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- PDB-6xod: Crystal structure of the PEX4-PEX22 protein complex from Arabidop... -

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Entry
Database: PDB / ID: 6xod
TitleCrystal structure of the PEX4-PEX22 protein complex from Arabidopsis thaliana
Components
  • Peroxisome biogenesis protein 22
  • Protein PEROXIN-4
KeywordsLIGASE/TRANSPORT PROTEIN / peroxin / E2 / ubiquitin-conjugating enzyme / LIGASE / TRANSFERASE / LIGASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


protein import into peroxisome matrix / peroxisome organization / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / fatty acid beta-oxidation / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-protein transferase activity / protein transport / membrane => GO:0016020 ...protein import into peroxisome matrix / peroxisome organization / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / fatty acid beta-oxidation / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-protein transferase activity / protein transport / membrane => GO:0016020 / protein ubiquitination / ATP binding / nucleus
Similarity search - Function
Peroxisome biogenesis protein 22 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Protein PEROXIN-4 / Peroxisome biogenesis protein 22
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsOlmos Jr., J.L. / Bradford, S.E. / Miller, M.D. / Xu, W. / Wright, Z.J. / Bartel, B. / Phillips Jr., G.N.
Funding support United States, 6items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130338 United States
Robert A. Welch FoundationC1309 United States
National Science Foundation (NSF, United States)GRFP 1450681 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115261 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA217255 United States
CitationJournal: Front Cell Dev Biol / Year: 2022
Title: The Structure of the Arabidopsis PEX4-PEX22 Peroxin Complex-Insights Into Ubiquitination at the Peroxisomal Membrane
Authors: Traver, M.S. / Bradford, S.E. / Olmos, J.L. / Wright, Z.J. / Miller, M.D. / Xu, W. / Phillips, G.N. / Bartel, B.
History
DepositionJul 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 2.0Mar 2, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine_ls_restr / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_details / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.seq_num / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Sequence discrepancy / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / software
Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PEROXIN-4
B: Peroxisome biogenesis protein 22


Theoretical massNumber of molelcules
Total (without water)38,2232
Polymers38,2232
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, gel filtration supports the assignment of a heterodimer between PEX4 and the soluble domain of PEX22
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-6 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.389, 100.484, 112.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

21B-352-

HOH

31B-368-

HOH

41B-373-

HOH

51B-377-

HOH

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Components

#1: Protein Protein PEROXIN-4 / AtPEX4 / E2 ubiquitin-conjugating enzyme 21 / Probable ubiquitin-conjugating enzyme E2 21 / ...AtPEX4 / E2 ubiquitin-conjugating enzyme 21 / Probable ubiquitin-conjugating enzyme E2 21 / Ubiquitin carrier protein 21


Mass: 18546.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PEX4, UBC21, At5g25760, F18A17.10 / Plasmid: pET-6XHIS-MBP-LIC-cloning-PEX4-PEX22-XLlinker
Details (production host): expressed as a chimera with MBP and PEX22 and was cleaved with TEV and Precission Proteases to form the final products
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8LGF7, E2 ubiquitin-conjugating enzyme
#2: Protein Peroxisome biogenesis protein 22 / Peroxin-22 / AtPEX22


Mass: 19676.396 Da / Num. of mol.: 1 / Fragment: Cytosolic domain, residues 111-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PEX22, At3g21865, MSD21.24 / Plasmid: pET-6XHIS-MBP-LIC-cloning-PEX4-PEX22-XLlinker
Details (production host): expressed as a chimera with MBP and PEX4 and was cleaved with TEV and Precission Proteases to form the final products
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LSX7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe construct was expressed as a fusion with an N-terminal TEV-cleavable 6-His MBP tag, the PEX 4 ...The construct was expressed as a fusion with an N-terminal TEV-cleavable 6-His MBP tag, the PEX 4 (residues 1-157), a linker containing a precision protease site (LEVLFQ/GP) and cytosolic domain of PEX 22 (residues 111-283 - lacking the predicted N-terminal luminal tail, transmembrane domain and unstructured tether). After purification, the N-terminal tag was removed with TEV-protease and the linker between PEX-4 and PEX-22 was cleaved with PreScission protease leaving the PEX-4 with an S remaining at the N-terminus after cleavage with TEV-protease and LEVLFQ from the linker at the C-terminus after cleavage with precision protease. The PEX-22(111-283) construct retains GP from the linker at its N-termius after cleavage.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100 mM NaCl, 100 mM Bis-Tris Propane, 25% (w/v) PEG 1,500

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.008→56.046 Å / Num. obs: 22014 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 43.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.041 / Rrim(I) all: 0.104 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.008-2.04261.5591.110790.4640.6961.711100
5.448-56.0466.10.05627.712010.9980.0250.06299.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NKZ

5nkz


Resolution: 2.01→49.83 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 1104 5.02 %
Rwork0.1936 20901 -
obs0.1958 22005 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 273 Å2 / Biso mean: 61.9435 Å2 / Biso min: 26.7 Å2
Refinement stepCycle: final / Resolution: 2.01→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 0 131 2675
Biso mean---54.98 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272620
X-RAY DIFFRACTIONf_angle_d0.56523557
X-RAY DIFFRACTIONf_chiral_restr0.0401402
X-RAY DIFFRACTIONf_plane_restr0.0052462
X-RAY DIFFRACTIONf_dihedral_angle_d16.072990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.01-2.10.32051130.278525822695
2.1-2.210.28151410.251125912732
2.21-2.350.28831420.238125492691
2.35-2.530.2641390.242225922731
2.53-2.780.24741370.213225972734
2.78-3.190.27671720.206225832755
3.19-4.010.24111210.17626512772
4.01-49.830.18951390.168827562895
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)
12.04670.16710.15311.1245-0.43021.91370.0070.12080.10970.02340.001-0.0694-0.03390.29320.01770.3366-0.01250.0050.37980.00720.385414.78433.103330.312
23.332.2096-0.91172.659-0.43641.63120.1317-0.2404-0.00460.0555-0.16460.21030.1592-0.14050.05230.4274-0.0085-0.02910.37130.03080.3676-8.8029-17.820347.7922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN 'B' AND RESID 118 THROUGH 283)B0
2X-RAY DIFFRACTION2(CHAIN 'A' AND RESID 1 THROUGH 154)A0

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