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Cryo-EM structure of Human DNA-PK Holoenzyme

by single particle reconstruction, at 6.6 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-6803, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5y3r
TitleCryo-EM structure of Human DNA-PK Holoenzyme
DescriptorPRKDC-Helix
DNA-dependent protein kinase catalytic subunit/DNA Complex
(X-ray repair cross-complementing protein ...) x 2
KeywordsDNA BINDING PROTEIN, Cryo-EM structure, DNA-PK, DNAPKcs, activation, NHEJ
AuthorsYin, X., Liu, M., Tian, Y., Wang, J., Xu, Y.
DateDeposition: 2017-07-29, Release: 2017-09-06
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-6803, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-6803

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Fit: target map of fitting

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Article
Citation - primary
ArticleCell Res., 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
Components
ID 1 : 5'-deoxyribose-5-phosphate lyase Ku70,5'-dRP lyase Ku70,70 kDa subunit of Ku antigen,ATP-dependent DNA helicase 2 subunit 1,ATP-dependent DNA helicase II 70 kDa subunit,CTC box-binding factor 75 kDa subunit,CTCBF,DNA repair protein XRCC6,Lupus Ku autoantigen protein p70,Ku70,Thyroid-lupus autoantigen,TLAA,X-ray repair complementing defective repair in Chinese hamster cells 6
DescriptionX-ray repair cross-complementing protein 6
Typepolypeptide(L)
FragmentUNP residues 34-534
Formula weight57619.352 Da
Number of molecules1
ID1
Ec3.6.4.-,4.2.99.-
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: Human, XRCC6, G22P1, ID:9606, Homo sapiens
Alt source flag: sample
Beg seq num: 1
End seq num: 501
Host: ID:9606, Homo sapiens
Seq type: Biological sequence
LinksUniProt: P12956, Sequence view
ID 2 : 86 kDa subunit of Ku antigen,ATP-dependent DNA helicase 2 subunit 2,ATP-dependent DNA helicase II 80 kDa subunit,CTC box-binding factor 85 kDa subunit,CTCBF,DNA repair protein XRCC5,Ku80,Ku86,Lupus Ku autoantigen protein p86,Nuclear factor IV,Thyroid-lupus autoantigen,TLAA,X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)
DescriptionX-ray repair cross-complementing protein 5
Typepolypeptide(L)
FragmentUNP residues 6-541
Formula weight60972.969 Da
Number of molecules1
ID2
Ec3.6.4.-
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: Human, XRCC5, G22P2, ID:9606, Homo sapiens
Alt source flag: sample
Beg seq num: 1
End seq num: 536
Host: ID:9606, Homo sapiens
Seq type: Biological sequence
LinksUniProt: P13010, Sequence view
ID 3 : PRKDC-Helix
DescriptionPRKDC-Helix
Typepolypeptide(L)
Formula weight1084.182 Da
Number of molecules1
ID3
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 15
Gene: ID:9606, Homo sapiens
Host: ID:9606, Homo sapiens
Seq type: Biological sequence
LinksSequence view
ID 4 : DNA (34-MER)
DescriptionDNA (34-MER)
Typepolydeoxyribonucleotide
Formula weight10502.785 Da
Number of molecules1
ID4
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 34
Gene: ID:9606, Homo sapiens
Host: ID:9606, Homo sapiens
Seq type: Biological sequence
LinksSequence view
ID 5 : DNA (36-MER)
DescriptionDNA (36-MER)
Typepolydeoxyribonucleotide
Formula weight11042.164 Da
Number of molecules1
ID5
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 36
Gene: ID:9606, Homo sapiens
Host: ID:9606, Homo sapiens
Seq type: Biological sequence
LinksSequence view
ID 6 : DNA-PKcs,DNPK1,p460
DescriptionDNA-dependent protein kinase catalytic subunit
Typepolypeptide(L)
FragmentUNP residues 10-4128
Formula weight468885.344 Da
Number of molecules1
ID6
Ec2.7.11.1
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: Human, PRKDC, HYRC, HYRC1, ID:9606, Homo sapiens
Alt source flag: sample
Beg seq num: 1
End seq num: 4119
Host: ID:9606, KIDNEY, Homo sapiens, HEK293F
Seq type: Biological sequence
LinksUniProt: P78527, Sequence view
Sample
Entity assembly
Entity id list1, 2, 3, 4, 5, 6
NamePRKDC-Helix
SourceRECOMBINANT
TypeCOMPLEX
Buffer
Specimen id1
PH7.4
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
Grid materialGOLD
Grid mesh size300
Grid typeQuantifoil R1.2/1.3
Vitrification
Specimen id1
Chamber temperature283
Cryogen nameETHANE
Humidity100
InstrumentFEI VITROBOT MARK IV
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TITAN KRIOS
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeOTHER
Lens
ModeBRIGHT FIELD
MagnificationNominal: 18000 X
CsNominal: 2.7 mm
Nominal defocusMax: 4700 nm, Min: 1700 nm
Specimen holder
Specimen holderModel: FEI TITAN KRIOS AUTOGRID HOLDER
Image scans
Image recording id1
Frames per image32
Used frames per image1-32
Processing
3D reconstruction
Image processing id1
Num class averages1
Number of particles53451
Resolution6.6 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
Refine
Refine idELECTRON MICROSCOPY
Software
Ordinal1
Classificationrefinement
NamePHENIX
Version1.10.1_2155
Download
PDB format
Allpdb5y3r.ent.gz
pdb5y3r.ent (uncompressed file)
Header onlypdb5y3r.ent.gz
mmCIF format
mmCIF5y3r.cif.gz
XML format
All5y3r.xml.gz
No-atom5y3r-noatom.xml.gz
Ext-atom5y3r-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 5.8 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 7 MB