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- EMDB-11857: Structure of the human THO - UAP56 complex (Map B) -

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Basic information

Entry
Database: EMDB / ID: EMD-11857
TitleStructure of the human THO - UAP56 complex (Map B)
Map dataMap B sharpened (Map sharpening B-factor -132 A2)
Sample
  • Complex: THO - UAP56
    • Complex: THO complex
      • 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: THOC2 anchor (putative)
    • Complex: Spliceosome RNA helicase DDX39B
      • Protein or peptide: Spliceosome RNA helicase DDX39B
Function / homology
Function and homology information


THO complex / THO complex part of transcription export complex / primitive hemopoiesis / transcription export complex / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / ATP-dependent activity, acting on RNA / U4 snRNA binding ...THO complex / THO complex part of transcription export complex / primitive hemopoiesis / transcription export complex / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / ATP-dependent activity, acting on RNA / U4 snRNA binding / mRNA 3'-end processing / RNA export from nucleus / ATP-dependent protein binding / U4 snRNP / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / positive regulation of DNA-templated transcription, elongation / poly(A)+ mRNA export from nucleus / generation of neurons / spliceosomal complex assembly / monocyte differentiation / blastocyst development / neuron development / U6 snRNA binding / RHOBTB2 GTPase cycle / mRNA export from nucleus / mRNA Splicing - Major Pathway / RNA splicing / regulation of DNA-templated transcription elongation / central nervous system development / spliceosomal complex / cell morphogenesis / mRNA splicing, via spliceosome / mRNA processing / nuclear matrix / 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. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Death-like domain superfamily / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 homolog / Spliceosome RNA helicase DDX39B / THO complex subunit 7 homolog / THO complex subunit 6 homolog / 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: 3.3 Å
AuthorsHohmann U / Puehringer T / Plaschka C
Funding support Austria, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationP2GEP3_188343 Austria
CitationJournal: Elife / Year: 2020
Title: Structure of the human core transcription-export complex reveals a hub for multivalent interactions.
Authors: Thomas Pühringer / Ulrich Hohmann / Laura Fin / Belén Pacheco-Fiallos / Ulla Schellhaas / Julius Brennecke / Clemens Plaschka /
Abstract: The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and ...The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and licenses mRNA for nuclear export by loading the export factor NXF1-NXT1. How TREX integrates these marks and achieves high selectivity for mature mRNA is poorly understood. Here, we report the cryo-electron microscopy structure of the human THO-UAP56/DDX39B complex at 3.3 Å resolution. The seven-subunit THO-UAP56/DDX39B complex multimerizes into a 28-subunit tetrameric assembly, suggesting that selective recognition of mature mRNA is facilitated by the simultaneous sensing of multiple, spatially distant mRNA regions and maturation marks. Two UAP56/DDX39B RNA helicases are juxtaposed at each end of the tetramer, which would allow one bivalent ALYREF protein to bridge adjacent helicases and regulate the TREX-mRNA interaction. Our structural and biochemical results suggest a conserved model for TREX complex function that depends on multivalent interactions between proteins and mRNA.
History
DepositionOct 17, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05257
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05257
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  • Surface view with fitted model
  • Atomic models: PDB-7apk
  • Surface level: 0.05257
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7apk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11857.png

Downloads & links

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Map

FileDownload / File: emd_11857.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap B sharpened (Map sharpening B-factor -132 A2)
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.05257 / Movie #1: 0.05257
Minimum - Maximum-0.10298025 - 0.27440223
Average (Standard dev.)-0.00020269188 (±0.0045365933)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z589.600589.600589.600
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.1030.274-0.000

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Supplemental data

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Additional map: Map B unsharpened

Fileemd_11857_additional_1.map
AnnotationMap B unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : THO - UAP56

EntireName: THO - UAP56
Components
  • Complex: THO - UAP56
    • Complex: THO complex
      • 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: THOC2 anchor (putative)
    • Complex: Spliceosome RNA helicase DDX39B
      • Protein or peptide: Spliceosome RNA helicase DDX39B

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Supramolecule #1: THO - UAP56

SupramoleculeName: THO - UAP56 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 1.836 MDa

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Supramolecule #2: THO complex

SupramoleculeName: THO complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6, #8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: Hi5

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Supramolecule #3: Spliceosome RNA helicase DDX39B

SupramoleculeName: Spliceosome RNA helicase DDX39B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 DE3 RIL

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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: 81.138383 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGKPIPNPLL GLDSTGSGKP IPNPLLGLDS TGSGKPIPNP LLGLDSTLEV LFQGPSPTPP LFSLPEARTR FTKSTREALN NKNIKPLLS TFSQVPGSEN EKKCTLDQAF RGILEEEIIN HSSCENVLAI ISLAIGGVTE GICTASTPFV LLGDVLDCLP L DQCDTIFT ...String:
MGKPIPNPLL GLDSTGSGKP IPNPLLGLDS TGSGKPIPNP LLGLDSTLEV LFQGPSPTPP LFSLPEARTR FTKSTREALN NKNIKPLLS TFSQVPGSEN EKKCTLDQAF RGILEEEIIN HSSCENVLAI ISLAIGGVTE GICTASTPFV LLGDVLDCLP L DQCDTIFT FVEKNVATWK SNTFYSAGKN YLLRMCNDLL RRLSKSQNTV FCGRIQLFLA RLFPLSEKSG LNLQSQFNLE NV TVFNTNE QESTLGQKHT EDREEGMDVE EGEMGDEEAP TTCSIPIDYN LYRKFWSLQD YFRNPVQCYE KISWKTFLKY SEE VLAVFK SYKLDDTQAS RKKMEELKTG GEHVYFAKFL TSEKLMDLQL SDSNFRRHIL LQYLILFQYL KGQVKFKSSN YVLT DEQSL WIEDTTKSVY QLLSENPPDG ERFSKMVEHI LNTEENWNSW KNEGCPSFVK ERTSDTKPTR IIRKRTAPED FLGKG PTKK ILMGNEELTR LWNLCPDNME ACKSETREHM PTLEEFFEEA IEQADPENMV ENEYKAVNNS NYGWRALRLL ARRSPH FFQ PTNQQFKSLP EYLENMVIKL AKELPPPSEE IKTGEDEDEE DNDALLKENE SPDVRRDKPV TGEQIEVFAN KLGEQWK IL APYLEMKDSE IRQIECDSED MKMRAKQLLV AWQDQEGVHA TPENLINALN KSGLSDLAES LTNDNETNS

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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: 141.584594 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKHHHHHHHH HHSAGLEVLF QGPMAAAAVV VPAEWIKNWE KSGRGEFLHL CRILSENKSH DSSTYRDFQQ ALYELSYHVI KGNLKHEQA SNVLSDISEF REDMPSILAD VFCILDIETN CLEEKSKRDY FTQLVLACLY LVSDTVLKER LDPETLESLG L IKQSQQFN ...String:
MKHHHHHHHH HHSAGLEVLF QGPMAAAAVV VPAEWIKNWE KSGRGEFLHL CRILSENKSH DSSTYRDFQQ ALYELSYHVI KGNLKHEQA SNVLSDISEF REDMPSILAD VFCILDIETN CLEEKSKRDY FTQLVLACLY LVSDTVLKER LDPETLESLG L IKQSQQFN QKSVKIKTKL FYKQQKFNLL REENEGYAKL IAELGQDLSG SITSDLILEN IKSLIGCFNL DPNRVLDVIL EV FECRPEH DDFFISLLES YMSMCEPQTL CHILGFKFKF YQEPNGETPS SLYRVAAVLL QFNLIDLDDL YVHLLPADNC IMD EHKREI AEAKQIVRKL TMVVLSSEKM DEREKEKEKE EEKVEKPPDN QKLGLLEALL KIGDWQHAQN IMDQMPPYYA ASHK LIALA ICKLIHITIE PLYRRVGVPK GAKGSPVNAL QNKRAPKQAE SFEDLRRDVF NMFCYLGPHL SHDPILFAKV VRIGK SFMK EFQSDGSKQE DKEKTEVILS CLLSITDQVL LPSLSLMDCN ACMSEELWGM FKTFPYQHRY RLYGQWKNET YNSHPL LVK VKAQTIDRAK YIMKRLTKEN VKPSGRQIGK LSHSNPTILF DYILSQIQKY DNLITPVVDS LKYLTSLNYD VLAYCII EA LANPEKERMK HDDTTISSWL QSLASFCGAV FRKYPIDLAG LLQYVANQLK AGKSFDLLIL KEVVQKMAGI EITEEMTM E QLEAMTGGEQ LKAEGGYFGQ IRNTKKSSQR LKDALLDHDL ALPLCLLMAQ QRNGVIFQEG GEKHLKLVGK LYDQCHDTL VQFGGFLASN LSTEDYIKRV PSIDVLCNEF HTPHDAAFFL SRPMYAHHIS SKYDELKKSE KGSKQQHKVH KYITSCEMVM APVHEAVVS LHVSKVWDDI SPQFYATFWS LTMYDLAVPH TSYEREVNKL KVQMKAIDDN QEMPPNKKKK EKERCTALQD K LLEEEKKQ MEHVQRVLQR LKLEKDNWLL AKSTKNETIT KFLQLCIFPR CIFSAIDAVY CARFVELVHQ QKTPNFSTLL CY DRVFSDI IYTVASCTEN EASRYGRFLC CMLETVTRWH SDRATYEKEC GNYPGFLTIL RATGFDGGNK ADQLDYENFR HVV HKWHYK LTKASVHCLE TGEYTHIRNI LIVLTKILPW YPKVLNLGQA LERRVHKICQ EEKEKRPDLY ALAMGYSGQL KSRK SYMIP ENEFHHKDPP PRNAVASVQN G

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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: 43.279445 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKTAGLEVL FQGPMAVPAA AMGPSALGQS GPGSMAPWCS VSSGPSRYVL GMQELFRGH SKTREFLAHS AKVHSVAWSC DGRRLASGSF DKTASVFLLE KDRLVKENNY RGHGDSVDQL CWHPSNPDLF V TASGDKTI ...String:
MKGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKTAGLEVL FQGPMAVPAA AMGPSALGQS GPGSMAPWCS VSSGPSRYVL GMQELFRGH SKTREFLAHS AKVHSVAWSC DGRRLASGSF DKTASVFLLE KDRLVKENNY RGHGDSVDQL CWHPSNPDLF V TASGDKTI RIWDVRTTKC IATVNTKGEN INICWSPDGQ TIAVGNKDDV VTFIDAKTHR SKAEEQFKFE VNEISWNNDN NM FFLTNGN GCINILSYPE LKPVQSINAH PSNCICIKFD PMGKYFATGS ADALVSLWDV DELVCVRCFS RLDWPVRTLS FSH DGKMLA SASEDHFIDI AEVETGDKLW EVQCESPTFT VAWHPKRPLL AFACDDKDGK YDSSREAGTV KLFGLPNDS

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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: 78.652898 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 IAHEDYMELH FTKDIVDAGL AGDTNLYYMA LIERGT AKL QAAVVLNPGY SSIPPIFQLC LNWKGEKTNS NDDNIRAMEG EVNVCYKELC GPWPSHQLLT NQLQRLCVLL DVYLETE SH DDSVEGPKEF PQEKMCLRLF RGPSRMKPFK YNHPQGFFSH R

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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

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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

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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: 51.612164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMKGSAWSH PQFEKLEVLF QGPMAENDVD NELLDYEDDE VETAAGGDGA EAPAKKDVKG SYVSIHSSGF RDFLLKPELL RAIVDCGFE HPSEVQHECI PQAILGMDVL CQAKSGMGKT AVFVLATLQQ LEPVTGQVSV LVMCHTRELA FQISKEYERF S KYMPNVKV ...String:
GPMKGSAWSH PQFEKLEVLF QGPMAENDVD NELLDYEDDE VETAAGGDGA EAPAKKDVKG SYVSIHSSGF RDFLLKPELL RAIVDCGFE HPSEVQHECI PQAILGMDVL CQAKSGMGKT AVFVLATLQQ LEPVTGQVSV LVMCHTRELA FQISKEYERF S KYMPNVKV AVFFGGLSIK KDEEVLKKNC PHIVVGTPGR ILALARNKSL NLKHIKHFIL DECDKMLEQL DMRRDVQEIF RM TPHEKQV MMFSATLSKE IRPVCRKFMQ DPMEIFVDDE TKLTLHGLQQ YYVKLKDNEK NRKLFDLLDV LEFNQVVIFV KSV QRCIAL AQLLVEQNFP AIAIHRGMPQ EERLSRYQQF KDFQRRILVA TNLFGRGMDI ERVNIAFNYD MPEDSDTYLH RVAR AGRFG TKGLAITFVS DENDAKILND VQDRFEVNIS ELPDEIDISS YIEQTR

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Macromolecule #8: THOC2 anchor (putative)

MacromoleculeName: THOC2 anchor (putative) / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.166895 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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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: 7.9
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHepes
50.0 mMKClpotassium chloride
1.0 mMC9H15O6PTCEP
2.0 %C3H8O3Glycerol
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 26303 / Average exposure time: 3.8 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1570265
CTF correctionSoftware - Name: Warp (ver. 1.07)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 195098

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7apk:
Structure of the human THO - UAP56 complex

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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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