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- PDB-4fmo: Structure of the C-terminal domain of the Saccharomyces cerevisia... -

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Basic information

Entry
Database: PDB / ID: 4fmo
TitleStructure of the C-terminal domain of the Saccharomyces cerevisiae MUTL alpha (MLH1/PMS1) heterodimer bound to a fragment of exo1
Components
  • (DNA mismatch repair protein ...) x 2
  • DNA repair peptide
KeywordsHYDROLASE / Mismatch repair / MUTL / endonuclease / Zn-binding protein / DNA damage / DNA repair
Function / homology
Function and homology information


meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / meiotic DNA double-strand break processing / gene conversion at mating-type locus / MutLalpha complex / telomeric 3' overhang formation / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / mismatched DNA binding ...meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / meiotic DNA double-strand break processing / gene conversion at mating-type locus / MutLalpha complex / telomeric 3' overhang formation / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / mismatched DNA binding / 5'-flap endonuclease activity / DNA double-strand break processing / mitotic G2/M transition checkpoint / reciprocal meiotic recombination / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / ATP-dependent DNA damage sensor activity / mismatch repair / telomere maintenance / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / Exonuclease-1, H3TH domain / Exonuclease 1-like, PIN-like domain / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain ...DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / Exonuclease-1, H3TH domain / Exonuclease 1-like, PIN-like domain / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / 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 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 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
Similarity search - Domain/homology
DNA mismatch repair protein PMS1 / DNA mismatch repair protein MLH1 / Exodeoxyribonuclease 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsGueneau, E. / Legrand, P. / Charbonnier, J.B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of the MutL alpha C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site.
Authors: Gueneau, E. / Dherin, C. / Legrand, P. / Tellier-Lebegue, C. / Gilquin, B. / Bonnesoeur, P. / Londino, F. / Quemener, C. / Le Du, M.H. / Marquez, J.A. / Moutiez, M. / Gondry, M. / Boiteux, S. / Charbonnier, J.B.
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 PMS1
C: DNA repair peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3736
Polymers62,2173
Non-polymers1553
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-26 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.700, 66.140, 74.470
Angle α, β, γ (deg.)90.00, 91.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA mismatch repair protein ... , 2 types, 2 molecules AB

#1: Protein DNA mismatch repair protein MLH1 / MutL protein homolog 1 / Post meiotic segregation protein 2


Mass: 33239.102 Da / Num. of mol.: 1 / Fragment: UNP residues 483-769
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MLH1, PMS2, YMR167W, YM8520.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P38920
#2: Protein DNA mismatch repair protein PMS1 / Postmeiotic segregation protein 1


Mass: 27948.195 Da / Num. of mol.: 1 / Fragment: UNP residues 635-873
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PMS1, YNL082W, N2317 / Production host: Escherichia coli (E. coli) / References: UniProt: P14242

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide DNA repair peptide / Exodeoxyribonuclease I / EXO I / Exonuclease I / Protein DHS1


Mass: 1030.201 Da / Num. of mol.: 1 / Fragment: UNP residues 443-450 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39875

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Non-polymers , 3 types, 59 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. all: 18310 / Num. obs: 18219 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 70.27 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 10
Reflection shellResolution: 3.04→3.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E4W

4e4w


Resolution: 3.04→48.41 Å / Cor.coef. Fo:Fc: 0.9304 / Cor.coef. Fo:Fc free: 0.9301 / SU R Cruickshank DPI: 0.691 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 1021 5.6 %RANDOM
Rwork0.1801 ---
obs0.181 18219 99.08 %-
all-18310 --
Displacement parametersBiso mean: 98.37 Å2
Baniso -1Baniso -2Baniso -3
1--28.4796 Å20 Å28.9781 Å2
2--14.1418 Å20 Å2
3---14.3378 Å2
Refine analyzeLuzzati coordinate error obs: 0.687 Å
Refinement stepCycle: LAST / Resolution: 3.04→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 3 56 3936
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013946HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185320HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1422SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes550HARMONIC5
X-RAY DIFFRACTIONt_it3946HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion20.2
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4308SEMIHARMONIC4
LS refinement shellResolution: 3.04→3.22 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2665 148 5.28 %
Rwork0.2264 2653 -
all0.2285 2801 -
obs--99.08 %
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)
10.8406-0.02541.48961.89220.45394.4015-0.0345-0.13990.02920.0846-0.0183-0.0670.107-0.28470.05280.3413-0.02570.0307-0.54980.0042-0.494847.5861-0.653416.3299
21.9072-0.37982.232.676-0.4915.67060.071-0.00420.1523-0.4263-0.09681.01520.1854-1.19940.02580.23650.0063-0.2003-0.2369-0.0093-0.097525.82443.0812-23.1287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A506 - 769
2X-RAY DIFFRACTION2{ B|* }B651 - 902

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