomal biogenesis factor 19


Theoretical massNumber of molelcules
Total (without water)39,8242
Polymers39,8242
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-10 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.470, 65.670, 61.580
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Peroxisomal biogenesis factor 3 / Peroxin-3 / Peroxisomal assembly protein PEX3


Mass: 37513.883 Da / Num. of mol.: 1 / Fragment: Cytosolic domain, UNP residues 41-373 / Mutation: C235S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEX3 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P56589
#2: Protein/peptide Peroxisomal biogenesis factor 19 / Peroxin-19 / Peroxisomal farnesylated protein / 33 kDa housekeeping protein


Mass: 2310.491 Da / Num. of mol.: 1 / Fragment: PEX19Pep, UNP residues 14-33 / Source method: obtained synthetically / Details: Synthesized peptide / References: UniProt: P40855
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 24% PEG 3350, 0.1M Bis-Tris, 0.2M NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2009 / Details: mirrors
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.42→25 Å / Num. obs: 11779 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 20.2
Reflection shellResolution: 2.42→2.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unrefined model of PEX3

Resolution: 2.42→24.97 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 19.09 / SU ML: 0.197 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.623 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23368 589 5 %RANDOM
Rwork0.19431 ---
obs0.19634 11190 100 %-
all-12726 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.488 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å21.77 Å2
2--0.66 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 2.42→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 0 67 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222403
X-RAY DIFFRACTIONr_bond_other_d0.0010.021591
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.983254
X-RAY DIFFRACTIONr_angle_other_deg0.85333909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0915298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67724.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87215436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5131515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02447
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.34441509
X-RAY DIFFRACTIONr_mcbond_other0.4794600
X-RAY DIFFRACTIONr_mcangle_it2.22242438
X-RAY DIFFRACTIONr_scbond_it2.9946894
X-RAY DIFFRACTIONr_scangle_it4.2366815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 41 -
Rwork0.289 793 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2488-0.8996-0.51372.41991.27952.0388-0.0747-0.0420.0150.13270.0769-0.03990.23390.1345-0.00210.1588-0.0225-0.01610.16620.0210.149920.9591.89150.274
21.3879-0.3643-1.31431.46061.43443.56470.01990.0296-0.0114-0.21360.03280.0225-0.1482-0.0531-0.05260.0977-0.0228-0.04330.04990.01840.073217.841-0.57141.533
36.1486-3.15242.707631.48821.140543.66080.15120.1395-0.0016-0.66610.4718-1.02530.88382.7356-0.6230.09230.06440.05090.3261-0.06940.073137.668-11.19518.947
40.6645-0.0413-0.3490.99870.62471.635-0.041-0.0263-0.0024-0.05850.0588-0.01460.10530.0081-0.01770.1865-0.033-0.02780.10120.00730.153218.880.93644.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 158
2X-RAY DIFFRACTION2A159 - 368
3X-RAY DIFFRACTION3B15 - 30
4X-RAY DIFFRACTION4A1 - 39
5X-RAY DIFFRACTION4A374 - 399
6X-RAY DIFFRACTION4B34 - 64

+
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