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- PDB-9q9e: Crystal structure of a TELSAM-SUMO1 fusion protein -

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Basic information

Entry
Database: PDB / ID: 9q9e
TitleCrystal structure of a TELSAM-SUMO1 fusion protein
ComponentsTranscription factor ETV6,Small ubiquitin-related modifier 1
KeywordsSIGNALING PROTEIN / SUMOylation / fusion protein-assisted crystallisation / TELSAM domain / SUMO1 protein
Function / homology
Function and homology information


protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization ...protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mesenchymal cell apoptotic process / vitellogenesis / nuclear stress granule / small protein activating enzyme binding / negative regulation of action potential / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / hematopoietic stem cell proliferation / ubiquitin-specific protease binding / transcription factor binding / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / potassium channel regulator activity / Regulation of IFNG signaling / nuclear pore / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / neurogenesis / Signaling by FLT3 fusion proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein stabilization / nuclear speck / nuclear body / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. ...Small ubiquitin-related modifier 1, Ubl domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Sterile alpha motif/pointed domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Transcription factor ETV6 / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCoste, F. / Mishra, A. / Suskiewicz, M.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101078837European Union
CitationJournal: Proteins / Year: 2025
Title: Fusion Protein-Assisted Crystallization of Human SUMO1.
Authors: Mishra, A. / Goffinont, S. / Coste, F. / Cisse, E.H. / Mance, L. / Castaing, B. / Suskiewicz, M.J.
History
DepositionFeb 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor ETV6,Small ubiquitin-related modifier 1
B: Transcription factor ETV6,Small ubiquitin-related modifier 1
C: Transcription factor ETV6,Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2976
Polymers58,7253
Non-polymers5723
Water3,747208
1
A: Transcription factor ETV6,Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0523
Polymers19,5751
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription factor ETV6,Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6702
Polymers19,5751
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription factor ETV6,Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)19,5751
Polymers19,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.726, 99.692, 113.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 Transcription factor ETV6,Small ubiquitin-related modifier 1 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / SUMO-1 / GAP-modifying protein 1 / ...ETS translocation variant 6 / ETS-related protein Tel1 / Tel / 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: 19575.162 Da / Num. of mol.: 3 / Mutation: V73E
Source method: isolated from a genetically manipulated source
Details: fusion protein: His Tag + ETV6/TEL (47-123) + SUMO1 (18-97),fusion protein: His Tag + ETV6/TEL (47-123) + SUMO1 (18-97)
Source: (gene. exp.) Homo sapiens (human)
Gene: ETV6, TEL, TEL1, SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43
Production host: Escherichia coli (E. coli) / References: UniProt: P41212, UniProt: P63165
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Na-phosphate/citric acid pH4.2, PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Feb 6, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.05→47.97 Å / Num. obs: 39816 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.25 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.08 / Net I/σ(I): 7.2
Reflection shellResolution: 2.05→2.11 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3081 / CC1/2: 0.404 / Rpim(I) all: 0.377 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47.97 Å / SU ML: 0.2131 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3975
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2312 1916 4.82 %
Rwork0.2094 37823 -
obs0.2104 39739 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.98 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 28 208 3664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193540
X-RAY DIFFRACTIONf_angle_d0.48714823
X-RAY DIFFRACTIONf_chiral_restr0.0409538
X-RAY DIFFRACTIONf_plane_restr0.0055631
X-RAY DIFFRACTIONf_dihedral_angle_d8.818498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.33461290.31212695X-RAY DIFFRACTION99.96
2.1-2.160.34861330.29172620X-RAY DIFFRACTION100
2.16-2.220.27491520.27022666X-RAY DIFFRACTION99.96
2.22-2.290.28971350.262673X-RAY DIFFRACTION100
2.29-2.380.27481230.23922685X-RAY DIFFRACTION99.96
2.38-2.470.24591450.24172654X-RAY DIFFRACTION100
2.47-2.580.24931300.22612684X-RAY DIFFRACTION100
2.58-2.720.27091310.21522687X-RAY DIFFRACTION99.96
2.72-2.890.23561380.21362683X-RAY DIFFRACTION99.86
2.89-3.110.26511560.21312670X-RAY DIFFRACTION100
3.11-3.430.21771320.18922746X-RAY DIFFRACTION99.93
3.43-3.920.18291450.17192716X-RAY DIFFRACTION99.83
3.92-4.940.17551370.1592755X-RAY DIFFRACTION99.86
4.94-47.970.21081300.20722889X-RAY DIFFRACTION99.41
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)
11.27068744902-0.1351889974360.4365304689710.1571265176340.1678569688980.40470354142-0.3914031012830.02900758629240.588915118916-0.4367927251320.0985238175782-0.3334332862150.1353568836490.115227263677-0.1091157849960.293221132692-0.05243890586880.05853543360310.17604530910.1146088072160.298872124719-30.40660848747.6303250053-19.7094909666
20.387369405135-0.215835957278-0.5969305767081.192674108550.8075702691830.6380683394680.1533842774210.148459121638-0.0299272755681-0.0371155434662-0.133291270050.06422704232470.0926929358172-0.01353559613770.0002978455610670.1491091566860.0164269182917-0.01031213419370.1548504168840.03476213524410.132459343975-34.584934560235.8062628446-15.8163931207
30.120512057893-0.224377981187-0.004116966328380.225868582613-0.02158107055260.08895816933350.05088265975360.1861405137790.345705281636-0.240156282069-0.1638346839190.336663124996-0.156133611942-0.138004344211-0.006227588137480.265094987487-0.0124655246781-0.02312676445510.4760458219090.1249692174450.404433217005-4.7659329088249.8210773912-27.3571373518
40.511295856822-0.2105674456480.3779848771940.789020769214-0.1888476467060.677805645156-0.2182593611690.1059842426180.09679614614730.0266274266240.3112224563040.1159215029840.330792244-0.3650259956340.003217363832360.2169143657630.0186481875818-0.0001626332721940.1914885702720.1133275457460.2443784287365.9091625736548.1082963931-25.9155460594
50.09400839538820.164222831609-0.02508687443570.2453719683080.1022127351410.0659490649855-0.08688958964360.708810515965-0.541263887208-0.5735438494790.0934630614181-0.6586198595080.5892766197570.1886886412350.00993604884860.3711027238240.1022899184450.07371418568430.385333195467-0.03156431861040.304914387641-19.02189279517.7318236449-28.4420132859
60.762813874866-0.8844286517490.1611846015960.841384184311-0.4546231014280.2880129956720.06139894320270.134634490279-0.150457730038-0.0108886328914-0.07650474879340.125842661507-0.00784113084088-0.1339811525260.0001116686736120.1695352556410.0246066442044-0.03668411283040.213381674312-0.005572702836360.168762187011-27.277304976316.9744782685-17.6442500737
70.278044854109-0.096374284042-0.2811775469750.5341242949240.450119889832-0.0920696778372-0.09241679702870.0119824276220.09630817618840.5253538128430.244757450642-0.0694285771551-0.20312876588-0.009525291760670.261150605801-0.0509324543694-0.0489000944846-0.1622120694930.231859904517-0.05032084424730.157153785509-8.6703351591816.8697759775-23.6275937762
80.8903786188180.2267803414230.1422040739050.419047883647-0.02256814129930.158835434117-0.2274695856770.2736474664970.00247724987442-0.3547774016930.113720591670.004994487743850.0152759907615-0.2770477519220.0002740677656290.304646315439-0.0355110125426-0.00875537520780.291224102974-0.09255998259620.31391916958215.041304307914.4229228118-35.0548971494
90.1334774739430.0004801007357820.1066684677080.0417076882212-0.04693152083530.107451397315-0.1109543570790.150076399671-0.247590859416-0.1613205238550.198781381141-0.174799198229-0.00319541067350.4279211841820.01039913786440.3004244620380.0832148795538-0.0578537447290.217517675346-0.06446029035290.227978842629-11.4667108633-2.41592038593-10.7347755082
100.693232367852-0.07920150187260.2596046208210.0939151306551-0.1392512231930.8747140732820.0421161227496-0.0832637905545-0.1270403869230.00454074615582-0.07035803991910.176200188837-0.00952500824282-0.189464077885-1.01721637388E-50.1848093688660.0219092483367-0.02248753121080.1343646434680.007575047041460.170956558769-18.17358859655.68103950494-1.76288140273
110.2675774176690.2750486046590.09459166235040.377077321394-0.1836459348930.0842029039301-0.0931755619061-0.496577301773-0.2782300666020.3459377003030.0721420362616-0.4006274966070.1280037047640.5268821974690.006218422119920.1745008917820.0584525773574-0.05445900563220.2796984469080.04145604090170.353810600463-1.816069293912.51221005783-4.52392562478
120.0386024466296-0.0278477350615-0.01730751868270.02940425087070.0130168962010.00507114215640.0567120442732-0.0291218210638-0.02053241878580.07527902128310.0881312469525-0.122939921154-0.002514639824860.01015113915290.0006345577694281.736328736390.1503676612410.3892755482141.61320231075-0.2625321980011.1281672422521.9758598065-23.3472967199-10.8278696099
130.0210129226347-0.00329383190293-0.0200491586335-0.0003090306684560.01044714707280.02176914348390.114150763475-0.308108435463-0.05386616110240.03321505186760.1848576667570.09066425621190.1356193608380.0102240248012.31720277347E-50.9521984526520.149496061840.06902353458770.7879598095960.3060044054991.2411500569616.8949175281-5.48665031533-5.99302427409
140.015614847371-0.0192606111005-0.03081544302530.168913136169-0.0243155284895-0.00107060041290.2316856619550.139535889033-0.04338977745070.09305562641970.2005210698-0.0132948611359-0.227975159592-0.02983060184970.1845912521460.929424583365-0.280902687845-0.4955876210610.5146293621710.6614363148121.4737001053126.9816276932-14.5651587313-0.821371421732
15-0.0143910990307-0.01436745371080.00847604441990.025772928699-0.01209503456060.00403907495024-0.2821679508990.271679658737-0.5051751211180.4264988318940.127838583686-0.2701239572210.0383509595228-0.0456181428390.0001065549590670.809015990274-0.03969851204330.01175452197860.765026076452-0.2879251521040.99850146271327.2449086741-7.79041308339-12.0541271263
160.05426448305190.00233334186312-0.03203291372040.0263196872968-0.05377435411820.1556774085230.1177461224930.233485047535-0.178965450817-0.02386095337640.2777672851730.197421621572-0.2778223956480.07900045106980.01168488923240.716740110677-0.119823001795-0.2632704337550.845334352208-0.1209211917591.2836215272221.184387533-6.23859317562-12.313501953
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 23 )AA11 - 231 - 13
22chain 'A' and (resid 24 through 83 )AA24 - 8314 - 73
33chain 'A' and (resid 84 through 109 )AA84 - 10974 - 99
44chain 'A' and (resid 110 through 164 )AA110 - 164100 - 154
55chain 'B' and (resid 8 through 23 )BB8 - 231 - 16
66chain 'B' and (resid 24 through 70 )BB24 - 7017 - 63
77chain 'B' and (resid 71 through 97 )BB71 - 9764 - 90
88chain 'B' and (resid 98 through 163 )BB98 - 16391 - 156
99chain 'C' and (resid 13 through 23 )CC13 - 231 - 11
1010chain 'C' and (resid 24 through 70 )CC24 - 7012 - 58
1111chain 'C' and (resid 71 through 96 )CC71 - 9659 - 84
1212chain 'C' and (resid 97 through 103 )CC97 - 10385 - 91
1313chain 'C' and (resid 104 through 114 )CC104 - 11492 - 102
1414chain 'C' and (resid 115 through 133 )CC115 - 133103 - 121
1515chain 'C' and (resid 134 through 143 )CC134 - 143122 - 131
1616chain 'C' and (resid 144 through 161 )CC144 - 161132 - 149

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