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- PDB-7kys: Crystal structure of human BCCIP beta (Native2) -

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Basic information

Entry
Database: PDB / ID: 7kys
TitleCrystal structure of human BCCIP beta (Native2)
ComponentsBRCA2 and CDKN1A-interacting protein
KeywordsTRANSFERASE / BRCA2 / eIF6 / cancer suppressor / ribosome biogenesis / GNAT / GCN5-related acetyltransferase
Function / homology
Function and homology information


microtubule anchoring / nuclear cyclin-dependent protein kinase holoenzyme complex / neuroendocrine cell differentiation / kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic spindle pole / establishment of mitotic spindle orientation / mitotic spindle assembly / centriole / tubulin binding ...microtubule anchoring / nuclear cyclin-dependent protein kinase holoenzyme complex / neuroendocrine cell differentiation / kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic spindle pole / establishment of mitotic spindle orientation / mitotic spindle assembly / centriole / tubulin binding / mitotic spindle organization / microtubule cytoskeleton organization / DNA repair / centrosome / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DI(HYDROXYETHYL)ETHER / BRCA2 and CDKN1A-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChoi, W.S. / Liu, B. / Shen, Z. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036146 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Structure of human BCCIP and implications for binding and modification of partner proteins.
Authors: Choi, W.S. / Liu, B. / Shen, Z. / Yang, W.
History
DepositionDec 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRCA2 and CDKN1A-interacting protein
B: BRCA2 and CDKN1A-interacting protein
C: BRCA2 and CDKN1A-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,65112
Polymers88,0493
Non-polymers6039
Water4,288238
1
A: BRCA2 and CDKN1A-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7227
Polymers29,3501
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BRCA2 and CDKN1A-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4562
Polymers29,3501
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BRCA2 and CDKN1A-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4743
Polymers29,3501
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.040, 67.000, 99.530
Angle α, β, γ (deg.)90.000, 91.031, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 60 through 75 or resid 77...
d_2ens_1(chain "B" and (resid 60 through 75 or resid 77...
d_3ens_1(chain "C" and (resid 60 through 75 or resid 77...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISLYSA2 - 17
d_12ens_1LEULEUA19 - 25
d_13ens_1ALAILEA27 - 39
d_14ens_1GLNLYSA41 - 49
d_15ens_1GLUTHRA55 - 66
d_16ens_1ARGARGA68
d_17ens_1GLYGLYA70
d_18ens_1GLNGLNA72 - 78
d_19ens_1LEUCYSA80 - 85
d_110ens_1ASNVALA88 - 94
d_111ens_1LEULEUA97 - 152
d_112ens_1ILEVALA154 - 159
d_113ens_1LEUVALA162 - 184
d_114ens_1THRASNA204 - 218
d_115ens_1ILEVALA220 - 230
d_21ens_1HISLYSB2 - 17
d_22ens_1LEULEUB19 - 25
d_23ens_1ALAILEB27 - 39
d_24ens_1GLNLYSB41 - 49
d_25ens_1GLUTHRB55 - 66
d_26ens_1ARGARGB68
d_27ens_1GLYGLYB70
d_28ens_1GLNGLNB72 - 78
d_29ens_1LEUCYSB80 - 85
d_210ens_1ASNVALB88 - 94
d_211ens_1LEULEUB98 - 153
d_212ens_1ILEVALB155 - 160
d_213ens_1LEUVALB163 - 185
d_214ens_1THRASNB206 - 220
d_215ens_1ILEVALB222 - 232
d_31ens_1HISLYSC2 - 17
d_32ens_1LEULEUC19 - 25
d_33ens_1ALAILEC27 - 39
d_34ens_1GLNLYSC41 - 49
d_35ens_1GLUTHRC55 - 66
d_36ens_1ARGARGC68
d_37ens_1GLYGLYC70
d_38ens_1GLNGLNC73 - 79
d_39ens_1LEUCYSC81 - 86
d_310ens_1ASNVALC89 - 95
d_311ens_1LEULEUC98 - 153
d_312ens_1ILEVALC156 - 161
d_313ens_1LEUVALC165 - 187
d_314ens_1THRASNC206 - 220
d_315ens_1ILEVALC222 - 232

NCS oper:
IDCodeMatrixVector
1given(0.972851876936, -0.0731377304113, -0.219567980206), (0.203814947064, -0.17866793352, 0.96256804273), (-0.109629799302, -0.981187363311, -0.158910871821)-14.9317271535, -78.4255893669, 36.5334308963
2given(-0.998748245431, -0.0262290455403, 0.0425908372565), (-0.011677476425, -0.705689388202, -0.708425101139), (0.0486372161262, -0.70803568028, 0.704499749225)39.7508724952, -3.62826440096, -31.193954651

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Components

#1: Protein BRCA2 and CDKN1A-interacting protein / P21- and CDK-associated protein 1 / Protein TOK-1


Mass: 29349.605 Da / Num. of mol.: 3 / Fragment: UNP residues 61-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCCIP, TOK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P287
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid, pH 4.5, 1-2% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 21, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 39873 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 52.75 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.59
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2987 / CC1/2: 0.467

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7KYQ

7kyq


Resolution: 2.2→29.73 Å / SU ML: 0.2822 / Cross valid method: FREE R-VALUE / σ(F): 0.96 / Phase error: 26.9465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 1053 2.64 %
Rwork0.2048 38807 -
obs0.2053 39860 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 0 39 238 5737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915621
X-RAY DIFFRACTIONf_angle_d1.26227574
X-RAY DIFFRACTIONf_chiral_restr0.0615866
X-RAY DIFFRACTIONf_plane_restr0.008965
X-RAY DIFFRACTIONf_dihedral_angle_d22.45932093
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.82036357458
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.796929374629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.33721410.33284884X-RAY DIFFRACTION99.84
2.3-2.420.30841260.30284837X-RAY DIFFRACTION99.74
2.42-2.570.27511330.28014869X-RAY DIFFRACTION99.68
2.57-2.770.28061330.25684874X-RAY DIFFRACTION99.74
2.77-3.050.30911310.24724890X-RAY DIFFRACTION99.9
3.05-3.490.21091330.20924886X-RAY DIFFRACTION99.58
3.49-4.40.17391270.17774790X-RAY DIFFRACTION97.46
4.4-29.730.21191290.17114777X-RAY DIFFRACTION94.8
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)
14.05976957818-0.2679352198110.601695369716.68482618110.7300853506583.214258601720.01662813048440.03390100455170.0251301800453-0.562676457716-0.08128332902030.4926609193690.00343047601604-0.5193942012740.02600183786740.3998928458460.0604265911575-0.08443344106860.4914176766390.0136222293120.41503764985417.8627385695-5.8132401917626.2240473142
22.99628169597-1.2136452391-0.1231007340562.595693267760.3202472888143.38655363103-0.0204789890458-0.168339830224-0.0006531719968070.0781327500728-0.16865889723-0.006233643187610.1044360221090.07049064220660.1760148523850.3002248563720.00214254430446-0.002147333703010.36400815760.01332947031550.31068335828626.9934776877-10.702064185336.6138305943
32.16556101648-0.8834801943641.684945851044.3226597801-4.221022684824.505078448040.147138635083-0.4060741163310.4001965866980.0598730025445-1.40422953552-0.1883837499090.5000240421350.8863706154981.076874868541.15781539289-0.1741537113380.03257598084821.011243712950.1090111662250.94671933393338.2306692535-4.9356453309417.6504163437
42.98832866186-0.941719847487-0.5422773542554.04825198994-0.4075519763663.25463561436-0.0969913920651-0.4483848509250.4682621781070.521113168394-0.163793419971-0.31426198755-0.3415415181620.2403839848180.2334849549420.345942620229-0.0270653172448-0.0785928254150.5197467285120.02498265627750.51990561671732.8535753149-2.8158076202240.6496002207
54.026077493550.0178068781344-1.528720011333.932448765990.04556759888877.47188554069-0.1896090422030.0888283172015-0.406968571947-0.2003435125130.03600270417820.5514765219410.960404091607-0.7918679857260.0559910640240.521707445895-0.101808559967-0.05427711648940.497427625731-0.0340666256990.624735310331-2.89296428691-48.534699685436.230184289
64.85408593476-0.250046475457-2.246031458364.69133200816-0.03170361085316.792375728710.02325246315080.458944266912-0.226386765986-0.435635324151-0.1872537225030.136906812694-0.0553944136727-0.6592676367250.2661127966280.24286040522-0.07163686596830.01657674637090.6635590456320.05113226694510.483697078353-3.86235151494-43.009277797637.6041932589
73.241776164564.52616854145-0.7759897957346.4169286724-0.993362633882.231446841450.170635743801-0.878129534817-0.6913256486690.435949447917-0.22740567346-0.591148999025-0.2653106545770.3546127605150.06956507647020.3653507994010.00637412289036-0.0387433012970.7352411940190.03862240600950.3819782402187.30823870564-38.024673832650.8689798915
81.593321745170.970051668360.6478786505064.42628717020.5778153162423.42225322528-0.105755457397-0.0134667383133-0.279426656307-0.178185633390.254799651993-0.253406845336-0.4549511606090.0568228315895-0.2768373893420.242377234826-0.05696065230.02422536518220.5114067220460.007774940881350.3901174115225.76235783954-32.596742512342.6880938309
93.488132631370.613102494097-0.7280829933084.08376292860.002138277250955.18863093790.02952500822120.1916972287420.0875040455397-0.3621704417080.08460633307810.40344444456-0.178339912254-0.322419253944-0.07520158260470.337586213271-0.0683666460516-0.03508182009970.4060943352190.009221019487770.3590382542794.70832050206-34.357109231432.9418727698
100.3193949022540.3394292237260.3484338660770.358177539860.3600592848210.365454467271-0.3164980837780.1572592614430.800325659343-0.439138551192-0.9952573212161.13894494940.2793148068520.3378468446071.159136521830.9417159555680.154973360014-0.2189913342830.852048198893-0.1240782844151.4530137926113.3182275869-52.481621846236.2857080819
112.542648975620.150776693271.207222135916.666298447022.377490559927.27936663359-0.421360683726-0.50667738742.14995144054-0.121451694929-0.0784194816783-1.07947576335-0.6654785745850.1251781958270.4971934799790.67836371667-0.0224349583018-0.08969775910070.592068577535-0.001100417288230.96459523093821.6787538783-54.118059032432.6906746097
123.915470095630.0871592918570.08054621194114.29792962103-0.830908231995.194522267480.1074723242950.8160333482490.0929111108338-1.110328496610.4410619862050.17674677116-0.0753285850344-0.234110395453-0.4177896745770.598634779471-0.02777811500150.04810202680020.6335045125790.03472263228480.4884636022458.26449390228-31.85342440129.3181412937
132.496959860682.155888390130.973865499023.503432148430.2009159233665.0531794324-0.08190903046650.321106233987-0.160668352614-0.3319378818150.0341963873088-0.376164036943-0.5825547424181.00851826037-0.09199633640830.7729149182420.07112793379660.1520517081920.8906671877210.02490053124410.73744253862423.2489621718-18.5907815279-7.96079189345
144.172521824170.4587744336952.018640179854.001208875810.2967606982383.7978634119-0.0897245830528-0.4323566858020.626771149395-0.3419278976550.0218859009819-0.0904027310037-0.5010008881990.002673404198460.1600421989520.6069448364130.00144098399564-0.03308677800610.458867776049-0.06686111717010.46781220180416.0894857344-15.69707738087.03943084549
151.093866022760.473473069927-1.055240516523.441027562811.723480504573.572744534330.2892285061790.1260714404640.0845631499886-0.00289718503908-0.270401029113-0.2342532969510.553455308585-0.045850921267-0.0101215329850.6526734402960.06250639690230.003010293774220.747961732744-0.0560549612550.42276433472313.6916044063-26.20230586151.52845751957
161.69493578406-0.31975601570.3513412894331.46565854445-1.530314582985.035491018390.0546898428796-0.381711110318-0.4424256199020.2121986723110.2119786816280.5265481101720.649729006322-0.990657954156-0.4636159335841.153734994360.126885969632-0.1339407043371.106766298520.166903000580.6438414451772.90040603123-12.5118837869-14.4046593667
172.2275108831.06419466413-0.9365042193293.331307607822.348716462412.99654155970.409118132594-0.216490163353-0.3402275610750.141187569453-0.509398513941-0.1221988228940.872687447951-0.7880844789950.1198595267890.977271133932-0.061050460014-0.07053610355350.721580611294-0.07522125708150.4940895271698.70812547092-31.05972728990.919941171308
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 59 through 108 )AA59 - 1081 - 50
22chain 'A' and (resid 109 through 267 )AA109 - 26751 - 183
33chain 'A' and (resid 268 through 287 )AA268 - 287184 - 203
44chain 'A' and (resid 288 through 314 )AA288 - 314204 - 230
55chain 'B' and (resid 59 through 108 )BB59 - 1081 - 50
66chain 'B' and (resid 109 through 139 )BB109 - 13951 - 71
77chain 'B' and (resid 140 through 156 )BB140 - 15672 - 88
88chain 'B' and (resid 157 through 188 )BB157 - 18889 - 121
99chain 'B' and (resid 189 through 267 )BB189 - 267122 - 184
1010chain 'B' and (resid 268 through 277 )BB268 - 277185 - 194
1111chain 'B' and (resid 278 through 287 )BB278 - 287195 - 205
1212chain 'B' and (resid 288 through 314 )BB288 - 314206 - 232
1313chain 'C' and (resid 59 through 109 )CC59 - 1091 - 51
1414chain 'C' and (resid 120 through 169 )CC120 - 16952 - 102
1515chain 'C' and (resid 170 through 267 )CC170 - 267103 - 186
1616chain 'C' and (resid 268 through 287 )CC268 - 287187 - 205
1717chain 'C' and (resid 288 through 314 )CC288 - 314206 - 232

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