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- EMDB-14980: NuA4 Histone Acetyltransferase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14980
TitleNuA4 Histone Acetyltransferase complex
Map data
Sample
  • Complex: NuA4 histone acetyltransferase complex
    • Protein or peptide: Tra1
    • Protein or peptide: Epl1
    • Protein or peptide: Swc4
    • Protein or peptide: Arp4
    • Protein or peptide: Eaf1
    • Protein or peptide: Act1
KeywordsNuA4 / histone acetyltransferase complex / Epigenetics / DNA repair / TRANSCRIPTION
Biological speciesKomagataella phaffii GS115 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsFrechard A / Hexnerova R / Crucifix C / Papai G / Smirnova E / Faux C / Lo Ying Ping F / Helmlinger D / Schultz P / Ben-shem A
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE12-0022 France
Citation
Journal: Nat Struct Mol Biol / Year: 2023
Title: The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification.
Authors: Alexander Fréchard / Céline Faux / Rozalie Hexnerova / Corinne Crucifix / Gabor Papai / Ekaterina Smirnova / Conor McKeon / Florie Lo Ying Ping / Dominique Helmlinger / Patrick Schultz / Adam Ben-Shem /
Abstract: Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa ...Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles in both transcription and DNA-damage repair. NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither the molecular mechanism of this activity nor its physiological importance are known. Here we report the structure of the Pichia pastoris NuA4 complex, with its core resolved at 3.4-Å resolution. Three subunits, Epl1, Eaf1 and Swc4, intertwine to form a stable platform that coordinates all other modules. The HAT module is firmly anchored into the core while retaining the ability to stretch out over a long distance. We provide structural, biochemical and genetic evidence that an unfolded linker region of the Epl1 subunit is critical for this long-range activity. Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. Our work lays the foundations for a mechanistic understanding of NuA4's regulatory role and elucidates how its essential long-range activity is attained.
#1: Journal: Res Sq / Year: 2022
Title: The structure of the NuA4/Tip60 complex reveals the mechanism and importance of long-range chromatin modification
Authors: Schultz P / Frechard A / Hexnerova R / Crucifix C / Papai G / Smirnova E / Faux C / Ping F / Helmlinger D / Ben-Shem A
History
DepositionMay 16, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14980.png

Downloads & links

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Map

FileDownload / File: emd_14980.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 448 pix.
= 386.176 Å		0.86 Å/pix.
x 448 pix.
= 386.176 Å		0.86 Å/pix.
x 448 pix.
= 386.176 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-3.799474 - 6.066793
Average (Standard dev.)0.010172429 (±0.100155026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 386.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14980_msk_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14980_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_14980_half_map_2.map
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Sample components

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Entire : NuA4 histone acetyltransferase complex

EntireName: NuA4 histone acetyltransferase complex
Components
  • Complex: NuA4 histone acetyltransferase complex
    • Protein or peptide: Tra1
    • Protein or peptide: Epl1
    • Protein or peptide: Swc4
    • Protein or peptide: Arp4
    • Protein or peptide: Eaf1
    • Protein or peptide: Act1

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Supramolecule #1: NuA4 histone acetyltransferase complex

SupramoleculeName: NuA4 histone acetyltransferase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Komagataella phaffii GS115 (fungus)

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Macromolecule #1: Tra1

MacromoleculeName: Tra1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
SequenceString: MLHVVQLDDF ATRLKAAEDY QSKHSVLSEI CDSLETFNAA QDYEYFLKSL IPLFIDVLKE VPVSFVANS PENKLRNITL EILHRIPAND ALQAYSNEIV DTLMDLLKVE NELNGILCMK A ITTLHKTF KASLQEKVHP FIDIVIEIYS NIPQVVEEQF NGNQIDSKEN ...String:
MLHVVQLDDF ATRLKAAEDY QSKHSVLSEI CDSLETFNAA QDYEYFLKSL IPLFIDVLKE VPVSFVANS PENKLRNITL EILHRIPAND ALQAYSNEIV DTLMDLLKVE NELNGILCMK A ITTLHKTF KASLQEKVHP FIDIVIEIYS NIPQVVEEQF NGNQIDSKEN VDSTSRPNSP SF SSQSDDS KQLAQAMFSF KTLAESPITM VSLYSSYKEL AASSLGNFIP HVMKVLSLEV AKQ AEARKA AEEKGIILVN VCKEITNRAN YGEFIIGQVK AASFLAYLFI RRQAQTFLEP YQQA IPDII IRLLQDCPSE LSAARKELLH ATRHILSTDF RKMFIPKIDL LFDLRVLIGE GFTAY ETLR PLAYSTVADF IHNVRDHLTP AQLWKSVSIY CKNLQDDSLA LTVQIMSAKL LLNLIE KIM RSESKTESRQ LLMVIIDAYT KRFKMLNSRY NGIMKQHATY EKEKQEKQNQ ERLLTNK LD GTTPSPSDDK KVELIDEDQD VKMEDPTPEI SDQETIKGDN DASTEPQDSE QQLADFMS L QEYLPIQVSV PPEIDLLKDS RYLFKTLMTF LKTIMIGLKN SNPPSSQNHF NAQNWNETA RGFSNEDINI LKSLFRECIL ALRFFSTSKT SLPASSMKQS FDITGPNLPI TSTKEEKDLM EIFATMFIH IDPASFNEIV REELPFMYKQ MLDFASLLHI PQFFLASVIT SSSFSGILIT F LKSKLVDL GEVNIIKSNI LIRLFKLCFM SVSLFPAANE SVILPHLNEL ILKSLKLSTT AK EPLVYFY LIRTLFRSIG GGRFENLYKE IMPLLQVLLE SLSKLIHEAR RPQERDIYVE LCL TVPVRL SVLVPHLSYL MKPLVYALNG SQESVSQGLR TLELCVDNLT AEYFDPIIEP VIDD VMEAL SKHLKPLPYY HQHSHTTLRI LGKLGGRNRT FIKPVDNLKT DSELFQNVEA MFKIH GLPN EVPLSITPGL SAAFSLLTDP RPRIHYRINS FKYISGIFQL FLGATQLPDD YANRLK ESM DIILEDTIAP DEPLNKLHHF PVKDIAKYDS QMELLVKLLE SIFYAVSLQE VREESKA LI RGTCNHFILL YFNKMVIDKR KFVRKFSVDN HEGNLFLNEN CIFDAIIYAL SSDNSAVR S MGLESVQLIY DSCVELFGNI DCALKFAPLN VMCSKFIHCC FEEPYHKKLA GCIGLEMML NSLDIPMKYF NARQLEIIRA LFYVLRDTAP ELPCEVTNTA KRLILNSLKE WNKELTRNDV FSSVFQNLV SSLIVDLPNA NEIVRATAQE ALRTLSETTQ VPIATMISPC KHILLAPIFG K PLRALPFQ MQIGNIDAIT FCMGLENSFL EYNEELNRLV QEALALVDAE DESLVSAHRI SE HKTSEQL VRLRVVCIQL LSLAITKPEF AAAQQRSNIR VKILVVFFKS LCGRSIEIIR AAH GGLKAV IDLKMKLPKE LLQNGLRPML MNLSDHKKLT VASLEALSGL LKLFISYFKV GIGS KLLDH LLAWAQPRTL QQLGSQDLEN NSTVQIIVAI LDVFHLLPPT AHKFMNDLMN ALLYL ENNL HRCQYSPFRE PLAKFLDRFP DESFEYFFNE FSKREITTRF VYFVGLDSCS SLRAKV LES LPRVRGLLHQ EGSAEEKCVR FSNLVDLCES LAASDKEWIK DKEELLGELL DAGSVCL TL KRSSNVVSPL YFQVDQGFET LQLLYIEYFK SQPLGHEKVF NFIDKISKEG LPFVLEFD D FIFNEVVKCQ DIPTVQQTLD TIIRMTPQVS SLDARVYLYK RIFLPICIYE SEMHGDLSR LSQTENNELP AWLKSFDSDV WKATGPLVDD YTSTLEDRYR LELMQLTALL IKGAPTALTD MRKDIIKFS WNYIKLDDNT SKQAAYVVTA YFISRFDTPS ELTTRIFVAL LRCHQIDTRY L VKQALELL APVLSERTNS ELDWLKWPRR VLSEDGFNIT QVANIYQLIV KFPDLFYPAR DH FIPNIIT AMGKLTVMSN TSLENQQLAI DLAELILKWE TKLPKSEKLG SAEETEKEKS VSE DKMDID VKEETKEDIA ERPKAEDQIG GDDSDSSNIL TSEDYEVSFA QREACVTFLI RYIC ISTQR PSENELGKRA LNILYELLGP KYWSEVTVKL QFFERFLMSS DLNQPSLLGY CLNAL EVLA VALKWKPTTW IIENVSYLQK LLEKCLRSDN QDIQEILQKV LGIILEAINK ETQGSE EDE PEEVTNFISL IVNIIGEDLS NMTSVAAGVS LCWTLSLYRP NALDSLLPSI MRTFNKL CR DHIAISLQGN QPQSGDFANI EFEAKVTTNL LEKILNLCAA RISSLDDQRR VFLSLLAQ L IDRSVDKDML LKVINIVTEW IFKTDFYPTT KEKAGILGKM MIFDLRGEPE LSKKFNQVI VDIFESKELA HTELTARMET AFLFGTRLSD VSIRKKLMSI LSDSLELDID KRLFYIIKDQ NWEYLSDYP WLNQALQLLY GSFHLDSPIR LSPEENTLSP LQSITEGLAR EKSPVEKAPQ N IIDFVAKH NEFLDSVRSL TAGDILNPLI DISYQSAETI HNAWVVVFPV AYSAIESRYE LE FTRALVK LLFKDYHIRQ QDARPNVIKS LLDGVGKCPG LHLPPHLVKY LGSNYNAWYG AIK LLEELS EGQGIDNQKI SDANQDALLE VYMSLQEDDM FYGTWRRRAK YFETNAALSY EQIG IWDKA LQLYEAAQIK ARSGVFPFGE SEYSLWEDHW IYCAEKLQHW EILTELAKHE GFTDL LLEC GWRGADWIAD REPLEQSVKT VMDIPTPRRQ IFQTFLALQG FSQQKDTLQD VSRLCD EGI QLTLRKWNAL PQRVTRAHIG LLHTFQQYVE LMEASQVYSS LVTTNAQNLD VKSQELK RV LQAWRERLPN VWDDINIWND LVTWRQHVFG VINRVYMPFV PVLQQSNGTN NGNSYAYR G YHEMAWVINR FAHVARKHEM PEVCINQLTK IYTLPNIEIQ EAFLKLREQA KCHYQNSSE LNTGLDVISN TNLVYFATQQ KAEFFTLKGM FLAKLNAKDE ANQAFATAVQ IDLNLPKAWA EWGFFNDRR FKENPEEIFH AKNAISCYLQ AAGLYKDGKT RKLLCRILWL ISLDDAAGSL A KTFEDHHG ESPVWYWITF VPQLLTSLSH KEAKIVRHIL IQIAKSYPQS LHFQLRTTKE DY QAIQRQA MAVNRAEEQS SNKQDTADSV LKNTNTPQPQ TRTETSGTTA ESDKKPSIPP KEE QGSPQP SRPATTQASP QAQSQENGES SQKHPPEIPT TDSRQPWQDV EEIMGILKTA YPLL ALSLE SLVDQLNQRF KCNADEDAYR LVIVLYNDGV QQMNRVANPR EEVKLPAATE ASISR FADS VLPKNIREVF EQDIIACNPN LETYISKLRK WRDCLEEKLD RSYGKADLER VSLHLS LFH HQKFEDIEIP GQYLLHKDNN NHFIKIERFL PTLDLVRGSN GCYKRMTIRG NDGSLHP FA VQFPAARHCR REERIFQLFR IFDDALSRKV QSRRRNISLT LPIAVPLSPH IRILNDDK R YTTLMGIYEE FCRRKGQSRD EPFAYTIQKL RAAFDPRLPK PDIVSVRAEV LASIQSTLV PSTLLKDYYT EKFSNYENYW LFRKQFTAQY ASFIFMTYIM CINSRQPQKI HINEGSGNIW TSEMLPTKV ATGKTHSTAY NNSTLDPAVK AGAPIFYNTE SVPFRLTPNI QKFIGEAGLE G ILSVYILV IANSLSDSEF DMEQYLSLFV RDEVISWFAQ QHRASAQTNQ LREIVRVNVE LL TKRVLQL NHIPNSQNVA TQFVLNLISQ AVNPRNLAYT DSAWMAYL

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Macromolecule #2: Epl1

MacromoleculeName: Epl1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
SequenceString: MVLPSAAGAR FRQRKISVKQ TLQVFKQSDI ADLETEDQQR ELQKIETGVE KGEEEEEHLQ RVINAAQAA VISGGKVEKA YIPTPDASQV WKDYDKYYRD KFQPPGTYIR FSATVEETTG C IYNLDEED ESFLKEVLNK NLANGIKPCT ETELEIVLQR FEVVIDKKQP ...String:
MVLPSAAGAR FRQRKISVKQ TLQVFKQSDI ADLETEDQQR ELQKIETGVE KGEEEEEHLQ RVINAAQAA VISGGKVEKA YIPTPDASQV WKDYDKYYRD KFQPPGTYIR FSATVEETTG C IYNLDEED ESFLKEVLNK NLANGIKPCT ETELEIVLQR FEVVIDKKQP FLAMDPSQIL TF EELHSAA LVVDPNSIEE IELSLEKQLG LHPFRTLLDG QRSQLSHRKL AELLRIFGQK IYD HWKQRR IARHGRPITA QLRFEDSSEK DDSDPYVCFR RREFRQARKT RRTDTQGSER LRKL HRELK QTRDLLLAVA QREVKRKEAI EVGHEVFQLR CSVKTLKRDL GVKGEEEDLV AHKRK KVVP TTDEDRKYRK GYNSGNYPNR NQAQAQQQQQ QLQQQQISKS GLNPVSIQPY VKLPMS RIP DMDLITVSTV LNEKDEAINR AVAEKLRQRK ESDRGWVNLT DDPFNPFLQF TNPDSIL EK GHFPYSSIAA ALFEVDQSNY FDPEITQLIK DKKPLPRTLC FKDNALTTPL PPSIYEVA S NNKLDVTAPI CKVRKRMGRR GLWIDRKMTV DEPLDEFLDF STFEKSLDAD ITDRNSAKS QQGMNVYDSV DDANSRLRSR FSFDRDVPLF NPVDPSELNQ ISSQTQSIRF GCMLLTKAYE QVHQAKQKL FLEQQQHQQK QQQKLLQQRQ KVQQKLQQQQ QQQQQAQQQN PKSNTNKVVN Q INNTKSPV KQSKIPSKVS KNISGVTTSA GKGA

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Macromolecule #3: Swc4

MacromoleculeName: Swc4 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
SequenceString: MSSDILDVLS ISGRSNLSNQ KKKITKDGPT KKKKQTAMSR ELFNLIGQNT PPLAVEKTVK FKEKLNVNN KPTPWSYVEF SNDARESKDG LKLHHWIKGS SELAKNSPYL FEKYNQKIQI P SFTKEEYD EFLKDLDLEC REREKRDKAL KEQEAKEAEK LEKEKENDKE ...String:
MSSDILDVLS ISGRSNLSNQ KKKITKDGPT KKKKQTAMSR ELFNLIGQNT PPLAVEKTVK FKEKLNVNN KPTPWSYVEF SNDARESKDG LKLHHWIKGS SELAKNSPYL FEKYNQKIQI P SFTKEEYD EFLKDLDLEC REREKRDKAL KEQEAKEAEK LEKEKENDKE RVNGDELGKE ED NASDFVP KKENVNDQIL PKIDEPQTNK KDDMESTEDV SKSDSQEVSK DVNPSEEVEA SWD YDETVH LFQLCEKWDL RWPIIVDRYE YDERSMEELK ERFYKVSERI LRHKYRNVTM DDKT SLLVQ TLSSFDKRRE TERKQYLRRL LSRSPTEIAE EESLVIEARK FELAAKKMLT ERASL LRLL DSPQSTGSIS QYLTSQGLTQ LYNTLMSADR SKRRKVETPT PPQIPPGASS SLHRTS MDL KRKAAKKIGP NALLENIKAT GNSVPPSGNA PQSAAIELIN TKMTPEEKEA YGIKIHQ EK LQPGVSLRSA RLPTFKPATQ AKIVVVLNEL EVSPKPTIPT AKVVAQYDNL LQTINVLL E TKKQVNKLEV ELNLLEGKEE DKES

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Macromolecule #4: Arp4

MacromoleculeName: Arp4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
SequenceString: MATAPQVYGA DEINAVVLDA SSYRTKIGYG SLDCPILNLP SYYGHQTKDG SEKFIFEENS MLIPRPDYE IKKIMKDGII DDFEGAVKQY NYMFDVLKLK PSEQPILVIE STQNEYEKKT A LLKQLLKE NKFVATFLIK NPTCVSFAHG RPNCLVVDLG HDLVTITPIL ...String:
MATAPQVYGA DEINAVVLDA SSYRTKIGYG SLDCPILNLP SYYGHQTKDG SEKFIFEENS MLIPRPDYE IKKIMKDGII DDFEGAVKQY NYMFDVLKLK PSEQPILVIE STQNEYEKKT A LLKQLLKE NKFVATFLIK NPTCVSFAHG RPNCLVVDLG HDLVTITPIL DGISLRKQVL GT HYAGAFL SQQLRQLLNH KGVEVVPVYK VKSKVPTYFP DEAKFEERKY DFDISESFEN FHK LRILRE MKETLLQALP DSETEKLKEQ ETEEDTRYFE FPNGLNVPFT KYERVRLANS LFNP SEPYT GESGPNIVVE GFSVETGKII NEDTITSREY VPLRRSKKTD SSSGRRSKDE PTDDK PRGL TSLVNQALNH LDVDLKPQLA NNIILTGATS LIPGVAERLN QELTAMNPGL KVRIHS SAN VIERTCSAWI GGSILSSLGT FHQLWVSENE YDEVGAKKLI MDRFR

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Macromolecule #5: Eaf1

MacromoleculeName: Eaf1 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
SequenceString: MSSLDSNVTA SSKHDSPKRQ PEDGSGTNDD PLQRILNERK RKLAELYCVS RLPLLPISPS QVSQIGENL MRFLERNDLE QGRQFNITTL TGDKSQKQPP VSKEVSTADQ LESPHWPVKE D EETTKDEP PRKKQKTAST SAEPQKATHK ESKMTMMHQE VTESEAPTLS ...String:
MSSLDSNVTA SSKHDSPKRQ PEDGSGTNDD PLQRILNERK RKLAELYCVS RLPLLPISPS QVSQIGENL MRFLERNDLE QGRQFNITTL TGDKSQKQPP VSKEVSTADQ LESPHWPVKE D EETTKDEP PRKKQKTAST SAEPQKATHK ESKMTMMHQE VTESEAPTLS SLIRKYAQDE VP IRPDDPT DRDLNFELLD RNKTIIQALP EIYPHKIADS ASLTELYYLT QTFPLAKLLP RSH KSLTTD AYESALLEGK IAVLYSRIEE LKRQRKWSLR QPKRFIDPFT RESPTHWDHL LAEM KWLSV DIMEERKFKA ASCVQLAQAV SDYWTYGKIV CIQRKPLIFL TDEEIKERTV TKVMK TEVD NENEHDHDDN DIFKDAQEEP RAMDQEQNQP FEENATIDVA KLLERPNPKD EIIPPA LPT YSMGDYKRLN QNAEPFKLHI GLDDFKKEDL VLVEKLPLSF IFDDNLSDSK KKLSEYE KA PIAAISTLLA PPEDDEWYKI VIRRDPASEL SASLDYQKGL FGASSQRRYN VLKPPKPP P IKNLELRTPT IWLPQDDKLL IRYVAEYAFN WDIISAHLSA RPARAYVANI ERRTPWQCF ERYIQLNDKF QFTDMRGQYA QSAQAWLEAA HKTQSTTKRR ISPLGVGIES IQRGHRRLRW GSMLDAMRK CMRRRENINR SSQVERKHTS DDKRTNVPTP EELSRLKYDR DKAIQEAYMH Q NSGTFSSA RPHTQSSALS PSKGKNAPLP TSAQQTGTHP YTNGIPPKGT LPKTTTPAPG VP STQPGTP NTRQPQVSSR VATSQNTTPV TNRTGTPNGN RPGPNNSFTQ EQLQHFLQAQ RHR QMMQTS AGTPVNKSNV PNRPAGITNT NVTTPANAVS SSTTPSKSAA TASQQQPSPS RGIN LTPAQ VNALINQIQA QNPNMSKDQV TKFAVAYIQN LQNQRERSSN GHSTPQVRTV PTPTR ATAG PPVSASPVTS NASPTTPASL TKEKLDALEN SPNLTPQQRQ QITLFKAMQA RNKMNQ VAN RGQESASASS NLSASPNTDT KQTTDTNK

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Macromolecule #6: Act1

MacromoleculeName: Act1 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
SequenceString: MDGEDVAALV IDNGSGMCKA GYAGDDAPHT VFPSVVGRPR HQGVMVGMGQ KDSFVGDEAQ SKRGILTLR YPIEHGIVTN WDDMEKIWHH TFYNELRLAP EEHPVLLTEA PMNPKSNREK M TQIMFETF NVPAFYVSIQ AVLSLYASGR TTGIVLDSGD GVTHVVPIYA ...String:
MDGEDVAALV IDNGSGMCKA GYAGDDAPHT VFPSVVGRPR HQGVMVGMGQ KDSFVGDEAQ SKRGILTLR YPIEHGIVTN WDDMEKIWHH TFYNELRLAP EEHPVLLTEA PMNPKSNREK M TQIMFETF NVPAFYVSIQ AVLSLYASGR TTGIVLDSGD GVTHVVPIYA GFSLPHAILR ID LAGRDLT DYLMKILSER GYTFSTSAER EIVRDIKEKL CYVALDFDQE LQTSSQSSSI EKS YELPDG QVITIGNERF RAPEALFHPS VLGLEASGID QTTYNSIMKC DVDVRKELYS NIVM SGGTT MFPGIAERMQ KELTALAPSS MKVKISAPPE RKYSVWIGGS ILASLGTFQQ MWISK QEYD ESGPSIVHLK CF

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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

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMKOAcPotassium acetate
5.0 mMMgOAcMagnesium acetate
2.0 mMTCEPtris(2-carboxyethyl)phosphine
5.0 mMNH4OAcAmmonium acetate
0.0025 %DDMDodecyl-maltoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1265830
Startup modelType of model: OTHER / Details: cryoSPARC ab-initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 518386
FSC plot (resolution estimation)

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  • 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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