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- EMDB-18992: MutSbeta bound to compound CHDI-00898647 in the canonical DNA-mis... -

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Basic information

Entry
Database: EMDB / ID: EMD-18992
TitleMutSbeta bound to compound CHDI-00898647 in the canonical DNA-mismatch bound form
Map data
Sample
  • Complex: MutSbeta in complex with the mismatched DNA and compound
    • Complex: MutSbeta
      • Protein or peptide: DNA mismatch repair protein Msh2
      • Protein or peptide: DNA mismatch repair protein Msh3
    • Complex: Double stranded DNA
      • DNA: DNA_61bp_Complement_Rev
      • DNA: DNA_61bp_CAG2_loop_Fwd
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ~{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
  • Ligand: SULFATE ION
KeywordsDNA REPAIR / MISMATCH RECOGNITION / ABC FAMILY ATPase / PROTEROS BIOSTRUCTURES GMBH / DNA BINDING PROTEIN
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 / positive regulation of helicase activity / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity ...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 / positive regulation of helicase activity / 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 / mitotic recombination / mismatched DNA binding / negative regulation of DNA recombination / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / oxidative phosphorylation / response to UV-B / postreplication repair / 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 / ATP-dependent activity, acting on DNA / response to X-ray / somatic hypermutation of immunoglobulin genes / mismatch repair / B cell differentiation / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / male gonad development / double-strand break repair / double-stranded DNA binding / negative regulation of neuron apoptotic process / in utero embryonic development / 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
DNA mismatch repair protein Msh3 / DNA mismatch repair protein Msh2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsHaque T / Brace G / Felsenfeld D / Tilack K / Schaertl S / Ballantyne G / Maillard M / Iyer R / Prasad B / Thomsen M ...Haque T / Brace G / Felsenfeld D / Tilack K / Schaertl S / Ballantyne G / Maillard M / Iyer R / Prasad B / Thomsen M / Wilkionson H / Plotnikov N / Ritzefeld M
Funding support United States, 1 items
OrganizationGrant numberCountry
CHDI Foundation United States
CitationJournal: To Be Published
Title: Identification of orthosteric inhibitors of MutSbeta ATPase function
Authors: Haque T / Brace G
History
DepositionNov 27, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18992.png

Downloads & links

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Map

FileDownload / File: emd_18992.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 320 pix.
= 292.544 Å		0.91 Å/pix.
x 320 pix.
= 292.544 Å		0.91 Å/pix.
x 320 pix.
= 292.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9142 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.16518424 - 1.9199643
Average (Standard dev.)0.0004581119 (±0.02376436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 292.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18992_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18992_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MutSbeta in complex with the mismatched DNA and compound

EntireName: MutSbeta in complex with the mismatched DNA and compound
Components
  • Complex: MutSbeta in complex with the mismatched DNA and compound
    • Complex: MutSbeta
      • Protein or peptide: DNA mismatch repair protein Msh2
      • Protein or peptide: DNA mismatch repair protein Msh3
    • Complex: Double stranded DNA
      • DNA: DNA_61bp_Complement_Rev
      • DNA: DNA_61bp_CAG2_loop_Fwd
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ~{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
  • Ligand: SULFATE ION

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Supramolecule #1: MutSbeta in complex with the mismatched DNA and compound

SupramoleculeName: MutSbeta in complex with the mismatched DNA and compound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: MutSbeta

SupramoleculeName: MutSbeta / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Double stranded DNA

SupramoleculeName: Double stranded DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA mismatch repair protein Msh2

MacromoleculeName: DNA mismatch repair protein Msh2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.861875 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT QGVIKYMGPA GAKNLQSVVL SKMNFESFV KDLLLVRQYR VEVYKNRAGN KASKENDWYL AYKASPGNLS QFEDILFGNN DMSASIGVVG VKMSAVDGQR Q VGVGYVDS ...String:
MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT QGVIKYMGPA GAKNLQSVVL SKMNFESFV KDLLLVRQYR VEVYKNRAGN KASKENDWYL AYKASPGNLS QFEDILFGNN DMSASIGVVG VKMSAVDGQR Q VGVGYVDS IQRKLGLCEF PDNDQFSNLE ALLIQIGPKE CVLPGGETAG DMGKLRQIIQ RGGILITERK KADFSTKDIY QD LNRLLKG KKGEQMNSAV LPEMENQVAV SSLSAVIKFL ELLSDDSNFG QFELTTFDFS QYMKLDIAAV RALNLFQGSV EDT TGSQSL AALLNKCKTP QGQRLVNQWI KQPLMDKNRI EERLNLVEAF VEDAELRQTL QEDLLRRFPD LNRLAKKFQR QAAN LQDCY RLYQGINQLP NVIQALEKHE GKHQKLLLAV FVTPLTDLRS DFSKFQEMIE TTLDMDQVEN HEFLVKPSFD PNLSE LREI MNDLEKKMQS TLISAARDLG LDPGKQIKLD SSAQFGYYFR VTCKEEKVLR NNKNFSTVDI QKNGVKFTNS KLTSLN EEY TKNKTEYEEA QDAIVKEIVN ISSGYVEPMQ TLNDVLAQLD AVVSFAHVSN GAPVPYVRPA ILEKGQGRII LKASRHA CV EVQDEIAFIP NDVYFEKDKQ MFHIITGPNM GGKSTYIRQT GVIVLMAQIG CFVPCESAEV SIVDCILARV GAGDSQLK G VSTFMAEMLE TASILRSATK DSLIIIDELG RGTSTYDGFG LAWAISEYIA TKIGAFCMFA THFHELTALA NQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLEREQG EKIIQEFLS KVKQMPFTEM SEENITIKLK QLKAEVIAKN NSFVNEIISR IKVTT

UniProtKB: DNA mismatch repair protein Msh2

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Macromolecule #2: DNA mismatch repair protein Msh3

MacromoleculeName: DNA mismatch repair protein Msh3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.634719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSRRKPASGG LAASSSAPAR QAVLSRFFQS TGSLKSTSSS TGAADQVDPG AAAAAAAAAA AAPPAPPAPA FPPQLPPHVA TEIDRRKKR PLENDGPVKK KVKKVQQKEG GSDLGMSGNS EPKKCLRTRN VSKSLEKLKE FCCDSALPQS RVQTESLQER F AVLPKCTD ...String:
MSRRKPASGG LAASSSAPAR QAVLSRFFQS TGSLKSTSSS TGAADQVDPG AAAAAAAAAA AAPPAPPAPA FPPQLPPHVA TEIDRRKKR PLENDGPVKK KVKKVQQKEG GSDLGMSGNS EPKKCLRTRN VSKSLEKLKE FCCDSALPQS RVQTESLQER F AVLPKCTD FDDISLLHAK NAVSSEDSKR QINQKDTTLF DLSQFGSSNT SHENLQKTAS KSANKRSKSI YTPLELQYIE MK QQHKDAV LCVECGYKYR FFGEDAEIAA RELNIYCHLD HNFMTASIPT HRLFVHVRRL VAKGYKVGVV KQTETAALKA IGD NRSSLF SRKLTALYTK STLIGEDVNP LIKLDDAVNV DEIMTDTSTS YLLCISENKE NVRDKKKGNI FIGIVGVQPA TGEV VFDSF QDSASRSELE TRMSSLQPVE LLLPSALSEQ TEALIHRATS VSVQDDRIRV ERMDNIYFEY SHAFQAVTEF YAKDT VDIK GSQIISGIVN LEKPVICSLA AIIKYLKEFN LEKMLSKPEN FKQLSSKMEF MTINGTTLRN LEILQNQTDM KTKGSL LWV LDHTKTSFGR RKLKKWVTQP LLKLREINAR LDAVSEVLHS ESSVFGQIEN HLRKLPDIER GLCSIYHKKC STQEFFL IV KTLYHLKSEF QAIIPAVNSH IQSDLLRTVI LEIPELLSPV EHYLKILNEQ AAKVGDKTEL FKDLSDFPLI KKRKDEIQ G VIDEIRMHLQ EIRKILKNPS AQYVTVSGQE FMIEIKNSAV SCIPTDWVKV GSTKAVSRFH SPFIVENYRH LNQLREQLV LDCSAEWLDF LEKFSEHYHS LCKAVHHLAT VDCIFSLAKV AKQGDYCRPT VQEERKIVIK NGRHPVIDVL LGEQDQYVPN NTDLSEDSE RVMIITGPNM GGKSSYIKQV ALITIMAQIG SYVPAEEATI GIVDGIFTRM GAADNIYKGR STFMEELTDT A EIIRKATS QSLVILDELG RGTSTHDGIA IAYATLEYFI RDVKSLTLFV THYPPVCELE KNYSHQVGNY HMGFLVSEDE SK LDPGTAE QVPDFVTFLY QITRGIAARS YGLNVAKLAD VPGEILKKAA HKSKELEGLI NTKRKRLKYF AKLWTMHNAQ DLQ KWTEEF NMEETQTSLL H

UniProtKB: DNA mismatch repair protein Msh3

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Macromolecule #3: DNA_61bp_Complement_Rev

MacromoleculeName: DNA_61bp_Complement_Rev / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.49185 KDa
SequenceString: (DG)(DA)(DA)(DT)(DT)(DG)(DG)(DG)(DT)(DA) (DC)(DC)(DG)(DC)(DT)(DG)(DA)(DA)(DT)(DT) (DG)(DC)(DA)(DC)(DC)(DG)(DA)(DG)(DC) (DT)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DG)(DA) (DT) (DG)(DA)(DT)(DC)(DC)(DT) ...String:
(DG)(DA)(DA)(DT)(DT)(DG)(DG)(DG)(DT)(DA) (DC)(DC)(DG)(DC)(DT)(DG)(DA)(DA)(DT)(DT) (DG)(DC)(DA)(DC)(DC)(DG)(DA)(DG)(DC) (DT)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DG)(DA) (DT) (DG)(DA)(DT)(DC)(DC)(DT)(DA)(DA) (DG)(DC)(DT)(DA)(DA)(DG)(DC)(DT)(DT)(DC) (DA)(DG)

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Macromolecule #4: DNA_61bp_CAG2_loop_Fwd

MacromoleculeName: DNA_61bp_CAG2_loop_Fwd / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.355037 KDa
SequenceString: (DC)(DT)(DG)(DA)(DA)(DG)(DC)(DT)(DT)(DA) (DG)(DC)(DT)(DT)(DA)(DG)(DG)(DA)(DT)(DC) (DA)(DT)(DC)(DG)(DA)(DG)(DG)(DA)(DT) (DC)(DC)(DA)(DG)(DC)(DA)(DG)(DA)(DG)(DC) (DT) (DC)(DG)(DG)(DT)(DG)(DC) ...String:
(DC)(DT)(DG)(DA)(DA)(DG)(DC)(DT)(DT)(DA) (DG)(DC)(DT)(DT)(DA)(DG)(DG)(DA)(DT)(DC) (DA)(DT)(DC)(DG)(DA)(DG)(DG)(DA)(DT) (DC)(DC)(DA)(DG)(DC)(DA)(DG)(DA)(DG)(DC) (DT) (DC)(DG)(DG)(DT)(DG)(DC)(DA)(DA) (DT)(DT)(DC)(DA)(DG)(DC)(DG)(DG)(DT)(DA) (DC)(DC) (DC)(DA)(DA)(DT)(DT)(DC)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #7: ~{N}-[3-[[2-[[3-fluoranyl-4-(4-methylpiperazin-1-yl)phenyl]amino]...

MacromoleculeName: ~{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
type: ligand / ID: 7 / Number of copies: 1 / Formula: YKQ
Molecular weightTheoretical: 487.529 Da

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Macromolecule #8: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.77 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 273352
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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