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- EMDB-29316: Cryo-EM structure of RNase-untreated RESC-B in trypanosomal RNA e... -

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Basic information

Entry
Database: EMDB / ID: EMD-29316
TitleCryo-EM structure of RNase-untreated RESC-B in trypanosomal RNA editing
Map data
Sample
  • Complex: RESC5-tagged isolate without RNase treatment
    • Protein or peptide: x 9 types
    • RNA: x 2 types
KeywordsHEAT repeat / trypanosoma / RNA editing substrate binding complex / gRNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / RNA modification / mitochondrial mRNA editing complex / ribonucleoprotein granule / mitochondrial RNA processing / RNA metabolic process / kinetoplast / cytoplasmic side of mitochondrial outer membrane ...regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / RNA modification / mitochondrial mRNA editing complex / ribonucleoprotein granule / mitochondrial RNA processing / RNA metabolic process / kinetoplast / cytoplasmic side of mitochondrial outer membrane / cytidine to uridine editing / 2-oxoglutarate-dependent dioxygenase activity / mRNA stabilization / post-transcriptional regulation of gene expression / RNA processing / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Mitochondrial RNA binding complex 1 subunit / Mitochondrial RNA binding protein / RNA-binding protein, putative / Mitochondrial RNA binding complex 1 subunit / Phytanoyl-CoA dioxygenase / Mitochondrial RNA binding complex 1 subunit / Mitochondrial RNA binding complex 1 subunit / Guide RNA binding protein / Mitochondrial RNA binding complex 1 subunit
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLiu S / Wang H / Li X / Zhang F / Lee JKJ / Li Z / Yu C / Zhao X / Hu JJ / Suematsu T ...Liu S / Wang H / Li X / Zhang F / Lee JKJ / Li Z / Yu C / Zhao X / Hu JJ / Suematsu T / Alvarez-Cabrera AL / Liu Q / Zhang L / Huang L / Aphasizheva I / Aphasizhev R / Zhou ZH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI101057 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI152408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
CitationJournal: Science / Year: 2023
Title: Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing.
Authors: Shiheng Liu / Hong Wang / Xiaorun Li / Fan Zhang / Jane K J Lee / Zihang Li / Clinton Yu / Jason J Hu / Xiaojing Zhao / Takuma Suematsu / Ana L Alvarez-Cabrera / Qiushi Liu / Liye Zhang / ...Authors: Shiheng Liu / Hong Wang / Xiaorun Li / Fan Zhang / Jane K J Lee / Zihang Li / Clinton Yu / Jason J Hu / Xiaojing Zhao / Takuma Suematsu / Ana L Alvarez-Cabrera / Qiushi Liu / Liye Zhang / Lan Huang / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou /
Abstract: In , the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial ...In , the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo-electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA-binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.
History
DepositionDec 27, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29316.png

Downloads & links

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Map

FileDownload / File: emd_29316.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.1818361 - 2.1610267
Average (Standard dev.)0.00050814333 (±0.04142595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29316_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29316_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : RESC5-tagged isolate without RNase treatment

EntireName: RESC5-tagged isolate without RNase treatment
Components
  • Complex: RESC5-tagged isolate without RNase treatment
    • Protein or peptide: RNA-editing substrate-binding complex protein 10 (RESC10)
    • Protein or peptide: RNA-editing substrate-binding complex protein 11 (RESC11)
    • Protein or peptide: RNA-editing substrate-binding complex protein 13 (RESC13)
    • Protein or peptide: RNA-editing substrate-binding complex protein 14 (RESC14)
    • Protein or peptide: RNA-editing substrate-binding complex protein 5 (RESC5)
    • Protein or peptide: RNA-editing substrate-binding complex protein 6 (RESC6)
    • Protein or peptide: RNA-editing substrate-binding complex protein 7 (RESC7)
    • Protein or peptide: RNA-editing substrate-binding complex protein 8 (RESC8)
    • Protein or peptide: RNA-editing substrate-binding complex protein 9 (RESC9)
    • RNA: gRNA
    • RNA: mRNA

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Supramolecule #1: RESC5-tagged isolate without RNase treatment

SupramoleculeName: RESC5-tagged isolate without RNase treatment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #8-#11, #3-#7, #2, #1
Details: CTS-tagged RESC5 purified from RNase-untreated mitochondrial extract by tandem affinity procedure
Source (natural)Organism: Trypanosoma brucei (eukaryote)

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Macromolecule #1: mRNA

MacromoleculeName: mRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 15.963094 KDa
SequenceString:
UAUAUAAUAG AAUAAGAUAA GUUUUUUUUU UUUUUUUUUU UUUUUUUUUU U

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Macromolecule #2: gRNA

MacromoleculeName: gRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 13.742247 KDa
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAUUU UUUUUUUUUU UUU

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Macromolecule #3: RNA-editing substrate-binding complex protein 5 (RESC5)

MacromoleculeName: RNA-editing substrate-binding complex protein 5 (RESC5)
type: protein_or_peptide / ID: 3
Details: RESC5 is tagged in situ in Trypanosoma brucei (5691), which shared the same native environment as other RESC proteins.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 43.469484 KDa
SequenceString: MLRHTSRNNA LHAFVRSPHY RTIPSAGPNG IVVNRDMLVH QFRDFYKTLQ HCSLVDKVHL MSERPSVEAL RVADQMVSIG ATFLEMPLT GMEHRATEFM ESMRYVRGAG GPSTLASYLQ DTENCRCNSG DVVCLPNGIA VGHGPRTNAV AHTTLKQLFE V KDDQFSFD ...String:
MLRHTSRNNA LHAFVRSPHY RTIPSAGPNG IVVNRDMLVH QFRDFYKTLQ HCSLVDKVHL MSERPSVEAL RVADQMVSIG ATFLEMPLT GMEHRATEFM ESMRYVRGAG GPSTLASYLQ DTENCRCNSG DVVCLPNGIA VGHGPRTNAV AHTTLKQLFE V KDDQFSFD VFTLEQEGDA PPLGDYFGFA GSNVLLTWKD EHGLLAVDQY QQKQPHTEMN VVYLEPGCHF LSFYGVDHTI DV LVQKGYE RSMDSIAAAG LNPIPVQWSE MDKLGISMRA AVLPLKFFKA NVGGMLSRNK SRGARWQTHQ LQKGSGSGSA SSG ASAAGS SGASASSGAS AAGSSGASAG HHHHHHHHHH SGSEDQVDPR LIDGKASAWS HPQFEKGGGS GGGSGGSAWS HPQF EK

UniProtKB: Mitochondrial RNA binding protein

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Macromolecule #4: RNA-editing substrate-binding complex protein 6 (RESC6)

MacromoleculeName: RNA-editing substrate-binding complex protein 6 (RESC6)
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 57.823484 KDa
SequenceString: MRSALRRCIL RHQGCLRMKQ SLSAFPTVVT GMTRHQGNSL IGTTHGAELS LAGDPQSVSH LSARNIATEA LQMKKLHQER GGNPMLAQQ ARRVLFATSI AGQNLDARSV ALLLNTAVYF GMESDAKLVR ECIDYCLKND KLITVDVLPI VVTACATLKS R DAREVIEM ...String:
MRSALRRCIL RHQGCLRMKQ SLSAFPTVVT GMTRHQGNSL IGTTHGAELS LAGDPQSVSH LSARNIATEA LQMKKLHQER GGNPMLAQQ ARRVLFATSI AGQNLDARSV ALLLNTAVYF GMESDAKLVR ECIDYCLKND KLITVDVLPI VVTACATLKS R DAREVIEM QAQKAARNAK FLDAKDVTNI ISAFSKTGIN HEKLFAFLSR RVQTLARVGE FEAAHLVILA NAFSRLRYRD KF LFGAIAR RAMSLRERVT VNELVPLIVA FSKIGLKDPK LSKRFATKAM EYVDQMNAEQ VASMFMAFAY FGIRYDQLFG VLT NRAVEL IDEFNAQYIS TTLNAFQRIG INNPELFDNL AERALAVVQD HDARDISKTV TALAHFGLKD EELFKRLASH AASI ADQFD AMGLVNTAHA FARTNFLQQD MAVALSERSV YVCRLLDAGE TRRLLWALAK FQVRDPKILT PVFNRCLALH YDFFA DPTG SEEIEEIFDF YGPNFCPPLY QLYISRGSTP QA

UniProtKB: Guide RNA binding protein

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Macromolecule #5: RNA-editing substrate-binding complex protein 7 (RESC7)

MacromoleculeName: RNA-editing substrate-binding complex protein 7 (RESC7)
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 18.669676 KDa
SequenceString:
MRSSRGILFL SGAFAIRGMS AYHSYQRLDT VSHTSKVYSL QMQRQTVHFT PITRLGVEAT ANPTTATNAT GQTGDGDGAT ALDVAMRVN KLKRLHQTGG GPSGKKQVEL DAWRDLNNLT EAQINSAEGK AVSLLLNSWA YFAKYWEKGA EGPSASLSEV T PSNDSSSA GEHGTQ

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #6: RNA-editing substrate-binding complex protein 8 (RESC8)

MacromoleculeName: RNA-editing substrate-binding complex protein 8 (RESC8)
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 61.109809 KDa
SequenceString: MLNVLSSTAS AALATVVVAR PSALHLIFER CKLNLVEFTA QDVYQICTTA YNMDTLGMLQ DPDFMRGLHD AFRRSDQTVI SPFQANLIA DTFRKVGINS MPKEVSVPEE DAISPESLIL VLRNMNITKQ RDERKINEVL KLMFPILDEF SPTQLSLTVT E LARLKSTN ...String:
MLNVLSSTAS AALATVVVAR PSALHLIFER CKLNLVEFTA QDVYQICTTA YNMDTLGMLQ DPDFMRGLHD AFRRSDQTVI SPFQANLIA DTFRKVGINS MPKEVSVPEE DAISPESLIL VLRNMNITKQ RDERKINEVL KLMFPILDEF SPTQLSLTVT E LARLKSTN ADFVGKLAKR IMEYNDDLSA LDISSAAVSL AYCPGISHNI LYRMMQIVEE RMGEFQPEDY INVLHALNTL GP KFVNTFR KIVECGLQHV ENMDAVTLTN YMVCFSTMDY KQREHIDIYA DALVEVATDL SEKDLVMAFI ALQRLRLLSD TMF GTMASC VIRYAAKMDP RNIAPIMDIC STVPHASDHL MKVLMDRAVE CTRILTANQL GDILDILGLY PPAREHPLVQ LFGK QARLR LDLMGPDALA NATRGLANLG YADPEYYAQA AETGFRYGFK DWTLLEPMLM GLSITGQCPP TMVRVLGSHI APMAR SMSL MEIERANRYL RRLGCEDDFV YKAMASRVLQ FVKEVTPEMP EDLQVLLQRG AVEPGAAPGV M

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #7: RNA-editing substrate-binding complex protein 9 (RESC9)

MacromoleculeName: RNA-editing substrate-binding complex protein 9 (RESC9)
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 96.668219 KDa
SequenceString: MLLPTLERLL ERCGRPIFSN VEDVRMVMAS LLDISAYVDR ASTKVIAKPL RRFCHKDPDT VASVMEAVPI DAAEPTHGRR AAMLLRCLP KHSCDEVIWE RAVAATLAGL KSRKWDLHDY RVAMAHAGRG GRHAPALAAA AEEFVSSSAR TASQSELPAL L VILTSLPE ...String:
MLLPTLERLL ERCGRPIFSN VEDVRMVMAS LLDISAYVDR ASTKVIAKPL RRFCHKDPDT VASVMEAVPI DAAEPTHGRR AAMLLRCLP KHSCDEVIWE RAVAATLAGL KSRKWDLHDY RVAMAHAGRG GRHAPALAAA AEEFVSSSAR TASQSELPAL L VILTSLPE LKRSPCLQVA ADRIVQLSEI LSPAAIGQIC ASVNKVSFRH TAMAIALQEE AIRFAEESDL FSAVQLFSFI CQ QEKEAIS PDAVKCLAER VIEGKDLDQE TVSVLCRALR SIPRPHRPEL LREIGEMMEF LGGEVKELLE LPVAKGGLKG DVS AGDIQS FISKFLSLDG LLPADHDRPG TYMAAIVACV DYITERLEDI VSDENPPFSI IPHLLNINME ETRRCGQAII REAA EQGIH FPTLQVFRFL LALGDHNMRD QRVYRHLRNE FAKTASDIPM IQLCAALKCF VRGLMQNVET QSLDEQVEHE LEKED MDAF LRFCVENLRR GFADGMEVKC VMAATESLYQ LGYTSTEFYE QVARYLGSKC SSASASVNSS ETATAVCLAL GEDILD RHP DVHTFLLEVE KSGLKGEASL SPTEWMNKND PANFITPLTE IQQEGWNIIN RMVETRAADT EKLTALANEY VAILKST RV DDLKYFFGVF EEKVFKQDRI LKQCLDYLVE SNAAVKLSAT SIGAMLNSLA AIRFTYHRSV KQFMIAISTE QWSEMDAS P LVKIVSAMAK LSLRLPQVLV HVGDRLLDVY TFLSPLDTAL VINSLQSIGY GNDEVLMMLM RHAASSARRW DEVSLTLLF GASGVHRLLR NVEVAAPLLE QAAGKTSSPH LRQRIAASLR RSALPRALVQ SSTSLLTGGA HEVVNNPPLQ LV

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #8: RNA-editing substrate-binding complex protein 10 (RESC10)

MacromoleculeName: RNA-editing substrate-binding complex protein 10 (RESC10)
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 60.563676 KDa
SequenceString: MRRRVVLCCQ DVGSLLSSKH SVHSGIGYHE RVFSRNLLYR RYPVVTVLPK AGFTVLDTKR WIASSGPPVT GSPLSPVTNP SLNVGTGGG EAVAMEGPLP VSYSPGSGVN GSLPVTSTAI TAHCDVLSEC VAKADELAVQ LKAQNALSAS AEILTQEGME E FVEELKTS ...String:
MRRRVVLCCQ DVGSLLSSKH SVHSGIGYHE RVFSRNLLYR RYPVVTVLPK AGFTVLDTKR WIASSGPPVT GSPLSPVTNP SLNVGTGGG EAVAMEGPLP VSYSPGSGVN GSLPVTSTAI TAHCDVLSEC VAKADELAVQ LKAQNALSAS AEILTQEGME E FVEELKTS ATNEMTALVK QMQTTPLLQR AGMHELRRTL YYTTSLKERD WLEEKQYTAA MRMLTVEVLR RDGDGVLSAD DV LYVTTHV VTANFYNRHL WNRMEKSLLK FSNYENIDMS SVKAFSTRLF KTRRGCAKET LDIRRKVLLA MSRRVGVLAN DFD LPSLLG VLQCYTVHDL TPFHLEPLAI RATNHVGDFT PHECATLAHV LRKWRTMRLE VCERLVERIC TSDQLTHHMA NAAM IAIRT CFNQVSDGGR NAMNAEPTRQ KLRAMGEQIG CRLDEVEYPA LPVILSILDV VVTLKIYVPK KCLQVIFSQA NDMVA IVME QKDDLVDPKT GKRVRPITAE EGRQLQALLS HYGNDLAPEL SQRMKEAFRE GVLPDEASL

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #9: RNA-editing substrate-binding complex protein 11 (RESC11)

MacromoleculeName: RNA-editing substrate-binding complex protein 11 (RESC11)
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 103.585086 KDa
SequenceString: MYRLYRRTVG YQSLHQRLSA CHVMCRHVST DNSDGTTPPK PRRSGIRRVV PSDEEMAELH DLEQEVASTT SSRSKQSALS GVMVEPMRF STSGGSGMEG DGDDLGELEA EGDEEGVGTN SLAEAENVYK RHNDGGALEK QGLAIPPSGK PTDPLLANRD D EGEGGAVP ...String:
MYRLYRRTVG YQSLHQRLSA CHVMCRHVST DNSDGTTPPK PRRSGIRRVV PSDEEMAELH DLEQEVASTT SSRSKQSALS GVMVEPMRF STSGGSGMEG DGDDLGELEA EGDEEGVGTN SLAEAENVYK RHNDGGALEK QGLAIPPSGK PTDPLLANRD D EGEGGAVP LSQAEEMTVS RSTLERQACV RSLSLEELVE AVTLYLRATK NPRLVSADEE HIFFPVLMER LNEFHVSQLL DV VECHWAR STLVRYGTTF KDMVRDRIAL IATAAAKSAS KRPAAAGKSG NDNRDGGAVE EEADDYDEQG DAVYVHEAEE KTS DLIILR AAEEMSPETV LRCIIVMGMS AGRRKRDLQF FQAMGMFLVH HINHYKDPHE LVRVLTAFAR AKIVPPKRFL ALLG RRFAV LNKRKKLGSL PSYRAFVNLY KMGHDQMNTF RFLADCILET IDSNIKAEKK RLRLAQLQSS SNITAATTNE NGATN ESGC GGSTSSSNPT VTNITGAGDL KATHTSEGAS DVAFIGDLDP HLLQNLRARE RFKRLTELKP SMFTKLLLVL ARFGAP HQQ YLRPTTVPLI LPTLRAFPPP SFTRLLRAMS LFRTTDLDLI EPVIDFMADS LGPTNVVPAD VLQMVRLVAP PDVPVPR NL VKLISLCEAV YSSSASFSHS DGKSSDSADA AACAMTTLSP IRPGDMCAVA VVLLKIQMKD DVPLEALDPL TRLMEFFA E RMYLLMKLHI VSLTHVDVFT DLCRQQQHPD VSGHIERLCA ERRRVNDAEG DDEYYSQLDI DVRETLHRIL IVNDYNTYG QYRPTPGVLQ VDFKQALTEV SAFDVLEAAD LFAQAFSNAL KPAVERHLSR SIIAKLDGGG EEVITEGNSI VLRPPRELLL TREDLGKFV CLLQRTPLRR VRASPVVWRF VEEKAKKLGM DDVLRVVENK LATAV

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #10: RNA-editing substrate-binding complex protein 13 (RESC13)

MacromoleculeName: RNA-editing substrate-binding complex protein 13 (RESC13)
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 32.445303 KDa
SequenceString: MKRTPVRVLN ATVAFLQGWG GGSSGGGWGS DDGPGNGSGG GGSGGRGGWG SGGGGGGGWG SGGGGNGGWG SGGGGGGGWG SGGGGRGSG GGSNGGWGSG RGGSAHGFSN PWNDGDAGWR GAATGARANR GRGGFRRGRG GADDGVWGQP NVVDEEAWTA A PPSFNPPV ...String:
MKRTPVRVLN ATVAFLQGWG GGSSGGGWGS DDGPGNGSGG GGSGGRGGWG SGGGGGGGWG SGGGGNGGWG SGGGGGGGWG SGGGGRGSG GGSNGGWGSG RGGSAHGFSN PWNDGDAGWR GAATGARANR GRGGFRRGRG GADDGVWGQP NVVDEEAWTA A PPSFNPPV RRVDPLTLTA VEVEIDGIKK LVGQRVQVSG LSDETTWHTL KDHLRQAGEV TFCKVFSGGR AVVEFVTPED AA RAITELQ ASELEGATLF LREDREDTVL VNTRRKIREV RDAQLRARKE EMEKKRREQA IAEGDCSAPA PPAEVAGDAS QKV

UniProtKB: RNA-binding protein, putative

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Macromolecule #11: RNA-editing substrate-binding complex protein 14 (RESC14)

MacromoleculeName: RNA-editing substrate-binding complex protein 14 (RESC14)
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 41.293148 KDa
SequenceString: MRSGRKLGCF TNRLRLPFFS PCSQITALTA SHRCKSYVLK FLRGQLPEDL KDVNGALGCL YGTLPDVDEF GQFVISPDVV NSFHQFGYV KMPIPVLDHQ QIDKLADEVN ELANNVEHHP KTERLYATSL ADLTGGPLFF CQGQWRAAWG MHDLIYLPTI T VAASQILN ...String:
MRSGRKLGCF TNRLRLPFFS PCSQITALTA SHRCKSYVLK FLRGQLPEDL KDVNGALGCL YGTLPDVDEF GQFVISPDVV NSFHQFGYV KMPIPVLDHQ QIDKLADEVN ELANNVEHHP KTERLYATSL ADLTGGPLFF CQGQWRAAWG MHDLIYLPTI T VAASQILN NSLVRLWYDE VFMKAARTGP CVPWQQNYAR WQHTKPVNHV TVMIALDTMN KDRGAPCLVP GSHRWREGGL LP PVSYDPT KDEAHQLNTI WEIINEEEGE MLMDTPPVTV DLRRGEALLI HPLTLFATHG NRSLDAVRCC FIHYMGEKTY AVQ NGPLLP HTTKFQADAM IQGPFYPVVF DPAMTEELTM LPTAPSEEEA

UniProtKB: Phytanoyl-CoA dioxygenase

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62372
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • 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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