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- PDB-7pb8: Crystal structure of the CENP-OPQUR complex -

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Basic information

Entry
Database: PDB / ID: 7pb8
TitleCrystal structure of the CENP-OPQUR complex
Components(Centromere protein ...) x 5
KeywordsCELL CYCLE / Inner kinetochore
Function / homology
Function and homology information


positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / centromere complex assembly / metaphase chromosome alignment / inner kinetochore / CENP-A containing chromatin assembly / chordate embryonic development / negative regulation of epithelial cell apoptotic process / centriolar satellite / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal ...positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / centromere complex assembly / metaphase chromosome alignment / inner kinetochore / CENP-A containing chromatin assembly / chordate embryonic development / negative regulation of epithelial cell apoptotic process / centriolar satellite / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / NRIF signals cell death from the nucleus / chromosome segregation / positive regulation of epithelial cell proliferation / RHO GTPases Activate Formins / Separation of Sister Chromatids / actin cytoskeleton / nuclear body / cell adhesion / cell division / apoptotic process / nucleolus / regulation of DNA-templated transcription / signal transduction / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Centromere protein R / Centromere protein Q / Centromere protein U / Centromere protein P / Kinetochore component, CENP-R / CENP-Q, a CENPA-CAD centromere complex subunit / CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P / CENP-A nucleosome associated complex (NAC) subunit / Centromere protein O / Cenp-O kinetochore centromere component
Similarity search - Domain/homology
Centromere protein R / Centromere protein P / Centromere protein U / Centromere protein Q / Centromere protein O
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.68 Å
AuthorsBellini, D. / Yatskevich, S. / Muir, K.W. / Barford, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Science / Year: 2022
Title: Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.
Authors: Stanislau Yatskevich / Kyle W Muir / Dom Bellini / Ziguo Zhang / Jing Yang / Thomas Tischer / Masa Predin / Tom Dendooven / Stephen H McLaughlin / David Barford /
Abstract: Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron ...Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-A reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A, and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle.
History
DepositionJul 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Centromere protein O
Q: Centromere protein Q
U: Centromere protein U
P: Centromere protein P
R: Centromere protein R


Theoretical massNumber of molelcules
Total (without water)151,1175
Polymers151,1175
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17500 Å2
ΔGint-152 kcal/mol
Surface area39460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.614, 51.299, 109.999
Angle α, β, γ (deg.)90.000, 117.490, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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Centromere protein ... , 5 types, 5 molecules OQUPR

#1: Protein Centromere protein O / CENPO / CENP-O / Interphase centromere complex protein 36


Mass: 33830.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPO, ICEN36, MCM21R / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): HighFive / References: UniProt: Q9BU64
#2: Protein Centromere protein Q / / CENP-Q


Mass: 15442.636 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPQ, C6orf139 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): HighFive / References: UniProt: Q7L2Z9
#3: Protein Centromere protein U / / CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV ...CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV latent nuclear antigen-interacting protein 1 / MLF1-interacting protein / Polo-box-interacting protein 1


Mass: 47609.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MAPRGRRRPRPHRSEGARRSKNTLERTHSMKDKAGQKCKPIDVFDFPDNSDVSSIGRLGE NEKDEETYETFDPPLHSTAIYADEEEFSKHCGLSLSSTPPGKEAKRSSDTSGNEASEIES VKISAKKPGRKLRPISDDSESIEESDTRRKVKSAEKISTQRHEVIRTTASSELSEKPAES ...Details: MAPRGRRRPRPHRSEGARRSKNTLERTHSMKDKAGQKCKPIDVFDFPDNSDVSSIGRLGE NEKDEETYETFDPPLHSTAIYADEEEFSKHCGLSLSSTPPGKEAKRSSDTSGNEASEIES VKISAKKPGRKLRPISDDSESIEESDTRRKVKSAEKISTQRHEVIRTTASSELSEKPAES VTSKKTGPLSAQPSVEKENLAIESQSKTQKKGKISHDKRKKSRSKAIGSDTSDIVHIWCP EGMKTSDIKELNIVLPEFEKTHLEHQQRIESKVCKAAIATFYVNVKEQFIKMLKESQMLT NLKRKNAKMISDIEKKRQRMIEVQDELLRLEPQLKQLQTKYDELKERKSSLRNAAYFLSN LKQLYQDYSDVQAQEPNVKETYDSSSLPALLFKARTLLGAESHLRNINHQLEKLLDQG
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): HighFive / References: UniProt: Q71F23
#4: Protein Centromere protein P / / CENP-P


Mass: 34005.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPP / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): HighFive / References: UniProt: Q6IPU0
#5: Protein Centromere protein R / / CENP-R / Beta-3-endonexin / Integrin beta-3-binding protein / Nuclear receptor-interacting factor 3


Mass: 20228.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3BP, CENPR, NRIF3 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): HighFive / References: UniProt: Q13352

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Non-polymers , 1 types, 1 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% PEG2kmme, 40 mM NaFormate, 200 mM bis-tris propane pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.68→46.3 Å / Num. obs: 6104 / % possible obs: 77.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 79.89 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.6
Reflection shellResolution: 3.68→3.9 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 6104

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QLF

6qlf


Resolution: 3.68→25.65 Å / SU ML: 0.6215 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3521 295 4.83 %
Rwork0.2563 5809 -
obs0.2608 6104 55.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.91 Å2
Refinement stepCycle: LAST / Resolution: 3.68→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5705 0 0 1 5706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00435792
X-RAY DIFFRACTIONf_angle_d0.75387791
X-RAY DIFFRACTIONf_chiral_restr0.0463897
X-RAY DIFFRACTIONf_plane_restr0.0042992
X-RAY DIFFRACTIONf_dihedral_angle_d6.37749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.68-4.630.4279650.281289X-RAY DIFFRACTION24.94
4.63-25.650.33452300.25094520X-RAY DIFFRACTION85.11
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)
14.64065533549-1.87388386843-2.11332787624.29259108463.155833251464.160213251440.337988359389-0.2428106005910.582109373588-0.6656129810560.880059646075-1.02987918260.06609979880081.91022168232-0.2676392655581.176020730830.03343325945230.3173741033221.94766280050.124075431890.44824404748657.40982446591.0232317938130.432612508
23.28927035703-1.165789133020.2207606613742.3438761449-0.6911539356291.86101628525-0.03062644055340.155607619164-0.566856418684-0.438143145422-0.3165656460450.1414313513230.964663975551-0.259468483489-0.006570951538870.800724742667-0.3323199231510.03198060024390.508461728281-0.3300344220960.28814429990636.3766877826-8.9013482726436.5769786261
32.53530871348-0.883292349437-0.5048059368492.17500132656-0.02730166398792.26804326663-0.5820207061080.312593282344-0.5747725027410.135132835209-0.1680996451240.5108750141460.585547611207-0.3102368430150.5337766259340.40842073139-0.02311070688740.3060320621080.52790761738-0.03378671074470.43941314088324.4128140137-1.3262423348736.3069352509
41.655577093610.5092211703981.623409378282.15043390283-1.119579575962.90531430431-0.283741636756-1.19694436997-0.1672664233110.345244126410.01383208117620.585254935288-0.229236436998-0.351412601903-0.2560419740490.298052411137-0.1799874090850.1302647754770.864330826643-0.1738701344550.78616371729511.01760123318.7748923450344.2376866955
53.7789153764-0.160912768155-1.185948566030.981814570341-0.7494194196360.99062811270.496602491805-0.377784555059-0.6064326852170.108992267607-0.4707520283430.829810318972-0.0380866931451-0.3757926931690.1938783330180.976597824288-0.5807212939510.004186161805340.728974920985-0.158994489260.50854004503411.36258219815.6138944892736.0464339775
62.616023382832.296777354761.867495346612.476872006372.780666698834.16187214756-0.40321570246-0.1530193749291.28452548734-1.011717058690.2529223568180.89526112776-0.930241891080.0232118153594-0.07876706196191.28245312248-0.269910167511-0.3390809024231.612120955621.107300367752.19952556768-1.6758638816513.278690538439.102432625
70.000682811534814-0.0663562257822-0.01915296005362.312373489030.6578332577530.1853871894170.274751763863-0.1822417804220.546601289344-0.209905810042-0.1706706233980.60154587364-0.50165885264-1.761068312640.1014505961860.371639538060.208177247973-0.3848744001961.383471795770.1701975063841.632888773264.1384266251216.54523930634.0378500758
81.22475531031.194782255093.477865125593.24249374263.433881331819.85806755546-1.22078159627-0.3090638883670.3855822566970.157877648163-0.5302868757220.981328922738-0.476810610151-0.7477115082470.2223248919540.467083532360.1282631970.2847517103870.407338981230.1604120328931.2077659823116.933119511918.226944874636.6421149135
91.80997000115-0.4796993470160.9543338503171.29448993572-0.8285192765952.030953731170.671763737506-1.18374912504-0.284290702045-0.186558019450.776752065003-0.132513434974-0.252267330631-0.9084849236-0.8037448423590.920679905313-0.248154079786-0.222696169091.005717381430.3269337265991.18307633687-5.61613258614-17.760486622729.7649668369
102.440466334931.282900090950.9205535759780.729340584402-0.01078271195583.752655978490.06893080713250.4740391311540.415630587331-0.166497330134-1.094750977130.0521646894789-0.2969174761730.1315442145311.108362972170.7144118312010.310301867469-0.007558594299970.561812420692-0.0732412089550.80678630093518.6037458972-16.40388575667.55749676566
113.644869939470.459980533259-0.8313157384660.0739418550989-0.3852454503772.989964954460.1565756694390.7528310779050.540351618740.3916371354540.686410207639-0.8907674536140.02481473210530.390489668424-0.6005190373321.33414129354-0.452143378601-0.2602173220950.6529156216290.07496421069411.2889947614622.86793361687.53151157133-4.72689891133
122.621139584610.1640196092-0.294462139061.79642469838-0.5805226658071.584490408930.538422989723-0.131518524232-0.2913905693730.0994549884691-0.1039295809950.160136423740.01871118364840.488732185409-0.3165730104980.335595626551-0.219951462872-0.1847603589270.968037818175-0.1823154162920.6716232773866.83743126209-7.487067528999.64565515846
133.81836766195-2.671798212491.750106889627.98884141101-0.5356050146894.49548804148-0.513818785304-0.541951813534-0.085665115878-0.2065961157871.586580883650.1437926642910.0106596286572-0.341659172807-1.275319908812.044978744360.2492773947380.3704075548421.560755742170.07725535041841.4050465698244.00133495979.12566183830.414531139713
141.902502307950.127422039616-0.01072572380972.694190840181.236068173541.31036911891-0.2078676411690.2439095781340.455911996334-0.497346370460.277958608728-0.211358114378-0.5833529360421.009930163130.04565394249051.07447203742-0.3934911918430.2616904102730.970887098573-0.1518956149650.641605710141.04186588315.9567056607425.9620911394
154.45662429909-1.42681035003-1.48124947240.6667404842590.0149094501141.469345222830.2379134443110.4507541337230.706900061039-0.2845878834820.60405114008-0.14577345809-0.3406050176740.796268145327-0.4873163438480.53561621871-0.1276965674240.03643100860591.11259856157-0.2095081726330.67131794004829.40365758-7.37704646858-2.97078696915
161.20065523854-0.462870152023-0.2026110047920.6667186743280.2277720284122.173967824150.6844464164470.702067581323-0.322839232634-0.3078937292440.0344232042485-0.130951499686-0.4015467167960.382402980162-0.3063700519711.10782253208-0.482576628386-0.3091548091180.902670525607-0.2615805340520.27399552754421.6799755567-0.1146416989463.28493805567
170.8225758829960.602106083203-0.8530791466523.431520960511.086272779212.29384056568-0.1582959001090.329905450120.378100718995-1.5221585167-0.5508134202240.221465596608-0.92584725266-0.6226874735110.3919284950671.140828722580.362015880117-0.442348335790.406627742584-0.131915918230.9329547827138.20519879354-0.784719379652-8.53159651528
180.670003547980.119881134588-0.8452848356420.0465711405016-0.1821524065021.104152083180.14291407140.648946461590.111170727889-0.2258319603160.1438899879960.1638429147560.402530543811-0.3322013531150.4777585853460.5766211434790.469612102583-0.7358332704990.657352463833-0.1373041119910.59841543550414.3418814821-9.309936726912.08962385759
192.62287524981-1.051421790091.055711881182.828760189552.205607709583.27005031022-0.4021994572891.539740663231.08913645408-0.3615103530151.32632773784-0.173539433552-1.148178011450.5648546080620.08623677590391.88493701593-0.6132907687280.5794351080621.503749286150.4092360711981.6688479469233.748837468216.6210676103-13.9889632788
202.587588170980.01919057213771.302890383313.06474453431.222466323431.135906113440.6488447185780.644856420537-0.0115520676327-0.198851112127-0.0574579403971-0.0841051322327-0.7688116159760.1160730369660.1530893688142.33192694372-0.02342247386990.1330531669512.56833930643-0.1785494746430.50319583823925.022603858517.78258018941.95693964442
215.759820046490.3046672020730.03008262989180.4940121026010.4189518475960.365577038217-0.08902700765690.4610243084560.858829578478-0.117215195273-0.273003021465-0.2221172783860.228489447967-0.0537658939768-0.2456031565051.30577060113-0.02638762449051.274667837152.302967830110.03771546916862.3359633999446.083246069513.0851309654-7.24230162383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|89-111 }O89 - 111
2X-RAY DIFFRACTION2{ A|112-160 }O112 - 160
3X-RAY DIFFRACTION3{ A|161-210 }O161 - 210
4X-RAY DIFFRACTION4{ A|211-230 }O211 - 230
5X-RAY DIFFRACTION5{ O|231-248 }O231 - 248
6X-RAY DIFFRACTION6{ O|249-261 }O249 - 261
7X-RAY DIFFRACTION7{ O|262-276 }O262 - 276
8X-RAY DIFFRACTION8{ O|277-289 }O277 - 289
9X-RAY DIFFRACTION9{ Q|153-198 }Q153 - 198
10X-RAY DIFFRACTION10{ Q|199-215 }Q199 - 215
11X-RAY DIFFRACTION11{ Q|216-268 }Q216 - 268
12X-RAY DIFFRACTION12{ U|315-398 }U315 - 398
13X-RAY DIFFRACTION13{ U|399-417 }U399 - 417
14X-RAY DIFFRACTION14{ P|53-184 }P54 - 184
15X-RAY DIFFRACTION15{ P|185-205 }P185 - 205
16X-RAY DIFFRACTION16{ P|206-235 }P206 - 235
17X-RAY DIFFRACTION17{ P|236-255 }P236 - 255
18X-RAY DIFFRACTION18{ P|256-283 }P256 - 283
19X-RAY DIFFRACTION19{ R|84-113 }R84 - 113
20X-RAY DIFFRACTION20{ R|114-130 }R114 - 130
21X-RAY DIFFRACTION21{ R|131-152 }R131 - 152

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