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- PDB-5cw4: Structure of CfBRCC36-CfKIAA0157 complex (Selenium Edge) -

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Basic information

Entry
Database: PDB / ID: 5cw4
TitleStructure of CfBRCC36-CfKIAA0157 complex (Selenium Edge)
Components
  • BRCA1/BRCA2-containing complex subunit 3
  • Protein FAM175B
KeywordsMETAL BINDING PROTEIN / Metal dependent enzyme
Function / homology
Function and homology information


BRISC complex / BRCA1-A complex / attachment of spindle microtubules to kinetochore / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / metal-dependent deubiquitinase activity / positive regulation of NLRP3 inflammasome complex assembly / mitotic spindle assembly / polyubiquitin modification-dependent protein binding / spindle pole / double-strand break repair ...BRISC complex / BRCA1-A complex / attachment of spindle microtubules to kinetochore / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / metal-dependent deubiquitinase activity / positive regulation of NLRP3 inflammasome complex assembly / mitotic spindle assembly / polyubiquitin modification-dependent protein binding / spindle pole / double-strand break repair / microtubule binding / cysteine-type deubiquitinase activity / cell cycle / cell division / proteolysis / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain / BRCA1-A complex subunit Abraxas 1 MPN domain / FAM175 family / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile.
Similarity search - Domain/homology
BRISC complex subunit FAM175B / Lys-63-specific deubiquitinase BRCC36
Similarity search - Component
Biological speciesCamponotus floridanus (Florida carpenter ant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.543 Å
AuthorsZeqiraj, E.
CitationJournal: Mol.Cell / Year: 2015
Title: Higher-Order Assembly of BRCC36-KIAA0157 Is Required for DUB Activity and Biological Function.
Authors: Zeqiraj, E. / Tian, L. / Piggott, C.A. / Pillon, M.C. / Duffy, N.M. / Ceccarelli, D.F. / Keszei, A.F. / Lorenzen, K. / Kurinov, I. / Orlicky, S. / Gish, G.D. / Heck, A.J. / Guarne, A. / ...Authors: Zeqiraj, E. / Tian, L. / Piggott, C.A. / Pillon, M.C. / Duffy, N.M. / Ceccarelli, D.F. / Keszei, A.F. / Lorenzen, K. / Kurinov, I. / Orlicky, S. / Gish, G.D. / Heck, A.J. / Guarne, A. / Greenberg, R.A. / Sicheri, F.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRCA1/BRCA2-containing complex subunit 3
B: Protein FAM175B
C: BRCA1/BRCA2-containing complex subunit 3
D: Protein FAM175B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4187
Polymers124,1684
Non-polymers2503
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20120 Å2
ΔGint-171 kcal/mol
Surface area42480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.106, 116.287, 231.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BRCA1/BRCA2-containing complex subunit 3


Mass: 29288.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camponotus floridanus (Florida carpenter ant)
Gene: EAG_15736 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: E2AXC7
#2: Protein Protein FAM175B


Mass: 32795.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camponotus floridanus (Florida carpenter ant)
Gene: EAG_01033 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: E2AB17
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na HEPES (pH 7.0), 10% w/v PEG4000 and 10% (v/v) 2-propanol
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.54→46.44 Å / Num. obs: 84216 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 71.92 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.059 / Χ2: 1.906 / Net I/σ(I): 13.74 / Num. measured all: 243850
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.54-2.610.4521.1691.0217408633960201.42595
2.61-2.680.5590.9581.2517983619761461.16899.2
2.68-2.760.6640.6871.7417210607760210.84199.1
2.76-2.840.7460.5052.2215543580557440.62698.9
2.84-2.940.8760.3613.2217089572356710.43999.1
2.94-3.040.9220.2644.4816189541053640.32199.1
3.04-3.150.9570.1766.3615679535852940.21598.8
3.15-3.280.9770.1328.3814543503949690.16298.6
3.28-3.430.990.08911.5913370489747970.1198
3.43-3.60.9930.06615.4612919471445810.08197.2
3.6-3.790.9960.05219.913010439743240.06498.3
3.79-4.020.9960.04423.1812156417541110.05398.5
4.02-4.30.9980.03427.2111198396238640.04297.5
4.3-4.640.9980.02930.059529369735670.03696.5
4.64-5.090.9980.02733.889836336332990.03398.1
5.09-5.690.9980.02932.78884305029930.03598.1
5.69-6.570.9980.02931.537359268426000.03696.9
6.57-8.040.9990.02336.576294227622010.02996.7
8.04-11.370.9990.01941.135054175717360.02398.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.543→46.44 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 2093 2.49 %
Rwork0.1889 82108 -
obs0.1901 84201 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 344.33 Å2 / Biso mean: 93.755 Å2 / Biso min: 37.28 Å2
Refinement stepCycle: final / Resolution: 2.543→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7606 0 29 4 7639
Biso mean--101.03 71.58 -
Num. residues----970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037763
X-RAY DIFFRACTIONf_angle_d0.55410480
X-RAY DIFFRACTIONf_chiral_restr0.0211251
X-RAY DIFFRACTIONf_plane_restr0.0021331
X-RAY DIFFRACTIONf_dihedral_angle_d12.8762854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5432-2.60240.41350.32525269540494
2.6024-2.66740.3761400.31875540568099
2.6674-2.73960.34391350.28055504563999
2.7396-2.82020.27291380.28265556569499
2.8202-2.91120.32341450.26725528567399
2.9112-3.01520.31951410.25355528566999
3.0152-3.13590.28771400.235573571399
3.1359-3.27860.24581370.21545449558699
3.2786-3.45140.25141390.19945472561198
3.4514-3.66760.24961360.18365441557798
3.6676-3.95060.2331430.17415499564298
3.9506-4.34790.21321410.15985447558898
4.3479-4.97640.18951400.14595444558497
4.9764-6.26730.25871380.18585471560998
6.2673-46.44760.2081450.16865387553297
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)
14.6832-0.71881.72296.0353-2.71856.21430.0462-0.05650.69230.16190.0515-0.0889-0.8008-0.0727-0.02510.39090.07970.04710.5076-0.03090.644756.9378128.7329-23.1642
23.98720.1228-0.43415.1337-0.84465.4580.16150.1240.29590.07890.07450.801-0.3364-0.4389-0.2630.39840.0523-0.01480.5469-0.04330.581549.1238124.0735-21.6246
32.23930.75411.55351.15791.1788.21490.06750.34870.1103-0.05020.1539-0.10450.03840.9153-0.23790.30710.07150.01140.6334-0.03790.558772.7212117.1043-19.8711
43.32421.20832.54524.5564-0.27627.68550.3380.4055-0.544-0.0102-0.08180.15150.84710.5085-0.37910.42980.1056-0.04550.4561-0.11250.515962.5612102.818-21.5806
51.41.15930.59383.94140.52386.46670.01460.1449-0.6806-0.31630.097-0.21350.88590.6157-0.02870.69540.1546-0.08380.6277-0.17080.761462.183196.0878-28.367
63.60033.5668-2.54549.92490.65413.31110.0294-0.1317-1.6622-0.00520.1305-0.32431.77240.84390.19111.11030.2021-0.11720.6326-0.13060.841559.88388.1721-27.8722
73.5553-1.12880.91346.9709-0.72364.11230.2245-0.0467-0.5772-0.00850.06850.34050.9154-0.1704-0.25150.4859-0.0180.05060.477-0.01350.500956.0701101.0371-17.4053
84.54912.7619-2.6372.6889-3.97046.50180.0204-0.6635-0.32930.30750.0389-0.22390.5431.12190.02940.52460.1751-0.02140.7379-0.16140.709782.9279109.9406-11.3768
95.20972.08795.62962.63332.07179.5247-0.10370.51640.2652-0.66350.05570.0358-0.0490.37010.01920.53160.17890.06350.6988-0.06580.654268.3112111.3884-38.3206
102.07790.5643-0.86864.0119-3.37723.24010.4748-0.2071-0.35320.32840.18110.61951.7391-0.1409-0.67841.1231-0.08190.03840.5013-0.02120.799866.8295108.143632.5122
116.1253-2.3876-1.27188.71280.89575.8767-0.1859-0.48320.16290.98550.4919-0.30181.9090.3403-0.33131.3350.0477-0.0870.5439-0.09120.755772.3463100.025632.5215
127.76836.5339-3.32855.8591-1.19859.6740.2192-0.10050.12180.4985-0.7407-1.14072.5421-0.7758-0.06391.5429-0.4959-0.17311.203-0.0311.477656.1308100.716827.5858
130.06440.49110.25330.9217-0.16076.68720.05730.0358-0.03960.28980.20560.33391.1731-0.0735-0.16240.72310.0564-0.03220.6429-0.02850.793570.2655111.010821.3718
144.9551-0.25212.97713.82.05093.0594-0.1665-0.53150.43730.58050.3276-0.1283-0.65591.51150.16740.8413-0.1880.1011.1263-0.13430.668983.6328128.128341.103
152.14791.06221.21393.4139-0.756.47220.1164-0.28480.71970.66310.06341.0066-1.781-0.2250.01211.01140.07160.30030.5497-0.0880.953867.8153133.701232.6161
167.3027-3.91871.96275.8586-4.55166.5430.2014-0.29530.75140.41750.0445-0.5752-0.90981.161-0.33940.9087-0.25690.04710.9619-0.20350.78882.2843127.613611.9169
171.8565-0.163-0.12751.6814-0.02072.6258-0.131-0.0349-0.37440.1664-0.01580.0890.73252.10460.31950.56660.1282-0.04841.0434-0.08570.626284.2384120.523637.7891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 82 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 166 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 250 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 42 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 112 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 113 through 129 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 188 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 189 through 223 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 224 through 272 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 42 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 43 through 97 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 98 through 117 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 118 through 218 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 219 through 251 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid 5 through 181 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 182 through 218 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 219 through 271 )D0

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