[English] 日本語
Yorodumi
- EMDB-43822: Human Drosha and DGCR8 in complex with Pri-let-7a1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43822
TitleHuman Drosha and DGCR8 in complex with Pri-let-7a1
Map data
Sample
  • Complex: RNAi_protein_a1
    • Protein or peptide: Isoform 4 of Drosha
    • Protein or peptide: Microprocessor complex subunit DGCR8
    • RNA: Pri-let-7a1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsRNAi / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / primary miRNA binding / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process / primary miRNA processing ...positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / primary miRNA binding / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process / primary miRNA processing / regulation of stem cell proliferation / ribonuclease III activity / microprocessor complex / pre-miRNA processing / MicroRNA (miRNA) biogenesis / SMAD binding / R-SMAD binding / lipopolysaccharide binding / rRNA processing / double-stranded RNA binding / site of double-strand break / protein-macromolecule adaptor activity / regulation of inflammatory response / defense response to Gram-negative bacterium / postsynaptic density / nuclear body / defense response to Gram-positive bacterium / glutamatergic synapse / heme binding / DNA damage response / positive regulation of gene expression / nucleolus / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RNase III, double-stranded RNA binding domain, animal / Microprocessor complex subunit DGCR8 / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif ...RNase III, double-stranded RNA binding domain, animal / Microprocessor complex subunit DGCR8 / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Microprocessor complex subunit DGCR8 / Ribonuclease 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGarg A / Joshua-Tor L
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 GM114147 United States
CitationJournal: To Be Published
Title: RNAi_protein_a1
Authors: Garg A / Joshua-Tor L
History
DepositionFeb 26, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43822.png

Downloads & links

-
Map

FileDownload / File: emd_43822.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. 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: 0.151
Minimum - Maximum-0.13468434 - 0.7728058
Average (Standard dev.)0.0012200162 (±0.020190137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_43822_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43822_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43822_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RNAi_protein_a1

EntireName: RNAi_protein_a1
Components
  • Complex: RNAi_protein_a1
    • Protein or peptide: Isoform 4 of Drosha
    • Protein or peptide: Microprocessor complex subunit DGCR8
    • RNA: Pri-let-7a1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: water

-
Supramolecule #1: RNAi_protein_a1

SupramoleculeName: RNAi_protein_a1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 300 KDa

-
Macromolecule #1: Isoform 4 of Drosha

MacromoleculeName: Isoform 4 of Drosha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease III
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 155.574297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMQGNTCHRM SFHPGRGCPR GRGGHGARPS APSFRPQNLR LLHPQQPPVQ YQYEPPSAPS TTFSNSPAPN FLPPRPDFVP FPPPMPPSA QGPLPPCPIR PPFPNHQMRH PFPVPPCFPP MPPPMPCPNN PPVPGAPPGQ GTFPFMMPPP SMPHPPPPPV M PQQVNYQY ...String:
MMQGNTCHRM SFHPGRGCPR GRGGHGARPS APSFRPQNLR LLHPQQPPVQ YQYEPPSAPS TTFSNSPAPN FLPPRPDFVP FPPPMPPSA QGPLPPCPIR PPFPNHQMRH PFPVPPCFPP MPPPMPCPNN PPVPGAPPGQ GTFPFMMPPP SMPHPPPPPV M PQQVNYQY PPGYSHHNFP PPSFNSFQNN PSSFLPSANN SSSPHFRHLP PYPLPKAPSE RRSPERLKHY DDHRHRDHSH GR GERHRSL DRRERGRSPD RRRQDSRYRS DYDRGRTPSR HRSYERSRER ERERHRHRDN RRSPSLERSY KKEYKRSGSR SPS REKKRA RWEEEKDRWS DNQSSGKDKN YTSIKEKEPE ETMPDKNEEE EEELLKPVWI RCTHSENYYS SDPMDQVGDS TVVG TSRLR DLYDKFEEEL GSRQEKAKAA RPPWEPPKTK LDEDLESSSE SECESDEDST CSSSSDSEVF DVIAEIKRKK AHPDR LHDE LWYNDPGQMN DGPLCKCSAK ARRTGIRHSI YPGEEAIKPC RPMTNNAGRL FHYRITVSPP TNFLTDRPTV IEYDDH EYI FEGFSMFAHA PLTNIPLCKV IRFNIDYTIH FIEEMMPENF CVKGLELFSL FLFRDILELY DWNLKGPLFE DSPPCCP RF HFMPRFVRFL PDGGKEVLSM HQILLYLLRC SKALVPEEEI ANMLQWEELE WQKYAEECKG MIVTNPGTKP SSVRIDQL D REQFNPDVIT FPIIVHFGIR PAQLSYAGDP QYQKLWKSYV KLRHLLANSP KVKQTDKQKL AQREEALQKI RQKNTMRRE VTVELSSQGF WKTGIRSDVC QHAMMLPVLT HHIRYHQCLM HLDKLIGYTF QDRCLLQLAM THPSHHLNFG MNPDHARNSL SNCGIRQPK YGDRKVHHMH MRKKGINTLI NIMSRLGQDD PTPSRINHNE RLEFLGDAVV EFLTSVHLYY LFPSLEEGGL A TYRTAIVQ NQHLAMLAKK LELDRFMLYA HGPDLCRESD LRHAMANCFE ALIGAVYLEG SLEEAKQLFG RLLFNDPDLR EV WLNYPLH PLQLQEPNTD RQLIETSPVL QKLTEFEEAI GVIFTHVRLL ARAFTLRTVG FNHLTLGHNQ RMEFLGDSIM QLV ATEYLF IHFPDHHEGH LTLLRSSLVN NRTQAKVAEE LGMQEYAITN DKTKRPVALR TKTLADLLES FIAALYIDKD LEYV HTFMN VCFFPRLKEF ILNQDWNDPK SQLQQCCLTL RTEGKEPDIP LYKTLQTVGP SHARTYTVAV YFKGERIGCG KGPSI QQAE MGAAMDALEK YNFPQMAHQK RFIERKYRQE LKEMRWEREH QEREPDETED IKK

UniProtKB: Ribonuclease 3

-
Macromolecule #2: Microprocessor complex subunit DGCR8

MacromoleculeName: Microprocessor complex subunit DGCR8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.171203 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: METDESPSPL PCGPAGEAVM ESRARPFQAL PREQSPPPPL QTSSGAEVMD VGSGGDGQSE LPAEDPFNFY GASLLSKGSF SKGRLLIDP NCSGHSPRTA RHAPAVRKFS PDLKLLKDVK ISVSFTESCR SKDRKVLYTG AERDVRAECG LLLSPVSGDV H ACPFGGSV ...String:
METDESPSPL PCGPAGEAVM ESRARPFQAL PREQSPPPPL QTSSGAEVMD VGSGGDGQSE LPAEDPFNFY GASLLSKGSF SKGRLLIDP NCSGHSPRTA RHAPAVRKFS PDLKLLKDVK ISVSFTESCR SKDRKVLYTG AERDVRAECG LLLSPVSGDV H ACPFGGSV GDGVGIGGES ADKKDEENEL DQEKRVEYAV LDELEDFTDN LELDEEGAGG FTAKAIVQRD RVDEEALNFP YE DDFDNDV DALLEEGLCA PKKRRTEEKY GGDSDHPSDG ETSVQPMMTK IKTVLKSRGR PPTEPLPDGW IMTFHNSGVP VYL HRESRV VTWSRPYFLG TGSIRKHDPP LSSIPCLHYK KMKDNEEREQ SSDLTPSGDV SPVKPLSRSA ELEFPLDEPD SMGA DPGPP DEKDPLGAEA APGALGQVKA KVEVCKDESV DLEEFRSYLE KRFDFEQVTV KKFRTWAERR QFNREMKRKQ AESER PILP ANQKLITLSV QDAPTKKEFV INPNGKSEVC ILHEYMQRVL KVRPVYNFFE CENPSEPFGA SVTIDGVTYG SGTASS KKL AKNKAARATL EILIPDFVKQ TSEEKPKDSE ELEYFNHISI EDSRVYELTS KAGLLSPYQI LHECLKRNHG MGDTSIK FE VVPGKNQKSE YVMACGKHTV RGWCKNKRVG KQLASQKILQ LLHPHVKNWG SLLRMYGRES SKMVKQETSD KSVIELQQ Y AKKNKPNLHI LSKLQEEMKR LAEEREETRK KPKMSIVASA QPGGEPLCTV DV

UniProtKB: Microprocessor complex subunit DGCR8

-
Macromolecule #3: Pri-let-7a1

MacromoleculeName: Pri-let-7a1 / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.174496 KDa
SequenceString:
UGGAUGUUCU CUUCACUGUG GGAUGAGGUA GUAGGUUGUA UAGUUUUAGG GUCACACCCA CCACUGGGAG AUAACUAUAC AAUCUACUG UCUUUCCUAA CGUGAUAGAA AAGUCUGCAU

GENBANK: GENBANK: AL158152.18

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 72.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 323645
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