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- EMDB-6862: Cryo-EM Structure of human ATR-ATRIP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6862
TitleCryo-EM Structure of human ATR-ATRIP complex
Map data
Sample
  • Complex: ATR-ATRIP complex
    • Protein or peptide: Serine/threonine-protein kinase ATR
    • Protein or peptide: ATR-interacting protein
Keywordscryo-EM / ATR-ATRIP / DNA damnage response / CELL CYCLE
Function / homology
Function and homology information


ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / MutSalpha complex binding / establishment of protein-containing complex localization to telomere / nuclear membrane disassembly / MutLalpha complex binding / response to arsenic-containing substance / regulation of double-strand break repair / mitotic G2/M transition checkpoint ...ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / MutSalpha complex binding / establishment of protein-containing complex localization to telomere / nuclear membrane disassembly / MutLalpha complex binding / response to arsenic-containing substance / regulation of double-strand break repair / mitotic G2/M transition checkpoint / positive regulation of DNA damage response, signal transduction by p53 class mediator / nucleobase-containing compound metabolic process / protein localization to chromosome, telomeric region / HDR through Single Strand Annealing (SSA) / K63-linked polyubiquitin modification-dependent protein binding / Impaired BRCA2 binding to RAD51 / negative regulation of DNA replication / replication fork processing / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / Regulation of HSF1-mediated heat shock response / interstrand cross-link repair / Activation of ATR in response to replication stress / response to mechanical stimulus / regulation of cellular response to heat / positive regulation of telomere maintenance via telomerase / Meiotic synapsis / telomere maintenance / DNA damage checkpoint signaling / TP53 Regulates Transcription of DNA Repair Genes / Fanconi Anemia Pathway / G2/M DNA damage checkpoint / cellular response to gamma radiation / PML body / cellular response to UV / nuclear envelope / double-strand break repair / peptidyl-serine phosphorylation / chromosome / Processing of DNA double-strand break ends / protein autophosphorylation / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA damage response / Golgi apparatus / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATR-interacting protein / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Serine/threonine-protein kinase ATR-like, HEAT repeats / HEAT repeat profile. / HEAT, type 2 / : / FATC domain / PIK-related kinase, FAT ...ATR-interacting protein / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Serine/threonine-protein kinase ATR-like, HEAT repeats / HEAT repeat profile. / HEAT, type 2 / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase ATR / ATR-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsRao Q / Liu M
Funding support China, 7 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500700 China
Ministry of Science and Technology (China)2016YFA0501100 China
Strategic Priority Research Program of Chinese Academy of Sciences(CAS))XDB08000000 China
National Natural Science Foundation of ChinaU1432242 China
National Natural Science Foundation of China31425008 China
National Natural Science Foundation of China91419301 China
Beijing Municipal Science & Technology CommissionZ161100000116034 China
CitationJournal: Cell Res / Year: 2018
Title: Cryo-EM structure of human ATR-ATRIP complex.
Authors: Qinhui Rao / Mengjie Liu / Yuan Tian / Zihan Wu / Yuhan Hao / Lei Song / Zhaoyu Qin / Chen Ding / Hong-Wei Wang / Jiawei Wang / Yanhui Xu /
Abstract: ATR (ataxia telangiectasia-mutated and Rad3-related) protein kinase and ATRIP (ATR-interacting protein) form a complex and play a critical role in response to replication stress and DNA damage. Here, ...ATR (ataxia telangiectasia-mutated and Rad3-related) protein kinase and ATRIP (ATR-interacting protein) form a complex and play a critical role in response to replication stress and DNA damage. Here, we determined the cryo-electron microscopy (EM) structure of the human ATR-ATRIP complex at 4.7 Å resolution and built an atomic model of the C-terminal catalytic core of ATR (residues 1 521-2 644) at 3.9 Å resolution. The complex adopts a hollow "heart" shape, consisting of two ATR monomers in distinct conformations. The EM map for ATRIP reveals 14 HEAT repeats in an extended "S" shape. The conformational flexibility of ATR allows ATRIP to properly lock the N-termini of the two ATR monomers to favor ATR-ATRIP complex formation and functional diversity. The isolated "head-head" and "tail-tail" each adopts a pseudo 2-fold symmetry. The catalytic pockets face outward and substrate access is not restricted by inhibitory elements. Our studies provide a structural basis for understanding the assembly of the ATR-ATRIP complex and a framework for characterizing ATR-mediated DNA repair pathways.
History
DepositionDec 11, 2017-
Header (metadata) releaseJan 31, 2018-
Map releaseJan 31, 2018-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-5yz0
  • Surface level: 0.02
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6862.png

Downloads & links

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Map

FileDownload / File: emd_6862.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.061650008 - 0.1427336
Average (Standard dev.)0.00072394306 (±0.005244613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0620.1430.001

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Supplemental data

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Sample components

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Entire : ATR-ATRIP complex

EntireName: ATR-ATRIP complex
Components
  • Complex: ATR-ATRIP complex
    • Protein or peptide: Serine/threonine-protein kinase ATR
    • Protein or peptide: ATR-interacting protein

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Supramolecule #1: ATR-ATRIP complex

SupramoleculeName: ATR-ATRIP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 700 kDa/nm

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Macromolecule #1: Serine/threonine-protein kinase ATR

MacromoleculeName: Serine/threonine-protein kinase ATR / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 301.756781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGEHGLELAS MIPALRELGS ATPEEYNTVV QKPRQILCQF IDRILTDVNV VAVELVKKTD SQPTSVMLLD FIQHIMKSSP LMFVNVSGS HEAKGSCIEF SNWIITRLLR IAATPSCHLL HKKICEVICS LLFLFKSKSP AIFGVLTKEL LQLFEDLVYL H RRNVMGHA ...String:
MGEHGLELAS MIPALRELGS ATPEEYNTVV QKPRQILCQF IDRILTDVNV VAVELVKKTD SQPTSVMLLD FIQHIMKSSP LMFVNVSGS HEAKGSCIEF SNWIITRLLR IAATPSCHLL HKKICEVICS LLFLFKSKSP AIFGVLTKEL LQLFEDLVYL H RRNVMGHA VEWPVVMSRF LSQLDEHMGY LQSAPLQLMS MQNLEFIEVT LLMVLTRIIA IVFFRRQELL LWQIGCVLLE YG SPKIKSL AISFLTELFQ LGGLPAQPAS TFFSSFLELL KHLVEMDTDQ LKLYEEPLSK LIKTLFPFEA EAYRNIEPVY LNM LLEKLC VMFEDGVLMR LKSDLLKAAL CHLLQYFLKF VPAGYESALQ VRKVYVRNIC KALLDVLGIE VDAEYLLGPL YAAL KMESM EIIEEIQCQT QQENLSSNSD GISPKRRRLS SSLNPSKRAP KQTEEIKHVD MNQKSILWSA LKQKAESLQI SLEYS GLKN PVIEMLEGIA VVLQLTALCT VHCSHQNMNC RTFKDCQHKS KKKPSVVITW MSLDFYTKVL KSCRSLLESV QKLDLE ATI DKVVKIYDAL IYMQVNSSFE DHILEDLCGM LSLPWIYSHS DDGCLKLTTF AANLLTLSCR ISDSYSPQAQ SRCVFLL TL FPRRIFLEWR TAVYNWALQS SHEVIRASCV SGFFILLQQQ NSCNRVPKIL IDKVKDDSDI VKKEFASILG QLVCTLHG M FYLTSSLTEP FSEHGHVDLF CRNLKATSQH ECSSSQLKAS VCKPFLFLLK KKIPSPVKLA FIDNLHHLCK HLDFREDET DVKAVLGTLL NLMEDPDKDV RVAFSGNIKH ILESLDSEDG FIKELFVLRM KEAYTHAQIS RNNELKDTLI LTTGDIGRAA KGDLVPFAL LHLLHCLLSK SASVSGAAYT EIRALVAAKS VKLQSFFSQY KKPICQFLVE SLHSSQMTAL PNTPCQNADV R KQDVAHQR EMALNTLSEI ANVFDFPDLN RFLTRTLQVL LPDLAAKASP AASALIRTLG KQLNVNRREI LINNFKYIFS HL VCSCSKD ELERALHYLK NETEIELGSL LRQDFQGLHN ELLLRIGEHY QQVFNGLSIL ASFASSDDPY QGPRDIISPE LMA DYLQPK LLGILAFFNM QLLSSSVGIE DKKMALNSLM SLMKLMGPKH VSSVRVKMMT TLRTGLRFKD DFPELCCRAW DCFV RCLDH ACLGSLLSHV IVALLPLIHI QPKETAAIFH YLIIENRDAV QDFLHEIYFL PDHPELKKIK AVLQEYRKET SESTD LQTT LQLSMKAIQH ENVDVRIHAL TSLKETLYKN QEKLIKYATD SETVEPIISQ LVTVLLKGCQ DANSQARLLC GECLGE LGA IDPGRLDFST TETQGKDFTF VTGVEDSSFA YGLLMELTRA YLAYADNSRA QDSAAYAIQE LLSIYDCREM ETNGPGH QL WRRFPEHVRE ILEPHLNTRY KSSQKSTDWS GVKKPIYLSK LGSNFAEWSA SWAGYLITKV RHDLASKIFT CCSIMMKH D FKVTIYLLPH ILVYVLLGCN QEDQQEVYAE IMAVLKHDDQ HTINTQDIAS DLCQLSTQTV FSMLDHLTQW ARHKFQALK AEKCPHSKSN RNKVDSMVST VDYEDYQSVT RFLDLIPQDT LAVASFRSKA YTRAVMHFES FITEKKQNIQ EHLGFLQKLY AAMHEPDGV AGVSAIRKAE PSLKEQILEH ESLGLLRDAT ACYDRAIQLE PDQIIHYHGV VKSMLGLGQL STVITQVNGV H ANRSEWTD ELNTYRVEAA WKLSQWDLVE NYLAADGKST TWSVRLGQLL LSAKKRDITA FYDSLKLVRA EQIVPLSAAS FE RGSYQRG YEYIVRLHML CELEHSIKPL FQHSPGDSSQ EDSLNWVARL EMTQNSYRAK EPILALRRAL LSLNKRPDYN EMV GECWLQ SARVARKAGH HQTAYNALLN AGESRLAELY VERAKWLWSK GDVHQALIVL QKGVELCFPE NETPPEGKNM LIHG RAMLL VGRFMEETAN FESNAIMKKY KDVTACLPEW EDGHFYLAKY YDKLMPMVTD NKMEKQGDLI RYIVLHFGRS LQYGN QFIY QSMPRMLTLW LDYGTKAYEW EKAGRSDRVQ MRNDLGKINK VITEHTNYLA PYQFLTAFSQ LISRICHSHD EVFVVL MEI IAKVFLAYPQ QAMWMMTAVS KSSYPMRVNR CKEILNKAIH MKKSLEKFVG DATRLTDKLL ELCNKPVDGS SSTLSMS TH FKMLKKLVEE ATFSEILIPL QSVMIPTLPS ILGTHANHAS HEPFPGHWAY IAGFDDMVEI LASLQKPKKI SLKGSDGK F YIMMCKPKDD LRKDCRLMEF NSLINKCLRK DAESRRRELH IRTYAVIPLN DECGIIEWVN NTAGLRPILT KLYKEKGVY MTGKELRQCM LPKSAALSEK LKVFREFLLP RHPPIFHEWF LRTFPDPTSW YSSRSAYCRS TAVMSMVGYI LGLGDRHGEN ILFDSLTGE CVHVDFNCLF NKGETFEVPE IVPFRLTHNM VNGMGPMGTE GLFRRACEVT MRLMRDQREP LMSVLKTFLH D PLVEWSKP VKGHSKAPLN ETGEVVNEKA KTHVLDIEQR LQGVIKTRNR VTGLPLSIEG HVHYLIQEAT DENLLCQMYL GW TPYM

UniProtKB: Serine/threonine-protein kinase ATR

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Macromolecule #2: ATR-interacting protein

MacromoleculeName: ATR-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.940664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGTSAPGSK RRSEPPAPRP GPPPGTGHPP SKRARGFSAA AAPDPDDPFG AHGDFTADDL EELDTLASQA LSQCPAAARD VSSDHKVHR LLDGMSKNPS GKNRETVPIK DNFELEVLQA QYKELKEKMK VMEEEVLIKN GEIKILRDSL HQTESVLEEQ R RSHFLLEQ ...String:
MAGTSAPGSK RRSEPPAPRP GPPPGTGHPP SKRARGFSAA AAPDPDDPFG AHGDFTADDL EELDTLASQA LSQCPAAARD VSSDHKVHR LLDGMSKNPS GKNRETVPIK DNFELEVLQA QYKELKEKMK VMEEEVLIKN GEIKILRDSL HQTESVLEEQ R RSHFLLEQ EKTQALSDKE KEFSKKLQSL QSELQFKDAE MNELRTKLQT SERANKLAAP SVSHVSPRKN PSVVIKPEAC SP QFGKTSF PTKESFSANM SLPHPCQTES GYKPLVGRED SKPHSLRGDS IKQEEAQKSF VDSWRQRSNT QGSILINLLL KQP LIPGSS LSLCHLLSSS SESPAGTPLQ PPGFGSTLAG MSGLRTTGSY DGSFSLSALR EAQNLAFTGL NLVARNECSR DGDP AEGGR RAFPLCQLPG AVHFLPLVQF FIGLHCQALQ DLAAAKRSGA PGDSPTHSSC VSSGVETNPE DSVCILEGFS VTALS ILQH LVCHSGAVVS LLLSGVGADS AAGEGNRSLV HRLSDGDMTS ALRGVADDQG QHPLLKMLLH LLAFSSAATG HLQASV LTQ CLKVLVKLAE NTSCDFLPRF QCVFQVLPKC LSPETPLPSV LLAVELLSLL ADHDQLAPQL CSHSEGCLLL LLYMYIT SR PDRVALETQW LQLEQEVVWL LAKLGVQSPL PPVTGSNCQC NVEVVRALTV MLHRQWLTVR RAGGPPRTDQ QRRTVRCL R DTVLLLHGLS QKDKLFMMHC VEVLHQFDQV MPGVSMLIRG LPDVTDCEEA ALDDLCAAET DVEDPEVECG

UniProtKB: ATR-interacting protein

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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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 266218
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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