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- PDB-6syf: Human Ubc9 with covalent isopeptide ligand -

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Basic information

Entry
Database: PDB / ID: 6syf
TitleHuman Ubc9 with covalent isopeptide ligand
Components
  • ACE-ILE-LYS-GLN-GLU
  • ACE-LEU-ARG-LEU-ARG-GLY-CYS
  • SUMO-conjugating enzyme UBC9
KeywordsLIGASE / Ubc9 / isopeptide / disulfide / ubiquitin / SUMO
Function / homology
Function and homology information


positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly ...positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / small protein activating enzyme binding / synaptonemal complex / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / nuclear export / SUMOylation of RNA binding proteins / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / nuclear pore / SUMOylation of DNA damage response and repair proteins / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Meiotic synapsis / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of endogenous retroelements by KRAB-ZFP proteins / transcription coregulator binding / chromosome segregation / SUMOylation of intracellular receptors / PKR-mediated signaling / protein modification process / PML body / Formation of Incision Complex in GG-NER / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHofmann, R. / Akimoto, G. / Wucherpfennig, T.G. / Zeymer, C. / Bode, J.W.
CitationJournal: Nat.Chem. / Year: 2020
Title: Lysine acylation using conjugating enzymes for site-specific modification and ubiquitination of recombinant proteins.
Authors: Hofmann, R. / Akimoto, G. / Wucherpfennig, T.G. / Zeymer, C. / Bode, J.W.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
B: SUMO-conjugating enzyme UBC9
C: SUMO-conjugating enzyme UBC9
D: SUMO-conjugating enzyme UBC9
E: ACE-LEU-ARG-LEU-ARG-GLY-CYS
F: ACE-ILE-LYS-GLN-GLU
G: ACE-LEU-ARG-LEU-ARG-GLY-CYS
H: ACE-ILE-LYS-GLN-GLU
I: ACE-LEU-ARG-LEU-ARG-GLY-CYS
J: ACE-ILE-LYS-GLN-GLU
K: ACE-LEU-ARG-LEU-ARG-GLY-CYS
L: ACE-ILE-LYS-GLN-GLU


Theoretical massNumber of molelcules
Total (without water)76,15612
Polymers76,15612
Non-polymers00
Water9,332518
1
A: SUMO-conjugating enzyme UBC9
E: ACE-LEU-ARG-LEU-ARG-GLY-CYS
F: ACE-ILE-LYS-GLN-GLU


Theoretical massNumber of molelcules
Total (without water)19,0393
Polymers19,0393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SUMO-conjugating enzyme UBC9
G: ACE-LEU-ARG-LEU-ARG-GLY-CYS
H: ACE-ILE-LYS-GLN-GLU


Theoretical massNumber of molelcules
Total (without water)19,0393
Polymers19,0393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SUMO-conjugating enzyme UBC9
I: ACE-LEU-ARG-LEU-ARG-GLY-CYS
J: ACE-ILE-LYS-GLN-GLU


Theoretical massNumber of molelcules
Total (without water)19,0393
Polymers19,0393
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SUMO-conjugating enzyme UBC9
K: ACE-LEU-ARG-LEU-ARG-GLY-CYS
L: ACE-ILE-LYS-GLN-GLU


Theoretical massNumber of molelcules
Total (without water)19,0393
Polymers19,0393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.700, 38.700, 97.800
Angle α, β, γ (deg.)90.000, 118.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SUMO-conjugating enzyme UBC9 / RING-type E3 SUMO transferase UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin ...RING-type E3 SUMO transferase UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / p18


Mass: 17750.363 Da / Num. of mol.: 4 / Mutation: K48A, K49A, E54A, C138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Production host: Escherichia coli (E. coli)
References: UniProt: P63279, Transferases; Acyltransferases; Aminoacyltransferases
#2: Protein/peptide
ACE-LEU-ARG-LEU-ARG-GLY-CYS


Mass: 744.951 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein/peptide
ACE-ILE-LYS-GLN-GLU


Mass: 543.633 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M trisodium citrate pH 5.0, 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47 Å / Num. obs: 49319 / % possible obs: 99.1 % / Redundancy: 3.307 % / Biso Wilson estimate: 23.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.074 / Χ2: 0.947 / Net I/σ(I): 13.2 / Num. measured all: 163079 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-23.2420.3943.4969460.8460.47399
2-2.53.3350.186.84205230.9740.21499.2
2.5-33.3970.08113.4791260.9950.09699.2
3-43.1670.03724.7572450.9990.04598.9
4-63.3350.02533.6137990.9990.0398.6
6-103.4310.02333.6612950.9990.02798.2
10-202.8930.01934.643360.9990.02397.7
20-501.8780.01325.74910.01696.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.3 (23-SEP-2019)refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f6e

5f6e


Resolution: 1.9→47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2466 5 %RANDOM
Rwork0.2129 ---
obs0.2153 49318 99.3 %-
Displacement parametersBiso max: 67.84 Å2 / Biso mean: 30.76 Å2 / Biso min: 10.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.7882 Å20 Å2-1.7025 Å2
2--4.4199 Å20 Å2
3----6.2081 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 1.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 0 518 5798
Biso mean---33.33 -
Num. residues----666
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1893SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes914HARMONIC5
X-RAY DIFFRACTIONt_it5495HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion689SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5179SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5495HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7445HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion16.62
LS refinement shellResolution: 1.9→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3305 49 4.96 %
Rwork0.3068 938 -
all0.308 987 -
obs--98.07 %
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)
13.1342-0.00750.8183.67780.331.95480.02730.2380.0017-0.23990.0038-0.02630.0420.0447-0.0311-0.22810.0006-0.0236-0.10780.0136-0.021455.256312.2398-8.9363
23.24670.130.48733.81330.68372.3644-0.06750.0623-0.0633-0.05120.040.05660.09730.02230.0275-0.3056-0.00610.0157-0.11620.02350.04997.871511.2361-8.773
33.75410.3453-0.74633.79410.21872.22030.0758-0.19380.11040.2039-0.07190.0614-0.1303-0.0144-0.004-0.2599-0.0021-0.0498-0.18250.00230.112978.9518.4705-34.041
42.3984-0.0588-0.39623.54180.68821.39630.043-0.16330.02260.1965-0.0266-0.1176-0.00160.0417-0.0164-0.1935-0.0033-0.0597-0.06250.0022-0.018331.35627.1511-33.8659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 157
2X-RAY DIFFRACTION2{ B|* }B2 - 157
3X-RAY DIFFRACTION3{ C|* }C2 - 157
4X-RAY DIFFRACTION4{ D|* }D5 - 157

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