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- PDB-9p4b: Crystal structure of MLH1-CTD with peptide QAVLSRFFQ -

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Basic information

Entry
Database: PDB / ID: 9p4b
TitleCrystal structure of MLH1-CTD with peptide QAVLSRFFQ
Components
  • DNA mismatch repair protein Mlh1
  • DNA mismatch repair protein Msh3
KeywordsDNA BINDING PROTEIN / MLH1 / MISMATCH REPAIR / DNA REPAIR
Function / homology
Function and homology information


chiasma / late recombination nodule / male meiosis chromosome segregation / meiotic metaphase I homologous chromosome alignment / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / negative regulation of mitotic recombination / MutLalpha complex / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 ...chiasma / late recombination nodule / male meiosis chromosome segregation / meiotic metaphase I homologous chromosome alignment / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / negative regulation of mitotic recombination / MutLalpha complex / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / Defective Mismatch Repair Associated With MSH2 / meiotic spindle midzone assembly / somatic recombination of immunoglobulin gene segments / guanine/thymine mispair binding / maintenance of DNA repeat elements / meiotic telomere clustering / nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of isotype switching to IgA isotypes / homologous chromosome pairing at meiosis / resolution of meiotic recombination intermediates / mismatched DNA binding / positive regulation of isotype switching to IgG isotypes / female meiosis chromosome segregation / synaptonemal complex / 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) / ATP-dependent DNA damage sensor activity / oogenesis / mismatch repair / somatic hypermutation of immunoglobulin genes / male germ cell nucleus / response to bacterium / TP53 Regulates Transcription of DNA Repair Genes / double-strand break repair via nonhomologous end joining / Meiotic recombination / intrinsic apoptotic signaling pathway in response to DNA damage / enzyme activator activity / chromosome / double-stranded DNA binding / spermatogenesis / DNA repair / chromatin binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair protein MutS-like, N-terminal ...DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA mismatch repair protein Msh3 / DNA mismatch repair protein Mlh1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsZhu, G. / Koszelak-Rosenblum, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Chemrxiv
Title: Cyclic Peptide Inhibitors of the MLH1-MSH3 Interaction as a Potential Therapeutic Strategy for Huntington's Disease
Authors: Haque, T.S. / Orvieto, F. / Tomaselli, S. / Turcano, L. / De Simone, D. / Francone, A. / Micaelli, M. / Movetti, S. / Piacenti, V. / Gambini, L. / Alli, C. / Fodale, V. / Bianchi, E. / ...Authors: Haque, T.S. / Orvieto, F. / Tomaselli, S. / Turcano, L. / De Simone, D. / Francone, A. / Micaelli, M. / Movetti, S. / Piacenti, V. / Gambini, L. / Alli, C. / Fodale, V. / Bianchi, E. / Toniatti, C. / Kawahara, D. / Ghosh, S. / Koszelak-Rosenblum, M. / Zhu, G. / Kintzel, S. / Williams, D. / Larocque, J. / Thieulin-Pardo, G. / Thomsen, M. / Dominguez, C. / Iyer, R.R. / Finley, M. / Felsenfeld, D. / Boudet, J. / Monteagudo, E. / Vogt, T.F. / Prasad, B.C.
History
DepositionJun 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: 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 Mlh1
B: DNA mismatch repair protein Mlh1
C: DNA mismatch repair protein Msh3
D: DNA mismatch repair protein Msh3
E: DNA mismatch repair protein Msh3


Theoretical massNumber of molelcules
Total (without water)64,6185
Polymers64,6185
Non-polymers00
Water1,13563
1
A: DNA mismatch repair protein Mlh1


Theoretical massNumber of molelcules
Total (without water)30,6651
Polymers30,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA mismatch repair protein Mlh1


Theoretical massNumber of molelcules
Total (without water)30,6651
Polymers30,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA mismatch repair protein Msh3


Theoretical massNumber of molelcules
Total (without water)1,0961
Polymers1,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA mismatch repair protein Msh3


Theoretical massNumber of molelcules
Total (without water)1,0961
Polymers1,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DNA mismatch repair protein Msh3


Theoretical massNumber of molelcules
Total (without water)1,0961
Polymers1,0961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.920, 70.920, 273.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA mismatch repair protein Mlh1 / MutL protein homolog 1


Mass: 30664.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLH1, COCA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P40692
#2: Protein/peptide DNA mismatch repair protein Msh3 / hMSH3 / Divergent upstream protein / DUP / Mismatch repair protein 1 / MRP1


Mass: 1096.258 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P20585
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 20K , 100 mM MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 27046 / % possible obs: 99.7 % / Redundancy: 12.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.036 / Rrim(I) all: 0.126 / Net I/σ(I): 14.4
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.906 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1858 / CC1/2: 0.42 / Rpim(I) all: 0.612 / Rrim(I) all: 2.007 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X7J

4x7j


Resolution: 2.44→49.25 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.933 / SU B: 20.54 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.367 / ESU R Free: 0.254
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1321 4.897 %Random selection
Rwork0.2056 25657 --
all0.208 ---
obs-25657 99.53 %-
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: 62.108 Å2
Baniso -1Baniso -2Baniso -3
1--1.689 Å20 Å20 Å2
2---1.689 Å20 Å2
3---3.377 Å2
Refinement stepCycle: LAST / Resolution: 2.44→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 0 63 4317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164127
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.8465904
X-RAY DIFFRACTIONr_angle_other_deg0.4371.7449532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.893519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48410766
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.3610209
X-RAY DIFFRACTIONr_chiral_restr0.0620.2658
X-RAY DIFFRACTIONr_chiral_restr_other0.0170.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02971
X-RAY DIFFRACTIONr_nbd_refined0.2170.2816
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23530
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22094
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2117
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.29
X-RAY DIFFRACTIONr_nbd_other0.1460.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.22
X-RAY DIFFRACTIONr_mcbond_it2.6294.5322080
X-RAY DIFFRACTIONr_mcbond_other2.6284.5322080
X-RAY DIFFRACTIONr_mcangle_it4.2738.1252586
X-RAY DIFFRACTIONr_mcangle_other4.2728.1252587
X-RAY DIFFRACTIONr_scbond_it2.9314.8312274
X-RAY DIFFRACTIONr_scbond_other2.9314.8312275
X-RAY DIFFRACTIONr_scangle_it4.8798.7663318
X-RAY DIFFRACTIONr_scangle_other4.8788.7663319
X-RAY DIFFRACTIONr_lrange_it7.00142.1394720
X-RAY DIFFRACTIONr_lrange_other7.00242.1364716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.5030.372760.3111770X-RAY DIFFRACTION96.1959
2.503-2.5720.348920.2881801X-RAY DIFFRACTION98.6451
2.572-2.6460.3870.2631765X-RAY DIFFRACTION99.5699
2.646-2.7270.302900.251720X-RAY DIFFRACTION99.8896
2.727-2.8160.317870.2561641X-RAY DIFFRACTION99.8844
2.816-2.9150.258680.2511621X-RAY DIFFRACTION99.9408
2.915-3.0250.315970.2351534X-RAY DIFFRACTION99.9387
3.025-3.1480.276700.2291527X-RAY DIFFRACTION99.9374
3.148-3.2870.291780.2241447X-RAY DIFFRACTION99.9345
3.287-3.4470.32700.2071396X-RAY DIFFRACTION100
3.447-3.6320.212690.191325X-RAY DIFFRACTION100
3.632-3.8510.211600.1881267X-RAY DIFFRACTION99.8495
3.851-4.1150.241650.1771191X-RAY DIFFRACTION99.9204
4.115-4.4420.159520.1431124X-RAY DIFFRACTION99.915
4.442-4.8620.165610.1411024X-RAY DIFFRACTION99.9079
4.862-5.430.202510.173952X-RAY DIFFRACTION100
5.43-6.2570.29560.214837X-RAY DIFFRACTION100
6.257-7.6320.233380.189737X-RAY DIFFRACTION100
7.632-10.6670.211310.164597X-RAY DIFFRACTION99.841
10.667-49.250.353230.322380X-RAY DIFFRACTION100
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)
10.89660.04670.25380.65930.10090.7801-0.00610.0366-0.0024-0.02570.07060.0383-0.01610.1191-0.06450.1846-0.016-0.01660.1374-0.01390.01121.855-11.43340.237
21.56550.79141.31461.56571.26211.80970.26550.0173-0.10860.193-0.1187-0.08730.37130.0076-0.14680.2774-0.0257-0.05480.1149-0.01080.0168-2.441-35.32965.829
310.1758-1.9165-1.01886.28371.57553.3302-0.53221.2246-0.3875-0.1630.05440.7220.0662-0.16090.47780.2242-0.068-0.04650.2241-0.01050.1311-10.286-26.14124.931
423.7645-5.2213-0.06562.69292.88835.34680.36140.7305-0.06870.2213-0.41860.0530.5836-0.47560.05720.3306-0.0592-0.07920.1188-0.0380.0536-17.325-45.68149.378
513.2979-3.97434.24651.2145-1.25631.36540.029-0.4412-0.88440.06120.23620.27650.0244-0.0867-0.26530.43580.1677-0.04680.47150.09760.1053-22.095-36.13244.461
Refinement TLS groupSelection: ALL

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