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- PDB-8u8m: X-ray crystal structure of TEBP-1 MCD2 homodimer -

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Basic information

Entry
Database: PDB / ID: 8u8m
TitleX-ray crystal structure of TEBP-1 MCD2 homodimer
ComponentsDouble-strand telomeric DNA-binding proteins 1
KeywordsPROTEIN BINDING / Telomeres / C. elegans / shelterin / DNA-binding protein / TEBP-1 / DTN-1 / homodimerization / MYB / homeodomain
Function / homologyDNA binding / : / Double-strand telomeric DNA-binding proteins 1
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNandakumar, J. / Padmanaban, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM148276 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Caenorhabditis elegans telomere-binding proteins TEBP-1 and TEBP-2 adapt the Myb module to dimerize and bind telomeric DNA.
Authors: Padmanaban, S. / Lambacher, N.J. / Tesmer, V.M. / Zhang, J. / Shibuya, H. / Nandakumar, J.
History
DepositionSep 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-strand telomeric DNA-binding proteins 1
B: Double-strand telomeric DNA-binding proteins 1
C: Double-strand telomeric DNA-binding proteins 1
D: Double-strand telomeric DNA-binding proteins 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9468
Polymers54,7104
Non-polymers2364
Water43224
1
A: Double-strand telomeric DNA-binding proteins 1
B: Double-strand telomeric DNA-binding proteins 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4734
Polymers27,3552
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-23 kcal/mol
Surface area13110 Å2
MethodPISA
2
C: Double-strand telomeric DNA-binding proteins 1
D: Double-strand telomeric DNA-binding proteins 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4734
Polymers27,3552
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-25 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.842, 59.965, 151.966
Angle α, β, γ (deg.)90.000, 101.823, 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
Double-strand telomeric DNA-binding proteins 1 / TEBP-1


Mass: 13677.616 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tebp-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O62329
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: TEBP-1 MCD2 + 1 M succinic acid, 9 mM cobalt chloride, 100 mM HEPES, pH 7.5, 16 degrees C, hanging drop, cryoprotectant: 1.2 M succinic acid, 7 mM cobalt chloride, 100 mM HEPES, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→148.74 Å / Num. obs: 35989 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 62.87 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.56 / Num. unique obs: 2686

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.58 Å / SU ML: 0.5208 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.7532
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2652 1831 5.09 %
Rwork0.2323 34158 -
obs0.234 35989 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.16 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 4 24 3832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283900
X-RAY DIFFRACTIONf_angle_d0.51125296
X-RAY DIFFRACTIONf_chiral_restr0.0407584
X-RAY DIFFRACTIONf_plane_restr0.0031668
X-RAY DIFFRACTIONf_dihedral_angle_d10.46041416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.53951360.47422550X-RAY DIFFRACTION98.68
2.77-2.850.4871610.45172690X-RAY DIFFRACTION98.45
2.85-2.950.43761210.40942548X-RAY DIFFRACTION97.87
2.95-3.050.3221750.35912624X-RAY DIFFRACTION97.49
3.05-3.170.37221470.32862549X-RAY DIFFRACTION97.89
3.17-3.320.29431170.2952651X-RAY DIFFRACTION98.44
3.32-3.490.27731570.26512656X-RAY DIFFRACTION98.43
3.49-3.710.26681810.24542566X-RAY DIFFRACTION98.67
3.71-40.24091030.21542669X-RAY DIFFRACTION99.64
4-4.40.22071500.2022661X-RAY DIFFRACTION99.82
4.4-5.040.21421600.17772627X-RAY DIFFRACTION99.93
5.04-6.340.2334990.19052687X-RAY DIFFRACTION99.89
6.35-49.580.19851240.16142680X-RAY DIFFRACTION99.08
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.16577410918-0.0389528967322.249209964861.857988540670.510635779399.083673489680.0306487060144-0.625924679523-0.8353696899990.1324386980250.7562837581590.6411713594580.771102104359-0.447976756768-0.484577103290.6955071457360.113810461675-0.1211359813320.6989220433390.001424659526530.624942599319-4.1160539011814.711881880739.0300207328
23.64896449469-0.342270329880.1094088417323.206093698773.549560186754.369659892760.8829664537690.270067982092-1.197967066960.3486519727180.857929185274-0.496749649931-1.40049511604-0.56171295467-0.245279068150.903430943730.5614723742060.07249846932341.006450787210.1030414199920.758729100619-6.5013046134230.080197397134.7769095098
33.611289262240.3730778487050.4358383716887.27569549495-1.88520981559.746368253950.286450491723-0.537988394136-0.2093217813210.3629478094050.374833712426-0.0520758675902-0.2680393926250.134715210635-0.5991219302350.4689761484620.229035711836-0.0005479034270150.828334614736-0.0009699141454240.636181072809-1.3819713701220.710453714840.1286461363
43.52969349034-1.088357481960.1430290566782.26230625721-2.218451471334.955511543110.5093964250280.893375887461-0.0493571450448-0.240667449972-0.005571030803860.152291018954-0.385772784901-0.0771007671459-0.3403675842131.054028906850.07658652316320.06664344754751.09137693445-0.1077149124440.7358255150452.2485350111925.37082792519.7066694859
52.597863049240.758068355379-1.070022054514.77856803055.153987981761.99563766931-0.149978474338-0.787571295076-0.394108925224-0.7228076253530.5630088237430.125662381926-1.704213634961.59010153678-0.04234237291471.199943144150.209837337343-0.2051157041610.8328445348460.03034133087840.748432851311-1.3944545627418.600922552755.7136359292
62.39083887119-2.889471261713.93495542295.79785901056-2.64044726479.751888839280.66563000479-0.348979894284-0.549812075789-0.3519300601720.2530360920731.139434193550.505449157533-1.26910463947-0.6540555648331.252258099810.181794063950.1273468448871.17281914250.2453908530510.849538710156-3.2663356255.2615422810763.2147483343
71.37747666473-1.24927066272-0.3439525229745.579543818660.505256991814.382822521420.1370868304560.087206326758-0.2190306724530.0942022304679-0.04434850870310.3396656897531.31945940236-0.14156520930.008246178430111.273724718890.4637913643320.09458491399050.5512452156140.2014152222060.8242814210027.003373700211.4682819276760.126351772
84.99804612089-2.953665931161.092480851977.69173766891-5.815158588154.76115358541.216070807190.478290181352-2.03044405826-1.298851254180.01741019657751.082291741961.87231220379-1.25098544398-1.474118132961.00323237210.125652527718-0.326537727321.04866708301-0.192432352671.02077452243-3.380742043536.5936361750448.8612499713
94.89059113784-1.69329990706-1.467431548280.5884604634710.6276661034381.984290323020.200582706320.4656986710860.902818710452-0.63827855831-0.257617516465-0.884674821402-2.829795460720.5423035562080.1614327666751.246383286770.05872614310740.07498457307240.895090977440.1565052018490.703013898265.632942348913.416324114259.7289792846
105.90264674216-2.8917954378-0.3697981995854.68396084706-0.1898226033225.53198214550.314438599866-1.56903999529-0.6105090305411.217204670710.2537941413040.634631457558-1.27454574983-1.54246251188-0.6217275149221.066762909520.4319602219940.09370538884181.114719066670.293116274420.8662261847640.9743982410118.3171184302872.5237037176
118.285360942870.2867541738382.2621283511.290917627661.903450112973.243522663151.04320953630.287404678149-0.606554248658-0.355147053985-0.245467949562-0.136967145709-0.112677002461-0.198215997279-0.7318538693691.1667283640.2736813259610.1237350144170.6871457709840.2035713394460.7203021108329.028574167952.5519630651875.377206501
129.35817231839-2.857732178171.914707573742.70503132120.4021779241958.37883982818-0.514251543164-1.6733962393-0.353650518330.8872098723370.676018826940.396373966522-1.05406396124-2.22831336425-0.2767116508381.595039242210.4323139404480.301570084981.197723893910.2769875482670.8569672554483.21994437339.9223781877582.0153720511
134.82603811632-1.84545076081-1.763237698173.25636371751-1.801751174347.986485136830.138719674783-0.8306871648990.531624143625-0.3518269243580.2595778657920.378497292437-0.412977687603-0.847874039863-0.6247907567131.487278815660.304696026670.1343773289941.001154874710.003140554952740.65083515690110.29306739148.2773382670484.1489221751
142.063174808420.4590728899280.07949999831782.48722983375-0.4734206717611.344667150150.320417297751-0.0292349555129-1.2575536727-1.03880309263-0.04934583294320.8395093388890.899367815004-0.134840754789-0.1544639921861.129920463920.2199357803720.00523223923940.5793908573080.1590977357610.9848426499889.380637847271.0481898792184.7652672614
155.191154981261.280069682113.596795459062.00895619191-1.982436467223.339418271632.176133222350.768009139387-0.5650792634310.398460637714-0.1015691062111.451388193321.813565064720.210899164681-2.286192898081.558024685610.6146896735-0.06886461862721.287021380010.2350447554270.67454610913617.73928454431.2840285431520.2722646678
169.92353895511-2.08466085098-0.1230360355563.244544229923.091754493933.336648520920.7936584145510.754135348706-0.158718440605-0.737091621361-0.2333559825340.472268166744-1.480711115460.238172113232-0.7550591587251.391803250810.5218032488350.06050154649791.427051962670.1621353653970.71248006744415.088018916710.8938404088.5275375629
173.976580180122.1826730773-2.828537919868.23635744291-0.4510136703778.18861536625-0.472400469029-0.7029761792090.705793691840.01534424272771.4171527897-1.10094598024-1.365717590753.69888977751-1.079942120891.58444157566-0.09207000193720.2568043034261.92467182509-0.2935893923570.84792080717127.409524752314.66624781854.00293863619
182.60288935726-1.166016958250.02440612126472.645211673163.370812828186.65692087891-0.915326636395-0.9868199053040.9083628393190.9856360740562.16519380436-1.02205335514-0.07185918967672.55883510621-1.249563446781.552951009220.34675148970.2094543263261.20099136554-0.0116617264640.81825672814520.698071368415.828072102816.9592335731
196.58433189115-1.418770186631.485628729651.300928094722.390759095067.758278846470.0156170572831-0.883639600048-1.425689252920.7169075758851.64180909538-0.7451760471561.013496733442.61218845892.124151732981.224461459871.123358526170.1050583952782.32729659076-0.3853120581210.6876068192524.61577452714.7851488212613.4628653234
206.28743250146-0.301860435438-2.07151679585.453423142382.316263240092.680781234360.2419743522920.1444323303080.323497251088-1.080973685380.1686516013250.153863316227-1.4579685060.142953474974-0.764689645911.33279033340.4007038738040.09456055114051.24700705140.09640640194850.61944600553321.94036767466.87177631192-2.06969063266
215.718352607660.936637001031-1.651111007387.145802789660.5232712863362.48143824329-0.167660079685-0.2458595314820.00327997531737-1.071037299680.07078896262750.5633085816670.692772189674-1.726811649150.02133107102171.093683880050.286777563223-0.03074450503311.132898393020.04735193652570.7490001660119.9856296650.0722909282228-8.17909337054
228.462095830532.88831361277-3.292298923417.617139067033.356934883554.30463167385-0.2068354425220.964221753565-0.253265236423-0.9818063854050.5706614189540.371085818584-1.019353555370.832682750952-0.5404769487611.044387866960.2025521491330.1300413638811.010395737730.02157603971790.6566491434426.26545921833.46194836057-12.6134558626
239.43107312401-1.5951651716-5.079231201869.68820350296.730033207136.407170645350.6335802987050.9903173258851.100252896511.117553081292.35012240502-0.485447458493-1.011301257030.184929420639-2.419498915881.597962326830.4114418206240.2580604061691.4159445787-0.03250085148710.76522100825624.172462376114.421416914825.9985100467
241.07335777544-0.997093253707-0.9333428437977.05999911849-0.9154566383054.852817611280.7788687402830.407477468740.888942251892-0.4705685925170.482583453470.48716191791-1.43334866527-0.4441404620791.57132632861.706119644221.036288485860.405563859920.7778415265690.03764809486620.88127743752114.519713804911.106072515237.6489038579
255.20661810881-1.18633680606-1.532843785615.09297181685-3.298928412338.66900302140.2730780524030.497086577216-0.54501407521-0.488465593663-0.3135524120570.07058485465441.23823057968-0.7093633782190.125747403371.181547539560.3015137674510.01967858124730.652126428024-0.0108438413450.72715350601717.0629289311-0.085060508604937.8962576382
260.395453629040.0674470336141.016756418160.7438872813010.3237725249532.641484223120.361772897405-0.8399393931910.06049168720770.7799666680151.336087376270.9489925710110.437948016516-3.00988612663-0.5718825236191.098566044230.755795075329-0.06537511541461.947609376030.422285416760.88865248008212.13606623786.5029800707324.1558999456
275.132381806281.28173070663-3.689696783095.940463198072.461800691675.256384621991.245007441441.520304600510.28313595797-0.311628995171-0.346106197462-0.6680146543790.1449746022382.15091010264-0.4328384359691.217532014730.5211299545640.147320276721.140025827070.0929805528910.71482135862125.37300123227.344878280132.7813880087
283.9007056496-1.427392866921.284023342994.80798861496-0.3637693359744.261586319370.538019062470.1078201010610.728815806904-0.409643939474-0.2449736764220.173418259314-1.75305381609-0.0348361555493-0.3880412507541.342075251310.1276186022860.3098830470240.5765737092340.02261041538990.6606682958423.61714235048.9133531124748.4859089349
295.69915805071.371174917522.45766791094.88719970053-2.493191733833.171391363541.06453446992-0.9502520427690.955087194522-0.0983352732961-0.153765435868-0.0950445020778-3.49459695729-0.299325908648-0.4817403890592.29396130607-0.06039124379330.4400026674540.810322228111-0.1788288800390.94121302830323.63095454715.611906898157.3904005141
300.7323648481671.419478235791.47921739172.74753283982.730009659916.115106171340.3243073756570.00568862931908-0.8584087162640.6725315725110.285107152535-1.49429392488-0.4663805898341.079121159640.1561268544671.5529697781-0.1897750833730.4437469949230.8904954319910.1682879358051.208837214436.30539372027.7588824137254.7294390829
315.4313843297-2.843769952861.527806800855.726006644140.8931843482521.347868062010.243286791845-1.22343167771-0.3667299235490.5401008711750.4919159024580.784158473647-0.238022299022-0.193771371566-0.4812016013811.40694799589-0.1938926744220.3069498702820.857391520520.07336080996480.67778685309923.29319108726.7779585516560.9139146667
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 166 through 184 )AA166 - 1841 - 19
22chain 'A' and (resid 185 through 190 )AA185 - 19020 - 25
33chain 'A' and (resid 191 through 236 )AA191 - 23626 - 71
44chain 'A' and (resid 237 through 282 )AA237 - 28172 - 116
55chain 'B' and (resid 166 through 171 )BB166 - 1711 - 6
66chain 'B' and (resid 172 through 184 )BB172 - 1847 - 19
77chain 'B' and (resid 185 through 206 )BB185 - 20620 - 41
88chain 'B' and (resid 207 through 214 )BB207 - 21442 - 49
99chain 'B' and (resid 215 through 225 )BB215 - 22550 - 60
1010chain 'B' and (resid 226 through 236 )BB226 - 23661 - 71
1111chain 'B' and (resid 237 through 246 )BB237 - 24672 - 81
1212chain 'B' and (resid 247 through 263 )BB247 - 26382 - 98
1313chain 'B' and (resid 264 through 274 )BB264 - 27499 - 109
1414chain 'B' and (resid 275 through 281 )BB275 - 281110 - 116
1515chain 'C' and (resid 166 through 171 )CC166 - 1711 - 6
1616chain 'C' and (resid 172 through 184 )CC172 - 1847 - 19
1717chain 'C' and (resid 185 through 196 )CC185 - 19620 - 31
1818chain 'C' and (resid 197 through 214 )CC197 - 21432 - 49
1919chain 'C' and (resid 215 through 225 )CC215 - 22550 - 60
2020chain 'C' and (resid 226 through 246 )CC226 - 24661 - 81
2121chain 'C' and (resid 247 through 263 )CC247 - 26382 - 98
2222chain 'C' and (resid 264 through 281 )CC264 - 28199 - 116
2323chain 'D' and (resid 166 through 171 )DD166 - 1711 - 6
2424chain 'D' and (resid 172 through 184 )DD172 - 1847 - 19
2525chain 'D' and (resid 185 through 206 )DD185 - 20620 - 41
2626chain 'D' and (resid 207 through 214 )DD207 - 21442 - 49
2727chain 'D' and (resid 215 through 225 )DD215 - 22550 - 60
2828chain 'D' and (resid 226 through 252 )DD226 - 25261 - 87
2929chain 'D' and (resid 253 through 269 )DD253 - 26988 - 104
3030chain 'D' and (resid 270 through 274 )DD270 - 274105 - 109
3131chain 'D' and (resid 275 through 281 )DD275 - 281110 - 116

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