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- PDB-8g0q: Crystal structure of the yeast Ndc80:Nuf2 head region with a boun... -

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Basic information

Entry
Database: PDB / ID: 8g0q
TitleCrystal structure of the yeast Ndc80:Nuf2 head region with a bound Dam1 segment
Components
  • DASH complex subunit DAM1,Kinetochore protein NUF2
  • Kinetochore protein NDC80
KeywordsCELL CYCLE / Cell division / chromosome segregation / kinetochore / Ndc80 complex / Ndc80 / Nuf2 / Dam1 / DASH-Dam1 complex / phospho-regulation
Function / homology
Function and homology information


mitotic spindle polar microtubule / centromere clustering / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / meiotic chromosome segregation / mitotic spindle pole body / positive regulation of attachment of spindle microtubules to kinetochore ...mitotic spindle polar microtubule / centromere clustering / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / meiotic chromosome segregation / mitotic spindle pole body / positive regulation of attachment of spindle microtubules to kinetochore / attachment of spindle microtubules to kinetochore / protein localization to chromosome, centromeric region / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / spindle pole body / positive regulation of microtubule polymerization / mitotic spindle organization / spindle microtubule / chromosome segregation / kinetochore / mitotic spindle / microtubule binding / cell division / protein-containing complex binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ncd80 complex, Ncd80 subunit / DASH complex subunit Dam1 / DASH complex subunit Dam1 / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / : ...Ncd80 complex, Ncd80 subunit / DASH complex subunit Dam1 / DASH complex subunit Dam1 / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / : / HEC/Ndc80p family / Domain of unknown function (DUF5595) / Actin-binding Protein, T-fimbrin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Kinetochore protein NUF2 / Kinetochore protein NDC80 / DASH complex subunit DAM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsZahm, J.A. / Jenni, S. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Open Biology / Year: 2023
Title: Structure of the Ndc80 complex and its interactions at the yeast kinetochore-microtubule interface.
Authors: Zahm, J.A. / Jenni, S. / Harrison, S.C.
History
DepositionFeb 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinetochore protein NDC80
B: DASH complex subunit DAM1,Kinetochore protein NUF2
C: Kinetochore protein NDC80
D: DASH complex subunit DAM1,Kinetochore protein NUF2


Theoretical massNumber of molelcules
Total (without water)122,0354
Polymers122,0354
Non-polymers00
Water00
1
A: Kinetochore protein NDC80
B: DASH complex subunit DAM1,Kinetochore protein NUF2


Theoretical massNumber of molelcules
Total (without water)61,0182
Polymers61,0182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-63 kcal/mol
Surface area30040 Å2
MethodPISA
2
C: Kinetochore protein NDC80
D: DASH complex subunit DAM1,Kinetochore protein NUF2


Theoretical massNumber of molelcules
Total (without water)61,0182
Polymers61,0182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-62 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.997, 129.997, 216.308
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Space group name HallP322(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: -y,-x,-z+1/3
#5: -x+y,y,-z+2/3
#6: x,x-y,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 115 through 684)
d_2ens_1chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPGLUA2 - 269
d_21ens_1ASPGLUC1 - 268

NCS oper: (Code: givenMatrix: (-0.461041106313, 0.0351179656091, -0.886683611432), (-0.0168689639251, -0.999382890624, -0.0308103226908), (-0.887218426514, 0.000752608594985, 0.461348997218)Vector: ...NCS oper: (Code: given
Matrix: (-0.461041106313, 0.0351179656091, -0.886683611432), (-0.0168689639251, -0.999382890624, -0.0308103226908), (-0.887218426514, 0.000752608594985, 0.461348997218)
Vector: 111.920838913, 12.9088176791, 68.1270123025)

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Components

#1: Protein Kinetochore protein NDC80 / 80 kDa spindle component protein / Nuclear division cycle protein 80 / Two-hybrid interaction with ...80 kDa spindle component protein / Nuclear division cycle protein 80 / Two-hybrid interaction with DMC1 protein 3


Mass: 34124.867 Da / Num. of mol.: 2 / Fragment: residues 106-318,residues 621-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NDC80, HEC1, TID3, YIL144W / Production host: Escherichia coli (E. coli) / References: UniProt: P40460
#2: Protein DASH complex subunit DAM1,Kinetochore protein NUF2 / DUO1 and MPS1-interacting protein 1 / Kinetochore assembly protein DAM1 / Outer kinetochore protein DAM1


Mass: 26892.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DAM1, YGR113W, G6153, NUF2, YOL069W / Production host: Escherichia coli (E. coli) / References: UniProt: P53267, UniProt: P33895

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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: 4.32 Å3/Da / Density % sol: 71.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M ADA buffer pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.22→99.9 Å / Num. obs: 24938 / % possible obs: 93.6 % / Redundancy: 70.6 % / Biso Wilson estimate: 80.04 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.021 / Rrim(I) all: 0.162 / Net I/σ(I): 16.2
Reflection shellResolution: 3.22→3.54 Å / Rmerge(I) obs: 3.44 / Num. unique obs: 1549 / CC1/2: 0.51 / Rpim(I) all: 0.418 / Rrim(I) all: 3.55 / % possible all: 75.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.22→99.86 Å / SU ML: 0.4157 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.6146
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2847 1236 4.96 %
Rwork0.2629 23699 -
obs0.264 24935 72.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.18 Å2
Refinement stepCycle: LAST / Resolution: 3.22→99.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7940 0 0 0 7940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00278075
X-RAY DIFFRACTIONf_angle_d0.561910875
X-RAY DIFFRACTIONf_chiral_restr0.03581210
X-RAY DIFFRACTIONf_plane_restr0.00491405
X-RAY DIFFRACTIONf_dihedral_angle_d4.95991034
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.65797192021 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.350.7362110.4449307X-RAY DIFFRACTION8.43
3.35-3.50.4203440.3801860X-RAY DIFFRACTION23.95
3.5-3.680.3268900.3251670X-RAY DIFFRACTION47.02
3.68-3.910.29411570.30352855X-RAY DIFFRACTION79.75
3.91-4.220.31611900.28713427X-RAY DIFFRACTION95.56
4.22-4.640.31141890.27233602X-RAY DIFFRACTION99.63
4.64-5.310.29311830.23933587X-RAY DIFFRACTION99.5
5.31-6.690.3451900.33013640X-RAY DIFFRACTION99.87
6.69-99.860.20461820.20823751X-RAY DIFFRACTION99.9
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)
10.429031188033-0.0267115709126-0.1697011128671.360191887950.5799616138940.470655021178-0.0263746704303-0.04716388093870.0836639513510.122648667504-0.1671579440810.330714335325-0.0591935994685-0.2233275491570.01258732617540.6240348024170.4652959488910.1169285974510.382484106541-0.2738726218440.1377046030632.168209383541.690780392824.2501886669
20.742402051194-0.538560933231-0.8189972644541.481639386861.107809059851.143772457620.07587729141030.1735799548970.0241204415156-0.0352398775875-0.1991549391370.290980759644-0.124052982436-0.435979832090.3122745612110.6249644899590.3868141510820.06400166461930.69993094776-0.4279352941660.2290719042324.187180206731.667842980617.8819070835
31.87961254181-1.45133795374-0.3776270134822.717851104120.4599274686060.557234106824-0.114104189869-0.00516567514407-0.111244896550.001097153555820.07094060315-0.118810742861-0.00789621659158-0.0509430418743-0.0237081111150.6128597715140.4099770644390.1093214981360.378337207523-0.2859437733960.3994072303135.48998146326.848071909528.5265493248
41.025699990140.1942686236161.483026177246.537943907650.8522782839582.18991346640.203990341103-1.35123397478-0.8152482752850.557244700088-0.2776157127580.3246412396620.883345282069-0.9108811750160.02438851192191.260294278520.1229130168540.4446999957020.8675741761730.4455442832661.2945557508148.4614500475-1.349747803838.0342935881
50.5490431786670.429441957159-0.2832227714731.14041125368-1.152911728421.268572430190.0967783609466-0.150836978312-0.1126508938930.0469524353424-0.250613316381-0.166033886706-0.06348928451620.162146063151-0.05755800996140.931112573524-0.1582532969920.8136201175210.01387645699250.4570794952540.40437278435655.3334575661-0.98715371418221.2697362659
60.5285965413380.126628580048-0.1100653390160.668394350689-0.2423330784940.649156552643-0.00738677030368-0.0620129599208-0.006534960839020.0306843304463-0.0563020008023-0.083483302818-0.0236000621843-0.0960243801893-0.06985331778131.06437468321-0.2162312304640.4107772838790.5376027331440.5768871941810.73074316678547.7997108483-48.878989252469.33731928
70.78709871892-0.01772760815570.1926612579211.74026528713-0.7701838837770.3859512951350.200072968517-0.0254260840411-0.377342799865-0.152984192448-0.1166684541890.1186204799350.229885827133-0.4190220137910.07861541392931.0716225578-0.2458047950870.2416818035790.862894616212-0.3517198932760.71879316492742.3924682817-8.7776941998411.7249854902
80.01836172178030.01003675858130.1335047940640.008450731077630.07785242438470.7898621155110.1771384302830.273334200486-0.147533449323-0.178433285075-0.2146480194150.1683905393670.153171870444-0.1435395489130.09134682028630.839910241893-0.05667057038270.3450969406050.449669764538-0.4129171142990.38510253106733.22806939045.8549465161210.9183252075
90.1346792102920.15192338918-0.1133463957460.462458745308-0.2008105157550.1132712598770.0682889280831-0.5420362969260.4744583174080.282638260326-0.38791392623-0.762050506526-0.189183638037-0.5368861495510.2977851286821.11341121040.2303731000570.4179449719441.27427404002-0.09027222192461.1211809664931.147222015624.945411825438.1049547493
100.260899910616-0.3595737271860.1419189899460.579801343795-0.2374384552090.09624855050610.06601388008430.0765382362452-0.0339236797358-0.250977194344-0.1806555685820.0836688497364-0.268707211769-0.353444455841-0.01472217137810.651400737760.02413259262980.385005273970.423934759859-0.4392080478070.27748753313635.142873321712.800059741912.9789462025
110.276127593155-0.0782993217502-0.02326529092480.538377201371-0.1238578903870.6517899807560.02923151033690.02127413772250.0210445191336-0.03932892904340.0151511007175-0.0221246607475-0.013190490028-0.00934122373555-0.03935325899570.655007841614-0.01474293156420.4060741094870.01834189750750.1441493165770.23326253008753.1325510254-11.361983636521.1691288628
120.582146967381-0.0272891425360.1612365890210.342956291620.1920305223990.3836376154410.01909724066270.07106561416180.0645007050624-0.111150447431-0.00750959540776-0.0787824462709-0.1202968445930.0199231344795-0.1111660578470.769103178306-0.2666182067870.2359848304530.3786717377080.5258284356820.50815135554140.9280605174-37.176311816862.46950655
130.364973608023-0.4437085915190.3111812124820.543891808403-0.3494433827190.2974276246880.1341025051910.1852789903280.0319071258127-0.338515280047-0.233825333945-0.4399180386690.2716909214540.2276659539970.0701654438371.647426267430.4712872566060.8330298071410.8030371138450.500870569451.6308734729277.2168788754-30.790812792150.3772402436
140.593571757875-0.902624033008-0.1505526931961.401750531010.4023899793181.00387401788-0.1061478126290.0217209561940.2859722145050.4595660046640.0571130936131-1.405233602980.4779946141730.4616513111640.2957814081131.310715718850.3246900431280.2718755941520.6964294043820.522241793122.1070075675784.3120393989-20.419848975354.5018661
152.108175644980.3169455203470.01532763145154.33714994783-0.7643341329283.02292032341-0.0269880006756-0.058699989201-0.003106008755130.0668145012750.09365478597290.2205439265950.00728486798613-0.0972668995305-0.08127638261850.987051065347-0.06886648991030.04404705097880.3344617094330.4071035520320.88591880427964.9114106807-6.3195038474943.7945715238
163.448022876860.4421946954981.823049350420.950752023610.4521969378882.80287867261-0.310836818695-0.8348620873280.04950205062840.8937289375840.2343654276820.326071207697-0.138885627211-0.8377362701520.002086659373740.9690362561030.1835749668310.5774415531530.5520252420570.09115293230161.050538982158.477300163116.047014872540.6642472416
171.00283656476-0.3485095692790.5714473474850.121055201483-0.1987574669540.326075783025-0.01833203691360.148504310145-0.0455703063673-0.247537447864-0.152097594914-0.2848490025530.2420269120060.150679173740.1548917125061.057813867590.09312811809060.8411035733570.4958477454750.101010740871.4959830641477.42735050176.1977187721323.9530223931
180.3342432742560.148610520739-0.1360546778140.278141816123-0.2492341699170.169459066065-0.203274780452-0.09832343235090.07433851698130.0798647128742-0.1918772985990.0293663003366-0.162183771448-0.272545043951-0.4789896541720.8053064463010.4547345208060.3858388126250.364708379943-0.6613910507980.44571100702133.739559216749.435412317150.8337110286
191.82940806644-0.676982645445-1.084367139241.358545481291.075699306651.052165292230.321751610001-0.255242953476-0.1264758732940.455483949219-0.2224919899360.149299827672-0.3474637858910.503890333393-0.1008570249061.27850132765-0.185104121136-0.1304722540421.005373837090.2878737920871.9827473271690.91214286599.0632840982646.8485671655
204.620032771183.98241833455-1.793961095318.8500935123-3.359697662574.61214718316-0.1987467011980.08320229361580.3677055867980.673695067416-0.24137892176-0.426287123201-0.6424577974440.3102187597420.3463760335040.9551202210370.01254316348610.1575219473380.4449091829450.2039653692621.6892465012272.83444093764.8732980883446.7198667283
211.489961495420.161193805787-0.8519743712733.66605013261-3.312544731086.33690072279-0.408677860745-0.229690492074-0.6096880040730.115563912222-0.463842584703-0.2367753759850.836436892211-0.4723718327860.7968926162470.878490215193-0.09973583354250.3327497739230.6491586905710.2206688462811.5093287844470.7559283551-8.9103636481150.2712991695
220.34281893735-0.3641983006440.01758003167142.10166532564-0.559459998520.163243692753-0.14002988464-0.279081018396-0.555741801140.0197294923943-0.336185485527-1.200803269710.1557467462190.5323264793840.6640150357341.04492524137-0.05063848996460.4294928466860.7423541908320.6233901178821.8674739964683.26718352847.6758683554836.7717679856
230.3381578677770.3780455914150.2233476852980.422590182610.2492775173710.148289382925-0.0179962725922-0.06133062540470.04175516809610.0573091167220.000134799935312-0.066871093457-0.08163793249780.028382052478-0.1962503234510.6013607012610.2722839417450.2813895414270.436679241644-0.2501639827790.5653253192351.978224154734.516946121941.8716920177
242.075894251710.49247691096-0.7285473470321.86556218359-0.0951479875582.640972590470.112434964005-0.131823551050.1327371588290.220519040549-0.03867928759540.160243014973-0.160036480198-0.00132562569816-0.06964559072170.6330477318150.3208480851140.09195422709520.465546965758-0.443996271430.43577908693833.64961700754.593403488766.6763257161
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 114:166)AA114 - 1661 - 53
22(chain A and resid 167:219)AA167 - 21954 - 106
33(chain A and resid 220:240)AA220 - 240107 - 127
44(chain A and resid 241:267)AA241 - 267128 - 154
55(chain A and resid 268:625)AA268 - 625155 - 210
66(chain A and resid 626:684)AA626 - 684211 - 269
77(chain B and resid 254:299)BB254 - 2991 - 27
88(chain B and resid 300:1064)BB300 - 106428 - 96
99(chain B and resid 1065:1082)BB1065 - 108297 - 114
1010(chain B and resid 1083:1132)BB1083 - 1132115 - 164
1111(chain B and resid 1133:1411)BB1133 - 1411165 - 190
1212(chain B and resid 1412:1451)BB1412 - 1451191 - 230
1313(chain C and resid 115:165)CC115 - 1651 - 51
1414(chain C and resid 166:229)CC166 - 22952 - 115
1515(chain C and resid 230:247)CC230 - 247116 - 133
1616(chain C and resid 248:280)CC248 - 280134 - 166
1717(chain C and resid 281:303)CC281 - 303167 - 189
1818(chain C and resid 304:684)CC304 - 684190 - 268
1919(chain D and resid 1009:1046)DD1009 - 10461 - 38
2020(chain D and resid 1047:1064)DD1047 - 106439 - 56
2121(chain D and resid 1065:1101)DD1065 - 110157 - 93
2222(chain D and resid 1102:1149)DD1102 - 114994 - 141
2323(chain D and resid 1150:1423)DD1150 - 1423142 - 162
2424(chain D and resid 1424:1451)DD1424 - 1451163 - 190

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