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- PDB-6xwt: drosophila melanogaster CENP-A/H4 bound to N-terminal CAL1 fragment -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6xwt
Titledrosophila melanogaster CENP-A/H4 bound to N-terminal CAL1 fragment
Components
  • 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
Centromere protein Scm3 / Histone, subunit A / Histone, subunit 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 protein Scm3 / Histone, subunit A / Histone, subunit 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 / Orthogonal Bundle / Mainly Alpha
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: 3.47 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
CitationJournal: 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.
History
DepositionJan 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Histone H3-like centromeric protein cid
D: Histone H4
E: Chromosome alignment defect 1
F: Chromosome alignment defect 1


Theoretical massNumber of molelcules
Total (without water)294,2816
Polymers294,2816
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-126 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.250, 178.250, 133.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUPHEPHE(chain 'A' and (resid 47 through 54 or resid 56...AA47 - 53147 - 153
121LEULEULYSLYS(chain 'A' and (resid 47 through 54 or resid 56...AA56 - 63156 - 163
131ASPASPARGARG(chain 'A' and (resid 47 through 54 or resid 56...AA67 - 71167 - 171
141THRTHRALAALA(chain 'A' and (resid 47 through 54 or resid 56...AA73 - 79173 - 179
151GLUGLUMETMET(chain 'A' and (resid 47 through 54 or resid 56...AA82 - 115182 - 215
161ILEILECYSCYS(chain 'A' and (resid 47 through 54 or resid 56...AA118 - 119218 - 219
271LEULEUPHEPHE(chain 'C' and (resid 47 through 54 or resid 56...CC47 - 53147 - 153
281LEULEULYSLYS(chain 'C' and (resid 47 through 54 or resid 56...CC56 - 63156 - 163
291ASPASPARGARG(chain 'C' and (resid 47 through 54 or resid 56...CC67 - 71167 - 171
2101THRTHRALAALA(chain 'C' and (resid 47 through 54 or resid 56...CC73 - 79173 - 179
2111GLUGLUMETMET(chain 'C' and (resid 47 through 54 or resid 56...CC82 - 115182 - 215
2121ILEILECYSCYS(chain 'C' and (resid 47 through 54 or resid 56...CC118 - 119218 - 219
1132LYSLYSVALVAL(chain 'B' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))BB32 - 4432 - 44
1142ILEILEILEILE(chain 'B' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))BB47 - 5147 - 51
1152GLUGLUTHRTHR(chain 'B' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))BB54 - 9754 - 97
2162LYSLYSVALVAL(chain 'D' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))DD32 - 4432 - 44
2172ILEILEILEILE(chain 'D' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))DD47 - 5147 - 51
2182GLUGLUTHRTHR(chain 'D' and (resid 32 through 45 or resid 47 through 52 or resid 54 through 98))DD54 - 9754 - 97
1193ARGARGALAALA(chain 'E' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))EE18 - 3018 - 30
1203GLUGLUVALVAL(chain 'E' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))EE33 - 4033 - 40
1213PHEPHEASNASN(chain 'E' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))EE43 - 4543 - 45
2223ARGARGALAALA(chain 'F' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))FF18 - 3018 - 30
2233GLUGLUVALVAL(chain 'F' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))FF33 - 4033 - 40
2243PHEPHEASNASN(chain 'F' and (resid 18 through 31 or resid 33 through 41 or resid 43 through 46))FF43 - 4543 - 45

NCS ensembles :
ID
1
2
3

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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.: 2
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.: 2
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


Mass: 109717.789 Da / Num. of mol.: 2
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

Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.01M Cobalt (II) Chloride hexahydrate, 0.1M MES pH 6.5 and 1.8 M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.47→100.88 Å / Num. obs: 10675 / % possible obs: 99.93 % / Redundancy: 7.6 % / Biso Wilson estimate: 137.49 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 10.46
Reflection shellResolution: 3.47→3.59 Å / Rmerge(I) obs: 1.96 / Num. unique obs: 1059

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Processing

Software
NameVersionClassification
xia21.17.1_3660data reduction
PHENIX1.17.1_3660refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PYO

2pyo


Resolution: 3.47→100.88 Å / SU ML: 0.5757 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.7683
RfactorNum. reflection% reflection
Rfree0.2863 542 5.08 %
Rwork0.2717 --
obs0.2724 10673 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 136.62 Å2
Refinement stepCycle: LAST / Resolution: 3.47→100.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 0 0 2803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392838
X-RAY DIFFRACTIONf_angle_d0.86463811
X-RAY DIFFRACTIONf_chiral_restr0.0462440
X-RAY DIFFRACTIONf_plane_restr0.0055479
X-RAY DIFFRACTIONf_dihedral_angle_d8.0201395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.47-3.820.40141260.35412511X-RAY DIFFRACTION100
3.82-4.370.35921470.32812495X-RAY DIFFRACTION99.96
4.37-5.510.2721340.29212522X-RAY DIFFRACTION99.96
5.51-100.880.24851350.22842603X-RAY DIFFRACTION99.82
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)
13.839594375440.9562311322520.7235153471983.695644446860.649659383626.548171770290.1403343472060.2131665193880.5815011012170.2802954963170.1371791470780.214240174015-0.812658503779-0.418277163919-0.2163716370150.8857716283180.1450298411320.1775034400990.7870489348970.04454452895291.0524028363625.0175366361-22.770643395839.3651146885
28.565917701680.8402433657494.792671669936.125059799173.730614896388.570134345480.02325956081561.74709523379-0.905280812042.978191861930.4091782594210.9567153616942.008879552352.48285525496-0.236019300771.289750872610.2880815097180.2001992367851.14822683226-0.089559683892.1217431757634.5537864846-14.809157514950.5139445063
36.03558736782-1.60717422653-0.1166469293772.5957661214-0.7651199222822.472659381850.218868482771.029003918571.35908278667-2.273417360260.02715362833470.870971755234-2.597027969450.135175301247-0.1283945857211.85646471147-0.1376581852360.1328911808111.38957651058-0.0151984257161.5971515322821.4723921509-11.136704270139.0305433889
44.20215051734-1.295118436092.296929434812.871447707673.449791397436.23634657032-0.3224980914621.283510798920.2008275672330.07152795575380.946530558878-2.68888023078-0.6915911359860.926833667051-0.41406756221.104217604780.03689409387220.2212897396531.28173305259-0.2037833800911.3872381781830.4271140509-26.718447655239.0058526596
54.93531162653-0.749527189470.7794074080232.83876475633-0.295638143559.660040913180.1047886418270.385883624905-1.939553222342.1315739171-0.5189903754261.510698051592.83522512211-1.184290090160.03953900285911.36554473244-0.05998490442410.2597555303240.997105417136-0.1278861241421.1817433205924.0412574941-40.657054233439.4855856467
67.724153565375.50340303512-5.110280874836.70754493848-1.495334984635.163077947931.30960158286-0.04149727120330.6758543180634.590479628130.253479056997-2.83051223659-1.28964049343-1.94262430025-1.656683281181.622184610470.270424660579-0.1298027278961.147447120290.1598878198120.7252303924727.9868336621-30.678636139150.0840622462
78.204078614141.657638559952.224690490843.41776079517-0.8604682887299.20684145386-0.657279868794-3.182408683912.451666124751.462312631250.4016542538890.780624511524-0.4909418171090.05391381714470.1819292675561.4902416665-0.1446657054870.2414007866781.4430550886-0.3775675479041.2247835344935.2456981661-29.322153791983.191286515
83.81386619013-3.195149677810.8821399057499.038013836630.8730963134532.157503134870.2408967098280.2180971770970.0328981957286-0.0251131943932-0.357490842066-0.319712800641-0.0110110406730.4036990481890.08633863691431.2000789524-0.06861013149180.1863682039970.840678302751-0.2134961334230.87681675767137.5561622263-22.978687148670.9523277371
95.436189886211.370109296570.2491374983092.178139870291.285031465474.05863161175-0.859380993501-0.852835665995-0.3372108357910.9753546144430.607300394521.173414825620.307521065685-0.4938825068850.07588491399341.25109527968-0.03669414422470.1117999971341.29541402326-0.04442974880631.6233805600528.7528038948-14.913921626363.9728493172
107.498353121631.66513122503-1.867173696799.01288418755-0.8010221481192.621935019940.492482200533-0.897120146675-2.028250523861.58331367338-0.0669712052506-1.277939970041.528655018081.52904137884-0.2372025851122.15915014780.22452285961-0.3433957619631.09595288213-0.09156068795071.2013452962342.8989215726-15.318507011277.4784336578
115.88686371223-2.12685651956-3.499449341899.49705548884-4.485008488178.447968057940.03363040639360.05028339713490.8065230043861.578559073950.1376306717412.43162050572-0.509747009048-0.877564364731-0.1653070102440.8312754508460.04668951690290.1019727229960.744742716257-0.02120088516290.83665694093933.2084586771-24.450502734773.4843134237
124.34032443251.666286915940.2544091804166.13980612045-0.9254003486622.652739479710.1033898693520.916662396322-2.59808550802-1.26394835118-1.0318505777-1.289252358842.782724071160.8737721857570.7183349301551.37290084075-0.2503052708610.2347316628290.8068481826660.01618333655981.1722524924436.2674230202-42.458620979372.4291343242
133.634460999133.8081519661-0.3705672214395.76574659675-3.240019077163.26510484858-1.846358909543.194471768520.88746133044-3.730718480131.681057269444.23263485071-2.08991738694-0.317668269896-0.1670520993551.5907503123-0.3817209232870.03513675172671.26840630380.1415142684571.0236885823834.3688426283-28.944757475461.9620535151
142.57235860824-0.8385552898170.8928815859746.488292862182.83808548797.505335664681.086587522830.6702721570060.0188134064976-1.594278460710.0220596567143-0.57838488408-0.2632998212891.75277030915-1.131751165091.51164978667-0.2186687986260.004833594704841.28495511065-0.05008379664351.1364256695545.7445488537-30.928926888763.0707014541
155.97259577629-0.815635481001-2.60818275044.67144100013-1.707133543071.967016187110.305733760934-0.183067390131-0.3859052580722.70907980069-0.6942076137350.0963674627922.56258522173-2.186901297320.140136216092.06870167517-0.422790403249-0.2477883820131.559915141990.1219940615891.2963683756442.1825552463-41.793937472982.1532868361
160.0776102802769-0.372583332612-0.2186188957393.998325016853.026431875182.44488896865-1.28467156326-2.860776471562.616255664410.792748280068-0.9903549154241.34741654391-1.75613553725-1.471258056091.934444773252.098680944291.279228052830.2251295275541.844370972291.012749104393.4252818597239.945967338-35.215182541891.297740739
179.787772164330.548141542009-3.13448993096.84915399028-2.676109192286.13031959021-1.037251769961.94846327037-1.287759449310.03308624257440.8599978466911.85902356933-0.0581529411286-1.86188718755-0.4627370634751.12822220143-0.08474385905490.1950499560781.17015609303-0.05803186607171.5498851122716.5944529592-29.649528766450.7127507887
187.92795304076-2.582454383573.032696852613.27879998861.366183658343.49404653737-0.370168735180.611675706528-1.00327058173-1.23793732124-0.734936379913.211327490480.6199835659611.346023810442.545278078221.661863436870.141593273269-0.1105747183311.22233823208-0.04816873386141.6351877638415.7427590507-38.765721074931.8470810316
192.992823585082.954585614521.061755890233.04464660710.746527472212.244745285650.09662554990261.753888128032.98629353206-3.597221030570.2480245792350.307164815083-0.4340433249061.724441043850.2406143339291.9489085262-0.159350871407-0.05468722608672.15905329921-0.2095204869751.5807855263720.4387020226-30.81832076221.7565397506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 120 )
3X-RAY DIFFRACTION3chain 'B' and (resid 27 through 48 )
4X-RAY DIFFRACTION4chain 'B' and (resid 49 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 47 through 63 )
8X-RAY DIFFRACTION8chain 'C' and (resid 64 through 108 )
9X-RAY DIFFRACTION9chain 'C' and (resid 109 through 120 )
10X-RAY DIFFRACTION10chain 'D' and (resid 29 through 41 )
11X-RAY DIFFRACTION11chain 'D' and (resid 42 through 76 )
12X-RAY DIFFRACTION12chain 'D' and (resid 77 through 92 )
13X-RAY DIFFRACTION13chain 'D' and (resid 93 through 99 )
14X-RAY DIFFRACTION14chain 'E' and (resid 17 through 29 )
15X-RAY DIFFRACTION15chain 'E' and (resid 30 through 40 )
16X-RAY DIFFRACTION16chain 'E' and (resid 41 through 46 )
17X-RAY DIFFRACTION17chain 'F' and (resid 17 through 29 )
18X-RAY DIFFRACTION18chain 'F' and (resid 30 through 38 )
19X-RAY DIFFRACTION19chain 'F' and (resid 39 through 47 )

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