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- PDB-2f4m: The Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of ... -

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Basic information

Entry
Database: PDB / ID: 2f4m
TitleThe Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of the Protein-Protein Interface Compared to its Yeast Orthologs
Components
  • UV excision repair protein RAD23 homolog B
  • peptide N-glycanase
KeywordsHYDROLASE / Glycoproteins / Ubiquitin-dependent protein degradation / Nucleotide excision repair / Peptide:N-glycanase / Transglutaminase
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / DNA Damage Recognition in GG-NER / XPC complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / glycoprotein catabolic process / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process ...peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / DNA Damage Recognition in GG-NER / XPC complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / glycoprotein catabolic process / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to interleukin-7 / proteasome binding / polyubiquitin modification-dependent protein binding / embryonic organ development / proteasome complex / ubiquitin binding / nucleotide-excision repair / spermatogenesis / collagen-containing extracellular matrix / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide N glycanase, PAW domain / PAW domain superfamily / PNGase C-terminal domain, mannose-binding module PAW / PAW domain profile. / domain present in PNGases and other hypothetical proteins / XPC-binding domain / C8orf32 fold - #30 / C8orf32 fold / : / RAD23A/RAD23B, UBA1 domain ...Peptide N glycanase, PAW domain / PAW domain superfamily / PNGase C-terminal domain, mannose-binding module PAW / PAW domain profile. / domain present in PNGases and other hypothetical proteins / XPC-binding domain / C8orf32 fold - #30 / C8orf32 fold / : / RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / PUB domain / PUB-like domain superfamily / PUB domain / domain in protein kinases, N-glycanases and other nuclear proteins / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / N-terminal domain of TfIIb - #10 / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / N-terminal domain of TfIIb / UBA-like superfamily / Single Sheet / Papain-like cysteine peptidase superfamily / Galactose-binding-like domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog B / Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.85 Å
AuthorsZhao, G. / Zhou, X. / Wang, L. / Kisker, C. / Lennarz, W.J. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of the mouse peptide N-glycanase-HR23 complex suggests co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways.
Authors: Zhao, G. / Zhou, X. / Wang, L. / Li, G. / Kisker, C. / Lennarz, W.J. / Schindelin, H.
History
DepositionNov 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,1534
Polymers42,0522
Non-polymers1012
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-30 kcal/mol
Surface area18340 Å2
MethodPISA
2
A: peptide N-glycanase
B: UV excision repair protein RAD23 homolog B
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)84,3068
Polymers84,1044
Non-polymers2024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5670 Å2
ΔGint-68 kcal/mol
Surface area34840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.225, 52.297, 82.548
Angle α, β, γ (deg.)90.00, 115.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein peptide N-glycanase


Mass: 34866.730 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 164-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL
References: UniProt: Q9JI78, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Protein UV excision repair protein RAD23 homolog B / mHR23B / XP-C repair complementing complex 58 kDa protein / p58


Mass: 7185.165 Da / Num. of mol.: 1 / Fragment: XPCB domain, residues 273-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rad23b, Mhr23b / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: P54728
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 28-32% PEG4000, 0.2 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 23, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 31216 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.051 / Net I/σ(I): 15.5
Reflection shellResolution: 1.85→1.91 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.4 / % possible all: 20.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.672 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.155 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1579 5.1 %RANDOM
Rwork0.186 ---
obs0.189 29636 96 %-
all-40360 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20.23 Å2
2--1.07 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 2 255 3210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213023
X-RAY DIFFRACTIONr_bond_other_d0.0020.022685
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9454086
X-RAY DIFFRACTIONr_angle_other_deg0.91536274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9095354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56124.146164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3715553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9251525
X-RAY DIFFRACTIONr_chiral_restr0.0930.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02614
X-RAY DIFFRACTIONr_nbd_refined0.2140.2642
X-RAY DIFFRACTIONr_nbd_other0.1960.22797
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21377
X-RAY DIFFRACTIONr_nbtor_other0.0840.21684
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2590.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1680.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3340.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.011.52333
X-RAY DIFFRACTIONr_mcbond_other0.2491.5715
X-RAY DIFFRACTIONr_mcangle_it1.21422881
X-RAY DIFFRACTIONr_scbond_it2.00931443
X-RAY DIFFRACTIONr_scangle_it2.7934.51205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 68 -
Rwork0.28 1474 -
obs--65.64 %
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)
18.69481.0772-4.7865.4009-0.63037.151-0.470.2366-0.7672-0.2132-0.0814-0.44451.06020.21780.55140.01270.01090.1361-0.1252-0.027-0.170543.53342.17597.4902
23.7935-0.7945-1.85053.26830.00785.21960.21540.24740.5588-0.17510.00660.0275-0.6417-0.352-0.222-0.16020.02820.0012-0.2330.0401-0.239527.818519.480619.2027
39.4823-3.5453-8.60584.40193.296721.1726-0.25490.7513-0.582-0.05930.02630.49180.5479-0.72780.2285-0.15320.10960.010.07530.0153-0.01594.034721.268537.64
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BB273 - 3331 - 61
2X-RAY DIFFRACTION2AA164 - 2411 - 78
3X-RAY DIFFRACTION2AA292 - 458129 - 295
4X-RAY DIFFRACTION3AA242 - 29179 - 128
5X-RAY DIFFRACTION3AC5011

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