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- PDB-6pgv: Human Josephin-2 in complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 6pgv
TitleHuman Josephin-2 in complex with ubiquitin
Components
  • Josephin-2
  • Polyubiquitin-B
KeywordsHYDROLASE / deubiquitinating enzyme / Josephin / ubiquitin
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / protein deubiquitination / Josephin domain DUBs / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / cytosol
Similarity search - Function
Josephin-1/2 / Josephin domain / Josephin / Josephin domain profile. / Josephin / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family
Similarity search - Domain/homology
ETHANAMINE / Tail fiber / Josephin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsGrasty, K.C. / Weeks, S.D. / Loll, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS065140 United States
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural insights into the activity and regulation of human Josephin-2
Authors: Grasty, K.C. / Weeks, S.D. / Loll, P.J.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 2, 2025Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Josephin-2
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4383
Polymers29,3922
Non-polymers451
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, No evidence for higher-order complex formation from gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-8 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.120, 102.120, 92.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Josephin-2 / Josephin domain-containing protein 2


Mass: 20872.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JOSD2, SBBI54 / Plasmid: pETHSUL-Jos2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8TAC2, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#3: Chemical ChemComp-NEH / ETHANAMINE


Mass: 45.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 0.2 M CaCl2, 22.5% (w/v) PEG 6000; microbatch under Al's Oil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.900, 0.9787, 0.9792, 0.9700, 1.0053, 1.0089
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 23, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97871
30.97921
40.971
51.00531
61.00891
ReflectionResolution: 2.3→20 Å / Num. obs: 12866 / % possible obs: 98.3 % / Redundancy: 77 % / Biso Wilson estimate: 50.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.007 / Rrim(I) all: 0.058 / Net I/σ(I): 81.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 46.2 % / Rmerge(I) obs: 0.99 / Num. unique obs: 1237 / CC1/2: 0.949 / Rpim(I) all: 0.145 / Rrim(I) all: 1 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSJan 26, 2018data reduction
XSCALEJan 26, 2018data scaling
PHENIX(1.14_3260)phasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.815 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1134 4.83 %random
Rwork0.201 ---
obs-23492 98.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 0 24 1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021832
X-RAY DIFFRACTIONf_angle_d0.4982478
X-RAY DIFFRACTIONf_dihedral_angle_d10.4551119
X-RAY DIFFRACTIONf_chiral_restr0.04287
X-RAY DIFFRACTIONf_plane_restr0.003319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40470.36161460.27292771X-RAY DIFFRACTION98
2.4047-2.53120.27981500.24782803X-RAY DIFFRACTION100
2.5312-2.68940.23771410.22592875X-RAY DIFFRACTION100
2.6894-2.89650.28391220.23822838X-RAY DIFFRACTION100
2.8965-3.18690.22181580.22972826X-RAY DIFFRACTION100
3.1869-3.64560.23611540.20892764X-RAY DIFFRACTION100
3.6456-4.58360.17761440.16772610X-RAY DIFFRACTION99
4.5836-19.81580.22121190.17772871X-RAY DIFFRACTION100
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)
1-1.84811.3053-5.14-2.4837-2.78676.6914-0.02880.56840.1666-0.22870.00220.0594-1.2391-0.5319-0.19770.7928-0.0233-0.04420.65520.04430.4825-20.170341.3088-8.4444
27.8562-5.09914.47483.275-3.47078.763-1.36760.02352.916-1.1443-0.0188-1.6713-1.75681.7852-0.33721.3594-0.15910.10430.49080.1621-0.0292-11.886347.8644-3.0673
35.4631-1.04531.14683.08471.31876.0117-0.21560.0581-0.621-0.27660.00060.02570.41980.80750.1770.33610.04980.12050.41610.04850.4338-11.853731.31466.2334
45.82310.38752.25064.55921.09347.2486-0.15010.6132-1.5855-0.2813-0.10560.24351.1302-0.08980.15160.63620.01610.09260.3815-0.12530.8361-18.988724.4728-1.0239
56.5302-0.90881.58575.252-1.06333.4122-0.106-1.0295-0.30630.43310.1866-0.6854-0.05630.22640.07290.3330.07190.00780.58430.14390.4846-12.525231.08313.7218
66.38961.52882.84388.101-1.89523.9798-0.24440.41160.33830.386-0.8367-0.62380.01811.5920.50340.42670.11380.01460.96960.23990.52855.294338.52879.3698
72.02831.30580.95061.8227-2.94792.5927-0.81582.00071.1570.195-0.8253-0.953-0.2511.99650.16220.5945-0.0177-0.04241.53210.37030.78578.463542.18015.4904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 13:45 )A13 - 45
2X-RAY DIFFRACTION2( CHAIN A AND RESID 46:68 )A46 - 68
3X-RAY DIFFRACTION3( CHAIN A AND RESID 69:111 )A69 - 111
4X-RAY DIFFRACTION4( CHAIN A AND RESID 122:167 )A122 - 167
5X-RAY DIFFRACTION5( CHAIN A AND RESID 168:186 )A168 - 186
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:49 )B1 - 49
7X-RAY DIFFRACTION7( CHAIN B AND ( RESID 50:75 OR RESID 101:101 ) )B50 - 75
8X-RAY DIFFRACTION7( CHAIN B AND ( RESID 50:75 OR RESID 101:101 ) )B101

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