[English] 日本語
Yorodumi
- PDB-4z2z: New crystal structure of yeast Ddi1 aspartyl protease reveals sub... -

+
Open data


ID or keywords:

Loading...

-
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 / protein secretion / polyubiquitin modification-dependent protein binding / vesicle-mediated transport / SNARE binding / ubiquitin binding / positive regulation of DNA replication / ubiquitin-dependent protein catabolic process ...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 / protein secretion / polyubiquitin modification-dependent protein binding / vesicle-mediated transport / SNARE binding / ubiquitin binding / positive regulation of DNA replication / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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