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- EMDB-45848: Focused map of the ligase IV catalytic domain in the ligation com... -

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Basic information

Entry
Database: EMDB / ID: EMD-45848
TitleFocused map of the ligase IV catalytic domain in the ligation complex in the NHEJ pathway
Map dataFocused map of ligase IV catalytic domain in the ligation complex I
Sample
  • Complex: Ligation complex in the NHEJ pathway
    • Protein or peptide: human ligase IV
    • DNA: DNA chain I
    • DNA: DNA chain J
    • DNA: DNA chain K
    • DNA: DNA chain L
KeywordsNHEJ / ligation / XLF / PAXX / DNA repair / Ligase IV / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 ligation complex in the NHEJ pathway
Authors: Li J / Liu L / Gellert M / Yang W
History
DepositionJul 21, 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_45848.png

Downloads & links

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Map

FileDownload / File: emd_45848.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of ligase IV catalytic domain in the ligation complex I
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: 0.26
Minimum - Maximum-0.57317394 - 1.2284999
Average (Standard dev.)-0.0013581559 (±0.022783875)
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_45848_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_45848_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_45848_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 : Ligation complex in the NHEJ pathway

EntireName: Ligation complex in the NHEJ pathway
Components
  • Complex: Ligation complex in the NHEJ pathway
    • 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: Ligation complex in the NHEJ pathway

SupramoleculeName: Ligation complex in the NHEJ pathway / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 854 KDa

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Macromolecule #1: human ligase IV

MacromoleculeName: human ligase IV / type: protein_or_peptide / ID: 1 / 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 GTHGDAGDFA MIAYFVLKPR CLQKGSLTIQ QVNDLLDSIA SNNSAKRKDL ...String:
GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHGDAGDFA MIAYFVLKPR CLQKGSLTIQ QVNDLLDSIA SNNSAKRKDL IKKSLLQLIT QSSALEQKWL IRMIIKDLKL GVSQQTIFSV FHNDAAELHN VTTDLEKVCR QLHDPSVGLS DISI TLFSA FKPMLAAIAD IEHIEKDMKH QSFYIETKLD GERMQMHKDG DVYKYFSRNG YNYTD QFGA SPTEGSLTPF IHNAFKADIQ ICILDGEMMA YNPNTQTFMQ KGTKFDIKRM VEDSDL QTC YCVFDVLMVN NKKLGHETLR KRYEILSSIF TPIPGRIEIV QKTQAHTKNE VIDALNE AI DKREEGIMVK QPLSIYKPDK RGEGWLKIKP EYVSGLMDEL DILIVGGYWG KGSRGGMM S HFLCAVAEKP PPGEKPSVFH TLSRVGSGCT MKELYDLGLK LAKYWKPFHR KAPPSSILC GTEKPEVYIE PCNSVIVQIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE QLRGKASGK LASKHLYIGG DDEPQEKKRK AAPKMKKVIG IIEHLKAPNL TNVNKISNIF E DVEFCVMS GTDSQPKPDL ENRIAEFGGY IVQNPGPDTY CVIAGSENIR VKNIILSNKH DV VKPAWLL ECFKTKSFVP WQPRFMIHMC PSTKEHFARE YDCYGDSYFI DTDLNQLKEV FSG IKNSNE QTPEEMASLI ADLEYRYSWD CSPLSMFRRH TVYLDSYAVI NDLSTKNEGT RLAI KALEL RFHGAKVVSC LAEGVSHVII GEDHSRVADF KAFRRTFKRK FKILKESWVT DSIDK CELQ EENQYLI

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Macromolecule #2: DNA chain I

MacromoleculeName: DNA chain I / type: dna / ID: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
CGCGCCCAGC TTTCCCAGCT AATAAACTAA AAACTATGCA TGCTCTACTG CTTCTGATCT AGTCGACC

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Macromolecule #3: DNA chain J

MacromoleculeName: DNA chain J / type: dna / ID: 3 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
CGCGCCCAGC TTTCCCAGCT AATAAACTAA AAACATTCGT TCACGTGAGT TCCAGTACAA GTCTGGTC

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Macromolecule #4: DNA chain K

MacromoleculeName: DNA chain K / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GACTAGATCA GAAGCAGTAG AGCATGCATA GTTTTTAGTT TATTGGGCGC G

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Macromolecule #5: DNA chain L

MacromoleculeName: DNA chain L / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
AGACTTGTAC TGGAACTCAC GTGAACGAAT GTTTTTAGTT TATTGGGCGC G

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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: 42.2 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104947
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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