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- PDB-5cw5: Structure of CfBRCC36-CfKIAA0157 complex (QSQ mutant) -

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Basic information

Entry
Database: PDB / ID: 5cw5
TitleStructure of CfBRCC36-CfKIAA0157 complex (QSQ mutant)
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 / polyubiquitin modification-dependent protein binding / mitotic spindle assembly / 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 / polyubiquitin modification-dependent protein binding / mitotic spindle assembly / spindle pole / double-strand break repair / microtubule binding / cysteine-type deubiquitinase activity / cell division / proteolysis / nucleus / metal ion binding / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.736 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 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)122,9094
Polymers122,9094
Non-polymers00
Water00
1
A: BRCA1/BRCA2-containing complex subunit 3
D: Protein FAM175B


Theoretical massNumber of molelcules
Total (without water)61,4552
Polymers61,4552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-49 kcal/mol
Surface area21460 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19000 Å2
ΔGint-126 kcal/mol
Surface area39550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.452, 124.173, 132.539
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: 28893.193 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: 32561.334 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

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M KCl, 0.1 M HEPES-Na (pH 7.5) and 15% PEG6000 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 2.736→50 Å / Num. obs: 37786 / % possible obs: 95.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 59.95 Å2 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.094 / Rrim(I) all: 0.158 / Χ2: 0.968 / Net I/av σ(I): 7.293 / Net I/σ(I): 4.2 / Num. measured all: 103925
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.75-2.852.60.92736220.50.6640.51393.2
2.85-2.962.70.78836900.5820.5520.53495.30.969
2.96-3.12.80.56337380.7720.3890.56296.10.689
3.1-3.262.70.38337170.8660.270.68195.30.472
3.26-3.462.80.27236940.9290.1880.83795.20.333
3.46-3.732.80.18938820.9540.1320.9898.70.232
3.73-4.112.80.13838310.9720.0951.16697.70.169
4.11-4.72.80.09137730.9850.0621.41395.10.112
4.7-5.922.80.0839410.9880.0551.34598.40.098
5.92-502.70.06538980.9920.0451.53393.30.08

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.736→48.939 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 1610 4.28 %
Rwork0.2309 36033 -
obs0.2329 37643 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.91 Å2 / Biso mean: 72.8552 Å2 / Biso min: 35.93 Å2
Refinement stepCycle: final / Resolution: 2.736→48.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 0 0 7019
Num. residues----900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027122
X-RAY DIFFRACTIONf_angle_d0.4939613
X-RAY DIFFRACTIONf_chiral_restr0.0181154
X-RAY DIFFRACTIONf_plane_restr0.0021220
X-RAY DIFFRACTIONf_dihedral_angle_d12.1592599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7363-2.81680.3641100.33952602271283
2.8168-2.90770.34831240.32962936306094
2.9077-3.01160.34731260.32523001312796
3.0116-3.13220.36611390.28662996313596
3.1322-3.27470.36421450.26822890303593
3.2747-3.44730.28931380.24853038317697
3.4473-3.66320.29771170.23123112322999
3.6632-3.9460.26011560.22373079323598
3.946-4.34280.25421380.2052946308493
4.3428-4.97070.22641340.17913182331699
4.9707-6.26050.26181350.2273095323097
6.2605-48.94670.25051480.20933156330494
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)
16.8809-2.8041-2.90625.30231.93825.474-0.5863-0.2907-0.07540.51790.2980.07370.6336-0.2380.34880.3546-0.0486-0.03290.49440.04470.438127.5112-13.3516-10.168
23.5345-3.0075-2.04253.88853.4213.14850.1798-0.30750.2358-0.0823-0.07460.5839-0.16270.084-0.15120.5989-0.0515-0.07640.6220.14390.548924.94-13.1031-17.4538
38.5845-4.2909-1.02153.0260.97412.59540.07940.70210.2172-0.0991-0.18140.76260.9965-0.8766-0.05550.5242-0.16520.05980.61270.12610.671421.4001-16.9584-18.5682
42.32762.2456-2.10832.03480.98337.90850.47-0.478-2.6523-0.9286-1.00530.91151.37510.60750.94070.7648-0.35580.08881.04360.07111.669715.0957-24.2705-14.7128
51.4825-1.9475-0.16639.449-0.10334.86381.7388-1.3324-0.94990.4929-1.39640.8753-0.74960.3876-0.31570.4539-0.182-0.0990.49290.11960.571521.2871-14.0861-14.9588
64.2554-2.22253.06056.75651.98864.3690.0474-0.60590.4586-0.89020.075-0.1496-0.26780.49580.18540.6292-0.02630.06770.60190.10020.297128.1403-7.0911-18.4079
74.38974.34151.99824.59651.92511.69680.34251.5536-0.7383-0.4249-0.2225-1.4799-0.7767-0.1436-0.3390.66320.040.11170.87180.1430.900246.6261-5.1186-17.5352
86.1965-3.194-0.41969.1185-0.27944.22840.160.1057-0.00030.1766-0.46360.2286-0.3641-0.03720.15890.3120.010.0650.4765-0.03880.372924.8112-7.3804-10.1574
91.3129-0.3419-1.73261.21721.03712.7416-0.45240.2989-0.3934-0.0523-0.24620.24830.9876-1.3820.86890.5735-0.14390.03370.61470.00680.670330.287-28.3892-28.8374
101.27640.1712-0.90953.04833.23473.4427-0.18850.02650.0452-0.1815-0.52470.42530.8776-0.05250.60040.7610.01330.0440.53910.03690.537740.6865-29.2655-36.043
112.12720.2560.67051.6507-2.2442.71660.2281-0.5763-0.53940.4176-0.2318-0.2392-0.68010.6080.24560.64820.0143-0.04650.62860.17140.613243.0071-29.42081.7119
122.64710.2616-1.89661.2660.98035.8234-0.0483-0.384-0.18390.19160.0847-0.22460.14210.734-0.0990.44240.0328-0.04440.67740.05630.536650.2291-18.5068-7.1289
133.03642.8671-0.75786.02-1.13823.96280.1046-0.5091-0.16330.5031-0.4752-0.55390.01330.28660.42930.39410.0101-0.06220.76670.00470.510453.9916-15.73180.4318
143.21870.71361.37021.98141.00191.5672-0.0671-0.03560.03050.02540.1166-0.38270.13360.6884-0.050.38360.0090.01530.6680.01050.503651.745-9.4451-9.6022
154.7221-1.9181-1.96631.72852.17762.96880.51630.00440.1547-0.4037-0.1005-0.8360.07240.0616-0.36190.54560.00990.04840.62330.09630.619852.2979-22.9997-28.0072
161.25860.4885-0.22971.7840.47655.9252-0.1446-0.3192-0.08420.1626-0.28050.21240.4293-0.02420.18740.61520.0256-0.04090.49460.09040.580537.7564-33.1741-8.4321
178.34761.8507-1.04455.3458-0.49370.6465-0.2972-0.29690.2483-0.00010.0907-0.28110.1650.47390.18310.41060.0496-0.03440.6018-0.04320.346264.4354-12.4817-62.8995
189.0284-4.8643-6.56226.08051.98468.2281-0.9681-0.5864-1.37520.8660.13120.04241.5761.89360.95550.640.1159-0.03560.91440.09851.164574.5481-22.2912-61.2718
195.0463-3.1982-4.47563.86922.13377.6267-0.0511.5033-0.07650.1285-0.5752-0.18320.1384-0.07680.26630.47920.05530.05710.82990.00280.569768.3152-12.7783-62.8733
206.97210.63891.69460.676-0.8691.6794-0.0966-0.62910.2790.2841-0.05680.3095-0.220.18410.130.628-0.04940.09040.6972-0.10020.63254.2123-3.7556-60.2971
213.97612.7716-1.37499.43870.77974.77020.1447-0.0411-0.2893-0.5018-0.2055-0.4099-0.32310.76020.05680.33630.0540.04980.83360.05680.643465.1258-7.0207-68.6602
223.12450.5959-2.25661.6878-1.0862.3239-0.2901-0.0563-0.7760.1532-0.5668-0.32671.20781.45410.77830.58560.1604-0.03660.58810.00830.711359.9249-26.3002-52.5894
232.91811.5997-3.32654.6873-4.1374.6426-0.5105-0.5663-0.13740.0572-0.8494-0.7950.22070.73131.26640.58140.0616-0.07010.4723-0.01430.530850.2279-29.7775-39.1535
242.38260.65570.95512.1219-2.18197.66360.22390.5625-0.1827-0.53790.21770.08370.0389-0.4835-0.34090.63340.04810.00770.4941-0.15830.547346.6079-27.2485-77.4495
253.1180.9036-1.76211.7452-2.1736.88610.1530.12320.1447-0.2918-0.08250.20450.04890.1639-0.17490.40140.0292-0.00910.61480.00970.474440.0796-16.9789-66.0927
262.11781.91310.1422.48241.56462.66780.74410.50022.0371-0.58860.02251.99591.7951-1.0508-0.46960.67480.0647-0.22971.30750.31611.063335.0966-14.6299-88.2168
274.8662-1.5804-0.41832.2389-0.35753.22470.04290.6816-0.009-0.5839-0.01410.27470.3932-0.0983-0.02620.48310.0166-0.05150.62140.00160.617235.7136-13.8759-77.6327
285.8242-0.7446-0.29421.1202-0.49432.13750.06530.41770.5906-0.01770.03820.1770.2371-0.2339-0.02090.40730.05790.01880.63310.00360.521537.4376-8.3428-67.5055
291.83311.084-0.27191.4185-1.47171.72940.02870.2164-0.27760.0870.31140.26890.0359-0.22-0.27150.5946-0.01280.0240.7364-0.08670.640837.1099-24.7854-53.7581
301.42640.23420.15512.9842-2.85594.4278-0.07560.2935-0.1352-0.5333-0.3303-0.34530.72270.01920.26860.71710.10340.0090.4953-0.12880.62452.0492-31.7147-69.2798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 25 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 42 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 67 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 83 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 97 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 128 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 129 through 140 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 141 through 166 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 167 through 196 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 197 through 218 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 219 through 249 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 5 through 81 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 82 through 127 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 176 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 177 through 203 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 204 through 264 )B0
17X-RAY DIFFRACTION17chain 'C' and (resid 4 through 66 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 67 through 83 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 84 through 97 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 98 through 147 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 148 through 166 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 167 through 191 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 192 through 218 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 219 through 247 )C0
25X-RAY DIFFRACTION25chain 'D' and (resid 5 through 66 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 67 through 81 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 82 through 126 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 127 through 176 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 177 through 205 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 206 through 264 )D0

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