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- EMDB-45839: Focused map of polymerase mu and ligase IV DBD in a gap-filling c... -

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Basic information

Entry
Database: EMDB / ID: EMD-45839
TitleFocused map of polymerase mu and ligase IV DBD in a gap-filling complex in the NHEJ pathway
Map dataFocused map of Pol mu and Ligase IV DBD in the gap-filling complex
Sample
  • Complex: A gap-filling complex with Pol mu engaged
    • Protein or peptide: human Pol mu
    • Protein or peptide: human Ligase IV
    • DNA: DNA chain I
    • DNA: DNA chain J
    • DNA: DNA chain K
    • DNA: DNA chain L
KeywordsNHEJ / DNA gap / fill-in synthesis / ligation / XLF / PAXX / Polymerase mu / DNA repair / Ligase IV / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLi J / Liu L / Gellert M / Yang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: The gap-filling complex with Pol mu engaged in the NHEJ pathway
Authors: Li J / Liu L / Gellert M / Yang W
History
DepositionJul 20, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45839.png

Downloads & links

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Map

FileDownload / File: emd_45839.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of Pol mu and Ligase IV DBD in the gap-filling complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.63073516 - 1.6040571
Average (Standard dev.)-0.0004733651 (±0.021975592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45839_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1 map

Fileemd_45839_half_map_1.map
Annotationhalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2 map

Fileemd_45839_half_map_2.map
Annotationhalf 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 : A gap-filling complex with Pol mu engaged

EntireName: A gap-filling complex with Pol mu engaged
Components
  • Complex: A gap-filling complex with Pol mu engaged
    • Protein or peptide: human Pol mu
    • Protein or peptide: human Ligase IV
    • DNA: DNA chain I
    • DNA: DNA chain J
    • DNA: DNA chain K
    • DNA: DNA chain L

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Supramolecule #1: A gap-filling complex with Pol mu engaged

SupramoleculeName: A gap-filling complex with Pol mu engaged / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 967 KDa

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Macromolecule #1: human Pol mu

MacromoleculeName: human Pol mu / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSSGL EVLFQGPHML PKRRRARVGS PSGDAASSTP PSTRFPGVAI YLVEPRMGRS RRAFLTGLAR SKGFRVLD A CSSEATHVVM EETSAEEAVS WQERRMAAAP PGCTPPALLD ISWLTESLGA GQPVPVECR HRLEVAGPRK GPLSPAWMPA YACQRPTPLT ...String:
HHHHHHSSGL EVLFQGPHML PKRRRARVGS PSGDAASSTP PSTRFPGVAI YLVEPRMGRS RRAFLTGLAR SKGFRVLD A CSSEATHVVM EETSAEEAVS WQERRMAAAP PGCTPPALLD ISWLTESLGA GQPVPVECR HRLEVAGPRK GPLSPAWMPA YACQRPTPLT HHNTGLSEAL EILAEAAGFE GSEGRLLTFC RAASVLKAL PSPVTTLSQL QGLPHFGEHS SRVVQELLEH GVCEEVERVR RSERYQTMKL F TQIFGVGV KTADRWYREG LRTLDDLREQ PQKLTQQQKA GLQHHQDLST PVLRSDVDAL QQ VVEEAVG QALPGATVTL TGGFRRGKLQ GHDVDFLITH PKEGQEAGLL PRVMCRLQDQ GLI LYHQHQ HSCCESPTRL AQQSHMDAFE RSFCIFRLPQ PPGAAVGGST RPCPSWKAVR VDLV VAPVS QFPFALLGWT GSKLFQRELR RFSRKEKGLW LNSHGLFDPE QKTFFQAASE EDIFR HLGL EYLPPEQRNA

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Macromolecule #2: human Ligase IV

MacromoleculeName: human Ligase IV / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHG DAGDF AMIAYFVLKP RCLQKGSLTI QQVNDLLDSI ASNNSAKRKD ...String:
GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHG DAGDF AMIAYFVLKP RCLQKGSLTI QQVNDLLDSI ASNNSAKRKD LIKKSLLQLI TQSSA LEQK WLIRMIIKDL KLGVSQQTIF SVFHNDAAEL HNVTTDLEKV CRQLHDPSVG LSDISI TLF SAFKPMLAAI ADIEHIEKDM KHQSFYIETK LDGERMQMHK DGDVYKYFSR NGYNYTD QF GASPTEGSLT PFIHNAFKAD IQICILDGEM MAYNPNTQTF MQKGTKFDIK RMVEDSDL Q TCYCVFDVLM VNNKKLGHET LRKRYEILSS IFTPIPGRIE IVQKTQAHTK NEVIDALNE AIDKREEGIM VKQPLSIYKP DKRGEGWLKI KPEYVSGLMD ELDILIVGGY WGKGSRGGMM SHFLCAVAE KPPPGEKPSV FHTLSRVGSG CTMKELYDLG LKLAKYWKPF HRKAPPSSIL C GTEKPEVY IEPCNSVIVQ IKAAEIVPSD MYKTGCTLRF PRIEKIRDDK EWHECMTLDD LE QLRGKAS GKLASKHLYI GGDDEPQEKK RKAAPKMKKV IGIIEHLKAP NLTNVNKISN IFE DVEFCV MSGTDSQPKP DLENRIAEFG GYIVQNPGPD TYCVIAGSEN IRVKNIILSN KHDV VKPAW LLECFKTKSF VPWQPRFMIH MCPSTKEHFA REYDCYGDSY FIDTDLNQLK EVFSG IKNS NEQTPEEMAS LIADLEYRYS WDCSPLSMFR RHTVYLDSYA VINDLSTKNE GTRLAI KAL ELRFHGAKVV SCLAEGVSHV IIGEDHSRVA DFKAFRRTFK RKFKILKESW VTDSIDK CE LQEENQYLI

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Macromolecule #3: DNA chain I

MacromoleculeName: DNA chain I / type: dna / ID: 3 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
CGCGCCCAGC TTTCCCAGCT AATAAACTAA AAACTATGCA TGCTCTACTG CTTCTGATCT AGTCGACT

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Macromolecule #4: DNA chain J

MacromoleculeName: DNA chain J / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
CGCGCCCAGC TTTCCCAGCT AATAAACTAA AAACATTCGT TCACGTGAGT TCCAGTACAA GTCTAGTC

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Macromolecule #5: DNA chain K

MacromoleculeName: DNA chain K / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GACTAGATCA GAAGCAGTAG AGCATGCATA GTTTTTAGTT TATTGGGCGC G

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Macromolecule #6: DNA chain L

MacromoleculeName: DNA chain L / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GACTTGTACT GGAACTCACG TGAACGAATG TTTTTAGTTT ATTGGGCGCG

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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

Concentration0.35 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

23509

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 891208
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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