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- EMDB-38720: The TRRAP module of human NuA4/TIP60 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38720
TitleThe TRRAP module of human NuA4/TIP60 complex
Map dataThe TRRAP module of human TIP60 complex
Sample
  • Complex: The TRRAP module of human NuA4/TIP60 complex
    • Protein or peptide: Isoform 2 of E1A-binding protein p400
    • Protein or peptide: Isoform 2 of Transformation/transcription domain-associated protein
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsRemodeler / Histone Acetyltransferase Complex / NuA4 / TIP60 / TRANSCRIPTION
Function / homology
Function and homology information


transcription factor TFTC complex / Swr1 complex / protein antigen binding / regulation of double-strand break repair / SAGA complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / regulation of RNA splicing / positive regulation of double-strand break repair via homologous recombination ...transcription factor TFTC complex / Swr1 complex / protein antigen binding / regulation of double-strand break repair / SAGA complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / regulation of RNA splicing / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / helicase activity / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / DNA Damage/Telomere Stress Induced Senescence / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosome / chromatin organization / HATs acetylate histones / regulation of apoptotic process / hydrolase activity / regulation of cell cycle / Ub-specific processing proteases / nuclear speck / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain ...E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / 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 / 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 / Helicase conserved C-terminal 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 / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E1A-binding protein p400 / Transformation/transcription domain-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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: Nat Commun / Year: 2024
Title: Structure of the human TIP60 complex.
Authors: Ke Chen / Li Wang / Zishuo Yu / Jiali Yu / Yulei Ren / Qianmin Wang / Yanhui Xu /
Abstract: Mammalian TIP60 is a multi-functional enzyme with histone acetylation and histone dimer exchange activities. It plays roles in diverse cellular processes including transcription, DNA repair, cell ...Mammalian TIP60 is a multi-functional enzyme with histone acetylation and histone dimer exchange activities. It plays roles in diverse cellular processes including transcription, DNA repair, cell cycle control, and embryonic development. Here we report the cryo-electron microscopy structures of the human TIP60 complex with the core subcomplex and TRRAP module refined to 3.2-Å resolution. The structures show that EP400 acts as a backbone integrating the motor module, the ARP module, and the TRRAP module. The RUVBL1-RUVBL2 hexamer serves as a rigid core for the assembly of EP400 ATPase and YL1 in the motor module. In the ARP module, an ACTL6A-ACTB heterodimer and an extra ACTL6A make hydrophobic contacts with EP400 HSA helix, buttressed by network interactions among DMAP1, EPC1, and EP400. The ARP module stably associates with the motor module but is flexibly tethered to the TRRAP module, exhibiting a unique feature of human TIP60. The architecture of the nucleosome-bound human TIP60 reveals an unengaged nucleosome that is located between the core subcomplex and the TRRAP module. Our work illustrates the molecular architecture of human TIP60 and provides architectural insights into how this complex is bound by the nucleosome.
History
DepositionJan 15, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38720.png

Downloads & links

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Map

FileDownload / File: emd_38720.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe TRRAP module of human TIP60 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 256 pix.
= 341.504 Å		1.33 Å/pix.
x 256 pix.
= 341.504 Å		1.33 Å/pix.
x 256 pix.
= 341.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.334 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028
Minimum - Maximum-0.1216683 - 0.2569335
Average (Standard dev.)0.0005591216 (±0.007871899)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 341.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map2 of the TRRAP module of human TIP60 complex

Fileemd_38720_half_map_1.map
Annotationhalf map2 of the TRRAP module of human TIP60 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1 of the TRRAP module of human TIP60 complex

Fileemd_38720_half_map_2.map
Annotationhalf map1 of the TRRAP module of human TIP60 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The TRRAP module of human NuA4/TIP60 complex

EntireName: The TRRAP module of human NuA4/TIP60 complex
Components
  • Complex: The TRRAP module of human NuA4/TIP60 complex
    • Protein or peptide: Isoform 2 of E1A-binding protein p400
    • Protein or peptide: Isoform 2 of Transformation/transcription domain-associated protein
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: The TRRAP module of human NuA4/TIP60 complex

SupramoleculeName: The TRRAP module of human NuA4/TIP60 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of E1A-binding protein p400

MacromoleculeName: Isoform 2 of 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: 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

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

MacromoleculeName: Isoform 2 of Transformation/transcription domain-associated protein
type: protein_or_peptide / ID: 2 / 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 #3: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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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:

7ktr

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 190003
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ktr


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8xvv:
The TRRAP module of human NuA4/TIP60 complex

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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