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- PDB-7m3p: Xrcc4-Spc110p(164-207) fusion -

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Basic information

Entry
Database: PDB / ID: 7m3p
TitleXrcc4-Spc110p(164-207) fusion
ComponentsXrcc4-Spc110p(164-207)
KeywordsCELL CYCLE / microtubule nucleation
Function / homology
Function and homology information


FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / spindle pole body / cellular response to lithium ion ...FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / spindle pole body / cellular response to lithium ion / 2-LTR circle formation / response to X-ray / SUMOylation of DNA damage response and repair proteins / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Spindle pole body component 110, C-terminal / Spindle pole body component 110 C-terminal domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal
Similarity search - Domain/homology
Spindle pole body component 110 / DNA repair protein XRCC4
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.00001856449 Å
AuthorsBrilot, A.F. / Lyon, A.S. / Zelter, A. / Viswanath, S. / Maxwell, A. / MacCoss, M.J. / Muller, E.G. / Sali, A. / Davis, T.N. / Agard, D.A.
Funding support United States, 13items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)David Agard United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM031627 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118099 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM105537 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103533 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM083960 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109824 United States
National Science Foundation (NSF, United States)1144247 United States
National Institutes of Health/Office of the Director1S10OD020054 United States
National Institutes of Health/Office of the Director1S10OD021741 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM124149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Elife / Year: 2021
Title: CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation.
Authors: Axel F Brilot / Andrew S Lyon / Alex Zelter / Shruthi Viswanath / Alison Maxwell / Michael J MacCoss / Eric G Muller / Andrej Sali / Trisha N Davis / David A Agard /
Abstract: Microtubule (MT) nucleation is regulated by the γ-tubulin ring complex (γTuRC), conserved from yeast to humans. In , γTuRC is composed of seven identical γ-tubulin small complex (γTuSC) sub- ...Microtubule (MT) nucleation is regulated by the γ-tubulin ring complex (γTuRC), conserved from yeast to humans. In , γTuRC is composed of seven identical γ-tubulin small complex (γTuSC) sub-assemblies, which associate helically to template MT growth. γTuRC assembly provides a key point of regulation for the MT cytoskeleton. Here, we combine crosslinking mass spectrometry, X-ray crystallography, and cryo-EM structures of both monomeric and dimeric γTuSCs, and open and closed helical γTuRC assemblies in complex with Spc110p to elucidate the mechanisms of γTuRC assembly. γTuRC assembly is substantially aided by the evolutionarily conserved CM1 motif in Spc110p spanning a pair of adjacent γTuSCs. By providing the highest resolution and most complete views of any γTuSC assembly, our structures allow phosphorylation sites to be mapped, surprisingly suggesting that they are mostly inhibitory. A comparison of our structures with the CM1 binding site in the human γTuRC structure at the interface between GCP2 and GCP6 allows for the interpretation of significant structural changes arising from CM1 helix binding to metazoan γTuRC.
History
DepositionMar 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xrcc4-Spc110p(164-207)
B: Xrcc4-Spc110p(164-207)


Theoretical massNumber of molelcules
Total (without water)41,4662
Polymers41,4662
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-36 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.131, 52.168, 55.916
Angle α, β, γ (deg.)100.804, 94.148, 112.831
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein Xrcc4-Spc110p(164-207) / X-ray repair cross-complementing protein 4 / Spindle pole body spacer protein SPC110


Mass: 20733.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: XRCC4, SCNYR20_0001052900, SCP684_0001052400 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: Q13426, UniProt: A0A6V8RX86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 13% PEG3350 and 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2→35.734 Å / Num. obs: 50099 / % possible obs: 93 % / Redundancy: 2.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03095 / Rrim(I) all: 0.0426 / Net I/σ(I): 17.36
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.1635 / Mean I/σ(I) obs: 5.45 / Num. unique obs: 5015 / CC1/2: 0.939 / Rrim(I) all: 0.2245

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEOctober 15, 2015data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.27data extraction
XDSOctober 15, 2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FU1

1fu1


Resolution: 2.00001856449→35.733970253 Å / SU ML: 0.229710874723 / Cross valid method: THROUGHOUT / σ(F): 1.98672757416 / Phase error: 24.5410731391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472931477 2717 6.02666193465 %
Rwork0.203945438763 42366 -
obs0.206492953569 45083 86.7280981878 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.8552882439 Å2
Refinement stepCycle: LAST / Resolution: 2.00001856449→35.733970253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2711 0 0 254 2965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047314159842754
X-RAY DIFFRACTIONf_angle_d0.5754657597053697
X-RAY DIFFRACTIONf_chiral_restr0.0379071301196413
X-RAY DIFFRACTIONf_plane_restr0.00301346748604469
X-RAY DIFFRACTIONf_dihedral_angle_d13.36275197981677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.00001856449-2.03640.3491211236881490.2788203561892043X-RAY DIFFRACTION82.0359281437
2.0364-2.07550.2589162888651290.2523790734962212X-RAY DIFFRACTION85.5003652301
2.0755-2.11790.2379851870051280.2514677468612266X-RAY DIFFRACTION85.9913793103
2.1179-2.1640.2724415057611580.2388149901682142X-RAY DIFFRACTION85.0591715976
2.164-2.21430.2547835349521290.2442845144372204X-RAY DIFFRACTION85.9616801769
2.2143-2.26960.2212317848021490.2199295846372202X-RAY DIFFRACTION86.1172161172
2.2696-2.3310.2424356826711490.2233500544062264X-RAY DIFFRACTION87.2378886479
2.331-2.39960.2779558624381400.2232822765332231X-RAY DIFFRACTION86.4067055394
2.3996-2.4770.3220598255421470.2223888876842208X-RAY DIFFRACTION87.5464684015
2.477-2.56550.2272863891841520.2343183263632309X-RAY DIFFRACTION87.5800711744
2.5655-2.66820.2610238491121310.2367407594012200X-RAY DIFFRACTION86.9776119403
2.6682-2.78960.2446250222731350.2304370194872246X-RAY DIFFRACTION86.897810219
2.7896-2.93660.2894530300351570.2141756036852280X-RAY DIFFRACTION87.5988497484
2.9366-3.12050.268228359191420.2177309063562227X-RAY DIFFRACTION86.9038884813
3.1205-3.36130.2384882170551390.1909864731242222X-RAY DIFFRACTION87.1217712177
3.3613-3.69920.2678280299561550.1890068913692235X-RAY DIFFRACTION86.5314989138
3.6992-4.23380.2104676031481360.1638604614722267X-RAY DIFFRACTION87.636761488
4.2338-5.33130.2308916438591380.1641544950392255X-RAY DIFFRACTION87.6556776557
5.3313-35.7339702530.2108605772781540.198929254072353X-RAY DIFFRACTION91.3629737609
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)
15.609688262615.079103340660.01217015100796.06777675150.05306884433896.266024172170.05374092850270.03368437117640.02910420205410.469308872303-0.0658458528380.8195180518690.091505547648-0.891173918391-0.1324585900330.3294941757670.03353866176240.01052052996170.2374043246120.008628474129930.511429695007-7.88596072547-30.97698630645.9819949359
21.876928603121.083927553642.22872592687.76719639071-1.851268139895.62045932455-0.09697666859990.14293043232-0.397887854084-0.018085337834-0.317856307661-1.07628787114-0.02529243474310.2141460718410.3516560369410.2434169575310.0302367117010.01164365737310.1990094860760.01289345258220.3834073838898.70642955386-26.11789563450.6990585304
36.253347674363.34096163304-2.548307793594.75177628369-0.1659545391495.31014459180.303070989823-0.519230737171-0.629244958919-0.2460163477990.4016792412170.5194429942940.366783268436-0.191389811671-0.766292092430.2824533559670.0112430716114-0.09861958886510.2618118489590.098550671510.636587407453-6.7021045259-39.626358681946.2134873929
40.313248039266-0.4393463763580.8221908239687.084554924080.3784853789852.4842092463-0.09601306957910.572060035443-0.531133760639-0.488719176240.272623040589-0.585407630280.4311338623010.189163676243-0.04149325416530.2844077218980.009949322011660.05175034612730.283881468901-0.1751205520120.5204570679496.76297577503-31.685172765241.164955684
51.46302500002-1.874240196032.09024675114.55472448864-4.656097994634.985216524990.142547328110.0216658053490.0941779725887-0.5892699055580.0315492762113-0.07658805255880.797143963682-0.415704328093-0.01154122018580.3410088449580.0110075897123-0.01038144682640.3291576055780.04992927104460.42758321594-0.789722324594-49.934135248950.3368320109
69.44548655419-3.77698233747-1.37529692634.54858786558-0.3411644221633.122957978510.4170645290370.04227124244471.01211407723-0.179495410564-0.2147262905730.155273934949-0.5717295669110.35552536320.1051435212670.3592497015660.0151209815203-0.0395750067310.3114406992280.0857661346360.4262777419570.326866663782-49.762315618459.2692472526
72.058220244931.63028316204-1.015822016557.432171974141.723265212985.84111846635-0.1429029412340.1776616470510.8010157976940.8452557274580.147947301467-0.2842249845060.03354122535330.0802334836146-0.08349100393940.3805671470640.04840030628220.03040553668890.296871406640.06920398351880.382608124729-2.79330536407-42.886928205458.541352038
84.738795825193.30676952972-1.146031297954.82145546501-2.174977980294.59640311975-0.345084876515-0.05276646326140.103182926730.405032579613-0.3280661128350.430315967301-1.01441416279-0.9918674593680.431620958860.3640725585730.06719515719670.01110673744060.3990793843660.07053842264490.661437605547-3.42045627405-34.888935127955.7192445788
94.48248113446-0.5628636614-2.159534639955.34356384172-1.956160565724.516426456460.462296833962-0.141869305645-1.22919423482-0.139731077841-0.5275602417-0.393670112294-0.1800836269540.2194363124590.1465438984680.3257601350820.00973735952512-0.1878286093010.26996542550.06305314524290.90478196773510.1687031072-36.111217359553.345334396
100.703079115501-0.623671221471-1.558720489692.740010632690.7618915813483.906850726770.47512493731-0.924029488975-1.148210732920.5310878453170.030205858042-0.6868888780320.3563875458110.34508000096-0.3725808278721.02233887052-0.166977092274-0.1171596104920.95336003447-0.1973525028281.242378612499.65397918946-35.970258195471.1948597251
112.487876142040.1698223558480.9666675769621.62048385611-1.530075141692.319039162810.3201238025430.0295452849922-1.35717271221-0.130196993491-0.0462647090299-0.5776531552050.8108053382670.244846759172-0.05565037920330.4380601427340.0530333128379-0.08688749317640.278494772789-0.06678171473831.004191215787.99850905484-40.336114501549.978356507
123.50212284983-3.61216247488-1.699317813274.401856733730.8799406007984.6059556767-0.03818212112340.649548961237-1.00209541134-0.4016617311870.03609195707360.01608089819670.239030344932-0.08165920117230.1688201544090.23422919148-0.02622656669590.05452850565420.278843755371-0.1649220032410.350856083202-2.87339756977-25.414966309237.4468073821
139.01806131975-6.55022244118-4.904262984916.856864440265.020956352845.052717661220.5070098376780.345422064982-0.103347600239-0.484910855343-0.2628810035230.091327813635-0.640224353348-0.150602107759-0.3119407948410.227327893507-0.01269700525970.01696988890730.1925294364150.05360847652220.174822676146-23.5409495434-12.84597869348.9818294641
143.81200446264-2.7379775556-3.046662014774.71353758931.853972619553.40035393385-0.136401469659-0.7483712346580.3921515763880.2749268058970.06539505300170.0736694721614-0.5754720599230.213192498179-0.1014164567320.3389204478170.0810376579696-0.01319547021560.343977775037-0.1068134001710.250649865813-44.9562380952-0.41784060784564.9968535013
153.068403202020.1398617446091.1355947674.66086238521-2.672420647852.01826670123-0.1043675441050.269833435404-0.156320929545-0.5302483067690.1788551622320.01123781964770.0484507678015-0.440241854934-0.09898857647040.263371658734-0.0148434230050.0301992579080.512158015441-0.01194314994780.173708265387-2.72357731456-14.183628269631.575171928
163.8061827123-2.83740587924-0.9083380867616.688768533144.657125690076.20067676645-0.1195022586090.9869675419080.1804549089020.0662941506064-0.4134202612420.743422565614-0.328851366337-0.780300073780.2841074245150.6726517977340.376093814581-0.01129346546371.34290914971-0.05807463815020.460685970577-4.661856892774.0440958288637.9400761819
171.28864752276-0.002652552570891.310589546962.13047449154-2.782479066145.01103171522-0.286877304630.1828523277590.354220144588-0.289766934547-0.255157395808-0.648096118045-1.10656504163-0.3542026085080.2952703721050.536197608020.0711007915373-0.09360973437430.433390710711-0.05772623066710.2490212710383.33325751549-1.8575324167230.448367145
182.85592231425-0.433980494073-4.603474906481.362938470630.9215489131077.45710766532-0.0286494246596-0.1701673056180.3371620887560.2010850316860.06548740382490.210931978528-1.59319764724-0.185432495740.3116621784041.162111185340.602876654033-0.1329521686451.5080374111-0.1742468497960.540596835112-7.994902741367.1713392630328.8079587079
194.629237205330.496549784842-2.82476013332.55545077050.5608660075387.06093055790.266548461590.2514445569960.09503111433260.228952124131-0.3689334862380.557862085657-0.155277352291-2.06331716427-0.5647935973360.6194125093580.184624427550.1273716638822.047352251210.1975741037430.513913801904-8.82143858597-2.6287105531631.9011431134
202.30521271643-1.220182137020.4726925392.47439240364-0.791059094752.301375259050.05460223778630.3301351718840.355584556006-0.9012027480780.5027305978340.1025405217030.167702240545-0.8065432913090.7313823128680.638345717755-0.239803526618-0.006365368195031.138490203350.3925742426420.126087448725-1.3973759304-7.7601283083222.6936518874
212.4964256922-1.559132799860.1197854165744.94863848989-0.7629614969461.32756035263-0.5419081484640.7581973141320.515244979451-0.4764708975760.400345672533-0.002322980239910.151166261641-0.7692154885410.02149301862250.425147524805-0.1261590491480.07468203786160.8105657560560.1530603555720.3684171891220.380562517751-5.0060191658123.8372736972
229.49126674071-0.452264674458-5.131733891551.09917053780.05839509473983.99702912610.233109617176-0.393786728141-0.1466028528210.108841625428-0.130791474002-0.142491733994-0.1539954988370.278400128024-0.1453743970830.196432433755-0.00410955859603-0.0004203327723190.229102373227-0.0006598588850540.191084621426-3.90899332027-16.807772943348.5441767047
235.03473024385-1.04400414557-3.81013895570.7156066624231.554253767264.06393154845-0.186915403518-0.728817100333-0.7808369300970.180698863274-0.03602617649460.07040826815860.036189408755-0.09547667242240.2726013239330.2614635199490.0001908827427130.05150231000960.3150692050870.06987907454980.216718300231-35.7587714586-12.74265075162.3044125688
245.36254264183-3.269102710862.099031218986.491844842150.2818610082489.64372563919-0.108601882727-1.49510435081-0.993659915640.1996788857760.5555842550610.402009667149-0.433977558247-0.500569630883-0.3084851853760.3246124324810.08247919713360.04530933113590.5694836787080.02430165711650.281588584315-56.9384073393-6.5903734161968.1980915643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:5)
2X-RAY DIFFRACTION2(chain A and resid 6:20)
3X-RAY DIFFRACTION3(chain A and resid 21:34)
4X-RAY DIFFRACTION4(chain A and resid 35:46)
5X-RAY DIFFRACTION5(chain A and resid 47:57)
6X-RAY DIFFRACTION6(chain A and resid 58:63)
7X-RAY DIFFRACTION7(chain A and resid 64:70)
8X-RAY DIFFRACTION8(chain A and resid 71:76)
9X-RAY DIFFRACTION9(chain A and resid 83:100)
10X-RAY DIFFRACTION10(chain A and resid 101:104)
11X-RAY DIFFRACTION11(chain A and resid 105:116)
12X-RAY DIFFRACTION12(chain A and resid 117:134)
13X-RAY DIFFRACTION13(chain A and resid 135:152)
14X-RAY DIFFRACTION14(chain A and resid 153:174)
15X-RAY DIFFRACTION15(chain B and resid 2:24)
16X-RAY DIFFRACTION16(chain B and resid 25:29)
17X-RAY DIFFRACTION17(chain B and resid 30:61)
18X-RAY DIFFRACTION18(chain B and resid 62:68)
19X-RAY DIFFRACTION19(chain B and resid 69:76)
20X-RAY DIFFRACTION20(chain B and resid 83:101)
21X-RAY DIFFRACTION21(chain B and resid 102:117)
22X-RAY DIFFRACTION22(chain B and resid 118:144)
23X-RAY DIFFRACTION23(chain B and resid 145:165)
24X-RAY DIFFRACTION24(chain B and resid 166:174)

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