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- PDB-1x3w: Structure of a peptide:N-glycanase-Rad23 complex -

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Basic information

Entry
Database: PDB / ID: 1x3w
TitleStructure of a peptide:N-glycanase-Rad23 complex
Components
  • UV excision repair protein RAD23
  • peptide:N-glycanase
KeywordsHYDROLASE / Protein-protein complex
Function / homology
Function and homology information


ubiquitin-dependent glycoprotein ERAD pathway / PNGase complex / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / nucleotide-excision repair factor 2 complex / nucleotide-excision repair, DNA damage recognition / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding ...ubiquitin-dependent glycoprotein ERAD pathway / PNGase complex / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / nucleotide-excision repair factor 2 complex / nucleotide-excision repair, DNA damage recognition / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding / ERAD pathway / ubiquitin binding / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #90 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #270 / XPC-binding domain / : / Rad4 transglutaminase-like domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Transglutaminase-like superfamily ...Rna Polymerase Sigma Factor; Chain: A - #90 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #270 / XPC-binding domain / : / Rad4 transglutaminase-like domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Rna Polymerase Sigma Factor; Chain: A / N-terminal domain of TfIIb - #10 / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / N-terminal domain of TfIIb / UBA-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single Sheet / Helix non-globular / Papain-like cysteine peptidase superfamily / Special / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
sucrose / UV excision repair protein RAD23 / Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsLee, J.-H. / Choi, J.M. / Lee, C. / Yi, K.J. / Cho, Y.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins.
Authors: Lee, J.H. / Choi, J.M. / Lee, C. / Yi, K.J. / Cho, Y.
History
DepositionMay 11, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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_atom_id / _atom_site.label_comp_id / _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.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_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide:N-glycanase
B: UV excision repair protein RAD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1986
Polymers47,1052
Non-polymers1,0924
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-14 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.235, 129.235, 128.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is protein-protein complex in asymmetric unit

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Components

#1: Protein peptide:N-glycanase


Mass: 39566.234 Da / Num. of mol.: 1 / Fragment: residues 8-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q02890, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Protein UV excision repair protein RAD23


Mass: 7539.189 Da / Num. of mol.: 1 / Fragment: XPC binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32628
#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 6.7 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: sodium chloride, MES, pH 6, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9794 Å
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 25391 / Num. obs: 25391 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.32 / % possible all: 68.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.9 / SU B: 37.386 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27418 1180 4.9 %RANDOM
Rwork0.24367 ---
all0.24516 22672 --
obs0.24516 22672 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.596 Å2
Baniso -1Baniso -2Baniso -3
1-5.4 Å22.7 Å20 Å2
2--5.4 Å20 Å2
3----8.1 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 70 17 3187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223243
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.9764394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1295375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45924.675169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.85715567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6291519
X-RAY DIFFRACTIONr_chiral_restr0.1170.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022441
X-RAY DIFFRACTIONr_nbd_refined0.2960.21965
X-RAY DIFFRACTIONr_nbtor_refined0.3430.22218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.22
X-RAY DIFFRACTIONr_mcbond_it1.0691.51912
X-RAY DIFFRACTIONr_mcangle_it1.93923041
X-RAY DIFFRACTIONr_scbond_it3.95331495
X-RAY DIFFRACTIONr_scangle_it3.4354.51353
X-RAY DIFFRACTIONr_rigid_bond_restr5.01733407
X-RAY DIFFRACTIONr_sphericity_free4.378318
X-RAY DIFFRACTIONr_sphericity_bonded1.94533170
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 75 -
Rwork0.42 1158 -
obs--67.86 %

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