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- PDB-6xws: Crystal Structure of Drosophila CAL1 1-160 bound to CENP-A/H4 -

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Basic information

Entry
Database: PDB / ID: 6xws
TitleCrystal Structure of Drosophila CAL1 1-160 bound to CENP-A/H4
Components
  • Chromosome alignment defect 1,Chromosome alignment defect 1
  • Histone H3-like centromeric protein cid
  • Histone H4
KeywordsCELL CYCLE / Centromere / Kinetochore / cell division
Function / homology
Function and homology information


HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / kinetochore organization / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / CENP-A containing chromatin assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / inner kinetochore / protein localization to kinetochore / chromatin-protein adaptor activity / mitotic metaphase chromosome alignment / nuclear chromosome / chromosome, centromeric region / spindle assembly / CENP-A containing nucleosome / chromosome segregation / kinetochore / structural constituent of chromatin / nucleosome / heterochromatin formation / mitotic cell cycle / nucleosome assembly / chromosome / chromatin organization / protein heterodimerization activity / nucleolus / DNA binding / nucleus
Similarity search - Function
TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 / Histone H3/CENP-A ...TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H4 / Histone H4 / Histone H3-like centromeric protein cid / Chromosome alignment defect 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.36 Å
AuthorsJeyaprakash, A.A. / Medina-Pritchard, B. / Lazou, V. / Zou, J. / Byron, O. / Abad, M.A. / Rappsilber, J. / Heun, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust202811 United Kingdom
Citation
Journal: Embo J. / Year: 2020
Title: Structural basis for centromere maintenance by Drosophila CENP-A chaperone CAL1.
Authors: Medina-Pritchard, B. / Lazou, V. / Zou, J. / Byron, O. / Abad, M.A. / Rappsilber, J. / Heun, P. / Jeyaprakash, A.A.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionJan 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3-like centromeric protein cid
B: Histone H4
C: Chromosome alignment defect 1,Chromosome alignment defect 1


Theoretical massNumber of molelcules
Total (without water)47,9243
Polymers47,9243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-64 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.700, 199.700, 76.754
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Histone H3-like centromeric protein cid / CENP-A homolog / Centromere identifier protein


Mass: 26014.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cid, CENP-A, CG13329 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V6Q2
#2: Protein Histone H4


Mass: 11408.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His4r, BcDNA:RH52884, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, CG3379, Dmel_CG3379
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4KFZ9, UniProt: P84040*PLUS
#3: Protein Chromosome alignment defect 1,Chromosome alignment defect 1


Mass: 10501.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: cal1, CAL1, Cal1, CLD2, Dmel\CG5148, CG5148, Dmel_CG5148
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VEN2

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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: 1.5 Å3/Da / Density % sol: 18.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5 and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 4.36→172.95 Å / Num. obs: 2322 / % possible obs: 89 % / Redundancy: 8.9 % / Biso Wilson estimate: 196.37 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.6
Reflection shellResolution: 4.36→5.186 Å / Rmerge(I) obs: 0.95 / Num. unique obs: 194

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHENIX1.17.1_3660refinement
STARANISOdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PYO

2pyo


Resolution: 4.36→172.95 Å / SU ML: 0.686 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 42.5351
Details: Completeness shown corresponds to ellipsoidal completeness. STARANISO defined anisotropic resolution limits are 7.1 A, 7.1 A and 4.0 A along a*, b* and c* axes, respectively.
RfactorNum. reflection% reflection
Rfree0.3229 117 5.04 %
Rwork0.3063 --
obs0.3072 2320 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 227.88 Å2
Refinement stepCycle: LAST / Resolution: 4.36→172.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 0 0 1715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451728
X-RAY DIFFRACTIONf_angle_d1.17542336
X-RAY DIFFRACTIONf_chiral_restr0.0563288
X-RAY DIFFRACTIONf_plane_restr0.0046298
X-RAY DIFFRACTIONf_dihedral_angle_d5.0917261
LS refinement shellResolution: 4.36→172.95 Å
RfactorNum. reflection% reflection
Rfree0.3229 117 -
Rwork0.3063 2203 -
obs--36.98 %
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)
15.427475754060.1905481343370.6744224329657.47419972005-4.644349942242.980775747321.291297453250.5932254270691.741057610891.06876105410.8112367373852.297299198623.1631852119-2.3085305716-1.427508381454.14546840376-1.251656397450.4450873444212.041241038830.4606756820552.8732793089273.4632115324-27.3277609622-11.2005887725
21.27481493753-1.473222733420.3989628158342.91289017017-1.414778420593.87507830355-0.4173831030270.3829410857510.4881837084040.08806489886390.759664460515-0.0850670528735-0.8720783302730.219578177255-1.242030582473.73397356929-0.143115671137-0.7709746354161.098396594260.2201910049832.165913107892.62357164-23.68401606174.26144753493
32.33993848437-1.335227058210.3562979594852.44176603266-1.297693180010.772051860829-0.332295016345-0.1991968948361.589307601770.881621142496-0.1760515628071.56530195340.92761978203-0.3093558010830.4697443294654.41293254057-1.465598096360.3570292860041.33986934018-0.2251000645252.5500820056385.7289802798-24.119417619612.0252780192
49.70325943131-0.55677771481-6.244442233753.806868478934.197868138697.89217500072-1.539516879282.678812162720.9434277538510.01946723115030.9571409885312.457383059391.27094649862-2.14910709916-0.1112413009543.1583045807-0.600618322376-0.4484335694871.466238498050.8108668159221.6915520964583.3333388776-24.1141892981-8.40023750741
59.98579691667-6.189432010122.005741911537.526419761626.979739693271.99806572325-3.762203169073.84914292289-0.514962795913-1.487585197191.208602713742.974532950512.30934548784-3.245332443362.050196411933.94277658293-0.988635584752-0.4266812368912.096489105470.4304033892162.1556148990883.4225391022-36.0244790466-16.3901969884
62.2760702374-0.420246513335-0.6992404278144.724255599240.3709207107370.226486354004-0.3398998333580.6636479521830.0707772340023-1.052884265070.7462694373630.8428414284521.640646173-0.680326467463-0.9885217504454.56426166344-0.164613371238-0.5602271604841.147029456280.918433658891.1740470346394.0607884647-27.6091023632-10.2133927634
73.42365757845-1.350107763860.7385787253894.87993520151.678210583612.56510688677-0.8377615771410.202518746409-0.1813015673540.623115953992-1.20440913373-0.2930112896342.64468155660.3179138983250.2039118240134.948151291720.790725071678-0.04594931080922.741485052680.03491044188971.08380598428100.90175011-32.2257110923-0.935652614015
89.216590938923.642313054490.3002673611618.664746984675.376581460143.834275360050.4834180277120.7558356236910.153213157019-1.47901825924-2.330466990672.641126578532.93143499821-0.7439521698542.109327571655.36836700175-1.00402566458-0.1793694830672.25680097488-0.2060350443452.3373827961676.2965396681-43.4078900786-9.54480068512
92.099268532512.044396028321.994238450022.093845813031.920254279391.98794320389-0.2456091975341.991348222770.669218602311-1.92467235318-0.4542709779051.28866693865-0.6729929611131.33801830260.692629048756.373939740050.192217908871-1.389074968974.092550459810.4030809948383.1683393032866.9812011519-31.6456960298-8.81653607833
101.193103672660.723537449426-0.4673753158771.655560687281.672695010482.676238392961.023115239441.39350446578-0.70706542969-0.87104340741-0.9861322409090.06163942777010.655218154136-0.481068938186-0.1839945869972.834652406181.35211475283-0.1567091293761.194885243840.09526733761692.6558919163187.749618395-11.90527525110.503491137779
114.69381154809-0.3726030432082.005547167563.57969552682-1.371741512383.798216788261.058961843780.4650094191810.1214279609770.861212729114-2.03770788602-0.6516720894111.068056816292.813961350980.4135616465624.20224940142-0.234695691768-1.259062191472.648750860651.632624723854.10563661275107.989279256-15.42032670180.0558636370604
124.52658323548-0.3444676474853.95281908360.0122826994665-0.2647178453693.420430112780.8342851477941.23959710533-2.03356016437-0.2265205866150.659056574940.5790112632851.88173110105-0.6078254928-0.585661861293.27983588394-0.413345781688-2.510613919481.798420891620.005777462092251.8435105456106.425461264-37.3435953907-9.58776492897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 118 )
3X-RAY DIFFRACTION3chain 'B' and (resid 31 through 50 )
4X-RAY DIFFRACTION4chain 'B' and (resid 51 through 76 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 92 )
6X-RAY DIFFRACTION6chain 'B' and (resid 93 through 98 )
7X-RAY DIFFRACTION7chain 'C' and (resid 4 through 29 )
8X-RAY DIFFRACTION8chain 'C' and (resid 30 through 38 )
9X-RAY DIFFRACTION9chain 'C' and (resid 39 through 44 )
10X-RAY DIFFRACTION10chain 'C' and (resid 45 through 99 )
11X-RAY DIFFRACTION11chain 'C' and (resid 100 through 117 )
12X-RAY DIFFRACTION12chain 'C' and (resid 118 through 148 )

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