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- PDB-9gau: Sumo-Darpin-C10-complex -

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Basic information

Entry
Database: PDB / ID: 9gau
TitleSumo-Darpin-C10-complex
Components
  • DARPin
  • Ubiquitin-like protein SMT3
KeywordsSIGNALING PROTEIN / Sumo / Darpin / Ankyrin repeats
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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / 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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / 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: 2.64 Å
AuthorsWolf, E. / Cakilkaya, B. / 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 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,1502
Polymers22,1502
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.461, 44.687, 47.602
Angle α, β, γ (deg.)90.000, 98.760, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein DARPin


Mass: 13211.627 Da / Num. of mol.: 1
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: 8938.099 Da / Num. of mol.: 1
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.: 31 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris. 16% (v/v)PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.64→47.05 Å / Num. obs: 5539 / % possible obs: 98.5 % / Redundancy: 5 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.144 / Rrim(I) all: 0.329 / Χ2: 1 / Net I/σ(I): 6.5
Reflection shellResolution: 2.64→2.77 Å / % possible obs: 95.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 1.614 / Num. measured all: 3612 / Num. unique obs: 695 / CC1/2: 0.401 / Rpim(I) all: 0.776 / Rrim(I) all: 1.798 / Χ2: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→47.05 Å / SU ML: 0.3983 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2883 554 10.02 %
Rwork0.233 4977 -
obs0.2385 5531 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.27 Å2
Refinement stepCycle: LAST / Resolution: 2.64→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 0 31 1537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221527
X-RAY DIFFRACTIONf_angle_d0.58912070
X-RAY DIFFRACTIONf_chiral_restr0.0407241
X-RAY DIFFRACTIONf_plane_restr0.0039275
X-RAY DIFFRACTIONf_dihedral_angle_d4.3494208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.910.3721330.30321190X-RAY DIFFRACTION96.29
2.91-3.330.3041370.28221241X-RAY DIFFRACTION98.57
3.33-4.190.31651420.21681270X-RAY DIFFRACTION99.86
4.19-47.050.23621420.20521276X-RAY DIFFRACTION97.73
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)
19.337516148411.40327772653-0.4796979281224.463300160684.406406602194.769763632380.735162439795-0.888779404394-0.7538755258752.26521901186-0.8045807130130.9320644279660.56004745063-0.3041165275840.1533516921330.8535911772560.008614967449550.06961138648920.449771811526-0.05320403071560.49274708520429.8224807361-17.26954040147.2515449984
25.383137911533.772099261751.295256160476.772595988772.399065360562.79908912903-0.913224193283-0.100913779472-0.263895659467-0.9784083395160.465989780776-0.0334062209562-0.314896063329-0.5169913243460.3024670218510.6859798735770.0654925985728-0.07438360433630.5757895829730.01903430509020.3134719955937.9492823854-17.68280189222.61103413085
33.03959042045-1.02423246715-1.444240908665.238610478910.2152660430665.370217220550.6524220459030.5278297011650.379083312791-0.514318733404-0.0288938125799-0.278562275639-0.0256619470469-0.0346443288982-0.5634006526720.4045814918970.0780126882441-0.01165262433480.319380106463-0.01714917052490.40848302098725.2669405094-9.925094548295.40757841965
45.270340652873.296118300664.75062674672.448426968473.152173363234.361379493810.359473537502-1.588178708060.4639225766520.645476739844-0.2205409160030.1945972241820.122918878494-0.930322546735-0.2471271138310.5413490681840.04668552251640.004943128055840.4584621147050.03172546662670.38204803557433.7047693934-6.3418108178910.4528316133
55.589068433191.620666904114.242514417067.907520399531.542203346153.47107621740.4637725175380.8076930214572.19430818069-0.11127475545-0.2169563462040.320720602843-0.01116070066250.605179437202-0.3850113195330.4190283251590.004540559067350.04517452943270.486674182286-0.02978610940330.63056884700539.7356531174-6.937721347782.51215790723
66.48101559962-3.76464907452-6.089782139224.888868547174.797419344826.3225673570.5960308379581.158516365580.708618317705-0.0179886665946-0.510288611233-0.0911960605384-0.261632211977-0.305017939860.0004212084802050.5585926814880.1494232932050.02342442975510.5503995081890.09182435970730.28317596174525.7116531348-0.9381116317925.70411494389
74.98394088891-4.13965099275-4.931709536317.649538479083.297245147575.58589363995-1.13601423371-1.421075204891.010048445570.4103524267380.603282285389-1.82650975286-0.3701434120181.52197969470.2378475562370.54503225240.167018210274-0.07847680260160.599007219673-0.08312797608020.73988754608633.5340527642.2956420227712.8632408786
86.211335805091.34839358024-1.563932053632.84649459355-0.6364588139118.314909875660.773068729777-0.1946253314140.9115036333850.7109872445060.0504673387762-0.474609743585-0.6960620230191.24199184073-0.504280400130.507517548828-0.0395291955512-0.04466579191070.4368791629270.03711753076560.5564903044540.35929448463.292777394694.87460067237
99.47979220571-4.8223200433-5.212247469944.354473589473.242319759423.425811491280.713935747926-0.05202379292042.61707832877-0.3881841102750.142384947041-1.03271837811-0.6135156736620.9125265326070.1122387786050.5381937196910.0011247837602-0.05040190142730.3861443067950.03644499929290.46954941285128.3850338068.702573755949.88638381088
107.27188404583-3.39136136745-4.661587957997.98267605350.3881662884633.49099555406-0.128359606401-1.000997774552.283766544540.519686678780.675907018009-1.85491840377-1.714649100571.49331134777-0.3110763928480.68727559727-0.08946529792420.1008727229250.494016063749-0.2470949278911.511382578539.87886724211.224535602511.7708080037
114.55043024523-2.11232024039-0.592613237566.05612702005-1.268625371210.590498121368-0.4009236358920.01699365461780.5721095178920.5473575227360.270878504785-1.03920235386-0.05391903114070.1516409918670.1518186547320.6005137789160.109397117893-0.1131801461730.391382176013-0.1192687015390.4016759400117.13282137182.9714468983318.9175707832
126.85206474121-3.874830931990.07926804179142.66170304091-1.899594752338.71064965919-0.0428727927541.048843441560.703052106801-0.192893337577-0.553215001739-0.331984674063-0.922097442714-0.56052480340.3325867640190.646231390256-0.03285048814330.06159906907870.554063084499-0.02177685089350.37527422963711.052215121410.357145815713.2022192858
137.97105994134-2.502729651770.9045203069448.1585439792-0.3974011336750.105955502373-0.1784586966540.8530830064580.893091308132-0.1111948586510.639416140869-0.669879946233-0.812100178388-0.727430062427-0.1868201287290.59425940426-0.00529377294747-0.04510772204230.5639714403970.0149435019660.1833918221563.8493270780211.138596579316.5410276669
149.561238000143.2203243042.913094506995.91773616876-1.4307853922.0992359672-1.02716661745-0.6529827028470.7573805852421.810132602040.5714408472820.3742235214920.9700123951660.3117979586160.2929234816951.231657778170.17103776126-0.01349418032410.499536675937-0.0445668782180.30715886056611.16785561678.0178997616727.7990557347
153.53594357817-1.138583641642.269506356215.30429530703-1.311427612167.23527002531-0.351110832301-0.395476158676-0.0595632124830.6013515533080.5201359388610.3489519663070.914732605995-0.614756761777-0.2622465027940.8182762692650.0427860245211-0.1549218279160.5971506689070.06419922268770.2240620389627.060304809632.543506662522.0892671341
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 26 )AA14 - 261 - 13
22chain 'A' and (resid 27 through 38 )AA27 - 3814 - 25
33chain 'A' and (resid 39 through 51 )AA39 - 5126 - 38
44chain 'A' and (resid 52 through 61 )AA52 - 6139 - 48
55chain 'A' and (resid 62 through 70 )AA62 - 7049 - 57
66chain 'A' and (resid 71 through 84 )AA71 - 8458 - 71
77chain 'A' and (resid 85 through 95 )AA85 - 9572 - 82
88chain 'A' and (resid 96 through 104 )AA96 - 10483 - 91
99chain 'A' and (resid 105 through 126 )AA105 - 12692 - 113
1010chain 'A' and (resid 127 through 136 )AA127 - 136114 - 123
1111chain 'B' and (resid 21 through 45 )BB21 - 451 - 25
1212chain 'B' and (resid 46 through 56 )BB46 - 5626 - 36
1313chain 'B' and (resid 57 through 66 )BB57 - 6637 - 46
1414chain 'B' and (resid 67 through 81 )BB67 - 8147 - 61
1515chain 'B' and (resid 82 through 96 )BB82 - 9662 - 76

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