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- EMDB-45857: Focused map of ligase IV catalytic domain in ligation complex II ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45857
TitleFocused map of ligase IV catalytic domain in ligation complex II in the NHEJ complex
Map dataFocused map of ligase IV catalytic domain in ligation complex II
Sample
  • Complex: Ligation complex like 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: 4.0 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 II in the NHEJ pathway
Authors: Li J / Liu L / Gellert M / Yang W
History
DepositionJul 22, 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_45857.png

Downloads & links

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Map

FileDownload / File: emd_45857.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of ligase IV catalytic domain in ligation complex II
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: 0.25
Minimum - Maximum-0.48394603 - 1.1247722
Average (Standard dev.)-0.00071129494 (±0.021862892)
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_45857_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_45857_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_45857_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 like in the NHEJ pathway

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

SupramoleculeName: Ligation complex like 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 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 #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 AGTCGACT

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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 GTCTAGTC

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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:
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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32621
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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