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- PDB-7r2e: Structure of human Senp7 with SUMO2 -

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Basic information

Entry
Database: PDB / ID: 7r2e
TitleStructure of human Senp7 with SUMO2
Components
  • Sentrin-specific protease 7
  • Small ubiquitin-related modifier 3
KeywordsHYDROLASE / Complex SUMO hydrolase / SENP7 / with a suicide substrate (SUMO-PA)
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / protein desumoylation / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of immune response proteins / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors ...SUMO-specific endopeptidase activity / protein desumoylation / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of immune response proteins / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / SUMOylation of DNA damage response and repair proteins / antiviral innate immune response / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / PML body / kinetochore / Formation of Incision Complex in GG-NER / protein tag activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic 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
prop-2-en-1-amine / Small ubiquitin-related modifier 3 / Sentrin-specific protease 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsReverter, D. / Li, Y.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Basis for the SUMO2 Isoform Specificity of SENP7.
Authors: Li, Y. / De Bolos, A. / Amador, V. / Reverter, D.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 2.0Mar 1, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_seq_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sentrin-specific protease 7
B: Sentrin-specific protease 7
C: Small ubiquitin-related modifier 3
D: Small ubiquitin-related modifier 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0396
Polymers97,9254
Non-polymers1142
Water5,855325
1
A: Sentrin-specific protease 7
D: Small ubiquitin-related modifier 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0193
Polymers48,9622
Non-polymers571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-2 kcal/mol
Surface area15920 Å2
2
B: Sentrin-specific protease 7
C: Small ubiquitin-related modifier 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0193
Polymers48,9622
Non-polymers571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-2 kcal/mol
Surface area15820 Å2
Unit cell
Length a, b, c (Å)36.413, 100.730, 93.037
Angle α, β, γ (deg.)90.000, 90.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sentrin-specific protease 7 / SUMO-1-specific protease 2 / Sentrin/SUMO-specific protease SENP7


Mass: 40185.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP7, KIAA1707, SSP2, SUSP2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BQF6, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Small ubiquitin-related modifier 3 / SUMO-3 / SMT3 homolog 1 / SUMO-2 / Ubiquitin-like protein SMT3A / Smt3A


Mass: 8776.925 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO3, SMT3A, SMT3H1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55854
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium HEPES 7.0, 15 % w/v PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.73→93.03 Å / Num. obs: 51898 / % possible obs: 92.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Net I/σ(I): 10.7
Reflection shellResolution: 1.73→1.9 Å / Num. unique obs: 2595 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EAY

3eay


Resolution: 1.74→50.36 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 2611 5.03 %
Rwork0.1841 49278 -
obs0.1863 51889 74.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.71 Å2 / Biso mean: 36.7846 Å2 / Biso min: 14.29 Å2
Refinement stepCycle: final / Resolution: 1.74→50.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 8 325 5639
Biso mean--29.62 41.13 -
Num. residues----639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.770.416880.370786943
1.77-1.80.3518170.37123133309
1.8-1.840.369320.31648251414
1.84-1.880.3753520.284572577721
1.88-1.920.2829790.28881339141839
1.92-1.970.2842930.27212049214260
1.97-2.020.30231810.24663087326889
2.02-2.080.27381710.23433389356099
2.08-2.150.27942020.22153431363398
2.15-2.230.26431840.21413394357899
2.23-2.310.25081560.20343435359199
2.31-2.420.26461740.19423440361499
2.42-2.550.24371870.1993437362499
2.55-2.710.24132150.20343412362799
2.71-2.920.24572120.20313398361099
2.92-3.210.25311550.1923454360999
3.21-3.670.23041470.17073463361098
3.67-4.630.18321850.14093432361799
4.63-50.360.181610.15673512367399
Refinement TLS params.Method: refined / Origin x: 9.1109 Å / Origin y: 1.9122 Å / Origin z: 22.9943 Å
111213212223313233
T0.1541 Å20.0111 Å2-0.0054 Å2-0.2125 Å20.0067 Å2--0.1816 Å2
L0.2092 °20.2571 °20.0436 °2-1.2846 °20.344 °2--0.2379 °2
S0.0262 Å °-0.0425 Å °-0.0075 Å °0.1092 Å °0.0034 Å °-0.0159 Å °0.0173 Å °0.0136 Å °-0.0276 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA678 - 981
2X-RAY DIFFRACTION1allB679 - 981
3X-RAY DIFFRACTION1allC17 - 93
4X-RAY DIFFRACTION1allD17 - 93
5X-RAY DIFFRACTION1allS1 - 329

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