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- PDB-4z2z: New crystal structure of yeast Ddi1 aspartyl protease reveals sub... -

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Basic information

Entry
Database: PDB / ID: 4z2z
TitleNew crystal structure of yeast Ddi1 aspartyl protease reveals substrate engagement mode
ComponentsDNA damage-inducible protein 1
KeywordsHYDROLASE / protease / Ddi1
Function / homology
Function and homology information


proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / polyubiquitin modification-dependent protein binding / protein secretion / vesicle-mediated transport / SNARE binding / positive regulation of DNA replication / ubiquitin binding / protein-macromolecule adaptor activity ...proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / polyubiquitin modification-dependent protein binding / protein secretion / vesicle-mediated transport / SNARE binding / positive regulation of DNA replication / ubiquitin binding / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / aspartic-type endopeptidase activity / plasma membrane / cytoplasm
Similarity search - Function
gag-polyprotein putative aspartyl protease / DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Peptidase A2A, retrovirus, catalytic ...gag-polyprotein putative aspartyl protease / DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA damage-inducible protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTrempe, J.-F. / Feng, X. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Sci Rep / Year: 2016
Title: Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.
Authors: Trempe, J.F. / Saskova, K.G. / Siva, M. / Ratcliffe, C.D. / Veverka, V. / Hoegl, A. / Menade, M. / Feng, X. / Shenker, S. / Svoboda, M. / Kozisek, M. / Konvalinka, J. / Gehring, K.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-inducible protein 1
B: DNA damage-inducible protein 1


Theoretical massNumber of molelcules
Total (without water)32,6642
Polymers32,6642
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-18 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.515, 50.051, 131.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA damage-inducible protein 1 / v-SNARE-master 1


Mass: 16331.970 Da / Num. of mol.: 2 / Fragment: UNP residues 185-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DDI1, VSM1, YER143W / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P40087
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M phosphate-citrate, pH 4.2, 0.4M NaCl, 20% PEG 8000, 8 mg/ml protein, 1:1 uL drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.8→50.06 Å / Num. obs: 25235 / % possible obs: 96.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 25.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 7 / % possible all: 79.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
PDB_EXTRACT3.15data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2I1A

2i1a


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.445 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21305 1285 5.1 %RANDOM
Rwork0.18287 ---
obs0.18438 23898 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.613 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---1.4 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 0 149 2152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9762930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7625.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68415385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2461511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211567
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0122.5021086
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6533.7381362
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4012.6671049
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.40821.2093181
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 73 -
Rwork0.197 1334 -
obs--74.96 %
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)
10.40080.73310.67452.18742.06082.0486-0.0686-0.0401-0.0534-0.50380.0683-0.0134-0.38460.0970.00030.2659-0.0121-0.02990.06170.00080.027813.011-0.836.226
20.6623-0.26140.65743.22470.37960.7852-0.0321-0.07920.0309-0.0315-0.04340.1496-0.042-0.09450.07550.06330.0047-0.02190.0942-0.01750.075211.73712.80727.806
310.092-9.007-1.162120.30652.31893.4730.03750.59630.1628-1.0263-0.1527-0.4078-0.1689-0.24980.11520.1781-0.0130.0050.09830.05510.14489.27235.614.834
41.3279-0.92970.115318.73752.31440.32910.03610.1120.0606-0.3348-0.12220.4406-0.0474-0.00410.08610.22590.0073-0.06330.0923-0.0240.09917.478-26.21116.063
50.18540.20690.26841.61240.43560.4165-0.0372-0.0320.0233-0.12660.0023-0.0032-0.046-0.01390.03480.0894-0.0078-0.030.09450.00870.062513.6158.30321.705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A200 - 324
2X-RAY DIFFRACTION2B200 - 325
3X-RAY DIFFRACTION3A189 - 199
4X-RAY DIFFRACTION4B188 - 199
5X-RAY DIFFRACTION5A401 - 453
6X-RAY DIFFRACTION5B401 - 496

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