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- PDB-8r7e: MutSbeta bound to compound CHDI-00898647 in the canonical DNA-mis... -

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Basic information

Entry
Database: PDB / ID: 8r7e
TitleMutSbeta bound to compound CHDI-00898647 in the canonical DNA-mismatch bound form
Components
  • (DNA mismatch repair protein ...) x 2
  • DNA (5'-D(*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
  • DNA (5'-D(*TP*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
KeywordsDNA BINDING PROTEIN / PROTEROS BIOSTRUCTURES GMBH / DNA mismatch Repair
Function / homology
Function and homology information


somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity / maintenance of DNA repeat elements ...somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity / maintenance of DNA repeat elements / positive regulation of isotype switching to IgA isotypes / centromeric DNA binding / positive regulation of isotype switching to IgG isotypes / mismatched DNA binding / mitotic recombination / negative regulation of DNA recombination / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / response to UV-B / oxidative phosphorylation / DNA damage tolerance / mitotic intra-S DNA damage checkpoint signaling / ATP-dependent DNA damage sensor activity / germ cell development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / ATP-dependent activity, acting on DNA / mismatch repair / somatic hypermutation of immunoglobulin genes / B cell differentiation / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / enzyme activator activity / male gonad development / double-strand break repair / double-stranded DNA binding / in utero embryonic development / negative regulation of neuron apoptotic process / damaged DNA binding / chromosome, telomeric region / DNA repair / chromatin binding / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV ...DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / DNA / DNA (> 10) / DNA mismatch repair protein Msh3 / DNA mismatch repair protein Msh2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.783 Å
AuthorsThomsen, M. / Thieulin-Pardo, G. / Steinbacher, S. / Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. ...Thomsen, M. / Thieulin-Pardo, G. / Steinbacher, S. / Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Witte, D. / Finley, M. / Prasad, B. / Monteagudo, E. / Plotnikov, N. / Pacifici, R. / Maillard, M. / Wilkinson, H. / Iyer, R. / Dominguez, C. / Vogt, T. / Felsenfeld, D. / Haque, T.
Funding support United States, 1items
OrganizationGrant numberCountry
CHDI Foundation United States
CitationJournal: Chemrxiv / Year: 2024
Title: Identification of orthosteric inhibitors of MutSbeta ATPase function
Authors: Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Thieulin-Pardo, G. / Steinbacher, S. / Thomsen, M. / Witte, D. ...Authors: Brace, G. / Tillack, K. / Johnson, P. / Ritzefeld, M. / Schaertl, S. / Frush, E. / Warfield, B. / Ballantyne, G. / Lee, J.-H. / Thieulin-Pardo, G. / Steinbacher, S. / Thomsen, M. / Witte, D. / Finley, M. / Prasad, B. / Monteagudo, E. / Plotnikov, N. / Pacifici, R. / Maillard, M. / Wilkinson, H. / Iyer, R. / Dominguez, C. / Vogt, T. / Felsenfeld, D. / Haque, T.
History
DepositionNov 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein Msh2
B: DNA mismatch repair protein Msh3
C: DNA (5'-D(*TP*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
D: DNA (5'-D(*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
E: DNA mismatch repair protein Msh2
F: DNA mismatch repair protein Msh3
G: DNA (5'-D(*TP*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
H: DNA (5'-D(*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,61227
Polymers446,8158
Non-polymers2,79719
Water2,108117
1
A: DNA mismatch repair protein Msh2
B: DNA mismatch repair protein Msh3
C: DNA (5'-D(*TP*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
D: DNA (5'-D(*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,86714
Polymers223,4074
Non-polymers1,46010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-165 kcal/mol
Surface area82340 Å2
MethodPISA
2
E: DNA mismatch repair protein Msh2
F: DNA mismatch repair protein Msh3
G: DNA (5'-D(*TP*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
H: DNA (5'-D(*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,74513
Polymers223,4074
Non-polymers1,3379
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15510 Å2
ΔGint-168 kcal/mol
Surface area81850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.473, 104.096, 122.016
Angle α, β, γ (deg.)109.331, 91.808, 109.505
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
32B
42F
53C
63G
74D
84H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERILEILEAA13 - 93013 - 930
221SERSERILEILEEE13 - 93013 - 930
332SERSERLYSLYSBB227 - 112111 - 905
442SERSERLYSLYSFF227 - 112111 - 905
553DCDCDGDGCC4 - 234 - 23
663DCDCDGDGGG4 - 234 - 23
774DCDCDGDGDD27 - 492 - 24
884DCDCDGDGHH27 - 492 - 24

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8

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Components

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DNA mismatch repair protein ... , 2 types, 4 molecules AEBF

#1: Protein DNA mismatch repair protein Msh2


Mass: 104431.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43246
#2: Protein DNA mismatch repair protein Msh3


Mass: 104260.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20585

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DNA chain , 2 types, 4 molecules CGDH

#3: DNA chain DNA (5'-D(*TP*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')


Mass: 7345.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')


Mass: 7369.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 136 molecules

#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-YKQ / Abivertinib / ~{N}-[3-[[2-[[3-fluoranyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]oxy]phenyl]prop-2-enamide


Mass: 487.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H26FN7O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 MES pH 6.5; 0.2 M NH4 Acetate; 20-25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.783→113.659 Å / Num. obs: 79309 / % possible obs: 92 % / Redundancy: 2.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.062 / Net I/σ(I): 9
Reflection shellResolution: 2.783→3.008 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3965 / CC1/2: 0.353 / Rpim(I) all: 0.643 / % possible all: 57.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.783→113.659 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.886 / SU B: 20.868 / SU ML: 0.395 / Cross valid method: FREE R-VALUE / ESU R Free: 0.507
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2657 3915 4.936 %
Rwork0.2226 75393 -
all0.225 --
obs-79308 72.825 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 60.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.266 Å2-0.193 Å20.096 Å2
2---0.035 Å2-0.067 Å2
3---0.356 Å2
Refinement stepCycle: LAST / Resolution: 2.783→113.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26824 1819 176 117 28936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01328281
X-RAY DIFFRACTIONr_bond_other_d0.0020.01726048
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0730.051
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.60138698
X-RAY DIFFRACTIONr_angle_other_deg1.1121.62959524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24153340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00422.91193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54615.0114349
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg6.018201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.21315121
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.934206
X-RAY DIFFRACTIONr_chiral_restr0.0470.23887
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0230746
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026326
X-RAY DIFFRACTIONr_nbd_refined0.1460.25178
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1420.223345
X-RAY DIFFRACTIONr_nbtor_refined0.1480.213165
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.212124
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2560
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.219
X-RAY DIFFRACTIONr_nbd_other0.1380.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.28
X-RAY DIFFRACTIONr_mcbond_it2.3526.7813453
X-RAY DIFFRACTIONr_mcbond_other2.3526.77913452
X-RAY DIFFRACTIONr_mcangle_it4.05310.15716762
X-RAY DIFFRACTIONr_mcangle_other4.05310.15716763
X-RAY DIFFRACTIONr_scbond_it1.957.03914828
X-RAY DIFFRACTIONr_scbond_other1.957.03914829
X-RAY DIFFRACTIONr_scangle_it3.43410.56721936
X-RAY DIFFRACTIONr_scangle_other3.43410.56721937
X-RAY DIFFRACTIONr_lrange_it6.38479.27130467
X-RAY DIFFRACTIONr_lrange_other6.38379.27230467
X-RAY DIFFRACTIONr_ncsr_local_group_10.0350.059490
X-RAY DIFFRACTIONr_ncsr_local_group_20.030.059802
X-RAY DIFFRACTIONr_ncsr_local_group_30.0410.05465
X-RAY DIFFRACTIONr_ncsr_local_group_40.0370.05536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.035160.05
12EX-RAY DIFFRACTIONLocal ncs0.035160.05
23BX-RAY DIFFRACTIONLocal ncs0.029650.05
24FX-RAY DIFFRACTIONLocal ncs0.029650.05
35CX-RAY DIFFRACTIONLocal ncs0.040950.05
36GX-RAY DIFFRACTIONLocal ncs0.040950.05
47DX-RAY DIFFRACTIONLocal ncs0.036970.05
48HX-RAY DIFFRACTIONLocal ncs0.036970.05
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.783-2.8550.378210.3494810.3580640.8050.7996.22520.343
2.855-2.9330.321590.34612280.34578730.7440.74316.3470.347
2.933-3.0180.3841400.3423780.34375960.6640.70933.1490.336
3.018-3.1110.3661730.30934180.31274410.7360.75948.25960.302
3.111-3.2130.3322100.29141880.29371950.7750.78761.12580.278
3.213-3.3260.3272580.27848040.2869130.8120.81173.22440.259
3.326-3.4510.3132740.26554510.26767440.8160.83384.89030.246
3.451-3.5920.2783190.24557580.24764530.8670.8794.17330.225
3.592-3.7520.2733200.23557430.23761690.8740.87898.28170.217
3.752-3.9350.2432790.21855770.21959150.9060.9199.00250.201
3.935-4.1470.252740.19853200.20156410.9090.92699.16680.186
4.147-4.3980.2222880.18649850.18853290.9320.93998.94910.18
4.398-4.7010.2332210.18347180.18549980.9210.93698.81950.182
4.701-5.0770.2312280.18343710.18546420.9250.9499.07370.184
5.077-5.5610.2742320.21540340.21842920.8880.91299.39420.218
5.561-6.2150.2941720.23836730.2438670.8930.9199.43110.242
6.215-7.1730.2951520.24232360.24534020.8970.90599.58850.257
7.173-8.7770.2351320.20727550.20929010.9220.92899.51740.237
8.777-12.3760.2421080.17521020.17822270.9280.9599.23660.22
12.376-113.6590.265550.28511730.28412400.9410.88699.03230.423

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