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- PDB-7s4a: MRG15 complex with PALB2 peptide -

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Basic information

Entry
Database: PDB / ID: 7s4a
TitleMRG15 complex with PALB2 peptide
Components
  • Mortality factor 4-like protein 1
  • Partner and localizer of BRCA2
KeywordsTRANSCRIPTION / Complex / Tumor suppressor / Recombination mediator
Function / homology
Function and homology information


regulation of double-strand break repair / post-anal tail morphogenesis / Impaired BRCA2 binding to PALB2 / DNA repair complex / 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 ...regulation of double-strand break repair / post-anal tail morphogenesis / Impaired BRCA2 binding to PALB2 / DNA repair complex / 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 / NuA4 histone acetyltransferase complex / inner cell mass cell proliferation / Sin3-type complex / positive regulation of double-strand break repair via homologous recombination / mesoderm development / embryonic organ development / somitogenesis / animal organ morphogenesis / double-strand break repair via homologous recombination / multicellular organism growth / HDR through Homologous Recombination (HRR) / KEAP1-NFE2L2 pathway / nucleosome / Neddylation / chromatin organization / HATs acetylate histones / fibroblast proliferation / regulation of apoptotic process / regulation of cell cycle / nuclear speck / apoptotic process / chromatin binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Partner and localiser of BRCA2, WD40 domain / Partner and localizer of BRCA2 / Partner and localizer of BRCA2 WD40 domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain ...Partner and localiser of BRCA2, WD40 domain / Partner and localizer of BRCA2 / Partner and localizer of BRCA2 WD40 domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo-like domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Partner and localizer of BRCA2 / Mortality factor 4-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.693 Å
AuthorsKorolev, S. / Deveryshetty, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private3950 United States
CitationJournal: Genes (Basel) / Year: 2021
Title: Structural Insight into the Mechanism of PALB2 Interaction with MRG15.
Authors: Redington, J. / Deveryshetty, J. / Kanikkannan, L. / Miller, I. / Korolev, S.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
A: Mortality factor 4-like protein 1
B: Partner and localizer of BRCA2
C: Mortality factor 4-like protein 1
D: Partner and localizer of BRCA2


Theoretical massNumber of molelcules
Total (without water)53,0054
Polymers53,0054
Non-polymers00
Water27015
1
A: Mortality factor 4-like protein 1
B: Partner and localizer of BRCA2


Theoretical massNumber of molelcules
Total (without water)26,5022
Polymers26,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-15 kcal/mol
Surface area10400 Å2
MethodPISA
2
C: Mortality factor 4-like protein 1
D: Partner and localizer of BRCA2


Theoretical massNumber of molelcules
Total (without water)26,5022
Polymers26,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-16 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.084, 60.157, 131.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 156 through 202 or resid 212 through 315))
21(chain C and (resid 156 through 202 or resid 212 through 315))
12(chain B and resid 597 through 610)
22(chain D and resid 597 through 610)
13(chain B and resid 611 through 628)
23(chain D and resid 611 through 628)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALLYSLYS(chain A and (resid 156 through 202 or resid 212 through 315))AA156 - 2025 - 51
121TYRTYRPROPRO(chain A and (resid 156 through 202 or resid 212 through 315))AA212 - 31561 - 164
211VALVALLYSLYS(chain C and (resid 156 through 202 or resid 212 through 315))CC156 - 2025 - 51
221TYRTYRPROPRO(chain C and (resid 156 through 202 or resid 212 through 315))CC212 - 31561 - 164
112METMETTHRTHR(chain B and resid 597 through 610)BB597 - 61024 - 37
212METMETTHRTHR(chain D and resid 597 through 610)DD597 - 61024 - 37
113ASPASPLYSLYS(chain B and resid 611 through 628)BB611 - 62838 - 55
213ASPASPLYSLYS(chain D and resid 611 through 628)DD611 - 62838 - 55

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Mortality factor 4-like protein 1 / MORF-related gene 15 protein / Protein MSL3-1 / Transcription factor-like protein MRG15


Mass: 19940.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORF4L1, MRG15, FWP006, HSPC008, HSPC061, PP368 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU8
#2: Protein Partner and localizer of BRCA2


Mass: 6561.436 Da / Num. of mol.: 2 / Fragment: UNP residues 597-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB2, FANCN / Production host: Escherichia coli (E. coli) / References: UniProt: Q86YC2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: Ammonium sulfate, Tris HCl

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.693→30 Å / Num. obs: 12298 / % possible obs: 98.7 % / Redundancy: 4.7 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.065 / Rrim(I) all: 0.146 / Χ2: 1.49 / Net I/σ(I): 10.1
Reflection shellResolution: 2.693→2.75 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 603 / CC1/2: 0.675 / CC star: 0.898 / Rpim(I) all: 0.434 / Rrim(I) all: 0.953 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AQL

2aql


Resolution: 2.693→29.671 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2969 1228 10.02 %
Rwork0.2265 11024 -
obs0.2336 12252 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.81 Å2 / Biso mean: 52.365 Å2 / Biso min: 23.23 Å2
Refinement stepCycle: final / Resolution: 2.693→29.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 0 15 3148
Biso mean---45.9 -
Num. residues----386
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A902X-RAY DIFFRACTION6.347TORSIONAL
12C902X-RAY DIFFRACTION6.347TORSIONAL
21B78X-RAY DIFFRACTION6.347TORSIONAL
22D78X-RAY DIFFRACTION6.347TORSIONAL
31B102X-RAY DIFFRACTION6.347TORSIONAL
32D102X-RAY DIFFRACTION6.347TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6934-2.80110.37831310.2885118098
2.8011-2.92850.43931340.3183119799
2.9285-3.08280.37571370.3112122499
3.0828-3.27570.36491340.2667121399
3.2757-3.52820.32841380.257123899
3.5282-3.88260.27741370.2146123299
3.8826-4.44280.2751360.1968122498
4.4428-5.59130.27581370.1924123097
5.5913-29.6710.22841440.1935128696

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