[English] 日本語
Yorodumi
- EMDB-45840: Focused map of Ku70/80 complex on the active side of a gap-fillin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45840
TitleFocused map of Ku70/80 complex on the active side of a gap-filling complex with Pol mu engaged in the NHEJ pathway
Map dataFocused map of the active Ku70/80 complex
Sample
  • Complex: A gap-filling complex with Pol mu engaged
    • Protein or peptide: human Ku70
    • Protein or peptide: human Ku80
    • DNA: DNA chain J
    • DNA: DNA chain L
    • Protein or peptide: human Polymerase mu
    • Protein or peptide: human PAXX
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: 2.9 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

-
Structure visualization

Supplemental images

emd_45840.png

Downloads & links

-
Map

FileDownload / File: emd_45840.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of the active Ku70/80 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-0.57432824 - 1.5542433
Average (Standard dev.)-0.00045094307 (±0.025409495)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_45840_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half 1 map

Fileemd_45840_half_map_1.map
Annotationhalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half 2 map

Fileemd_45840_half_map_2.map
Annotationhalf 2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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 Ku70
    • Protein or peptide: human Ku80
    • DNA: DNA chain J
    • DNA: DNA chain L
    • Protein or peptide: human Polymerase mu
    • Protein or peptide: human PAXX

-
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: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 967 KDa

-
Macromolecule #1: human Ku70

MacromoleculeName: human Ku70 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMSGWESY YKTEGDEEAE EEQEENLEAS GDYKYSGRDS LIFLVDASKA MFESQSEDEL TPF DMSIQC IQSVYISKII SSDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELD QFKGQ QGQKRFQDMM GHGSDYSLSE VLWVCANLFS DVQFKMSHKR ...String:
GPVMSGWESY YKTEGDEEAE EEQEENLEAS GDYKYSGRDS LIFLVDASKA MFESQSEDEL TPF DMSIQC IQSVYISKII SSDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELD QFKGQ QGQKRFQDMM GHGSDYSLSE VLWVCANLFS DVQFKMSHKR IMLFTNEDNP HGNDS AKAS RARTKAGDLR DTGIFLDLMH LKKPGGFDIS LFYRDIISIA EDEDLRVHFE ESSKLE DLL RKVRAKETRK RALSRLKLKL NKDIVISVGI YNLVQKALKP PPIKLYRETN EPVKTKT RT FNTSTGGLLL PSDTKRSQIY GSRQIILEKE ETEELKRFDD PGLMLMGFKP LVLLKKHH Y LRPSLFVYPE ESLVIGSSTL FSALLIKCLE KEVAALCRYT PRRNIPPYFV ALVPQEEEL DDQKIQVTPP GFQLVFLPFA DDKRKMPFTE KIMATPEQVG KMKAIVEKLR FTYRSDSFEN PVLQQHFRN LEALALDLME PEQAVDLTLP KVEAMNKRLG SLVDEFKELV YPPDYNPEGK V TKRKHDNE GSGSKRPKVE YSEEELKTHI SKGTLGKFTV PMLKEACRAY GLKSGLKKQE LL EALTKHF QD

-
Macromolecule #2: human Ku80

MacromoleculeName: human Ku80 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLS GGDQYQNITV HRHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ H ETIGKKFE KRHIEIFTDL SSRFSKSQLD IIIHSLKKCD ISLQFFLPFS ...String:
MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLS GGDQYQNITV HRHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ H ETIGKKFE KRHIEIFTDL SSRFSKSQLD IIIHSLKKCD ISLQFFLPFS LGKEDGSGDR GD GPFRLGG HGPSFPLKGI TEQQKEGLEI VKMVMISLEG EDGLDEIYSF SESLRKLCVF KKI ERHSIH WPCRLTIGSN LSIRIAAYKS ILQERVKKTW TVVDAKTLKK EDIQKETVYC LNDD DETEV LKEDIIQGFR YGSDIVPFSK VDEEQMKYKS EGKCFSVLGF CKSSQVQRRF FMGNQ VLKV FAARDDEAAA VALSSLIHAL DDLDMVAIVR YAYDKRANPQ VGVAFPHIKH NYECLV YVQ LPFMEDLRQY MFSSLKNSKK YAPTEAQLNA VDALIDSMSL AKKDEKTDTL EDLFPTT KI PNPRFQRLFQ CLLHRALHPR EPLPPIQQHI WNMLNPPAEV TTKSQIPLSK IKTLFPLI E AKKKDQVTAQ EIFQDNHEDG PTAKKLKTEQ GGAHFSVSSL AEGSVTSVGS VNPAENFRV LVKQKKASFE EASNQLINHI EQFLDTNETP YFMKSIDCIR AFREEAIKFS EEQRFNNFLK ALQEKVEIK QLNHFWEIVV QDGITLITKE EASGSSVTAE EAKKFLAPKD KPSGDTAAVF E EGGDVDDL LDMI

-
Macromolecule #5: human Polymerase mu

MacromoleculeName: human Polymerase mu / type: protein_or_peptide / ID: 5 / 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

-
Macromolecule #6: human PAXX

MacromoleculeName: human PAXX / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAAL KARFG LSAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPR LRAL TLGLAKRVWS LERRLAAAEE TAVSPRKSPR ...String:
MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAAL KARFG LSAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPR LRAL TLGLAKRVWS LERRLAAAEE TAVSPRKSPR PAGPQLFLPD PDPQRGGPGP GVRRRC PGE SLINPGFKSK KPAGGVDFDE T

-
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

-
Macromolecule #4: DNA chain L

MacromoleculeName: DNA chain L / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GACTTGTACT GGAACTCACG TGAACGAATG TTTTTAGTTT ATTGGGCGCG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

23509

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more