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- PDB-6m14: Crystal Structure of the BARD1 BRCT Mutant -

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Basic information

Entry
Database: PDB / ID: 6m14
TitleCrystal Structure of the BARD1 BRCT Mutant
ComponentsBRCA1-associated RING domain protein 1
KeywordsTRANSFERASE / BRCT / disease mutation / OLA1 / ANTITUMOR PROTEIN
Function / homology
Function and homology information


negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / homologous recombination ...negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / homologous recombination / tissue homeostasis / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / regulation of phosphorylation / Impaired BRCA2 binding to PALB2 / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / regulation of DNA repair / ubiquitin ligase complex / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Metalloprotease DUBs / kinase binding / cytoplasmic ribonucleoprotein granule / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / UCH proteinases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / protein ubiquitination / nuclear speck / positive regulation of apoptotic process / protein heterodimerization activity / DNA repair / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ankyrin repeats (3 copies) ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88001831059 Å
AuthorsChen, T. / Huang, W.T.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 108-2311-B-007-002-MY3 Taiwan
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2022
Title: BARD1 is an ATPase activating protein for OLA1.
Authors: Chen, T. / Yeh, H.W. / Chen, P.P. / Huang, W.T. / Wu, C.Y. / Liao, T.C. / Lin, S.L. / Chen, Y.Y. / Lin, K.T. / Hsu, S.D. / Cheng, H.C.
History
DepositionFeb 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
B: BRCA1-associated RING domain protein 1
A: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3303
Polymers48,2342
Non-polymers961
Water6,287349
1
B: BRCA1-associated RING domain protein 1


Theoretical massNumber of molelcules
Total (without water)24,1171
Polymers24,1171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11300 Å2
MethodPISA
2
A: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2132
Polymers24,1171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.850, 75.254, 116.824
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

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 569 - 777 / Label seq-ID: 2 - 210

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AB
22chain 'B'BA

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Components

#1: Protein BRCA1-associated RING domain protein 1 / BARD-1 / RING-type E3 ubiquitin transferase BARD1


Mass: 24116.938 Da / Num. of mol.: 2 / Mutation: V695L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARD1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q99728, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulfate,22% PEG 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88001831059→27.7540799692 Å / Num. obs: 41860 / % possible obs: 99.1 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Χ2: 0.865 / Net I/σ(I): 21.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88001831059-1.957.40.23540910.9760.0920.2520.91998.6
1.95-2.037.40.15541040.9890.0610.1670.92898.9
2.03-2.127.40.10541500.9940.0410.1130.93899.1
2.12-2.237.40.07841100.9960.030.0840.91598.6
2.23-2.377.40.0641650.9970.0240.0640.90999.5
2.37-2.557.40.04541690.9980.0180.0480.82999.3
2.55-2.817.30.03441930.9990.0140.0370.7499.5
2.81-3.217.20.03142460.9980.0120.0340.81499.5
3.21-4.0570.02842630.9990.0110.030.93799.7
4.05-27.75407996926.60.02644230.9980.0110.0290.71498.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NTE

2nte


Resolution: 1.88001831059→27.7540799692 Å / SU ML: 0.157701932175 / Cross valid method: FREE R-VALUE / σ(F): 1.3435291979 / Phase error: 19.9417164219
RfactorNum. reflection% reflection
Rfree0.197539814327 2306 3.85193599038 %
Rwork0.16990566604 --
obs0.170982188006 41860 74.7297465984 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.1768193221 Å2
Refinement stepCycle: LAST / Resolution: 1.88001831059→27.7540799692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 5 349 3734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01095652081933468
X-RAY DIFFRACTIONf_angle_d1.109330506114694
X-RAY DIFFRACTIONf_chiral_restr0.0643043705954512
X-RAY DIFFRACTIONf_plane_restr0.00908310883213592
X-RAY DIFFRACTIONf_dihedral_angle_d10.89898816692096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88001831059-1.92090.256929000364980.2141731531142444X-RAY DIFFRACTION51.1057498995
1.9209-1.96560.2198852444331000.1983527613362470X-RAY DIFFRACTION51.4308585151
1.9656-2.01470.2084174339721000.1927793687272479X-RAY DIFFRACTION51.1097899326
2.0147-2.06920.1974946208791000.1852628927752474X-RAY DIFFRACTION51.2035010941
2.0692-2.130.1946658270421000.1905976646222472X-RAY DIFFRACTION51.8234938545
2.13-2.19870.237527577032990.1880548277932489X-RAY DIFFRACTION51.6773162939
2.1987-2.27730.2020081803151060.1811586704062585X-RAY DIFFRACTION53.4458788481
2.2773-2.36840.2075876897121290.1683733297963342X-RAY DIFFRACTION69.4477791116
2.3684-2.47620.2093671131031750.1617033197414463X-RAY DIFFRACTION92.7971188475
2.4762-2.60660.1859787419841880.1601643384444672X-RAY DIFFRACTION97.0253543621
2.6066-2.76980.2110067213271890.169329587414708X-RAY DIFFRACTION97.5303724358
2.7698-2.98340.1923573615211870.1714074396874687X-RAY DIFFRACTION97.8911427998
2.9834-3.28320.1784295058931920.1631510537324665X-RAY DIFFRACTION96.4073044859
3.2832-3.75730.2017610456821800.1623922858524524X-RAY DIFFRACTION93.9297124601
3.7573-4.730.1698961675941830.1488173874354441X-RAY DIFFRACTION92.48
4.73-27.75407996920.2143664612881800.1855916156454645X-RAY DIFFRACTION96.4421347192
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)
11.643507066410.2637746490531.08077276834.930332906982.012327185643.19038443704-0.02157763423090.0877686537590.0690944848588-0.267147255328-0.05139072131390.0648114714144-0.6759829064870.1554519384230.06099065688670.292362371642-0.05917824450280.04984783189580.19706345816-0.02848628601920.16982785801141.029693690216.21901988318.60108533101
23.665301101340.4352148566631.351721563112.671464680073.661596089215.610223884380.244648382917-0.183990547395-0.01667423681030.723216483630.156280212677-0.4853828324780.112401075860.351880560382-0.1380151466490.308534041229-0.0425256307909-0.007741512390410.163690885956-0.02500804143780.19337142596245.225042295312.833490435119.195355358
32.49538964230.7764448616751.191048492211.070560937321.534605947073.118175203435.94594652391E-5-0.1713807148560.3025648035860.2088129619390.205366577289-0.469883330488-0.1614500638940.6312953956120.002311609289260.178532484262-0.0169676629868-0.04335148584640.220477475178-0.07914112807240.27288962317748.7236348833-0.4908360444583.40342953342
43.26458800623-0.5666848660860.2493028178452.909450535060.2543440501672.39451415703-0.05072819457570.4101297007250.193077089702-0.2484932509190.0379239285081-0.122123131806-0.1976314206960.063023386942-0.05320611571720.1377871268080.0001118873519430.0227906648140.1627045197840.007673168057830.12317060286337.1856937664-4.288717324-11.2918142229
56.14556304606-0.819410075193-0.1194582407143.418247423110.1726390689392.47556507998-0.0731753459083-0.0160657402069-0.199752585939-0.07367159177540.1778478715260.1893341788590.0385174039001-0.2302362388320.01670877223380.0906659292560.01602306453650.004405348001240.1055198293180.02761053063610.06621099457331.637692092-11.6705066348-8.3497737812
64.479685033320.02406701221080.9328763866852.920532929151.507133585414.247215067250.0201803373402-0.3549389139480.2007875055170.2012084694670.0254530053145-0.0307275993637-0.0282393711788-0.119286360737-0.1167980927160.08790936212120.02614570821540.01897553655770.101118518831-0.007252734886020.085296178452435.1372900882-7.31273931405-0.634494245114
73.360580469221.070809143630.04819253852743.584941319440.9391315855193.839617309170.0898785098419-0.1624084272560.346067501787-0.120701283018-0.0390325790881-0.0253221310456-0.4490493834850.1050960271990.02034177746560.146830047784-0.04044791160190.03957429376180.176069214403-0.07585235091780.21454088831521.884559021814.485328404637.2128557357
80.9924722464550.101994288447-0.3829394026652.30534620451.498305601763.173151351760.0343080127566-0.1992873314790.367110295794-0.0772900331609-0.126308316990.122763786675-0.178432126627-0.00124992518387-0.2133294182710.115061037016-0.007917938937550.1272551122860.102289784492-0.2433507798570.23756847111916.058187777211.046608188537.6655373499
92.01703346041-1.17752377862-0.8866740857941.714622196910.7236468425794.16377275813-0.00878238130942-0.2073124912620.1379673850620.0844744113934-0.06880198025660.0654583093613-0.02027912784220.231706593769-0.07887820595780.097813814838-0.0278604953860.0671944725440.214963046737-0.1147420220770.18693895326811.2974983538.2240865903342.8080559078
100.550546551851-0.743215650577-0.9194529354491.25581235181.161007984673.00444564958-0.0399475981773-0.193402025838-0.005251108684190.501404603903-0.2363161033330.2032072628420.230890789073-0.0901923621736-0.5550560822880.261033943697-0.1435834286270.06803644239160.240277409018-0.122555955520.09465541068716.0884971299-5.105906210431.3870286026
112.444592369220.659336280837-0.8116692785453.418681254410.02184915914833.303879621960.1388689515910.08218275978620.137684198007-0.143367935115-0.0568366348003-0.026852610194-0.04140239422480.0929088022981-0.1173056030050.07820441782510.004810001844630.01245337543360.165242025826-0.03176859626580.11391231374122.7294177538-5.8502314198614.59919836
123.839278026030.771368974577-0.2321624016634.06117149960.1062078174273.430326677360.06931783929790.3465480964610.387537151131-0.513557395359-0.1165422156450.462808956863-0.313663854039-0.319628911755-0.1989660605750.1721285902510.0297734700774-0.04724789826820.166350551782-0.01933207139560.15782315179415.0695372218-5.302707758137.76923201303
131.77067859288-0.786514111009-1.458610422291.660224669080.6947015138584.353406705120.04783295945550.003930008127290.316713825858-0.0401952842367-0.2753426962250.439441578101-0.242411851967-0.4748189281680.1134659139410.139428000333-0.00214758158770.009943356945550.161388978283-0.08874977374880.21097582422212.6958905726-1.785283114416.2858987861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 569 through 628 )
2X-RAY DIFFRACTION2chain 'B' and (resid 629 through 655 )
3X-RAY DIFFRACTION3chain 'B' and (resid 656 through 675 )
4X-RAY DIFFRACTION4chain 'B' and (resid 676 through 728 )
5X-RAY DIFFRACTION5chain 'B' and (resid 729 through 754 )
6X-RAY DIFFRACTION6chain 'B' and (resid 755 through 777 )
7X-RAY DIFFRACTION7chain 'A' and (resid 569 through 617 )
8X-RAY DIFFRACTION8chain 'A' and (resid 618 through 642 )
9X-RAY DIFFRACTION9chain 'A' and (resid 643 through 655 )
10X-RAY DIFFRACTION10chain 'A' and (resid 656 through 675 )
11X-RAY DIFFRACTION11chain 'A' and (resid 676 through 728 )
12X-RAY DIFFRACTION12chain 'A' and (resid 729 through 754 )
13X-RAY DIFFRACTION13chain 'A' and (resid 755 through 777 )

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