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- PDB-9qtg: Simkania negevensis CE-clan virulence factor SnCE1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9qtg
TitleSimkania negevensis CE-clan virulence factor SnCE1 in complex with hsSUMO1
Components
  • Deubiquitinase and deneddylase ChlaDub2
  • Small ubiquitin-related modifier 1
KeywordsHYDROLASE / cysteine protease / CE-clan / Ubl protease / deSUMOylase / SUMO pathway / virulence factor / bacterial virulence / pathogenesis
Function / homology
Function and homology information


SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / negative regulation of transcription initiation by RNA polymerase II / small protein activating enzyme binding / regulation of calcium ion transmembrane transport ...SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / negative regulation of transcription initiation by RNA polymerase II / small protein activating enzyme binding / regulation of calcium ion transmembrane transport / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA methylation proteins / negative regulation of protein import into nucleus / Maturation of nucleoprotein / XY body / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / roof of mouth development / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / cellular response to cadmium ion / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / ubiquitin-like protein ligase binding / nuclear pore / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / transporter activator activity / postsynaptic cytosol / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / cysteine-type peptidase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / Maturation of DENV proteins / regulation of protein stability / positive regulation of protein-containing complex assembly / PML body / PKR-mediated signaling / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / host cell / cellular response to heat / nuclear membrane / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear body / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / nuclear speck / protein stabilization / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA repair / nucleolus / negative regulation of transcription by RNA polymerase II / glutamatergic synapse / enzyme binding / proteolysis / RNA binding / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / prop-2-en-1-amine / DeSUMOylase CE1 / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesSimkania negevensis Z (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchmoeker, O. / Girbardt, B. / Palm, G.J. / Hoppen, J. / Schulze, S. / Lammers, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)443535983 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Reprogramming of bacterial virulence by lysine acetylation.
Authors: Schmoker, O. / Girbardt, B. / Schulze, S. / Palm, G.J. / Berndt, L. / Hoppen, J. / Kara, N. / Schops, X. / Al-Abdulla, R. / Garz, K. / Junker, H. / Wolfgramm, S. / Steil, L. / Hentschker, C. ...Authors: Schmoker, O. / Girbardt, B. / Schulze, S. / Palm, G.J. / Berndt, L. / Hoppen, J. / Kara, N. / Schops, X. / Al-Abdulla, R. / Garz, K. / Junker, H. / Wolfgramm, S. / Steil, L. / Hentschker, C. / Schoknecht, K. / Mayer, L.M. / Speth, L. / Lachmayer, V. / Dorr, M. / Kemnitz, S. / Muller, S. / Lackmann, J.W. / Kruger, M. / Hofmann, K. / Bornscheuer, U.T. / Volker, U. / Kruger, E. / Kozjak-Pavlovic, V. / Lammers, M.
History
DepositionApr 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deubiquitinase and deneddylase ChlaDub2
B: Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6675
Polymers37,5112
Non-polymers1563
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.967, 56.164, 148.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Deubiquitinase and deneddylase ChlaDub2


Mass: 28392.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Starting amino acids GPLGS correspond to expression tag, residues 1 - 39 not resolved
Source: (gene. exp.) Simkania negevensis Z (bacteria) / Gene: cdu2, SNE_A10940 / Plasmid: pGEX6P.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8L4W9
#2: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 9118.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: amino acids 1-19 not cloned / Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Plasmid: pTXB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63165

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Non-polymers , 4 types, 271 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#5: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M calcium acetate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 22, 2025
RadiationMonochromator: SILICON111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→49.55 Å / Num. obs: 43672 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 22.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.049 / Rrim(I) all: 0.127 / Χ2: 1 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.49-49.559.70.04439.33390.9990.0180.0470.8699.6
1.55-1.5811.41.3971.721400.3520.6241.5320.85100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Coot0.9.6model building
PHASERphasing
XDSdata reduction
XDSdata scaling
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→37.19 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.203 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2163 2250 5.164 %
Rwork0.1534 41325 -
all0.157 --
obs-43575 99.938 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.865 Å2
Baniso -1Baniso -2Baniso -3
1-2.018 Å20 Å2-0 Å2
2---0.068 Å2-0 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 13 268 2636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132434
X-RAY DIFFRACTIONr_bond_other_d0.0050.0162280
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.6533275
X-RAY DIFFRACTIONr_angle_other_deg1.4421.5895256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5765280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98622.986144
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg10.01101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53415439
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.585151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4691513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022746
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02600
X-RAY DIFFRACTIONr_nbd_refined0.2370.2448
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22054
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2179
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.211
X-RAY DIFFRACTIONr_nbd_other0.2640.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0440.22
X-RAY DIFFRACTIONr_mcbond_it3.2232.5231121
X-RAY DIFFRACTIONr_mcbond_other3.2252.5241119
X-RAY DIFFRACTIONr_mcangle_it3.6923.7761397
X-RAY DIFFRACTIONr_mcangle_other3.6923.7761397
X-RAY DIFFRACTIONr_scbond_it4.1652.9031313
X-RAY DIFFRACTIONr_scbond_other4.1632.9041314
X-RAY DIFFRACTIONr_scangle_it4.8284.1871877
X-RAY DIFFRACTIONr_scangle_other4.8274.1881878
X-RAY DIFFRACTIONr_lrange_it4.67129.6012807
X-RAY DIFFRACTIONr_lrange_other4.62829.012750
X-RAY DIFFRACTIONr_rigid_bond_restr3.6834714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.4321670.3643030X-RAY DIFFRACTION99.9687
1.59-1.6330.2981430.3142904X-RAY DIFFRACTION100
1.633-1.6810.2981460.2652858X-RAY DIFFRACTION100
1.681-1.7320.2721570.2312787X-RAY DIFFRACTION100
1.732-1.7890.2511580.1952697X-RAY DIFFRACTION100
1.789-1.8520.2321590.1912575X-RAY DIFFRACTION100
1.852-1.9220.2071150.1642540X-RAY DIFFRACTION99.9623
1.922-20.241260.1462437X-RAY DIFFRACTION99.961
2-2.0890.2211300.1332348X-RAY DIFFRACTION99.8388
2.089-2.1910.1721290.1152230X-RAY DIFFRACTION99.8307
2.191-2.310.2011090.1222110X-RAY DIFFRACTION99.91
2.31-2.450.1771040.1112047X-RAY DIFFRACTION99.9535
2.45-2.6190.2241090.1221880X-RAY DIFFRACTION99.8996
2.619-2.8280.2231060.1361780X-RAY DIFFRACTION100
2.828-3.0980.21940.1491657X-RAY DIFFRACTION99.8859
3.098-3.4640.221900.151501X-RAY DIFFRACTION99.7492
3.464-3.9990.184640.1311334X-RAY DIFFRACTION99.8571
3.999-4.8970.156610.1111148X-RAY DIFFRACTION100
4.897-6.9220.22540.143922X-RAY DIFFRACTION100
6.922-37.190.22290.184540X-RAY DIFFRACTION99.4755
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)
10.12990.00680.13440.21640.02170.40240.00380.0031-0.00260.0009-0.00280.0041-0.0137-0.0031-0.0010.00150.00010.00220.02010.00120.0276-13.10249.8384-23.8593
20.0143-0.008-0.06970.02130.2493.4008-0.023-0.0090.00720.02810.01450.00490.29540.10550.00840.0580.01780.00880.02580.00130.0336-16.3435-2.00871.2842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA40 - 242
2X-RAY DIFFRACTION2ALLB1 - 77
3X-RAY DIFFRACTION2ALLB101

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