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- EMDB-38703: Structure of human NuA4/TIP60 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38703
TitleStructure of human NuA4/TIP60 complex
Map datahuman TIP60 complex overall half map1
Sample
  • Complex: Structure of human NuA4/TIP60 complex
    • Protein or peptide: x 9 types
  • Ligand: x 2 types
KeywordsRemodeler / Histone Acetyltransferase Complex / NuA4 / TIP60 / TRANSCRIPTION
Function / homology
Function and homology information


ATP-dependent H2AZ histone chaperone activity / piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / histone chaperone activity / sperm DNA condensation / establishment of protein localization to chromatin / npBAF complex / brahma complex ...ATP-dependent H2AZ histone chaperone activity / piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / histone chaperone activity / sperm DNA condensation / establishment of protein localization to chromatin / npBAF complex / brahma complex / R2TP complex / transcription factor TFTC complex / dynein axonemal particle / chromatin-protein adaptor activity / RPAP3/R2TP/prefoldin-like complex / GBAF complex / protein antigen binding / Swr1 complex / regulation of G0 to G1 transition / neural retina development / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex / RSC-type complex / blastocyst formation / Regulation of MITF-M-dependent genes involved in pigmentation / enzyme-substrate adaptor activity / protein folding chaperone complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / SAGA complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of gene expression, epigenetic / spinal cord development / regulation of chromosome organization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / regulation of RNA splicing / somatic stem cell population maintenance / TFIID-class transcription factor complex binding / negative regulation of cell differentiation / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / spermatid development / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of myoblast differentiation / regulation of DNA repair / histone acetyltransferase activity / Deposition of new CENPA-containing nucleosomes at the centromere / TBP-class protein binding / DNA helicase activity / positive regulation of DNA repair / telomere maintenance / transcription initiation-coupled chromatin remodeling / replication fork / helicase activity / cellular response to estradiol stimulus / positive regulation of cell differentiation / transcription coregulator activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / euchromatin / DNA Damage/Telomere Stress Induced Senescence / chromatin DNA binding / kinetochore / ADP binding / RMTs methylate histone arginines / nuclear matrix / beta-catenin binding / positive regulation of protein import into nucleus / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / protein folding / chromatin organization / nervous system development / site of double-strand break / HATs acetylate histones / histone binding / ATPase binding / spermatogenesis / nuclear membrane / DNA helicase
Similarity search - Function
Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 ...Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / 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 / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / 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. / : / PIK-related kinase, FAT / FAT domain / FATC / : / FATC domain / PIK-related kinase / FAT domain profile. / FATC 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 / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic 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 / Armadillo-like helical / 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 / Armadillo-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACTB protein / Actin-like protein 6A / 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 / Transformation/transcription domain-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsChen K / Wang L / Yu Z / Yu J / Ren Y / Wang Q / Xu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the human TIP60 complex
Authors: Chen K / Wang L / Yu Z / Yu J / Ren Y / Wang Q / Xu Y
History
DepositionJan 15, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38703.png

Downloads & links

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Map

FileDownload / File: emd_38703.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman TIP60 complex overall half map1
Voxel sizeX=Y=Z: 2.668 Å
Density
Contour LevelBy AUTHOR: 0.027
Minimum - Maximum-0.056272987 - 0.1032619
Average (Standard dev.)-0.000031704683 (±0.0056330934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 533.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: human TIP60 complex overall half map1

Fileemd_38703_half_map_1.map
Annotationhuman TIP60 complex overall half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: human TIP60 complex overall half map2

Fileemd_38703_half_map_2.map
Annotationhuman TIP60 complex overall half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of human NuA4/TIP60 complex

EntireName: Structure of human NuA4/TIP60 complex
Components
  • Complex: Structure of human NuA4/TIP60 complex
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: DNA methyltransferase 1-associated protein 1
    • Protein or peptide: Isoform 2 of E1A-binding protein p400
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: ACTB protein (Fragment)
    • Protein or peptide: Isoform 2 of Transformation/transcription domain-associated protein
    • Protein or peptide: Isoform 2 of Enhancer of polycomb homolog 1
    • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Structure of human NuA4/TIP60 complex

SupramoleculeName: Structure of human NuA4/TIP60 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#7, #1, #8-#9
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Transformation/transcription domain-associated protein

MacromoleculeName: Isoform 2 of Transformation/transcription domain-associated protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 434.949906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFVATQGAT VVDQTTLMKK YLQFVAALTD VNTPDETKLK MMQEVSENFE NVTSSPQYST FLEHIIPRFL TFLQDGEVQF LQEKPAQQL RKLVLEIIHR IPTNEHLRPH TKNVLSVMFR FLETENEENV LICLRIIIEL HKQFRPPITQ EIHHFLDFVK Q IYKELPKV ...String:
MAFVATQGAT VVDQTTLMKK YLQFVAALTD VNTPDETKLK MMQEVSENFE NVTSSPQYST FLEHIIPRFL TFLQDGEVQF LQEKPAQQL RKLVLEIIHR IPTNEHLRPH TKNVLSVMFR FLETENEENV LICLRIIIEL HKQFRPPITQ EIHHFLDFVK Q IYKELPKV VNRYFENPQV IPENTVPPPE MVGMITTIAV KVNPEREDSE TRTHSIIPRG SLSLKVLAEL PIIVVLMYQL YK LNIHNVV AEFVPLIMNT IAIQVSAQAR QHKLYNKELY ADFIAAQIKT LSFLAYIIRI YQELVTKYSQ QMVKGMLQLL SNC PAETAH LRKELLIAAK HILTTELRNQ FIPCMDKLFD ESILIGSGYT ARETLRPLAY STLADLVHHV RQHLPLSDLS LAVQ LFAKN IDDESLPSSI QTMSCKLLLN LVDCIRSKSE QESGNGRDVL MRMLEVFVLK FHTIARYQLS AIFKKCKPQS ELGAV EAAL PGVPTAPAAP GPAPSPAPVP APPPPPPPPP PATPVTPAPV PPFEKQGEKD KEDKQTFQVT DCRSLVKTLV CGVKTI TWG ITSCKAPGEA QFIPNKQLQP KETQIYIKLV KYAMQALDIY QVQIAGNGQT YIRVANCQTV RMKEEKEVLE HFAGVFT MM NPLTFKEIFQ TTVPYMVERI SKNYALQIVA NSFLANPTTS ALFATILVEY LLDRLPEMGS NVELSNLYLK LFKLVFGS V SLFAAENEQM LKPHLHKIVN SSMELAQTAK EPYNYFLLLR ALFRSIGGGS HDLLYQEFLP LLPNLLQGLN MLQSGLHKQ HMKDLFVELC LTVPVRLSSL LPYLPMLMDP LVSALNGSQT LVSQGLRTLE LCVDNLQPDF LYDHIQPVRA ELMQALWRTL RNPADSISH VAYRVLGKFG GSNRKMLKES QKLHYVVTEV QGPSITVEFS DCKASLQLPM EKAIETALDC LKSANTEPYY R RQAWEVIK CFLVAMMSLE DNKHALYQLL AHPNFTEKTI PNVIISHRYK AQDTPARKTF EQALTGAFMS AVIKDLRPSA LP FVASLIR HYTMVAVAQQ CGPFLLPCYQ VGSQPSTAMF HSEENGSKGM DPLVLIDAIA ICMAYEEKEL CKIGEVALAV IFD VASIIL GSKERACQLP LFSYIVERLC ACCYEQAWYA KLGGVVSIKF LMERLPLTWV LQNQQTFLKA LLFVMMDLTG EVSN GAVAM AKTTLEQLLM RCATPLKDEE RAEEIVAAQE KSFHHVTHDL VREVTSPNST VRKQAMHSLQ VLAQVTGKSV TVIME PHKE VLQDMVPPKK HLLRHQPANA QIGLMEGNTF CTTLQPRLFT MDLNVVEHKV FYTELLNLCE AEDSALTKLP CYKSLP SLV PLRIAALNAL AACNYLPQSR EKIIAALFKA LNSTNSELQE AGEACMRKFL EGATIEVDQI HTHMRPLLMM LGDYRSL TL NVVNRLTSVT RLFPNSFNDK FCDQMMQHLR KWMEVVVITH KGGQRSDGNE MKICSAIINL FHLIPAAPQT LVKPLLEV V MKTERAMLIE AGSPFREPLI KFLTRHPSQT VELFMMEATL NDPQWSRMFM SFLKHKDARP LRDVLAANPN RFITLLLPG GAQTAVRPGS PSTSTMRLDL QFQAIKIISI IVKNDDSWLA SQHSLVSQLR RVWVSENFQE RHRKENMAAT NWKEPKLLAY CLLNYCKRN YGDIELLFQL LRAFTGRFLC NMTFLKEYME EEIPKNYSIA QKRALFFRFV DFNDPNFGDE LKAKVLQHIL N PAFLYSFE KGEGEQLLGP PNPEGDNPES ITSVFITKVL DPEKQADMLD SLRIYLLQYA TLLVEHAPHH IHDNNKNRNS KL RRLMTFA WPCLLSKACV DPACKYSGHL LLAHIIAKFA IHKKIVLQVF HSLLKAHAME ARAIVRQAMA ILTPAVPARM EDG HQMLTH WTRKIIVEEG HTVPQLVHIL HLIVQHFKVY YPVRHHLVQH MVSAMQRLGF TPSVTIEQRR LAVDLSEVVI KWEL QRIKD QQPDSDMDPN SSGEGVNSVS SSIKRGLSVD SAQEVKRFRT ATGAISAVFG RSQSLPGADS LLAKPIDKQH TDTVV NFLI RVACQVNDNT NTAGSPGEVL SRRCVNLLKT ALRPDMWPKS ELKLQWFDKL LMTVEQPNQV NYGNICTGLE VLSFLL TVL QSPAILSSFK PLQRGIAACM TCGNTKVLRA VHSLLSRLMS IFPTEPSTSS VASKYEELEC LYAAVGKVIY EGLTNYE KA TNANPSQLFG TLMILKSACS NNPSYIDRLI SVFMRSLQKM VREHLNPQAA SGSTEATSGT SELVMLSLEL VKTRLAVM S MEMRKNFIQA ILTSLIEKSP DAKILRAVVK IVEEWVKNNS PMAANQTPTL REKSILLVKM MTYIEKRFPE DLELNAQFL DLVNYVYRDE TLSGSELTAK LEPAFLSGLR CAQPLIRAKF FEVFDNSMKR RVYERLLYVT CSQNWEAMGN HFWIKQCIEL LLAVCEKST PIGTSCQGAM LPSITNVINL ADSHDRAAFA MVTHVKQEPR ERENSESKEE DVEIDIELAP GDQTSTPKTK E LSEKDIGN QLHMLTNRHD KFLDTLREVK TGALLSAFVQ LCHISTTLAE KTWVQLFPRL WKILSDRQQH ALAGEISPFL CS GSHQVQR DCQPSALNCF VEAMSQCVPP IPIRPCVLKY LGKTHNLWFR STLMLEHQAF EKGLSLQIKP KQTTEFYEQE SIT PPQQEI LDSLAELYSL LQEEDMWAGL WQKRCKYSET ATAIAYEQHG FFEQAQESYE KAMDKAKKEH ERSNASPAIF PEYQ LWEDH WIRCSKELNQ WEALTEYGQS KGHINPYLVL ECAWRVSNWT AMKEALVQVE VSCPKEMAWK VNMYRGYLAI CHPEE QQLS FIERLVEMAS SLAIREWRRL PHVVSHVHTP LLQAAQQIIE LQEAAQINAG LQPTNLGRNN SLHDMKTVVK TWRNRL PIV SDDLSHWSSI FMWRQHHYQA IVTAYENSSQ HDPSSNNAML GVHASASAII QYGKIARKQG LVNVALDILS RIHTIPT VP IVDCFQKIRQ QVKCYLQLAG VMGKNECMQG LEVIESTNLK YFTKEMTAEF YALKGMFLAQ INKSEEANKA FSAAVQMH D VLVKAWAMWG DYLENIFVKE RQLHLGVSAI TCYLHACRHQ NESKSRKYLA KVLWLLSFDD DKNTLADAVD KYCIGVPPI QWLAWIPQLL TCLVGSEGKL LLNLISQVGR VYPQAVYFPI RTLYLTLKIE QRERYKSDPG PIRATAPMWR CSRIMHMQRE LHPTLLSSL EGIVDQMVWF RENWHEEVLR QLQQGLAKCY SVAFEKSGAV SDAKITPHTL NFVKKLVSTF GVGLENVSNV S TMFSSAAS ESLARRAQAT AQDPVFQKLK GQFTTDFDFS VPGSMKLHNL ISKLKKWIKI LEAKTKQLPK FFLIEEKCRF LS NFSAQTA EVEIPGEFLM PKPTHYYIKI ARFMPRVEIV QKHNTAARRL YIRGHNGKIY PYLVMNDACL TESRREERVL QLL RLLNPC LEKRKETTKR HLFFTVPRVV AVSPQMRLVE DNPSSLSLVE IYKQRCAKKG IEHDNPISRY YDRLATVQAR GTQA SHQVL RDILKEVQSN MVPRSMLKEW ALHTFPNATD YWTFRKMFTI QLALIGFAEF VLHLNRLNPE MLQIAQDTGK LNVAY FRFD INDATGDLDA NRPVPFRLTP NISEFLTTIG VSGPLTASMI AVARCFAQPN FKVDGILKTV LRDEIIAWHK KTQEDT SSP LSAAGQPENM DSQQLVSLVQ KAVTAIMTRL HNLAQFEGGE SKVNTLVAAA NSLDNLCRMD PAWHPWL

UniProtKB: Transformation/transcription domain-associated protein

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Macromolecule #2: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.296914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 #3: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.222465 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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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Macromolecule #4: DNA methyltransferase 1-associated protein 1

MacromoleculeName: DNA methyltransferase 1-associated protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.090699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 #5: Isoform 2 of E1A-binding protein p400

MacromoleculeName: Isoform 2 of E1A-binding protein p400 / type: protein_or_peptide / ID: 5 / 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: 340.198062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 QQALAGSLVA GAGSTVETDL FKRQQAMPST GMAEQ SKRP RLEVGHQGVV FQHPGADAGV PLQQLMPTAQ GGMPPTPQAA QLAGQRQSQQ QYDPSTGPPV QNAASLHTPL PQLPGR LPP AGVPTAALSS ALQFAQQPQV VEAQTQLQIP VKTQQPNVPI PAPPSSQLPI PPSQPAQLAL HVPTPGKVQV QASQLSS LP QMVASTRLPV DPAPPCPRPL PTSSTSSLAP VSGSGPGPSP ARSSPVNRPS SATNKALSPV TSRTPGVVAS APTKPQSP A QNATSSQDSS QDTLTEQITL ENQVHQRIAE LRKAGLWSQR RLPKLQEAPR PKSHWDYLLE EMQWMATDFA QERRWKVAA AKKLVRTVVR HHEEKQLREE RGKKEEQSRL RRIAASTARE IECFWSNIEQ VVEIKLRVEL EEKRKKALNL QKVSRRGKEL RPKGFDALQ ESSLDSGMSG RKRKASISLT DDEVDDEEET IEEEEANEGV VDHQTELSNL AKEAELPLLD LMKLYEGAFL P SSQWPRPK PDGEDTSGEE DADDCPGDRE SRKDLVLIDS LFIMDQFKAA ERMNIGKPNA KDIADVTAVA EAILPKGSAR VT TSVKFNA PSLLYGALRD YQKIGLDWLA KLYRKNLNGI LADEAGLGKT VQIIAFFAHL ACNEGNWGPH LVVVRSCNIL KWE LELKRW CPGLKILSYI GSHRELKAKR QEWAEPNSFH VCITSYTQFF RGLTAFTRVR WKCLVIDEMQ RVKGMTERHW EAVF TLQSQ QRLLLIDSPL HNTFLELWTM VHFLVPGISR PYLSSPLRAP SEESQDYYHK VVIRLHRVTQ PFILRRTKRD VEKQL TKKY EHVLKCRLSN RQKALYEDVI LQPGTQEALK SGHFVNVLSI LVRLQRICNH PGLVEPRHPG SSYVAGPLEY PSASLI LKA LERDFWKEAD LSMFDLIGLE NKITRHEAEL LSKKKIPRKL MEEISTSAAP AARPAAAKLK ASRLFQPVQY GQKPEGR TV AFPSTHPPRT AAPTTASAAP QGPLRGRPPI ATFSANPEAK AAAAPFQTSQ ASASAPRHQP ASASSTAASP AHPAKLRA Q TTAQASTPGQ PPPQPQAPSH AAGQSALPQR LVLPSQAQAR LPSGEVVKIA QLASITGPQS RVAQPETPVT LQFQGSKFT LSHSQLRQLT AGQPLQLQGS VLQIVSAPGQ PYLRAPGPVV MQTVSQAGAV HGALGSKPPA GGPSPAPLTP QVGVPGRVAV NALAVGEPG TASKPASPIG GPTQEEKTRL LKERLDQIYL VNERRCSQAP VYGRDLLRIC ALPSHGRVQW RGSLDGRRGK E AGPAHSYT SSSESPSELM LTLCRCGESL QDVIDRVAFV IPPVVAAPPS LRVPRPPPLY SHRMRILRQG LREHAAPYFQ QL RQTTAPR LLQFPELRLV QFDSGKLEAL AILLQKLKSE GRRVLILSQM ILMLDILEMF LNFHYLTYVR IDENASSEQR QEL MRSFNR DRRIFCAILS THSRTTGINL VEADTVVFYD NDLNPVMDAK AQEWCDRIGR CKDIHIYRLV SGNSIEEKLL KNGT KDLIR EVAAQGNDYS MAFLTQRTIQ ELFEVYSPMD DAGFPVKAEE FVVLSQEPSV TETIAPKIAR PFIEALKSIE YLEED AQKS AQEGVLGPHT DALSSDSENM PCDEEPSQLE ELADFMEQLT PIEKYALNYL ELFHTSIEQE KERNSEDAVM TAVRAW EFW NLKTLQEREA RLRLEQEEAE LLTYTREDAY SMEYVYEDVD GQTEVMPLWT PPTPPQDDSD IYLDSVMCLM YEATPIP EA KLPPVYVRKE RKRHKTDPSA AGRKKKQRHG EAVVPPRSLF DRATPGLLKI RREGKEQKKN ILLKQQVPFA KPLPTFAK P TAEPGQDNPE WLISEDWALL QAVKQLLELP LNLTIVSPAH TPNWDLVSDV VNSCSRIYRS SKQCRNRYEN VIIPREEGK SKNNRPLRTS QIYAQDENAT HTQLYTSHFD LMKMTAGKRS PPIKPLLGMN PFQKNPKHAS VLAESGINYD KPLPPIQVAS LRAERIAKE KKALADQQKA QQPAVAQPPP PQPQPPPPPQ QPPPPLPQPQ AAGSQPPAGP PAVQPQPQPQ PQTQPQPVQA P AKAQPAIT TGGSAAVLAG TIKTSVTGTS MPTGAVSGNV IVNTIAGVPA ATFQSINKRL ASPVAPGALT TPGGSAPAQV VH TQPPPRA VGSPATATPD LVSMATTQGV RAVTSVTASA VVTTNLTPVQ TPARSLVPQV SQATGVQLPG KTITPAHFQL LRQ QQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQTTTTSQVQ VPQIQGQAQS PAQIKAVGKL TPEHLIKMQK QKLQMPPQPP PPQA QSAPP QPTAQVQVQT SQPPQQQSPQ LTTVTAPRPG ALLTGTTVAN LQVARLTRVP TSQLQAQGQM QTQAPQPAQV ALAKP PVVS VPAAVVSSPG VTTLPMNVAG ISVAIGQPQK AAGQTVVAQP VHMQQLLKLK QQAVQQQKAI QPQAAQGPAA VQQKIT AQQ ITTPGAQQKV AYAAQPALKT QFLTTPISQA QKLAGAQQVQ TQIQVAKLPQ VVQQQTPVAS IQQVASASQQ ASPQTVA LT QATAAGQQVQ MIPAVTATAQ VVQQKLIQQQ VVTTASAPLQ TPGAPNPAQV PASSDSPSQQ PKLQMRVPAV RLKTPTKP P CQ

UniProtKB: E1A-binding protein p400

+
Macromolecule #6: Actin-like protein 6A

MacromoleculeName: Actin-like protein 6A / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.509812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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: ACTB protein (Fragment)

MacromoleculeName: ACTB protein (Fragment) / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.78266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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: ACTB protein

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Macromolecule #8: Isoform 2 of Enhancer of polycomb homolog 1

MacromoleculeName: Isoform 2 of Enhancer of polycomb homolog 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.988273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 NSSTNTSQGF VSKTLDSASA QFAASAL VT SEQLMGFKMK DDVVLGIGVN GVLPASGVYK GLHLSSTTPT ALVHTSPSTA GSALLQPSNI TQTSSSHSAL SHQVTAAN S ATTQVLIGNN IRLTVPSSVA TVNSIAPINA RHIPRTLSAV PSSALKLAAA ANCQVSKVPS SSSVDSVPRE NHESEKPAL NNIADNTVAM EVT

UniProtKB: Enhancer of polycomb homolog 1

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Macromolecule #9: Vacuolar protein sorting-associated protein 72 homolog

MacromoleculeName: Vacuolar protein sorting-associated protein 72 homolog
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.658363 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

+
Macromolecule #10: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 9 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6igm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20275
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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