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- PDB-5cw3: Structure of CfBRCC36-CfKIAA0157 complex (Zn Edge) -

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Basic information

Entry
Database: PDB / ID: 5cw3
TitleStructure of CfBRCC36-CfKIAA0157 complex (Zn 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 / protein K63-linked deubiquitination / positive regulation of NLRP3 inflammasome complex assembly / polyubiquitin modification-dependent protein binding / mitotic spindle assembly / spindle pole ...BRISC complex / BRCA1-A complex / attachment of spindle microtubules to kinetochore / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / 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
BRISC complex subunit FAM175B, helical domain / Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain / FAM175 family / BRCA1-A complex subunit Abraxas 1 MPN domain / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain ...BRISC complex subunit FAM175B, helical domain / Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain / FAM175 family / BRCA1-A complex subunit Abraxas 1 MPN domain / : / 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 / Resolution: 2.55 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0806
Polymers122,9494
Non-polymers1312
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19410 Å2
ΔGint-211 kcal/mol
Surface area43220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.930, 116.580, 226.080
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: 28913.229 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2824 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: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.55→48.755 Å / Num. obs: 80922 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 64.79 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.123 / Χ2: 1.194 / Net I/σ(I): 7.22 / Num. measured all: 277108
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.55-2.650.4341.2761.0130610915589741.49498
2.65-2.830.6380.8041.74381013184128960.93897.8
2.83-3.050.8360.443.144259012229120570.50798.6
3.05-3.350.9440.2465.553909611949115740.28596.9
3.35-3.750.980.1389.363627410505103190.15998.2
3.75-4.30.9850.10112.0827693878184070.11895.7
4.3-5.30.9880.08214.927071810578850.09597.3
5.3-7.50.9930.07314.6219138597156960.08495.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.55→48.755 Å / FOM work R set: 0.8108 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 2044 2.53 %
Rwork0.2113 78868 -
obs0.2125 80912 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.56 Å2 / Biso mean: 76.52 Å2 / Biso min: 29.01 Å2
Refinement stepCycle: final / Resolution: 2.55→48.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7524 0 2 24 7550
Biso mean--111.02 62.16 -
Num. residues----978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027650
X-RAY DIFFRACTIONf_angle_d0.50410353
X-RAY DIFFRACTIONf_chiral_restr0.0331252
X-RAY DIFFRACTIONf_plane_restr0.0021321
X-RAY DIFFRACTIONf_dihedral_angle_d11.9732749
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 (%)
2.55-2.60930.35671350.31885324545998
2.6093-2.67460.37931380.31375253539197
2.6746-2.74690.31611370.28995261539897
2.7469-2.82770.31321410.28165330547199
2.8277-2.9190.37581360.27395366550299
2.919-3.02330.33221330.26325284541798
3.0233-3.14430.28381360.2475313544998
3.1443-3.28740.28261350.23275158529396
3.2874-3.46060.22761360.21135293542998
3.4606-3.67740.22951390.2015292543198
3.6774-3.96120.24241340.19915291542597
3.9612-4.35960.28621350.18455077521295
4.3596-4.98990.2171380.16715319545798
4.9899-6.28470.2521360.21745146528295
6.2847-48.7640.22891350.19365161529696
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)
16.547-0.6502-1.8825.4591.00246.5681-0.00820.1667-0.7022-0.087-0.02280.01840.8059-0.0925-0.0120.36790.0341-0.06340.3585-0.00480.5295-7.7943-12.5267-23.7439
24.3049-0.9308-1.00035.54420.46233.7577-0.0624-0.0172-0.4157-0.06590.0412-0.70860.31550.2431-0.05030.35220.0125-0.00850.40390.04120.51220.0853-7.6256-21.4899
31.92130.8925-1.61610.73-0.73084.3979-0.04950.2338-0.1421-0.03570.16180.12480.2-0.6245-0.15360.35850.0314-0.02980.53880.02060.4505-24.031-1.269-19.1047
42.03970.9798-0.88393.9857-0.49484.38790.06840.27620.4162-0.32560.0616-0.1581-0.7704-0.069-0.18520.52650.07430.07360.43490.10810.4376-13.253717.7724-26.1286
52.8790.16730.1974.817-1.4565.1442-0.0024-0.05930.39110.2580.0858-0.0379-1.3106-0.123-0.08880.5654-0.06980.00740.39890.03430.4939-6.951520.0381-21.7689
61.29310.2537-1.15753.35931.71912.7758-0.4663-0.3780.31781.11070.4124-0.3693-0.5679-0.1672-0.0670.51690.06320.00280.53250.03860.5327-23.267410.9924-6.3997
76.37353.2494-4.6243.9403-2.58755.3682-0.06230.3758-0.1174-0.34650.1040.12450.2121-0.3915-0.08260.30560.0718-0.15310.51830.07050.4775-23.39064.5109-32.9605
83.29720.88021.91843.6187-2.11543.8278-0.1777-0.19040.3970.74640.3243-0.1633-1.6382-0.2845-0.12661.11320.0778-0.04780.48170.07290.7567-20.828812.618631.1291
90.81040.2750.36020.9216-0.98445.3581-0.0276-0.05970.12560.46620.0886-0.3637-1.0578-0.1848-0.04770.76410.1455-0.05790.51840.01040.6903-22.33823.193625.8952
102.24580.5087-1.39744.8977-1.52995.6377-0.0745-0.1305-0.31710.3773-0.0706-0.95180.82880.01880.04570.59810.0557-0.23410.44220.00160.8048-18.4467-17.091831.362
116.8157-4.5138-2.7975.35555.4197.9402-0.3384-0.5524-0.12420.63410.25170.64730.9764-1.11170.0440.5623-0.1826-0.03080.82570.27180.7794-35.9925-12.012813.0909
123.6178-1.45892.07821.4815-1.28196.6954-0.1192-0.45270.21540.3880.3476-0.0371-0.6157-2.1331-0.36150.5449-0.0545-0.0070.73070.04710.4703-34.4608-5.323639.3908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 83 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 166 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 250 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 112 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 113 through 176 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 177 through 203 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 204 through 272 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 97 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 98 through 250 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 5 through 188 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 189 through 221 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 222 through 271 )D0

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