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- PDB-9g8i: Sumo-Darpin-A10-complex -

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Basic information

Entry
Database: PDB / ID: 9g8i
TitleSumo-Darpin-A10-complex
Components
  • DARPin
  • Ubiquitin-like protein SMT3
KeywordsSIGNALING PROTEIN / ankyrin repeat / sumo
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / protein tag activity / identical protein binding / nucleus
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciessynthetic construct (others)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsCakilkaya, B. / Wolf, E. / Boergel, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Cell Rep / Year: 2025
Title: Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast.
Authors: Troster, V. / Wong, R.P. / Borgel, A. / Cakilkaya, B. / Renz, C. / Mockel, M.M. / Eifler-Olivi, K. / Marinho, J. / Reinberg, T. / Furler, S. / Schaefer, J.V. / Pluckthun, A. / Wolf, E. / Ulrich, H.D.
History
DepositionJul 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jun 11, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_ref_seq / symmetry
Item: _cell.volume / _entity.formula_weight ..._cell.volume / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _symmetry.space_group_name_Hall
Description: Model orientation/position / Details: C terminus of DARPin structures are re-refined. / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DARPin
C: Ubiquitin-like protein SMT3
B: DARPin
D: Ubiquitin-like protein SMT3


Theoretical massNumber of molelcules
Total (without water)51,2944
Polymers51,2944
Non-polymers00
Water1,00956
1
A: DARPin
C: Ubiquitin-like protein SMT3


Theoretical massNumber of molelcules
Total (without water)25,6472
Polymers25,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DARPin
D: Ubiquitin-like protein SMT3


Theoretical massNumber of molelcules
Total (without water)25,6472
Polymers25,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.972, 94.747, 120.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DARPin


Mass: 16821.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Ubiquitin-like protein SMT3


Mass: 8824.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMT3, YDR510W, D9719.15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12306
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Bis-Tris pH 6.5, 23% (v/v) PEG 3350

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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 / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→47.37 Å / Num. obs: 17608 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 61.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.028 / Rrim(I) all: 0.101 / Χ2: 0.98 / Net I/σ(I): 17.7 / Num. measured all: 229854
Reflection shellResolution: 2.51→2.61 Å / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 1.496 / Num. measured all: 24989 / Num. unique obs: 1948 / CC1/2: 0.897 / Rpim(I) all: 0.433 / Rrim(I) all: 1.558 / Χ2: 0.96 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→44.11 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.16 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3015 1744 9.97 %
Rwork0.2428 --
obs0.2486 17493 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 0 56 3506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023503
X-RAY DIFFRACTIONf_angle_d0.5924759
X-RAY DIFFRACTIONf_dihedral_angle_d3.856477
X-RAY DIFFRACTIONf_chiral_restr0.045557
X-RAY DIFFRACTIONf_plane_restr0.004633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.580.45051400.35191262X-RAY DIFFRACTION99
2.58-2.670.3941440.34431304X-RAY DIFFRACTION99
2.67-2.760.44931400.36781267X-RAY DIFFRACTION99
2.76-2.870.41711430.36081301X-RAY DIFFRACTION99
2.87-30.3271410.31711282X-RAY DIFFRACTION100
3-3.160.36761430.29851295X-RAY DIFFRACTION99
3.16-3.360.3691460.29411305X-RAY DIFFRACTION100
3.36-3.620.3261450.27821311X-RAY DIFFRACTION100
3.62-3.980.29631470.20811315X-RAY DIFFRACTION100
3.98-4.560.24991480.19231334X-RAY DIFFRACTION100
4.56-5.740.24531490.21151346X-RAY DIFFRACTION100
5.75-44.110.26951580.21121427X-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)
10.7408-0.01572.27919.95090.37517.5294-0.3744-1.0914-0.090.74381.1518-2.36591.151.3021-0.75391.16020.6351-0.38061.5864-0.44380.9342-7.3136-21.2735-3.9822
27.562-4.2207-4.153.30190.98164.17440.82320.5369-0.97760.8459-0.60941.24232.7922-0.0339-0.33730.99890.0823-0.21480.7882-0.10880.6591-15.8494-18.40381.4544
33.06950.13350.83166.82031.31767.9379-0.1260.0927-0.029-0.2991-0.16180.26550.2238-0.210.31350.4660.1637-0.0930.9216-0.08030.4486-14.8736-5.5668-3.1961
45.0492-1.1161-1.76556.64070.48198.651-0.1412-0.09760.4294-0.4704-0.44070.8064-0.8577-0.57160.63050.68940.1335-0.19350.9016-0.14910.5679-16.08638.68960.0489
56.2127-5.5731-0.82519.34022.38745.5008-0.2107-0.29471.80531.45030.4522-1.2185-0.67732.0538-0.38030.8168-0.0157-0.27771.0722-0.17610.8878-10.266316.01053.6672
63.08232.6129-1.26923.5689-2.52262.0822-0.6331-1.16872.0809-0.567-0.1064-0.3362-0.16420.38960.89391.00010.0525-0.28750.8262-0.21890.4974-14.639218.2771-4.6912
71.1026-1.1720.9192.33280.69798.1145-0.0170.72110.0184-0.20290.15260.0930.5793-0.716-0.01140.67760.1074-0.22541.1663-0.00180.6827-1.7706-1.93294.7067
89.15743.6821-0.16066.1469-3.40543.9014-0.1262-0.92860.32970.71510.3602-0.1578-0.619-0.6194-0.24580.66620.0482-0.02810.9534-0.11570.4847-5.92334.79519.8117
94.91561.18540.61413.5938-3.55975.33290.0167-1.6191.00290.725-0.2336-0.3132-0.5298-0.2750.21990.67980.0121-0.08071.1316-0.17270.5731-1.50322.609817.4155
104.33573.3730.83636.15380.19618.32670.0351-0.367-0.2806-0.1525-0.3239-0.4263-0.45070.85320.24860.48640.0745-0.14221.0672-0.0550.60772.5586-1.002512.5517
115.6209-1.81372.89467.89970.27327.20971.7716-0.32941.19320.3501-0.092-1.5278-1.21151.4286-1.12681.0714-0.48920.34931.9936-0.06660.529812.40437.094534.6269
124.05442.60014.32839.67712.58266.91380.3157-0.55761.08031.1412-0.31860.6943-1.16960.69550.10750.9306-0.0880.26441.1371-0.14770.83278.76176.040237.0502
132.2009-0.094-2.83348.61684.90318.52640.5437-2.08820.85110.96580.2474-0.5234-0.24580.5519-0.8080.70910.06940.0121.1894-0.13660.477611.6127-2.610940.5396
147.44580.2968-6.99298.30682.42337.7385-0.6297-0.5062-0.14560.70710.09030.55230.08-0.41310.52630.45740.08330.06351.0950.08690.60636.4543-8.779438.0312
153.62930.1725-3.06263.36591.52787.8112-0.352-0.575-0.09950.754-0.25870.7310.751-0.96060.69320.5445-0.11290.16471.07850.00050.65034.6704-17.151233.4352
165.58342.142-4.02796.59711.95278.67790.0749-0.6508-0.87081.694-0.9343-0.26411.4040.92320.8580.97530.19060.19191.03130.22880.77418.5464-21.741743.3326
175.64786.5085-5.40737.9458-6.4175.31320.2091-0.7010.2079-0.07380.65180.6497-0.98881.7349-1.03280.9417-0.14440.12111.0648-0.00270.69480.7729-24.778129.3429
186.4522-2.38964.41792.1105-0.84443.55980.34540.2023-3.3009-0.76310.9457-0.44460.3123.2434-1.0021.18630.25610.44461.49130.02281.3789.8475-29.229429.1544
191.7191-0.9434-2.51433.2392.19464.15151.34210.7054-1.6550.4703-0.1566-0.73341.38611.7029-1.14581.3813-0.1194-0.17321.06420.24281.045211.1152-31.187537.4488
207.04951.1046-0.65587.94761.5156.5193-0.3286-0.4743-0.73860.28260.341-0.02970.1251-0.34430.00040.4620.160.01540.8591-0.0330.486616.9373-14.76724.6932
217.57177.5336-6.11778.8658-7.91737.4505-1.08281.1336-0.5282-1.59831.2495-0.85872.0109-0.5315-0.17170.71010.25280.12031.3429-0.16120.641425.355-17.337317.7807
229.1367-2.28223.95097.8465-5.75599.04870.29370.52630.0673-0.4777-0.5089-0.40011.45121.86490.26970.59920.11720.07731.0079-0.20140.427824.4634-13.399622.4306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 117 )
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 162 )
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 171 )
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 40 )
8X-RAY DIFFRACTION8chain 'C' and (resid 41 through 56 )
9X-RAY DIFFRACTION9chain 'C' and (resid 57 through 77 )
10X-RAY DIFFRACTION10chain 'C' and (resid 78 through 95 )
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 26 )
12X-RAY DIFFRACTION12chain 'B' and (resid 27 through 51 )
13X-RAY DIFFRACTION13chain 'B' and (resid 52 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 103 )
15X-RAY DIFFRACTION15chain 'B' and (resid 104 through 127 )
16X-RAY DIFFRACTION16chain 'B' and (resid 128 through 137 )
17X-RAY DIFFRACTION17chain 'B' and (resid 138 through 150 )
18X-RAY DIFFRACTION18chain 'B' and (resid 151 through 159 )
19X-RAY DIFFRACTION19chain 'B' and (resid 160 through 168 )
20X-RAY DIFFRACTION20chain 'D' and (resid 21 through 66 )
21X-RAY DIFFRACTION21chain 'D' and (resid 67 through 76 )
22X-RAY DIFFRACTION22chain 'D' and (resid 77 through 95 )

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