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Cryo-EM structure of Human DNA-PK Holoenzyme

by single particle reconstruction, at 6.6 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.03, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.03, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5y3r, Surface level: 0.03, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 6803
TitleCryo-EM structure of Human DNA-PK Holoenzyme
MapNone
SamplePRKDC-Helix
AuthorsYin X, Liu M
DateDeposition: 2017-07-29, Header release: 2017-09-06, Map release: 2017-09-06, Last update: 2017-11-15
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.03, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.03, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5y3r, Surface level: 0.03, Imaged by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-5y3r

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleCell Res., Vol. 27, Issue 11, Page 1341-1350, Year 2017
TitleCryo-EM structure of human DNA-PK holoenzyme.
AuthorsXiaotong Yin, Mengjie Liu, Yuan Tian, Jiawei Wang, Yanhui Xu
Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
LinksPubMed: 28840859, DOI: 10.1038/cr.2017.110, PMC: PMC5674154
Map
Fileemd_6803.map.gz ( map file in CCP4 format, 108001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.3 A/pix
= 390. A
300 pix
1.3 A/pix
= 390. A
300 pix
1.3 A/pix
= 390. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum: -0.052921083 - 0.13899168
Average (Standard dev.): 0.0004368765 (0.00405337)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
Unit CellA= B= C: 390 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.3 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.31.31.3
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z390.000390.000390.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0530.1390.000
Annotation DetailsNone
Supplement
Images
Images
FSC
FSC
Sample
NamePRKDC-Helix
Number of Components7
Component #1: protein - PRKDC-Helix
Scientific namePRKDC-Helix
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Component #2: protein - X-ray repair cross-complementing protein 6
Scientific nameX-ray repair cross-complementing protein 6
Theoretical Mass0.057619352 MDa
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Component #3: protein - X-ray repair cross-complementing protein 5
Scientific nameX-ray repair cross-complementing protein 5
Theoretical Mass0.060972969 MDa
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Component #4: protein - PRKDC-Helix
Scientific namePRKDC-Helix
Theoretical Mass0.001084182 MDa
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Component #5: nucleic-acid - DNA (34-MER)
Scientific nameDNA (34-MER)
Theoretical Mass0.010502785 MDa
SyntheticNo
Sequence(DT)(DA)(DA)(DA)(DA)(DA)(DC)(DT)(DA)(DT)(DT)(DA)(DT)(DT)(DA)(DT)(DG)(DG)(DT)(DA) (DT)(DT)(DA)(DT)(DG)(DG)(DC)(DC)(DT)(DT)(DG)(DG)(DG)(DC)
ClassDNA
StructureOTHER
Component #6: nucleic-acid - DNA (36-MER)
Scientific nameDNA (36-MER)
Theoretical Mass0.011042164 MDa
SyntheticNo
Sequence(DC)(DA)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DG)(DC)(DC)(DA)(DT)(DA)(DA)(DT)(DA)(DC)(DC) (DA)(DT)(DA)(DA)(DT)(DA)(DA)(DT)(DA)(DG)(DT)(DT)(DT)(DT)(DT)(DA)
ClassDNA
StructureOTHER
Component #7: protein - DNA-dependent protein kinase catalytic subunit
Scientific nameDNA-dependent protein kinase catalytic subunit
Theoretical Mass0.468885344 MDa
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc0.6 mg/ml
BufferpH: 7.4
Vitrification
Cryogen NameETHANE
Humidity100
Temperature283 Kelvin
InstrumentFEI VITROBOT MARK IV
Imaging
MicroscopeFEI TITAN KRIOS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose50 e/A**2
Illumination ModeOTHER
Lens
MagnificationNominal: 18000
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Defocus1700 nm - 4700 nm
Specimen Holder
ModelFEI TITAN KRIOS AUTOGRID HOLDER
Camera
DetectorGATAN K2 (4k x 4k)
Image Acquisition
#1
Number of Digital Images3496
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareRELION
Resolution By Author
6.6 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Number of Projections53451
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-6803-v19.xml (8.9 KB)
emd-6803-v20.xml (18.8 KB)
emd-6803.xml (8.9 KB)
Map dataemd_6803.map.gz (6.6 MB)
Imagesemd_6803.png (116.9 KB)
FSC (resolution estimation)emd_6803_fsc.xml (10.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-6803
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.8 MB
Session file for UCSF-Chimera, 26.8 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 7 MB
Session file for UCSF-Chimera, 3.8 MB