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- EMDB-18611: Cryo-EM structure of the human Tip60 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-18611
TitleCryo-EM structure of the human Tip60 complex
Map dataComposite map of the human Tip60 complex
Sample
  • Cell: Tip60 complex
    • Protein or peptide: E1A-binding protein p400
    • Protein or peptide: Enhancer of polycomb homolog 1
    • Protein or peptide: DNA methyltransferase 1-associated protein 1
    • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
KeywordsEukaryotic transcription / Histone acetyltransferase / chromatin remodeling / Complex / TRANSCRIPTION
Function / homology
Function and homology information


ATP-dependent H2AZ histone chaperone activity / piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / histone chaperone activity / sperm DNA condensation ...ATP-dependent H2AZ histone chaperone activity / piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / histone chaperone activity / sperm DNA condensation / establishment of protein localization to chromatin / morphogenesis of a polarized epithelium / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / brahma complex / nBAF complex / protein localization to adherens junction / R2TP complex / postsynaptic actin cytoskeleton / dynein axonemal particle / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / chromatin-protein adaptor activity / Regulation of MITF-M-dependent genes involved in pigmentation / RPAP3/R2TP/prefoldin-like complex / GBAF complex / neural retina development / protein antigen binding / dense body / Swr1 complex / regulation of G0 to G1 transition / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / blastocyst formation / RHOF GTPase cycle / Adherens junctions interactions / tight junction / enzyme-substrate adaptor activity / protein folding chaperone complex / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of gene expression, epigenetic / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / regulation of chromosome organization / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / Transcriptional Regulation by E2F6 / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / somatic stem cell population maintenance / calyx of Held / negative regulation of cell differentiation / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / spermatid development / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of myoblast differentiation / regulation of DNA repair / DNA helicase activity / Deposition of new CENPA-containing nucleosomes at the centromere / EPHB-mediated forward signaling / substantia nigra development
Similarity search - Function
Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / E1A-binding protein p400, N-terminal / Vps72/YL1, N-terminal / E1A-binding protein p400, N-terminal / DNA methyltransferase 1-associated 1 / Vps72/YL1 family / DNA methyltransferase 1-associated protein 1 (DMAP1) / YL1 nuclear protein / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 ...Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / E1A-binding protein p400, N-terminal / Vps72/YL1, N-terminal / E1A-binding protein p400, N-terminal / DNA methyltransferase 1-associated 1 / Vps72/YL1 family / DNA methyltransferase 1-associated protein 1 (DMAP1) / YL1 nuclear protein / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Enhancer of polycomb protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / Myb-like domain profile. / domain in helicases and associated with SANT domains / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / SANT/Myb domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Actin-like protein 6A / Actin, cytoplasmic 1 / Vacuolar protein sorting-associated protein 72 homolog / E1A-binding protein p400 / Enhancer of polycomb homolog 1 / DNA methyltransferase 1-associated protein 1 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLi C / Smirnova E / Schnitzler C / Crucifix C / Concordet JP / Brion A / Poterszman A / Schultz P / Papai G / Ben-Shem A
Funding support France, 1 items
OrganizationGrant numberCountry
La ligue contre le cancer France
CitationJournal: Nature / Year: 2024
Title: Structure of human TIP60-C histone exchange and acetyltransferase complex
Authors: Li C / Smirnova E / Schnitzler C / Crucifix C / Concordet JP / Brion A / Poterszman A / Schultz P / Papai G / Ben-Shem A
History
DepositionOct 6, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18611.png

Downloads & links

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Map

FileDownload / File: emd_18611.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the human Tip60 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 686 pix.
= 500.78 Å		0.73 Å/pix.
x 686 pix.
= 500.78 Å		0.73 Å/pix.
x 686 pix.
= 500.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-28.889392999999998 - 74.696235999999999
Average (Standard dev.)-0.0031860704 (±1.0691456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions686686686
Spacing686686686
CellA=B=C: 500.78 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tip60 complex

EntireName: Tip60 complex
Components
  • Cell: Tip60 complex
    • Protein or peptide: E1A-binding protein p400
    • Protein or peptide: Enhancer of polycomb homolog 1
    • Protein or peptide: DNA methyltransferase 1-associated protein 1
    • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2

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Supramolecule #1: Tip60 complex

SupramoleculeName: Tip60 complex / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Strain: K562

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Macromolecule #1: E1A-binding protein p400

MacromoleculeName: E1A-binding protein p400 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 343.867312 KDa
SequenceString: MHHGTGPQNV QHQLQRSRAC PGSEGEEQPA HPNPPPSPAA PFAPSASPSA PQSPSYQIQQ LMNRSPATGQ NVNITLQSVG PVVGGNQQI TLAPLPLPSP TSPGFQFSAQ PRRFEHGSPS YIQVTSPLSQ QVQTQSPTQP SPGPGQALQN VRAGAPGPGL G LCSSSPTG ...String:
MHHGTGPQNV QHQLQRSRAC PGSEGEEQPA HPNPPPSPAA PFAPSASPSA PQSPSYQIQQ LMNRSPATGQ NVNITLQSVG PVVGGNQQI TLAPLPLPSP TSPGFQFSAQ PRRFEHGSPS YIQVTSPLSQ QVQTQSPTQP SPGPGQALQN VRAGAPGPGL G LCSSSPTG GFVDASVLVR QISLSPSSGG HFVFQDGSGL TQIAQGAQVQ LQHPGTPITV RERRPSQPHT QSGGTIHHLG PQ SPAAAGG AGLQPLASPS HITTANLPPQ ISSIIQGQLV QQQQVLQGPP LPRPLGFERT PGVLLPGAGG AAGFGMTSPP PPT SPSRTA VPPGLSSLPL TSVGNTGMKK VPKKLEEIPP ASPEMAQMRK QCLDYHYQEM QALKEVFKEY LIELFFLQHF QGNM MDFLA FKKKHYAPLQ AYLRQNDLDI EEEEEEEEEE EEKSEVINDE VKVVTGKDGQ TGTPVAIATQ LPPKVSAAFS SQQQP FQQA LAGSLVAGAG STVETDLFKR QQAMPSTGMA EQSKRPRLEV GHQGVVFQHP GADAGVPLQQ LMPTAQGGMP PTPQAA QLA GQRQSQQQYD PSTGPPVQNA ASLHTPLPQL PGRLPPAGVP TAALSSALQF AQQPQVVEAQ TQLQIPVKTQ QPNVPIP AP PSSQLPIPPS QPAQLALHVP TPGKVQVQAS QLSSLPQMVA STRLPVDPAP PCPRPLPTSS TSSLAPVSGS GPGPSPAR S SPVNRPSSAT NKALSPVTSR TPGVVASAPT KPQSPAQNAT SSQDSSQDTL TEQITLENQV HQRIAELRKA GLWSQRRLP KLQEAPRPKS HWDYLLEEMQ WMATDFAQER RWKVAAAKKL VRTVVRHHEE KQLREERGKK EEQSRLRRIA ASTAREIECF WSNIEQVVE IKLRVELEEK RKKALNLQKV SRRGKELRPK GFDALQESSL DSGMSGRKRK ASISLTDDEV DDEEETIEEE E ANEGVVDH QTELSNLAKE AELPLLDLMK LYEGAFLPSS QWPRPKPDGE DTSGEEDADD CPGDRESRKD LVLIDSLFIM DQ FKAAERM NIGKPNAKDI ADVTAVAEAI LPKGSARVTT SVKFNAPSLL YGALRDYQKI GLDWLAKLYR KNLNGILADE AGL GKTVQI IAFFAHLACN EGNWGPHLVV VRSCNILKWE LELKRWCPGL KILSYIGSHR ELKAKRQEWA EPNSFHVCIT SYTQ FFRGL TAFTRVRWKC LVIDEMQRVK GMTERHWEAV FTLQSQQRLL LIDSPLHNTF LELWTMVHFL VPGISRPYLS SPLRA PSEE SQDYYHKVVI RLHRVTQPFI LRRTKRDVEK QLTKKYEHVL KCRLSNRQKA LYEDVILQPG TQEALKSGHF VNVLSI LVR LQRICNHPGL VEPRHPGSSY VAGPLEYPSA SLILKALERD FWKEADLSMF DLIGLENKIT RHEAELLSKK KIPRKLM EE ISTSAAPAAR PAAAKLKASR LFQPVQYGQK PEGRTVAFPS THPPRTAAPT TASAAPQGPL RGRPPIATFS ANPEAKAA A APFQTSQASA SAPRHQPASA SSTAASPAHP AKLRAQTTAQ ASTPGQPPPQ PQAPSHAAGQ SALPQRLVLP SQAQARLPS GEVVKIAQLA SITGPQSRVA QPETPVTLQF QGSKFTLSHS QLRQLTAGQP LQLQGSVLQI VSAPGQPYLR APGPVVMQTV SQAGAVHGA LGSKPPAGGP SPAPLTPQVG VPGRVAVNAL AVGEPGTASK PASPIGGPTQ EEKTRLLKER LDQIYLVNER R CSQAPVYG RDLLRICALP SHGRVQWRGS LDGRRGKEAG PAHSYTSSSE SPSELMLTLC RCGESLQDVI DRVAFVIPPV VA APPSLRV PRPPPLYSHR MRILRQGLRE HAAPYFQQLR QTTAPRLLQF PELRLVQFDS GKLEALAILL QKLKSEGRRV LIL SQMILM LDILEMFLNF HYLTYVRIDE NASSEQRQEL MRSFNRDRRI FCAILSTHSR TTGINLVEAD TVVFYDNDLN PVMD AKAQE WCDRIGRCKD IHIYRLVSGN SIEEKLLKNG TKDLIREVAA QGNDYSMAFL TQRTIQELFE VYSPMDDAGF PVKAE EFVV LSQEPSVTET IAPKIARPFI EALKSIEYLE EDAQKSAQEG VLGPHTDALS SDSENMPCDE EPSQLEELAD FMEQLT PIE KYALNYLELF HTSIEQEKER NSEDAVMTAV RAWEFWNLKT LQEREARLRL EQEEAELLTY TREDAYSMEY VYEDVDG QT EVMPLWTPPT PPQDDSDIYL DSVMCLMYEA TPIPEAKLPP VYVRKERKRH KTDPSAAGRK KKQRHGEAVV PPRSLFDR A TPGLLKIRRE GKEQKKNILL KQQVPFAKPL PTFAKPTAEP GQDNPEWLIS EDWALLQAVK QLLELPLNLT IVSPAHTPN WDLVSDVVNS CSRIYRSSKQ CRNRYENVII PREEGKSKNN RPLRTSQIYA QDENATHTQL YTSHFDLMKM TAGKRSPPIK PLLGMNPFQ KNPKHASVLA ESGINYDKPL PPIQVASLRA ERIAKEKKAL ADQQKAQQPA VAQPPPPQPQ PPPPPQQPPP P LPQPQAAG SQPPAGPPAV QPQPQPQPQT QPQPVQAPAK AQPAITTGGS AAVLAGTIKT SVTGTSMPTG AVSGNVIVNT IA GVPAATF QSINKRLASP VAPGALTTPG GSAPAQVVHT QPPPRAVGSP ATATPDLVSM ATTQGVRAVT SVTASAVVTT NLT PVQTPA RSLVPQVSQA TGVQLPGKTI TPAHFQLLRQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQTT TTSQVQVPQI QGQA QSPAQ IKAVGKLTPE HLIKMQKQKL QMPPQPPPPQ AQSAPPQPTA QVQVQTSQPP QQQSPQLTTV TAPRPGALLT GTTVA NLQV ARLTRVPTSQ LQAQGQMQTQ APQPAQVALA KPPVVSVPAA VVSSPGVTTL PMNVAGISVA IGQPQKAAGQ TVVAQP VHM QQLLKLKQQA VQQQKAIQPQ AAQGPAAVQQ KITAQQITTP GAQQKVAYAA QPALKTQFLT TPISQAQKLA GAQQVQT QI QVAKLPQVVQ QQTPVASIQQ VASASQQASP QTVALTQATA AGQQVQMIPA VTATAQVVQQ KLIQQQVVTT ASAPLQTP G APNPAQVPAS SDSPSQQPKL QMRVPAVRLK TPTKPPCQ

UniProtKB: E1A-binding protein p400

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Macromolecule #2: Enhancer of polycomb homolog 1

MacromoleculeName: Enhancer of polycomb homolog 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.589172 KDa
SequenceString: MSKLSFRARA LDASKPLPVF RCEDLPDLHE YASINRAVPQ MPTGMEKEEE SEHHLQRAIS AQQVYGEKRD NMVIPVPEAE SNIAYYESI YPGEFKMPKQ LIHIQPFSLD AEQPDYDLDS EDEVFVNKLK KKMDICPLQF EEMIDRLEKG SGQQPVSLQE A KLLLKEDD ...String:
MSKLSFRARA LDASKPLPVF RCEDLPDLHE YASINRAVPQ MPTGMEKEEE SEHHLQRAIS AQQVYGEKRD NMVIPVPEAE SNIAYYESI YPGEFKMPKQ LIHIQPFSLD AEQPDYDLDS EDEVFVNKLK KKMDICPLQF EEMIDRLEKG SGQQPVSLQE A KLLLKEDD ELIREVYEYW IKKRKNCRGP SLIPSVKQEK RDGSSTNDPY VAFRRRTEKM QTRKNRKNDE ASYEKMLKLR RD LSRAVTI LEMIKRREKS KRELLHLTLE IMEKRYNLGD YNGEIMSEVM AQRQPMKPTY AIPIIPITNS SQFKHQEAMD VKE FKVNKQ DKADLIRPKR KYEKKPKVLP SSAAATPQQT SPAALPVFNA KDLNQYDFPS SDEEPLSQVL SGSSEAEEDN DPDG PFAFR RKAGCQYYAP HLDQTGNWPW TSPKDGGLGD VRYRYCLTTL TVPQRCIGFA RRRVGRGGRV LLDRAHSDYD SVFHH LDLE MLSSPQHSPV NQFANTSETN TSDKSFSKDL SQILVNIKSC RWRHFRPRTP SLHDSDNDEL SCRKLYRSIN RTGTAQ PGT QTCSTSTQSK SSSGSAHFAF TAEQYQQHQQ QLALMQKQQL AQIQQQQANS NSSTNTSQNL ASNQQKSGFR LNIQGLE RT LQGFVSKTLD SASAQFAASA LVTSEQLMGF KMKDDVVLGI GVNGVLPASG VYKGLHLSST TPTALVHTSP STAGSALL Q PSNITQTSSS HSALSHQVTA ANSATTQVLI GNNIRLTVPS SVATVNSIAP INARHIPRTL SAVPSSALKL AAAANCQVS KVPSSSSVDS VPRENHESEK PALNNIADNT VAMEVT

UniProtKB: Enhancer of polycomb homolog 1

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Macromolecule #3: DNA methyltransferase 1-associated protein 1

MacromoleculeName: DNA methyltransferase 1-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.090699 KDa
SequenceString: MATGADVRDI LELGGPEGDA ASGTISKKDI INPDKKKSKK SSETLTFKRP EGMHREVYAL LYSDKKDAPP LLPSDTGQGY RTVKAKLGS KKVRPWKWMP FTNPARKDGA MFFHWRRAAE EGKDYPFARF NKTVQVPVYS EQEYQLYLHD DAWTKAETDH L FDLSRRFD ...String:
MATGADVRDI LELGGPEGDA ASGTISKKDI INPDKKKSKK SSETLTFKRP EGMHREVYAL LYSDKKDAPP LLPSDTGQGY RTVKAKLGS KKVRPWKWMP FTNPARKDGA MFFHWRRAAE EGKDYPFARF NKTVQVPVYS EQEYQLYLHD DAWTKAETDH L FDLSRRFD LRFVVIHDRY DHQQFKKRSV EDLKERYYHI CAKLANVRAV PGTDLKIPVF DAGHERRRKE QLERLYNRTP EQ VAEEEYL LQELRKIEAR KKEREKRSQD LQKLITAADT TAEQRRTERK APKKKLPQKK EAEKPAVPET AGIKFPDFKS AGV TLRSQR MKLPSSVGQK KIKALEQMLL ELGVELSPTP TEELVHMFNE LRSDLVLLYE LKQACANCEY ELQMLRHRHE ALAR AGVLG GPATPASGPG PASAEPAVTE PGLGPDPKDT IIDVVGAPLT PNSRKRRESA SSSSSVKKAK KP

UniProtKB: DNA methyltransferase 1-associated protein 1

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Macromolecule #4: Vacuolar protein sorting-associated protein 72 homolog

MacromoleculeName: Vacuolar protein sorting-associated protein 72 homolog
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.658363 KDa
SequenceString: MSLAGGRAPR KTAGNRLSGL LEAEEEDEFY QTTYGGFTEE SGDDEYQGDQ SDTEDEVDSD FDIDEGDEPS SDGEAEEPRR KRRVVTKAY KEPLKSLRPR KVNTPAGSSQ KAREEKALLP LELQDDGSDS RKSMRQSTAE HTRQTFLRVQ ERQGQSRRRK G PHCERPLT ...String:
MSLAGGRAPR KTAGNRLSGL LEAEEEDEFY QTTYGGFTEE SGDDEYQGDQ SDTEDEVDSD FDIDEGDEPS SDGEAEEPRR KRRVVTKAY KEPLKSLRPR KVNTPAGSSQ KAREEKALLP LELQDDGSDS RKSMRQSTAE HTRQTFLRVQ ERQGQSRRRK G PHCERPLT QEELLREAKI TEELNLRSLE TYERLEADKK KQVHKKRKCP GPIITYHSVT VPLVGEPGPK EENVDIEGLD PA PSVSALT PHAGTGPVNP PARCSRTFIT FSDDATFEEW FPQGRPPKVP VREVCPVTHR PALYRDPVTD IPYATARAFK IIR EAYKKY ITAHGLPPTA SALGPGPPPP EPLPGSGPRA LRQKIVIK

UniProtKB: Vacuolar protein sorting-associated protein 72 homolog

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Macromolecule #5: Actin, cytoplasmic 1, N-terminally processed

MacromoleculeName: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.78266 KDa
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #6: Actin-like protein 6A

MacromoleculeName: Actin-like protein 6A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.509812 KDa
SequenceString: MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLK NGMVEDWDSF QAILDHTYKM HVKSEASLHP VLMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA F ANGRSTGL ...String:
MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLK NGMVEDWDSF QAILDHTYKM HVKSEASLHP VLMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA F ANGRSTGL ILDSGATHTT AIPVHDGYVL QQGIVKSPLA GDFITMQCRE LFQEMNIELV PPYMIASKEA VREGSPANWK RK EKLPQVT RSWHNYMCNC VIQDFQASVL QVSDSTYDEQ VAAQMPTVHY EFPNGYNCDF GAERLKIPEG LFDPSNVKGL SGN TMLGVS HVVTTSVGMC DIDIRPGLYG SVIVAGGNTL IQSFTDRLNR ELSQKTPPSM RLKLIANNTT VERRFSSWIG GSIL ASLGT FQQMWISKQE YEEGGKQCVE RKCP

UniProtKB: Actin-like protein 6A

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Macromolecule #7: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.296914 KDa
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EYVPLPKGDV HKKKEIIQDV TL HDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALE SSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQTEGINI SEEALNHLGE IGTK TTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

UniProtKB: RuvB-like 1

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Macromolecule #8: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.222465 KDa
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FTRARDYDAM GSQTKFVQCP DGELQKRKEV VH TVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKVAEWREEG KAEIIPGVLF IDEVHMLDIE SFSFLNRALE SDM APVLIM ATNRGITRIR GTSYQSPHGI PIDLLDRLLI VSTTPYSEKD TKQILRIRCE EEDVEMSEDA YTVLTRIGLE TSLR YAIQL ITAASLVCRK RKGTEVQVDD IKRVYSLFLD ESRSTQYMKE YQDAFLFNEL KGETMDTS

UniProtKB: RuvB-like 2

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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

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
20.0 mMHEPES
250.0 mMNaCl
2.0 mMMgCl2
20.0 mMBiotin
1.0 %Trehalose
2.0 mMDTT
0.0125 %DDM
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON IV (4k x 4k) / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 284286
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 180397
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qr1:
Cryo-EM structure of the human Tip60 complex

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