[English] 日本語
Yorodumi
- EMDB-14808: Structure of the human TREX core THO-UAP56 complex (map D) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14808
TitleStructure of the human TREX core THO-UAP56 complex (map D)
Map dataSharpened map
Sample
  • Complex: THO-UAP56
    • Protein or peptide: THO complex subunit 1
    • Protein or peptide: THO complex subunit 2
    • Protein or peptide: THO complex subunit 3
    • Protein or peptide: THO complex subunit 5 homolog
    • Protein or peptide: THO complex subunit 6 homolog
    • Protein or peptide: THO complex subunit 7 homolog
    • Protein or peptide: Spliceosome RNA helicase DDX39B
Keywordstranscription and export complex / TREX / RNA export / RNA packaging / RNA binding protein / gene expression / GENE REGULATION
Function / homology
Function and homology information


THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / ATP-dependent protein binding / mRNA 3'-end processing ...THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / ATP-dependent protein binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / U4 snRNA binding / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNP / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus / generation of neurons / spliceosomal complex assembly / monocyte differentiation / blastocyst development / neuron development / RHOBTB2 GTPase cycle / mRNA export from nucleus / U6 snRNA binding / mRNA Splicing - Major Pathway / RNA splicing / central nervous system development / spliceosomal complex / cell morphogenesis / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / Signaling by CSF1 (M-CSF) in myeloid cells / negative regulation of neuron projection development / regulation of gene expression / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / mRNA binding / apoptotic process / signal transduction / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
THO complex, subunit 5 / THO complex subunit 6 / Fms-interacting protein/Thoc5 / TREX component Tex1/THOC3 / THO complex subunit 7/Mft1 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Tho complex subunit 7 ...THO complex, subunit 5 / THO complex subunit 6 / Fms-interacting protein/Thoc5 / TREX component Tex1/THOC3 / THO complex subunit 7/Mft1 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Tho complex subunit 7 / Transcription factor/nuclear export subunit protein 2 / Transcription- and export-related complex subunit / THO complex subunit 2 N-terminus / THO complex, subunit THOC1 / THO complex subunit 1 transcription elongation factor / WD40-like beta propeller / WD40-like Beta Propeller Repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
THO complex subunit 5 / Spliceosome RNA helicase DDX39B / THO complex subunit 7 / THO complex subunit 6 / THO complex subunit 2 / THO complex subunit 1 / THO complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsPacheco-Fiallos FB / Vorlaender MK / Plaschka C
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
European Molecular Biology Organization (EMBO)623-2020European Union
CitationJournal: Nature / Year: 2023
Title: mRNA recognition and packaging by the human transcription-export complex.
Authors: Belén Pacheco-Fiallos / Matthias K Vorländer / Daria Riabov-Bassat / Laura Fin / Francis J O'Reilly / Farja I Ayala / Ulla Schellhaas / Juri Rappsilber / Clemens Plaschka /
Abstract: Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the ...Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.
History
DepositionApr 21, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14808.png

Downloads & links

-
Map

FileDownload / File: emd_14808.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 440 pix.
= 589.6 Å		1.34 Å/pix.
x 440 pix.
= 589.6 Å		1.34 Å/pix.
x 440 pix.
= 589.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-4.5229445 - 6.604897
Average (Standard dev.)0.0025976128 (±0.04813204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 589.60004 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_14808_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_14808_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_14808_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : THO-UAP56

EntireName: THO-UAP56
Components
  • Complex: THO-UAP56
    • Protein or peptide: THO complex subunit 1
    • Protein or peptide: THO complex subunit 2
    • Protein or peptide: THO complex subunit 3
    • Protein or peptide: THO complex subunit 5 homolog
    • Protein or peptide: THO complex subunit 6 homolog
    • Protein or peptide: THO complex subunit 7 homolog
    • Protein or peptide: Spliceosome RNA helicase DDX39B

-
Supramolecule #1: THO-UAP56

SupramoleculeName: THO-UAP56 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.8 MDa

-
Macromolecule #1: THO complex subunit 1

MacromoleculeName: THO complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.752156 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSPTPPLFSL PEARTRFTKS TREALNNKNI KPLLSTFSQV PGSENEKKCT LDQAFRGILE EEIINHSSCE NVLAIISLAI GGVTEGICT ASTPFVLLGD VLDCLPLDQC DTIFTFVEKN VATWKSNTFY SAGKNYLLRM CNDLLRRLSK SQNTVFCGRI Q LFLARLFP ...String:
MSPTPPLFSL PEARTRFTKS TREALNNKNI KPLLSTFSQV PGSENEKKCT LDQAFRGILE EEIINHSSCE NVLAIISLAI GGVTEGICT ASTPFVLLGD VLDCLPLDQC DTIFTFVEKN VATWKSNTFY SAGKNYLLRM CNDLLRRLSK SQNTVFCGRI Q LFLARLFP LSEKSGLNLQ SQFNLENVTV FNTNEQESTL GQKHTEDREE GMDVEEGEMG DEEAPTTCSI PIDYNLYRKF WS LQDYFRN PVQCYEKISW KTFLKYSEEV LAVFKSYKLD DTQASRKKME ELKTGGEHVY FAKFLTSEKL MDLQLSDSNF RRH ILLQYL ILFQYLKGQV KFKSSNYVLT DEQSLWIEDT TKSVYQLLSE NPPDGERFSK MVEHILNTEE NWNSWKNEGC PSFV KERTS DTKPTRIIRK RTAPEDFLGK GPTKKILMGN EELTRLWNLC PDNMEACKSE TREHMPTLEE FFEEAIEQAD PENMV ENEY KAVNNSNYGW RALRLLARRS PHFFQPTNQQ FKSLPEYLEN MVIKLAKELP PPSEEIKTGE DEDEEDNDAL LKENES PDV RRDKPVTGEQ IEVFANKLGE QWKILAPYLE MKDSEIRQIE CDSEDMKMRA KQLLVAWQDQ EGVHATPENL INALNKS GL SDLAESLTND NETNS

UniProtKB: THO complex subunit 1

-
Macromolecule #2: THO complex subunit 2

MacromoleculeName: THO complex subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 183.087734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAAAVVVPA EWIKNWEKSG RGEFLHLCRI LSENKSHDSS TYRDFQQALY ELSYHVIKGN LKHEQASNVL SDISEFREDM PSILADVFC ILDIETNCLE EKSKRDYFTQ LVLACLYLVS DTVLKERLDP ETLESLGLIK QSQQFNQKSV KIKTKLFYKQ Q KFNLLREE ...String:
MAAAAVVVPA EWIKNWEKSG RGEFLHLCRI LSENKSHDSS TYRDFQQALY ELSYHVIKGN LKHEQASNVL SDISEFREDM PSILADVFC ILDIETNCLE EKSKRDYFTQ LVLACLYLVS DTVLKERLDP ETLESLGLIK QSQQFNQKSV KIKTKLFYKQ Q KFNLLREE NEGYAKLIAE LGQDLSGSIT SDLILENIKS LIGCFNLDPN RVLDVILEVF ECRPEHDDFF ISLLESYMSM CE PQTLCHI LGFKFKFYQE PNGETPSSLY RVAAVLLQFN LIDLDDLYVH LLPADNCIMD EHKREIAEAK QIVRKLTMVV LSS EKMDER EKEKEKEEEK VEKPPDNQKL GLLEALLKIG DWQHAQNIMD QMPPYYAASH KLIALAICKL IHITIEPLYR RVGV PKGAK GSPVNALQNK RAPKQAESFE DLRRDVFNMF CYLGPHLSHD PILFAKVVRI GKSFMKEFQS DGSKQEDKEK TEVIL SCLL SITDQVLLPS LSLMDCNACM SEELWGMFKT FPYQHRYRLY GQWKNETYNS HPLLVKVKAQ TIDRAKYIMK RLTKEN VKP SGRQIGKLSH SNPTILFDYI LSQIQKYDNL ITPVVDSLKY LTSLNYDVLA YCIIEALANP EKERMKHDDT TISSWLQ SL ASFCGAVFRK YPIDLAGLLQ YVANQLKAGK SFDLLILKEV VQKMAGIEIT EEMTMEQLEA MTGGEQLKAE GGYFGQIR N TKKSSQRLKD ALLDHDLALP LCLLMAQQRN GVIFQEGGEK HLKLVGKLYD QCHDTLVQFG GFLASNLSTE DYIKRVPSI DVLCNEFHTP HDAAFFLSRP MYAHHISSKY DELKKSEKGS KQQHKVHKYI TSCEMVMAPV HEAVVSLHVS KVWDDISPQF YATFWSLTM YDLAVPHTSY EREVNKLKVQ MKAIDDNQEM PPNKKKKEKE RCTALQDKLL EEEKKQMEHV QRVLQRLKLE K DNWLLAKS TKNETITKFL QLCIFPRCIF SAIDAVYCAR FVELVHQQKT PNFSTLLCYD RVFSDIIYTV ASCTENEASR YG RFLCCML ETVTRWHSDR ATYEKECGNY PGFLTILRAT GFDGGNKADQ LDYENFRHVV HKWHYKLTKA SVHCLETGEY THI RNILIV LTKILPWYPK VLNLGQALER RVHKICQEEK EKRPDLYALA MGYSGQLKSR KSYMIPENEF HHKDPPPRNA VASV QNGPG GGPSSSSIGS ASKSDESSTE ETDKSRERSQ CGVKAVNKAS STTPKGNSSN GNSGSNSNKA VKENDKEKGK EKEKE KKEK TPATTPEARV LGKDGKEKPK EERPNKDEKA RETKERTPKS DKEKEKFKKE EKAKDEKFKT TVPNAESKST QERERE KEP SRERDIAKEM KSKENVKGGE KTPVSGSLKS PVPRSDIPEP EREQKRRKID THPSPSHSST VKDSLIELKE SSAKLYI NH TPPPLSKSKE REMDKKDLDK SRERSREREK KDEKDRKERK RDHSNNDREV PPDLTKRRKE ENGTMGVSKH KSESPCES P YPNEKDKEKN KSKSSGKEKG SDSFKSEKMD KISSGGKKES RHDKEKIEKK EKRDSSGGKE EKKHHKSSDK HR

UniProtKB: THO complex subunit 2

-
Macromolecule #3: THO complex subunit 3

MacromoleculeName: THO complex subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.817617 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAVPAAAMGP SALGQSGPGS MAPWCSVSSG PSRYVLGMQE LFRGHSKTRE FLAHSAKVHS VAWSCDGRRL ASGSFDKTAS VFLLEKDRL VKENNYRGHG DSVDQLCWHP SNPDLFVTAS GDKTIRIWDV RTTKCIATVN TKGENINICW SPDGQTIAVG N KDDVVTFI ...String:
MAVPAAAMGP SALGQSGPGS MAPWCSVSSG PSRYVLGMQE LFRGHSKTRE FLAHSAKVHS VAWSCDGRRL ASGSFDKTAS VFLLEKDRL VKENNYRGHG DSVDQLCWHP SNPDLFVTAS GDKTIRIWDV RTTKCIATVN TKGENINICW SPDGQTIAVG N KDDVVTFI DAKTHRSKAE EQFKFEVNEI SWNNDNNMFF LTNGNGCINI LSYPELKPVQ SINAHPSNCI CIKFDPMGKY FA TGSADAL VSLWDVDELV CVRCFSRLDW PVRTLSFSHD GKMLASASED HFIDIAEVET GDKLWEVQCE SPTFTVAWHP KRP LLAFAC DDKDGKYDSS REAGTVKLFG LPNDS

UniProtKB: THO complex subunit 3

-
Macromolecule #4: THO complex subunit 5 homolog

MacromoleculeName: THO complex subunit 5 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.624852 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSESSKKRK PKVIRSDGAP AEGKRNRSDT EQEGKYYSEE AEVDLRDPGR DYELYKYTCQ ELQRLMAEIQ DLKSRGGKDV AIEIEERRI QSCVHFMTLK KLNRLAHIRL KKGRDQTHEA KQKVDAYHLQ LQNLLYEVMH LQKEITKCLE FKSKHEEIDL V SLEEFYKE ...String:
MSSESSKKRK PKVIRSDGAP AEGKRNRSDT EQEGKYYSEE AEVDLRDPGR DYELYKYTCQ ELQRLMAEIQ DLKSRGGKDV AIEIEERRI QSCVHFMTLK KLNRLAHIRL KKGRDQTHEA KQKVDAYHLQ LQNLLYEVMH LQKEITKCLE FKSKHEEIDL V SLEEFYKE APPDISKAEV TMGDPHQQTL ARLDWELEQR KRLAEKYREC LSNKEKILKE IEVKKEYLSS LQPRLNSIMQ AS LPVQEYL FMPFDQAHKQ YETARHLPPP LYVLFVQATA YGQACDKTLS VAIEGSVDEA KALFKPPEDS QDDESDSDAE EEQ TTKRRR PTLGVQLDDK RKEMLKRHPL SVMLDLKCKD DSVLHLTFYY LMNLNIMTVK AKVTTAMELI TPISAGDLLS PDSV LSCLY PGDHGKKTPN PANQYQFDKV GILTLSDYVL ELGHPYLWVQ KLGGLHFPKE QPQQTVIADH SLSASHMETT MKLLK TRVQ SRLALHKQFA SLEHGIVPVT SDCQYLFPAK VVSRLVKWVT VAHEDYMELH FTKDIVDAGL AGDTNLYYMA LIERGT AKL QAAVVLNPGY SSIPPVFQLC LNWKGEKTNS NDDNIRAMEG EVNVCYKELC GPWPSHQLLT NQLQRLCVLL DVYLETE SH DDSVEGPKEF PQEKMCLRLF RGPSRMKPFK YNHPQGFFSH R

UniProtKB: THO complex subunit 5

-
Macromolecule #5: THO complex subunit 6 homolog

MacromoleculeName: THO complex subunit 6 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.577875 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MERAVPLAVP LGQTEVFQAL QRLHMTIFSQ SVSPCGKFLA AGNNYGQIAI FSLSSALSSE AKEESKKPVV TFQAHDGPVY SMVSTDRHL LSAGDGEVKA WLWAEMLKKG CKELWRRQPP YRTSLEVPEI NALLLVPKEN SLILAGGDCQ LHTMDLETGT F TRVLRGHT ...String:
MERAVPLAVP LGQTEVFQAL QRLHMTIFSQ SVSPCGKFLA AGNNYGQIAI FSLSSALSSE AKEESKKPVV TFQAHDGPVY SMVSTDRHL LSAGDGEVKA WLWAEMLKKG CKELWRRQPP YRTSLEVPEI NALLLVPKEN SLILAGGDCQ LHTMDLETGT F TRVLRGHT DYIHCLALRE RSPEVLSGGE DGAVRLWDLR TAKEVQTIEV YKHEECSRPH NGRWIGCLAT DSDWMVCGGG PA LTLWHLR SSTPTTIFPI RAPQKHVTFY QDLILSAGQG RCVNQWQLSG ELKAQVPGSS PGLLSLSLNQ QPAAPECKVL TAA GNSCRV DVFTNLGYRA FSLSF

UniProtKB: THO complex subunit 6

-
Macromolecule #6: THO complex subunit 7 homolog

MacromoleculeName: THO complex subunit 7 homolog / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.782014 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGAVTDDEVI RKRLLIDGDG AGDDRRINLL VKSFIKWCNS GSQEEGYSQY QRMLSTLSQC EFSMGKTLLV YDMNLREMEN YEKIYKEIE CSIAGAHEKI AECKKQILQA KRIRKNRQEY DALAKVIQHH PDRHETLKEL EALGKELEHL SHIKESVEDK L ELRRKQFH ...String:
MGAVTDDEVI RKRLLIDGDG AGDDRRINLL VKSFIKWCNS GSQEEGYSQY QRMLSTLSQC EFSMGKTLLV YDMNLREMEN YEKIYKEIE CSIAGAHEKI AECKKQILQA KRIRKNRQEY DALAKVIQHH PDRHETLKEL EALGKELEHL SHIKESVEDK L ELRRKQFH VLLSTIHELQ QTLENDEKLS EVEEAQEASM ETDPKP

UniProtKB: THO complex subunit 7

-
Macromolecule #7: Spliceosome RNA helicase DDX39B

MacromoleculeName: Spliceosome RNA helicase DDX39B / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.05625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAENDVDNEL LDYEDDEVET AAGGDGAEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQA KSGMGKTAVF VLATLQQLEP VTGQVSVLVM CHTRELAFQI SKEYERFSKY MPNVKVAVFF GGLSIKKDEE V LKKNCPHI ...String:
MAENDVDNEL LDYEDDEVET AAGGDGAEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQA KSGMGKTAVF VLATLQQLEP VTGQVSVLVM CHTRELAFQI SKEYERFSKY MPNVKVAVFF GGLSIKKDEE V LKKNCPHI VVGTPGRILA LARNKSLNLK HIKHFILDEC DKMLEQLDMR RDVQEIFRMT PHEKQVMMFS ATLSKEIRPV CR KFMQDPM EIFVDDETKL TLHGLQQYYV KLKDNEKNRK LFDLLDVLEF NQVVIFVKSV QRCIALAQLL VEQNFPAIAI HRG MPQEER LSRYQQFKDF QRRILVATNL FGRGMDIERV NIAFNYDMPE DSDTYLHRVA RAGRFGTKGL AITFVSDEND AKIL NDVQD RFEVNISELP DEIDISSYIE QTR

UniProtKB: Spliceosome RNA helicase DDX39B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

-
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: 3.7 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

11857

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 246457
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more