[English] 日本語
- PDB-5ejj: Crystal structure of UfSP from C.elegans -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 5ejj
TitleCrystal structure of UfSP from C.elegans
ComponentsUfm1-specific protease
KeywordsHYDROLASE / Ufm1 / UfSP / Deufmylation
Function / homology
Function and homology information

protein localization to non-motile cilium / UFM1 hydrolase activity / positive regulation of chemotaxis / chemotaxis / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / response to ethanol / proteolysis / endoplasmic reticulum membrane / perinuclear region of cytoplasm / protein-containing complex
Similarity search - Function
Peptidase C78, ubiquitin fold modifier-specific peptidase 1/ 2 / Peptidase family C78 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ufm1-specific protease
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
AuthorsKim, K. / Ha, B. / Kim, E.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future PlanningNRF 20110021713 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: The MPN domain of Caenorhabditis elegans UfSP modulates both substrate recognition and deufmylation activity
Authors: Ha, B.H. / Kim, K.H. / Yoo, H.M. / Lee, W. / Kim, E.E.
DepositionNov 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: Ufm1-specific protease
B: Ufm1-specific protease

Theoretical massNumber of molelcules
Total (without water)128,1902
A: Ufm1-specific protease

Theoretical massNumber of molelcules
Total (without water)64,0951
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
B: Ufm1-specific protease

Theoretical massNumber of molelcules
Total (without water)64,0951
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
A: Ufm1-specific protease

B: Ufm1-specific protease

Theoretical massNumber of molelcules
Total (without water)128,1902
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_764-x+5/2,-y+1,z-1/21
Buried area1440 Å2
ΔGint-13 kcal/mol
Surface area47520 Å2
Unit cell
Length a, b, c (Å)77.531, 149.808, 226.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121


#1: Protein Ufm1-specific protease / UfSP / Odorant response abnormal protein 8

Mass: 64095.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: odr-8, ufsp-2, F38A5.1 / Plasmid: pET28a / Cell line (production host): BL21RIL / Production host: Escherichia coli (E. coli)
References: UniProt: Q94218, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION

Sample preparation

CrystalDensity Matthews: 5.13 Å3/Da / Density % sol: 76.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Bicine, Ammonium phosphate

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 66417 / % possible obs: 93.8 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1.65 / % possible all: 77.3


HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.278 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 3723 3.21 %
Rwork0.2056 --
obs0.2066 62217 91.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→41.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8307 0 0 223 8530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018502
X-RAY DIFFRACTIONf_angle_d1.30111517
X-RAY DIFFRACTIONf_dihedral_angle_d16.8553095
X-RAY DIFFRACTIONf_chiral_restr0.0931257
X-RAY DIFFRACTIONf_plane_restr0.0051485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7924-2.82770.3489850.34542621X-RAY DIFFRACTION58
2.8277-2.86490.33951130.32333332X-RAY DIFFRACTION73
2.8649-2.90420.34441140.30283554X-RAY DIFFRACTION79
2.9042-2.94560.37131230.30483672X-RAY DIFFRACTION80
2.9456-2.98960.33671240.30273708X-RAY DIFFRACTION82
2.9896-3.03630.35851240.28393809X-RAY DIFFRACTION85
3.0363-3.08610.2771280.27153871X-RAY DIFFRACTION85
3.0861-3.13930.29941310.27133931X-RAY DIFFRACTION87
3.1393-3.19630.31231380.26614028X-RAY DIFFRACTION88
3.1963-3.25780.29751360.24364037X-RAY DIFFRACTION89
3.2578-3.32430.30581380.24054181X-RAY DIFFRACTION92
3.3243-3.39650.26781410.22174253X-RAY DIFFRACTION93
3.3965-3.47550.27471380.22044266X-RAY DIFFRACTION94
3.4755-3.56230.24531410.21594336X-RAY DIFFRACTION96
3.5623-3.65860.20751500.19614416X-RAY DIFFRACTION97
3.6586-3.76620.20591450.19344436X-RAY DIFFRACTION98
3.7662-3.88770.24651480.18254450X-RAY DIFFRACTION98
3.8877-4.02650.21311520.17984497X-RAY DIFFRACTION99
4.0265-4.18760.24081470.17784485X-RAY DIFFRACTION99
4.1876-4.37790.19231500.17084532X-RAY DIFFRACTION100
4.3779-4.60850.18771520.16514530X-RAY DIFFRACTION100
4.6085-4.89680.21681530.16314544X-RAY DIFFRACTION100
4.8968-5.27420.21731500.1684506X-RAY DIFFRACTION100
5.2742-5.80360.25291470.19144539X-RAY DIFFRACTION100
5.8036-6.64040.23421520.21134515X-RAY DIFFRACTION100
6.6404-8.35480.20161530.21384551X-RAY DIFFRACTION100
8.3548-41.28270.22351500.21474502X-RAY DIFFRACTION99

About Yorodumi


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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search


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