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Yorodumi- EMDB-17925: Cryo-EM structure of human Elp123 in complex with 5'-deoxyadenosi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17925 | |||||||||
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Title | Cryo-EM structure of human Elp123 in complex with 5'-deoxyadenosine and methionine | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Elongator / tRNA modification / acetyl-CoA hydrolysis / TRANSLATION | |||||||||
Function / homology | Function and homology information phosphorylase kinase regulator activity / tRNA uridine(34) acetyltransferase activity / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of receptor signaling pathway via JAK-STAT / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription elongation factor complex / central nervous system development ...phosphorylase kinase regulator activity / tRNA uridine(34) acetyltransferase activity / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of receptor signaling pathway via JAK-STAT / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription elongation factor complex / central nervous system development / transcription elongation by RNA polymerase II / neuron migration / : / regulation of translation / 4 iron, 4 sulfur cluster binding / HATs acetylate histones / tRNA binding / positive regulation of cell migration / nucleolus / regulation of transcription by RNA polymerase II / protein kinase binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.58 Å | |||||||||
Authors | Abbassi N / Jaciuk M / Lin T-Y / Glatt S | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human Elp123 in complex with 5'-deoxyadenosine and methionine Authors: Abbassi N / Jaciuk M / Lin T-Y / Glatt S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17925.map.gz | 15.1 MB | EMDB map data format | |
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Header (meta data) | emd-17925-v30.xml emd-17925.xml | 23.1 KB 23.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17925_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_17925.png | 60.4 KB | ||
Masks | emd_17925_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-17925.cif.gz | 8 KB | ||
Others | emd_17925_half_map_1.map.gz emd_17925_half_map_2.map.gz | 194.3 MB 194 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17925 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17925 | HTTPS FTP |
-Related structure data
Related structure data | 8ptyMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17925.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17925_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17925_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17925_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human Elp123 in complex with 5'-deoxyadenosine and methionine
Entire | Name: Human Elp123 in complex with 5'-deoxyadenosine and methionine |
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Components |
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-Supramolecule #1: Human Elp123 in complex with 5'-deoxyadenosine and methionine
Supramolecule | Name: Human Elp123 in complex with 5'-deoxyadenosine and methionine type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 610 KDa |
-Macromolecule #1: Elongator complex protein 1
Macromolecule | Name: Elongator complex protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 150.427484 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MRNLKLFRTL EFRDIQGPGN PQCFSLRTEQ GTVLIGSEHG LIEVDPVSRE VKNEVSLVAE GFLPEDGSGR IVGVQDLLDQ ESVCVATAS GDVILCSLST QQLECVGSVA SGISVMSWSP DQELVLLATG QQTLIMMTKD FEPILEQQIH QDDFGESKFI T VGWGRKET ...String: MRNLKLFRTL EFRDIQGPGN PQCFSLRTEQ GTVLIGSEHG LIEVDPVSRE VKNEVSLVAE GFLPEDGSGR IVGVQDLLDQ ESVCVATAS GDVILCSLST QQLECVGSVA SGISVMSWSP DQELVLLATG QQTLIMMTKD FEPILEQQIH QDDFGESKFI T VGWGRKET QFHGSEGRQA AFQMQMHESA LPWDDHRPQV TWRGDGQFFA VSVVCPETGA RKVRVWNREF ALQSTSEPVA GL GPALAWK PSGSLIASTQ DKPNQQDIVF FEKNGLLHGH FTLPFLKDEV KVNDLLWNAD SSVLAVWLED LQREESSIPK TCV QLWTVG NYHWYLKQSL SFSTCGKSKI VSLMWDPVTP YRLHVLCQGW HYLAYDWHWT TDRSVGDNSS DLSNVAVIDG NRVL VTVFR QTVVPPPMCT YQLLFPHPVN QVTFLAHPQK SNDLAVLDAS NQISVYKCGD CPSADPTVKL GAVGGSGFKV CLRTP HLEK RYKIQFENNE DQDVNPLKLG LLTWIEEDVF LAVSHSEFSP RSVIHHLTAA SSEMDEEHGQ LNVSSSAAVD GVIISL CCN SKTKSVVLQL ADGQIFKYLW ESPSLAIKPW KNSGGFPVRF PYPCTQTELA MIGEEECVLG LTDRCRFFIN DIEVASN IT SFAVYDEFLL LTTHSHTCQC FCLRDASFKT LQAGLSSNHV SHGEVLRKVE RGSRIVTVVP QDTKLVLQMP RGNLEVVH H RALVLAQIRK WLDKLMFKEA FECMRKLRIN LNLIYDHNPK VFLGNVETFI KQIDSVNHIN LFFTELKEED VTKTMYPAP VTSSVYLSRD PDGNKIDLVC DAMRAVMESI NPHKYCLSIL TSHVKKTTPE LEIVLQKVHE LQGNAPSDPD AVSAEEALKY LLHLVDVNE LYDHSLGTYD FDLVLMVAEK SQKDPKEYLP FLNTLKKMET NYQRFTIDKY LKRYEKAIGH LSKCGPEYFP E CLNLIKDK NLYNEALKLY SPSSQQYQDI SIAYGEHLMQ EHMYEPAGLM FARCGAHEKA LSAFLTCGNW KQALCVAAQL NF TKDQLVG LGRTLAGKLV EQRKHIDAAM VLEECAQDYE EAVLLLLEGA AWEEALRLVY KYNRLDIIET NVKPSILEAQ KNY MAFLDS QTATFSRHKK RLLVVRELKE QAQQAGLDDE VPHGQESDLF SETSSVVSGS EMSGKYSHSN SRISARSSKN RRKA ERKKH SLKEGSPLED LALLEALSEV VQNTENLKDE VYHILKVLFL FEFDEQGREL QKAFEDTLQL MERSLPEIWT LTYQQ NSAT PVLGPNSTAN SIMASYQQQK TSVPVLDAEL FIPPKINRRT QWKLSLLD UniProtKB: Elongator complex protein 1 |
-Macromolecule #2: Elongator complex protein 2
Macromolecule | Name: Elongator complex protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 92.597766 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MVAPVLETSH VFCCPNRVRG VLNWSSGPRG LLAFGTSCSV VLYDPLKRVV VTNLNGHTAR VNCIQWICKQ DGSPSTELVS GGSDNQVIH WEIEDNQLLK AVHLQGHEGP VYAVHAVYQR RTSDPALCTL IVSAAADSAV RLWSKKGPEV MCLQTLNFGN G FALALCLS ...String: MVAPVLETSH VFCCPNRVRG VLNWSSGPRG LLAFGTSCSV VLYDPLKRVV VTNLNGHTAR VNCIQWICKQ DGSPSTELVS GGSDNQVIH WEIEDNQLLK AVHLQGHEGP VYAVHAVYQR RTSDPALCTL IVSAAADSAV RLWSKKGPEV MCLQTLNFGN G FALALCLS FLPNTDVPIL ACGNDDCRIH IFAQQNDQFQ KVLSLCGHED WIRGVEWAAF GRDLFLASCS QDCLIRIWKL YI KSTSLET QDDDNIRLKE NTFTIENESV KIAFAVTLET VLAGHENWVN AVHWQPVFYK DGVLQQPVRL LSASMDKTMI LWA PDEESG VWLEQVRVGE VGGNTLGFYD CQFNEDGSMI IAHAFHGALH LWKQNTVNPR EWTPEIVISG HFDGVQDLVW DPEG EFIIT VGTDQTTRLF APWKRKDQSQ VTWHEIARPQ IHGYDLKCLA MINRFQFVSG ADEKVLRVFS APRNFVENFC AITGQ SLNH VLCNQDSDLP EGATVPALGL SNKAVFQGDI ASQPSDEEEL LTSTGFEYQQ VAFQPSILTE PPTEDHLLQN TLWPEV QKL YGHGYEIFCV TCNSSKTLLA SACKAAKKEH AAIILWNTTS WKQVQNLVFH SLTVTQMAFS PNEKFLLAVS RDRTWSL WK KQDTISPEFE PVFSLFAFTN KITSVHSRII WSCDWSPDSK YFFTGSRDKK VVVWGECDST DDCIEHNIGP CSSVLDVG G AVTAVSVCPV LHPSQRYVVA VGLECGKICL YTWKKTDQVP EINDWTHCVE TSQSQSHTLA IRKLCWKNCS GKTEQKEAE GAEWLHFASC GEDHTVKIHR VNKCAL UniProtKB: Elongator complex protein 2 |
-Macromolecule #3: Elongator complex protein 3
Macromolecule | Name: Elongator complex protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 65.740539 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MRQKRKGDLS PAELMMLTIG DVIKQLIEAH EQGKDIDLNK VKTKTAAKYG LSAQPRLVDI IAAVPPQYRK VLMPKLKAKP IRTASGIAV VAVMCKPHRC PHISFTGNIC VYCPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPFLQTR HRIEQLKQLG H SVDKVEFI ...String: MRQKRKGDLS PAELMMLTIG DVIKQLIEAH EQGKDIDLNK VKTKTAAKYG LSAQPRLVDI IAAVPPQYRK VLMPKLKAKP IRTASGIAV VAVMCKPHRC PHISFTGNIC VYCPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPFLQTR HRIEQLKQLG H SVDKVEFI VMGGTFMALP EEYRDYFIRN LHDALSGHTS NNIYEAVKYS ERSLTKCIGI TIETRPDYCM KRHLSDMLTY GC TRLEIGV QSVYEDVARD TNRGHTVKAV CESFHLAKDS GFKVVAHMMP DLPNVGLERD IEQFTEFFEN PAFRPDGLKL YPT LVIRGT GLYELWKSGR YKSYSPSDLV ELVARILALV PPWTRVYRVQ RDIPMPLVSS GVEHGNLREL ALARMKDLGI QCRD VRTRE VGIQEIHHKV RPYQVELVRR DYVANGGWET FLSYEDPDQD ILIGLLRLRK CSEETFRFEL GGGVSIVREL HVYGS VVPV SSRDPTKFQH QGFGMLLMEE AERIAREEHG SGKIAVISGV GTRNYYRKIG YRLQGPYMVK MLKGLEGSAW SHPQFE KGG GSGGGSGGSA WSHPQFEK UniProtKB: Elongator complex protein 3 |
-Macromolecule #4: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Macromolecule #5: 5'-DEOXYADENOSINE
Macromolecule | Name: 5'-DEOXYADENOSINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: 5AD |
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Molecular weight | Theoretical: 251.242 Da |
Chemical component information | ChemComp-5AD: |
-Macromolecule #6: METHIONINE
Macromolecule | Name: METHIONINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: MET |
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Molecular weight | Theoretical: 149.211 Da |
Chemical component information | ChemComp-MET: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Details: 8 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 15 s wait time, blot force 5, 5 s blot time. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Software | Name: EPU |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 5300 / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: SwissModel / Chain - Initial model type: in silico model / Details: Based on PDB 6QK7 |
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Software | Name: UCSF ChimeraX |
Output model | PDB-8pty: |