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- PDB-6xwv: Crystal structure of drosophila melanogaster CENP-C bound to CAL1 -

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Basic information

Entry
Database: PDB / ID: 6xwv
TitleCrystal structure of drosophila melanogaster CENP-C bound to CAL1
Components
  • Calmodulin
  • Ryanodine Receptor 2
KeywordsCELL CYCLE / Centromere / Kinetochore / Cell Division
Function / homology
Function and homology information


CENP-A containing chromatin assembly / regulation of centromere complex assembly / female meiosis chromosome segregation / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / chromatin-protein adaptor activity / protein localization to kinetochore / regulation of stem cell differentiation / mitotic metaphase chromosome alignment ...CENP-A containing chromatin assembly / regulation of centromere complex assembly / female meiosis chromosome segregation / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / chromatin-protein adaptor activity / protein localization to kinetochore / regulation of stem cell differentiation / mitotic metaphase chromosome alignment / chromosome, centromeric region / chromosome segregation / kinetochore / nucleolus
Similarity search - Function
RE68959p / Chromosome alignment defect 1 / Centromeric protein-C, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 1.2May 1, 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: Calmodulin
E: Ryanodine Receptor 2
B: Calmodulin
C: Calmodulin
D: Calmodulin


Theoretical massNumber of molelcules
Total (without water)741,6675
Polymers741,6675
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS and AUC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-50 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.273, 86.444, 88.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLYGLY(chain 'A' and (resid 1274 through 1281 or (resid 1282...AA1274 - 12891274 - 1289
12VALVALILEILE(chain 'A' and (resid 1274 through 1281 or (resid 1282...AA1306 - 14091306 - 1409
23ASPASPGLYGLY(chain 'B' and (resid 1274 through 1281 or (resid 1282...BC1274 - 12891274 - 1289
24VALVALILEILE(chain 'B' and (resid 1274 through 1281 or (resid 1282...BC1306 - 14091306 - 1409
35ASPASPGLYGLY(chain 'C' and (resid 1274 through 1281 or (resid 1282...CD1274 - 12891274 - 1289
36VALVALILEILE(chain 'C' and (resid 1274 through 1281 or (resid 1282...CD1306 - 14091306 - 1409
47ASPASPGLYGLY(chain 'D' and (resid 1274 through 1327 or (resid 1328...DE1274 - 12891274 - 1289
48VALVALILEILE(chain 'D' and (resid 1274 through 1327 or (resid 1328...DE1306 - 14091306 - 1409

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Components

#1: Protein
Calmodulin


Mass: 157987.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG31258 / Production host: Escherichia coli (E. coli) / References: UniProt: A8WHM0, UniProt: Q9VHP9*PLUS
#2: Protein Ryanodine Receptor 2


Mass: 109717.789 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Calcium acetate, 0.1M Na Cacodylate, pH 6.5, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.27→29.08 Å / Num. obs: 30957 / % possible obs: 98.4 % / Redundancy: 13.1 % / Biso Wilson estimate: 45.64 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 21.2
Reflection shellResolution: 2.27→2.35 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 2932

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS1.17.1_3660data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: dmCENP-C cupin

Resolution: 2.27→29.08 Å / SU ML: 0.2985 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.4926
RfactorNum. reflection% reflection
Rfree0.2655 1961 6.38 %
Rwork0.2371 --
obs0.2389 30725 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.09 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4211 0 0 18 4229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064279
X-RAY DIFFRACTIONf_angle_d1.1875760
X-RAY DIFFRACTIONf_chiral_restr0.0635642
X-RAY DIFFRACTIONf_plane_restr0.0072735
X-RAY DIFFRACTIONf_dihedral_angle_d5.0915580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.41871340.351909X-RAY DIFFRACTION92.65
2.33-2.390.35691430.32531997X-RAY DIFFRACTION97.67
2.39-2.460.33061440.30311997X-RAY DIFFRACTION98.39
2.46-2.540.34561410.30042027X-RAY DIFFRACTION97.7
2.54-2.630.29991330.28542036X-RAY DIFFRACTION98.73
2.63-2.740.30571350.28242037X-RAY DIFFRACTION98.24
2.74-2.860.34791460.27222012X-RAY DIFFRACTION98
2.86-3.010.28921320.26742049X-RAY DIFFRACTION98.87
3.01-3.20.28551370.26122073X-RAY DIFFRACTION99.15
3.2-3.440.29091360.24162083X-RAY DIFFRACTION99.42
3.44-3.790.27221480.22522076X-RAY DIFFRACTION99.29
3.79-4.340.22321340.20992106X-RAY DIFFRACTION99.87
4.34-5.460.2041430.18822132X-RAY DIFFRACTION99.74
5.46-29.080.24371550.2262230X-RAY DIFFRACTION99.79
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)
17.19414062108-1.59684436973-1.847660066854.02416156192-0.2596033060992.38826190419-0.751403275041-1.19285123826-0.6224884309090.2879820427320.492660964691-0.4452166557690.05924616410970.6014870203120.07164659994620.4674711764780.0776462791319-0.0008691739767660.6613696938750.1354778979620.51026094558228.0823363314-0.50305995553631.7728999489
25.248525222621.168935710390.3705456226752.77204144589-0.2578251393192.5492552701-0.0358461788508-0.109697200628-0.0622723421015-0.123893419889-0.08861221066570.3167088735360.0204547863-0.03701148555060.05185063440050.3935265953240.0490836656213-0.03483216450110.318579367878-0.003212147906010.3978955806420.671737447911.013157142523.8663774182
36.166262237780.2379499621820.06816161740840.202734880621-1.268801891612.37370918515-0.02755592904320.463771473669-0.7599610438130.3006977480230.3013052082430.139252687135-0.274201415464-0.36745609956-0.08969574979320.476247943238-0.01285421798890.01485947384620.4475303719850.009791700116160.5691933611468.374894039122.0223928484219.7085508976
43.194098857470.525272079557-1.368751820121.961851371121.057424158584.063687190630.742506915631.69645471864-2.03541744453-0.353471347687-0.6185952824890.7864894690531.1612499323-1.575735691140.237016488510.494242424256-0.116660471657-0.07505426258731.25727705395-0.458424526130.8353032072671.93809838218-3.1157759475212.5177140815
54.996165054551.276136980590.6416803429081.87544728316-0.3305552446935.03441377704-0.0352914007190.570944883624-0.468496690291-0.204570907160.5810980106520.450746156223-0.00252462717593-0.432602888373-0.2870890699550.4140213594420.000747777423224-0.06607801791090.529489688207-0.06434592435510.60993798814710.56637889490.94650080888618.379234371
67.371568410491.59512804115-3.348395125014.03985769734-2.602946467033.418251634560.2523247874590.1554250699820.8918511307380.01180323235250.2294019661810.623976771996-0.218708067245-0.161370860759-0.2486394880260.549439008394-0.00492835801304-0.03080649120920.365842738742-0.1386819539940.52358998927322.780857918622.139519726423.2001452577
77.5060464975-1.10751982462-0.6312252647375.11505115771-0.4663028649144.44579767071-0.829885302181-0.207465777468-1.8847399860.6018342098110.0991182052920.2193419677120.111802439775-0.3843928635610.554943789660.685800149846-0.04390085315920.1685367500440.509131269002-0.07993863914471.2081403543822.2154664758-12.207941841721.5985963698
83.789835562920.03538870102780.7417929404462.607756903760.2627399916472.137391892-0.2539625280831.09047308137-0.0722136234029-0.7522778129170.190330546038-0.4902888258010.102960192042-0.1475623362390.2249509295480.652907761477-0.07771982377640.02298086066280.695290944968-0.2792114185680.74966331539526.3740237574-6.35185137577.36991596353
94.36623231272-1.85536473360.5004148625426.4647420929-4.504047068673.290521109630.005227067772971.49668386226-0.534820994156-0.777137466062-0.5049649813630.05901548329911.10005863097-0.05710901924180.1793861118620.4763218824820.0126770487254-0.04796798085620.72044647968-0.08641136930640.3747914601637.14711361721.281751042257.10426233599
103.582786584151.68813498191-1.270238604955.59415576158-2.746253874053.45679853146-0.147239878541-0.177929664178-0.458826760436-0.04586989760220.10890897366-0.4156566435510.08635701907230.0713398122640.24488045940.4098620958240.01156427455160.02126460827620.3495474137350.001341196855390.5594041020234.74612673163.5069239529415.7313285632
114.497000318990.1149824855670.6454830560815.35880540227-1.371406845297.220431630930.02469855278210.804377928883-0.144569776378-0.971752364227-1.24910996655-0.115671064462-0.9439930796931.246418705270.2924495399390.7331242017850.0210968368739-0.05775945854340.519886976123-0.01209083673410.54382851089541.709718713413.779739395911.8023774511
125.467098717072.16811493377-3.399316904198.13099483749-2.492188400512.26082044019-0.112813083377-0.151765184132-0.2399286303650.880486576137-0.3098303768190.0552139721917-1.01253919769-0.3120931239230.7286391455720.442959781964-0.02050296511780.02244752060170.3732197048290.01245980436650.42908758088931.67040611626.9468554573318.603227552
136.086264573794.35715197054-2.170357495335.69367084525-2.163398777482.79150129815-0.3357507491291.22384269342-0.5066867575410.212985597770.1096943544440.0141829863379-0.2065165188-0.08680533611810.6856018480620.4850066871110.02078019647620.04279697857840.6029191412160.01012187815790.41135802829236.6114938667.660839309897.75909818517
144.77591778618-0.4761589637182.615811409894.18238288128-1.44716067234.97280341189-0.02854529578050.629072328714-1.23751749518-0.486703170951-0.37841638512-0.3161138827640.665820189171-0.03636852300410.5041089151540.468154117437-0.00343408310340.05155239145730.417709730389-0.02705146314450.56979625154333.0618827952-2.1991630665115.999677514
152.10917900604-0.5969111832970.3027441207751.498006786922.654681429444.97492001278-0.286347088262-1.281978840341.662250900560.4720646267940.11080431636-0.343503986274-0.225310654281-0.324155664126-0.1772723839590.6334734583240.01151548445460.02789177585370.686136320394-0.1981919347190.7687860752413.744520711947.273012341825.6149605212
167.64133296312-0.1123410416851.557544914073.75684334419-1.023845427872.075061164380.125411424272-0.444655410975-0.1477488677720.09578031269250.149469525775-0.1196224604480.0290250516247-0.190001059691-0.1879633642020.433002144538-0.012963583956-0.02512255304850.333959269671-0.04786349160860.36950548777722.382598251934.768637539621.023635021
172.149996123980.3541906718970.9242627179710.9200874267772.099975445173.43693785153-0.101134376720.254657401916-0.1915416542710.0203090229521-0.6060095240931.159638362470.449014746895-0.7620899564920.5165690741040.623255858650.0687204337782-0.03033242635430.646066917068-0.2301663788290.53788004446237.19428946538.205693455215.8389825988
189.56348563882-2.89837026985-1.478214769025.356371480712.492979060136.50095349411-0.7137371923710.4785829625071.748305621080.3591688532250.722377054467-0.391682470471-0.2806207270931.154858132420.05239673208260.438645383536-0.03630816132060.007649510367270.5485227866390.1525581640760.5540607881332.490399990746.01516468213.7341052783
195.648323251420.8363666394420.6215650773572.08846166003-0.3730853907352.60551922220.1437837863242.37441119851.04512895087-0.326207359149-0.140728791616-0.7349690603680.007904070670340.761642099988-0.3965135575460.533133048778-0.04227723027230.1643108095541.135385063610.2384879018670.90826053845636.670834528947.25589619558.31041722903
204.009066932210.01127732168881.310719278842.99583497910.7266460093365.025104933050.03229884074290.6517930584260.354242092193-0.1755218752930.364874694263-0.7031097815340.03935040243970.210818890443-0.3000805785810.446526366592-0.08913429063170.03220868982620.4943194198270.01109857100390.56344479854433.307877746641.947048075214.576536909
213.239333307050.42914097624.443862637942.505237861291.73946427067.94888789688-0.2359971687120.06466886793681.872403613530.8330391426730.482370619660.750533967680.3454963072620.63869326444-0.2499875729090.8104190069210.0689152744203-0.192496211380.701583872646-0.02694417429471.6875519645619.779166254556.651624726819.2335849522
225.490198031090.4566887616031.109179572813.31805291861-2.060999372091.68842362212-0.50801979851.689739763791.32858438217-0.5952476143280.3363017654780.0809863314201-0.175773935678-0.1978243525350.01631108249180.559631892614-0.0963827144998-0.06263829409560.8885586473430.4369425316630.86822621092417.586110861850.51497079572.94904937843
235.00049001541-0.5301052569910.5061787856514.482408411761.274613743652.39488365082-0.1724859770290.7173284120910.6014146388360.0851205408018-0.052051159025-0.0896361038256-0.06109719015470.2780871042250.2121636429510.395535248741-0.0240071616272-5.378060936E-50.5594649077570.122694493880.5859749208457.2772687686941.28628712066.62822498817
244.486109931310.844837383072.61244280208-0.4773809790410.7528527637584.26813565266-0.2227615345090.831614117110.168631479932-0.09750359637480.08151306215680.03180057664760.4591028972170.02899022404860.2592729090080.474372101033-0.01448654750790.04280720370840.62448077773-0.08567689615420.4768681485865.9525122428934.15345298547.3963741809
254.400226967381.635458460892.991937255193.23355591230.02244722820672.28261825939-0.1204372503050.8625710705471.41018590864-0.442534281035-0.0272394676744-0.341983987439-0.6261822779650.05702854513140.4232218550850.58257823844-0.0420872795364-0.0384706729230.4933972136750.10777985320.70610151866510.501587378645.82312117810.3519636775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1274 through 1297 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1302 through 1338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1339 through 1368 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1369 through 1381 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1382 through 1410 )
6X-RAY DIFFRACTION6chain 'E' and (resid 890 through 913 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1274 through 1308 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1309 through 1338 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1339 through 1353 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1354 through 1368 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1369 through 1380 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1381 through 1388 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1389 through 1398 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1399 through 1411 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1274 through 1287 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1288 through 1338 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1339 through 1353 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1354 through 1368 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1369 through 1388 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1389 through 1411 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1274 through 1288 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1289 through 1338 )
23X-RAY DIFFRACTION23chain 'D' and (resid 1339 through 1368 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1369 through 1398 )
25X-RAY DIFFRACTION25chain 'D' and (resid 1399 through 1411 )

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