[English] 日本語
Yorodumi
- EMDB-51383: Human 80S ribosome in complex with NatA in proximal and distal po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51383
TitleHuman 80S ribosome in complex with NatA in proximal and distal position
Map data
Sample
  • Complex: human 80S ribosome in complex with NatA and Ebp1
    • Protein or peptide: x 10 types
    • RNA: x 2 types
  • Protein or peptide: x 3 types
  • Ligand: x 1 types
Keywordshuman 80S ribosome / N-terminal acetylation (NTA) / N-acety-transferase A (NatA) in proximal and distal position / TRANSLATION
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / N-acetyltransferase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / N-acetyltransferase activity / acetyltransferase activator activity / translation at presynapse / eukaryotic 80S initiation complex / regulation of translation involved in cellular response to UV / axial mesoderm development / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / alpha-beta T cell differentiation / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / protein acetylation / middle ear morphogenesis / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / chromosome organization / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-RNA complex assembly / rough endoplasmic reticulum / cytosolic ribosome / ossification / positive regulation of translation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / skeletal system development / DNA damage response, signal transduction by p53 class mediator / sensory perception of sound / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / cellular response to UV / heparin binding / regulation of translation / presynapse / ribosome binding / cell body / angiogenesis / transcription regulator complex / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / rRNA binding / postsynaptic density / protein stabilization / nuclear body / structural constituent of ribosome / cadherin binding / translation / intracellular membrane-bounded organelle / ribonucleoprotein complex / focal adhesion / mRNA binding / synapse / dendrite / regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / glutamatergic synapse / endoplasmic reticulum / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Tetratricopeptide repeat / Ribosomal protein L28e / Gcn5-related N-acetyltransferase (GNAT) domain profile. / Ribosomal protein L23 ...N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Tetratricopeptide repeat / Ribosomal protein L28e / Gcn5-related N-acetyltransferase (GNAT) domain profile. / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / GNAT domain / TPR repeat region circular profile. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L6e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / TPR repeat profile. / Ribosomal Protein L6, KOW domain / 60S ribosomal protein L35 / Acyl-CoA N-acyltransferase / 60S ribosomal protein L19 / Ribosomal protein L6e / 60S ribosomal protein L6E / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Tetratricopeptide repeats / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Tetratricopeptide repeat / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Tetratricopeptide-like helical domain superfamily / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / Ribosomal protein L23 / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L25/L23 / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL38 ...Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL6 / N-alpha-acetyltransferase 15, NatA auxiliary subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsKlein MA / Wild K / Sinning I
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: structure of human RAF complexes
Authors: Klein MA / Wild K / Sinning I
History
DepositionAug 21, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51383.png

Downloads & links

-
Map

FileDownload / File: emd_51383.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 640 pix.
= 782.72 Å		1.22 Å/pix.
x 640 pix.
= 782.72 Å		1.22 Å/pix.
x 640 pix.
= 782.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.223 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.1480317 - 2.758073
Average (Standard dev.)-0.0014309352 (±0.11491571)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 782.72003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_51383_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51383_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : human 80S ribosome in complex with NatA and Ebp1

EntireName: human 80S ribosome in complex with NatA and Ebp1
Components
  • Complex: human 80S ribosome in complex with NatA and Ebp1
    • Protein or peptide: N-alpha-acetyltransferase 10
    • RNA: 28S rRNA
    • RNA: 5.8S rRNA
    • Protein or peptide: 60S ribosomal protein L4
    • Protein or peptide: Large ribosomal subunit protein eL6
    • Protein or peptide: 60S ribosomal protein L38
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: 60S ribosomal protein L35
    • Protein or peptide: 60S ribosomal protein L23a
    • Protein or peptide: 60S ribosomal protein L19
    • Protein or peptide: 60S ribosomal protein L28
    • Protein or peptide: Large ribosomal subunit protein eL22
  • Protein or peptide: N-alpha-acetyltransferase 15, NatA auxiliary subunit
  • Protein or peptide: 60S ribosomal protein L31
  • Protein or peptide: 60S ribosomal protein L17
  • Ligand: INOSITOL HEXAKISPHOSPHATE

+
Supramolecule #1: human 80S ribosome in complex with NatA and Ebp1

SupramoleculeName: human 80S ribosome in complex with NatA and Ebp1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#13
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: N-alpha-acetyltransferase 10

MacromoleculeName: N-alpha-acetyltransferase 10 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: N-terminal amino-acid Nalpha-acetyltransferase NatA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.496564 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNIRNARPED LMNMQHCNLL CLPENYQMKY YFYHGLSWPQ LSYIAEDENG KIVGYVLAKM EEDPDDVPHG HITSLAVKRS HRRLGLAQK LMDQASRAMI ENFNAKYVSL HVRKSNRAAL HLYSNTLNFQ ISEVEPKYYA DGEDAYAMKR DLTQMADELR R HLELKEKG ...String:
MNIRNARPED LMNMQHCNLL CLPENYQMKY YFYHGLSWPQ LSYIAEDENG KIVGYVLAKM EEDPDDVPHG HITSLAVKRS HRRLGLAQK LMDQASRAMI ENFNAKYVSL HVRKSNRAAL HLYSNTLNFQ ISEVEPKYYA DGEDAYAMKR DLTQMADELR R HLELKEKG RHVVLGAIEN KVESKGNSPP SSGEACREEK GLAAEDSGGD SKDLSEVSET TESTDVKDSS EASDSAS

UniProtKB: N-alpha-acetyltransferase 10

+
Macromolecule #2: N-alpha-acetyltransferase 15, NatA auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 15, NatA auxiliary subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.658648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPAVSLPPKE NALFKRILRC YEHKQYRNGL KFCKQILSNP KFAEHGETLA MKGLTLNCLG KKEEAYELVR RGLRNDLKSH VCWHVYGLL QRSDKKYDEA IKCYRNALKW DKDNLQILRD LSLLQIQMRD LEGYRETRYQ LLQLRPAQRA SWIGYAIAYH L LEDYEMAA ...String:
MPAVSLPPKE NALFKRILRC YEHKQYRNGL KFCKQILSNP KFAEHGETLA MKGLTLNCLG KKEEAYELVR RGLRNDLKSH VCWHVYGLL QRSDKKYDEA IKCYRNALKW DKDNLQILRD LSLLQIQMRD LEGYRETRYQ LLQLRPAQRA SWIGYAIAYH L LEDYEMAA KILEEFRKTQ QTSPDKVDYE YSELLLYQNQ VLREAGLYRE ALEHLCTYEK QICDKLAVEE TKGELLLQLC RL EDAADVY RGLQERNPEN WAYYKGLEKA LKPANMLERL KIYEEAWTKY PRGLVPRRLP LNFLSGEKFK ECLDKFLRMN FSK GCPPVF NTLRSLYKDK EKVAIIEELV VGYETSLKSC RLFNPNDDGK EEPPTTLLWV QYYLAQHYDK IGQPSIALEY INTA IESTP TLIELFLVKA KIYKHAGNIK EAARWMDEAQ ALDTADRFIN SKCAKYMLKA NLIKEAEEMC SKFTREGTSA VENLN EMQC MWFQTECAQA YKAMNKFGEA LKKCHEIERH FIEITDDQFD FHTYCMRKIT LRSYVDLLKL EDVLRQHPFY FKAARI AIE IYLKLHDNPL TDENKEHEAD TANMSDKELK KLRNKQRRAQ KKAQIEEEKK NAEKEKQQRN QKKKKDDDDE EIGGPKE EL IPEKLAKVET PLEEAIKFLT PLKNLVKNKI ETHLFAFEIY FRKEKFLLML QSVKRAFAID SSHPWLHECM IRLFNTVC E SKDLSDTVRT VLKQEMNRLF GATNPKNFNE TFLKRNSDSL PHRLSAAKMV YYLDPSSQKR AIELATTLDE SLTNRNLQT CMEVLEALYD GSLGDCKEAA EIYRANCHKL FPYALAFMPP

UniProtKB: N-alpha-acetyltransferase 15, NatA auxiliary subunit

+
Macromolecule #5: 60S ribosomal protein L4

MacromoleculeName: 60S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.804621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MACARPLISV YSEKGESSGK NVTLPAVFKA PIRPDIVNFV HTNLRKNNRQ PYAVSELAGH QTSAESWGTG RAVARIPRVR GGGTHRSGQ GAFGNMCRGG RMFAPTKTWR RWHRRVNTTQ KRYAICSALA ASALPALVMS KGHRIEEVPE LPLVVEDKVE G YKKTKEAV ...String:
MACARPLISV YSEKGESSGK NVTLPAVFKA PIRPDIVNFV HTNLRKNNRQ PYAVSELAGH QTSAESWGTG RAVARIPRVR GGGTHRSGQ GAFGNMCRGG RMFAPTKTWR RWHRRVNTTQ KRYAICSALA ASALPALVMS KGHRIEEVPE LPLVVEDKVE G YKKTKEAV LLLKKLKAWN DIKKVYASQR MRAGKGKMRN RRRIQRRGPC IIYNEDNGII KAFRNIPGIT LLNVSKLNIL KL APGGHVG RFCIWTESAF RKLDELYGTW RKAASLKSNY NLPMHKMINT DLSRILKSPE IQRALRAPRK KIHRRVLKKN PLK NLRIML KLNPYAKTMR RNTILRQARN HKLRVDKAAA AAAALQAKSD EKAAVAGKKP VVGKKGKKAA VGVKKQKKPL VGKK AAATK KPAPEKKPAE KKPTTEEKKP AA

UniProtKB: Large ribosomal subunit protein uL4

+
Macromolecule #6: Large ribosomal subunit protein eL6

MacromoleculeName: Large ribosomal subunit protein eL6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.810176 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGEKVEKPD TKEKKPEAKK VDAGGKVKKG NLKAKKPKKG KPHCSRNPVL VRGIGRYSRS AMYSRKAMYK RKYSAAKSKV EKKKKEKVL ATVTKPVGGD KNGGTRVVKL RKMPRYYPTE DVPRKLLSHG KKPFSQHVRK LRASITPGTI LIILTGRHRG K RVVFLKQL ...String:
MAGEKVEKPD TKEKKPEAKK VDAGGKVKKG NLKAKKPKKG KPHCSRNPVL VRGIGRYSRS AMYSRKAMYK RKYSAAKSKV EKKKKEKVL ATVTKPVGGD KNGGTRVVKL RKMPRYYPTE DVPRKLLSHG KKPFSQHVRK LRASITPGTI LIILTGRHRG K RVVFLKQL ASGLLLVTGP LVLNRVPLRR THQKFVIATS TKIDISNVKI PKHLTDAYFK KKKLRKPRHQ EGEIFDTEKE KY EITEQRK IDQKAVDSQI LPKIKAIPQL QGYLRSVFAL TNGIYPHKLV F

UniProtKB: Large ribosomal subunit protein eL6

+
Macromolecule #7: 60S ribosomal protein L38

MacromoleculeName: 60S ribosomal protein L38 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.238948 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MPRKIEEIKD FLLTARRKDA KSVKIKKNKD NVKFKVRCSR YLYTLVITDK EKAEKLKQSL PPGLAVKELK

UniProtKB: Large ribosomal subunit protein eL38

+
Macromolecule #8: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.303363 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MKFNPFVTSD RSKNRKRHFN APSHIRRKIM SSPLSKELRQ KYNVRSMPIR KDDEVQVVRG HYKGQQIGKV VQVYRKKYVI YIERVQREK ANGTTVHVGI HPSKVVITRL KLDKDRKKIL ERKAKSRQVG KEKGKYKEET IEKMQE

UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #9: 60S ribosomal protein L35

MacromoleculeName: 60S ribosomal protein L35 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.462429 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AKIKARDLRG KKKEELLKQL DDLKVELSQL RVAKVTGGAA SKLSKIRVVR KSIARVLTVI NQTQKENLRK FYKGKKYKPL DLRPKKTRA MRRRLNKHEE NLKTKKQQRK ERLYPLRKYA VKA

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #10: 60S ribosomal protein L23a

MacromoleculeName: 60S ribosomal protein L23a / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.740193 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAPKAKKEAP APPKAEAKAK ALKAKKAVLK GVHSHKKKKI RTSPTFRRPK TLRLRRQPKY PRKSAPRRNK LDHYAIIKFP LTTESAMKK IEDNNTLVFI VDVKANKHQI KQAVKKLYDI DVAKVNTLIR PDGEKKAYVR LAPDYDALDV ANKIGII

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #11: 60S ribosomal protein L19

MacromoleculeName: 60S ribosomal protein L19 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.535281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSMLRLQKRL ASSVLRCGKK KVWLDPNETN EIANANSRQQ IRKLIKDGLI IRKPVTVHSR ARCRKNTLAR RKGRHMGIGK RKGTANARM PEKVTWMRRM RILRRLLRRY RESKKIDRHM YHSLYLKVKG NVFKNKRILM EHIHKLKADK ARKKLLADQA E ARRSKTKE ...String:
MSMLRLQKRL ASSVLRCGKK KVWLDPNETN EIANANSRQQ IRKLIKDGLI IRKPVTVHSR ARCRKNTLAR RKGRHMGIGK RKGTANARM PEKVTWMRRM RILRRLLRRY RESKKIDRHM YHSLYLKVKG NVFKNKRILM EHIHKLKADK ARKKLLADQA E ARRSKTKE ARKRREERLQ AKKEEIIKTL SKEEETKK

UniProtKB: Large ribosomal subunit protein eL19

+
Macromolecule #12: 60S ribosomal protein L28

MacromoleculeName: 60S ribosomal protein L28 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.784622 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSAHLQWMVV RNCSSFLIKR NKQTYSTEPN NLKARNSFRY NGLIHRKTVG VEPAADGKGV VVVIKRRSGQ RKPATSYVRT TINKNARAT LSSIRHMIRK NKYRPDLRMA AIRRASAILR SQKPVMVKRK RTRPTKSS

UniProtKB: Large ribosomal subunit protein eL28

+
Macromolecule #13: Large ribosomal subunit protein eL22

MacromoleculeName: Large ribosomal subunit protein eL22 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.681819 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
APVKKLVVKG GKKKKQVLKF TLDCTHPVED GIMDAANFEQ FLQERIKVNG KAGNLGGGVV TIERSKSKIT VTSEVPFSKR YLKYLTKKY LKKNNLRDWL RVVANSKESY ELRYFQINQD EEEEEDED

UniProtKB: Large ribosomal subunit protein eL22

+
Macromolecule #14: 60S ribosomal protein L31

MacromoleculeName: 60S ribosomal protein L31 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.494938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAPAKKGGEK KKGRSAINEV VTREYTINIH KRIHGVGFKK RAPRALKEIR KFAMKEMGTP DVRIDTRLNK AVWAKGIRNV PYRIRVRLS RKRNEDEDSP NKLYTLVTYV PVTTFKNLQT VNVDEN

UniProtKB: Large ribosomal subunit protein eL31

+
Macromolecule #15: 60S ribosomal protein L17

MacromoleculeName: 60S ribosomal protein L17 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.44317 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVRYSLDPEN PTKSCKSRGS NLRVHFKNTR ETAQAIKGMH IRKATKYLKD VTLQKQCVPF RRYNGGVGRC AQAKQWGWTQ GRWPKKSAE FLLHMLKNAE SNAELKGLDV DSLVIEHIQV NKAPKMRRRT YRAHGRINPY MSSPCHIEMI LTEKEQIVPK P EEEVAQKK KISQKKLKKQ KLMARE

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #3: 28S rRNA

MacromoleculeName: 28S rRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.640222125 MDa
SequenceString: CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAAC GGCGAGUGAA CAGGGAAGAG CCCAGCGCCG AAUCCCCGCC CCGCGGCGGG GCGCGGGACA UGUGGCGUAC G GAAGACCC ...String:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAAC GGCGAGUGAA CAGGGAAGAG CCCAGCGCCG AAUCCCCGCC CCGCGGCGGG GCGCGGGACA UGUGGCGUAC G GAAGACCC GCUCCCCGGC GCCGCUCGUG GGGGGCCCAA GUCCUUCUGA UCGAGGCCCA GCCCGUGGAC GGUGUGAGGC CG GUAGCGG CCCCCGGCGC GCCGGGCCCG GGUCUUCCCG GAGUCGGGUU GCUUGGGAAU GCAGCCCAAA GCGGGUGGUA AAC UCCAUC UAAGGCUAAA UACCGGCACG AGACCGAUAG UCAACAAGUA CCGUAAGGGA AAGUUGAAAA GAACUUUGAA GAGA GAGUU CAAGAGGGCG UGAAACCGUU AAGAGGUAAA CGGGUGGGGU CCGCGCAGUC CGCCCGGAGG AUUCAACCCG GCGGC GGGU CCGGCCGUGU CGGCGGCCCG GCGGAUCUUU CCCGCCCCCC GUUCCUCCCG ACCCCUCCAC CCGCCCUCCC UUCCCC CGC CGCCCCUCCU CCUCCUCCCC GGAGGGGGCG GGCUCCGGCG GGUGCGGGGG UGGGCGGGCG GGGCCGGGGG UGGGGUC GG CGGGGGACCG UCCCCCGACC GGCGACCGGC CGCCGCCGGG CGCAUUUCCA CCGCGGCGGU GCGCCGCGAC CGGCUCCG G GACGGCUGGG AAGGCCCGGC GGGGAAGGUG GCUCGGGGGG CCCCGUCCGU CCGUCCGUCC GUCCUCCUCC UCCCCCGUC UCCGCCCCCC GGCCCCGCGU CCUCCCUCGG GAGGGCGCGC GGGUCGGGGC GGCGGCGGCG GCGGCGGUGG CGGCGGCGGC GGCGGCGGC GGGACCGAAA CCCCCCCCGA GUGUUACAGC CCCCCCGGCA GCAGCACUCG CCGAAUCCCG GGGCCGAGGG A GCGAGACC CGUCGCCGCG CUCUCCCCCC UCCCGGCGCC CACCCCCGCG GGGAAUCCCC CGCGAGGGGG GUCUCCCCCG CG GGGGCGC GCCGGCGUCU CCUCGUGGGG GGGCCGGGCC ACCCCUCCCA CGGCGCGACC GCUCUCCCAC CCCUCCUCCC CGC GCCCCC GCCCCGGCGA CGGGGGGGGU GCCGCGCGCG GGUCGGGGGG CGGGGCGGAC UGUCCCCAGU GCGCCCCGGG CGGG UCGCG CCGUCGGGCC CGGGGGAGGU UCUCUCGGGG CCACGCGCGC GUCCCCCGAA GAGGGGGACG GCGGAGCGAG CGCAC GGGG UCGGCGGCGA CGUCGGCUAC CCACCCGACC CGUCUUGAAA CACGGACCAA GGAGUCUAAC ACGUGCGCGA GUCGGG GGC UCGCACGAAA GCCGCCGUGG CGCAAUGAAG GUGAAGGCCG GCGCGCUCGC CGGCCGAGGU GGGAUCCCGA GGCCUCU CC AGUCCGCCGA GGGCGCACCA CCGGCCCGUC UCGCCCGCCG CGCCGGGGAG GUGGAGCACG AGCGCACGUG UUAGGACC C GAAAGAUGGU GAACUAUGCC UGGGCAGGGC GAAGCCAGAG GAAACUCUGG UGGAGGUCCG UAGCGGUCCU GACGUGCAA AUCGGUCGUC CGACCUGGGU AUAGGGGCGA AAGACUAAUC GAACCAUCUA GUAGCUGGUU CCCUCCGAAG UUUCCCUCAG GAUAGCUGG CGCUCUCGCA GACCCGACGC ACCCCCGCCA CGCAGUUUUA UCCGGUAAAG CGAAUGAUUA GAGGUCUUGG G GCCGAAAC GAUCUCAACC UAUUCUCAAA CUUUAAAUGG GUAAGAAGCC CGGCUCGCUG GCGUGGAGCC GGGCGUGGAA UG CGAGUGC CUAGUGGGCC ACUUUUGGUA AGCAGAACUG GCGCUGCGGG AUGAACCGAA CGCCGGGUUA AGGCGCCCGA UGC CGACGC UCAUCAGACC CCAGAAAAGG UGUUGGUUGA UAUAGACAGC AGGACGGUGG CCAUGGAAGU CGGAAUCCGC UAAG GAGUG UGUAACAACU CACCUGCCGA AUCAACUAGC CCUGAAAAUG GAUGGCGCUG GAGCGUCGGG CCCAUACCCG GCCGU CGCC GGCAGUCGAG AGUGGACGGG AGCGGCGGGG GCGGCGCGCG CGCGCGCGCG UGUGGUGUGC GUCGGAGGGC GGCGGC GGC GGCGGCGGCG GGGGUGUGGG GUCCUUCCCC CGCCCCCCCC CCCACGCCUC CUCCCCUCCU CCCGCCCACG CCCCGCU CC CCGCCCCCGG AGCCCCGCGG ACGCUACGCC GCGACGAGUA GGAGGGCCGC UGCGGUGAGC CUUGAAGCCU AGGGCGCG G GCCCGGGUGG AGCCGCCGCA GGUGCAGAUC UUGGUGGUAG UAGCAAAUAU UCAAACGAGA ACUUUGAAGG CCGAAGUGG AGAAGGGUUC CAUGUGAACA GCAGUUGAAC AUGGGUCAGU CGGUCCUGAG AGAUGGGCGA GCGCCGUUCC GAAGGGACGG GCGAUGGCC UCCGUUGCCC UCGGCCGAUC GAAAGGGAGU CGGGUUCAGA UCCCCGAAUC CGGAGUGGCG GAGAUGGGCG C CGCGAGGC GUCCAGUGCG GUAACGCGAC CGAUCCCGGA GAAGCCGGCG GGAGCCCCGG GGAGAGUUCU CUUUUCUUUG UG AAGGGCA GGGCGCCCUG GAAUGGGUUC GCCCCGAGAG AGGGGCCCGU GCCUUGGAAA GCGUCGCGGU UCCGGCGGCG UCC GGUGAG CUCUCGCUGG CCCUUGAAAA UCCGGGGGAG AGGGUGUAAA UCUCGCGCCG GGCCGUACCC AUAUCCGCAG CAGG UCUCC AAGGUGAACA GCCUCUGGCA UGUUGGAACA AUGUAGGUAA GGGAAGUCGG CAAGCCGGAU CCGUAACUUC GGGAU AAGG AUUGGCUCUA AGGGCUGGGU CGGUCGGGCU GGGGCGCGAA GCGGGGCUGG GCGCGCGCCG CGGCUGGACG AGGCGC CGC CGCCCCCCCC ACGCCCGGGG CACCCCCCUC GCGGCCCUCC CCCGCCCCAC CCCGCGCGCG CCGCUCGCUC CCUCCCC GC CCCGCGCCCU CUCUCUCUCU CUCUCCCCCG CUCCCCGUCC UCCCCCCUCC CCGGGGGAGC GCCGCGUGGG GGCGGCGG C GGGGGGAGAA GGGUCGGGGC GGCAGGGGCC GGCGGCGGCC CGCCGCGGGG CCCCGGCGGC GGGGGCACGG UCCCCCGCG AGGGGGGCCC GGGCACCCGG GGGGCCGGCG GCGGCGGCGA CUCUGGACGC GAGCCGGGCC CUUCCCGUGG AUCGCCCCAG CUGCGGCGG GCGUCGCGGC CGCCCCCGGG GAGCCCGGCG GGCGCCGGCG CGCCCCCCCC CCCACCCCAC GUCUCGUCGC G CGCGCGUC CGCUGGGGGC GGGGAGCGGU CGGGCGGCGG CGGUCGGCGG GCGGCGGGGC GGGGCGGUUC GUCCCCCCGC CC UACCCCC CCGGCCCCGU CCGCCCCCCG UUCCCCCCUC CUCCUCGGCG CGCGGCGGCG GCGGCGGCAG GCGGCGGAGG GGC CGCGGG CCGGUCCCCC CCGCCGGGUC CGCCCCCGGG GCCGCGGUUC CGCGCGGCGC CUCGCCUCGG CCGGCGCCUA GCAG CCGAC UUAGAACUGG UGCGGACCAG GGGAAUCCGA CUGUUUAAUU AAAACAAAGC AUCGCGAAGG CCCGCGGCGG GUGUU GACG CGAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAU GAAGCGCGGG UAAACGGCGG GAGUAA CUA UGACUCUCUU AAGGUAGCCA AAUGCCUCGU CAUCUAAUUA GUGACGCGCA UGAAUGGAUG AACGAGAUUC CCACUGU CC CUACCUACUA UCCAGCGAAA CCACAGCCAA GGGAACGGGC UUGGCGGAAU CAGCGGGGAA AGAAGACCCU GUUGAGCU U GACUCUAGUC UGGCACGGUG AAGAGACAUG AGAGGUGUAG AAUAAGUGGG AGGCCCCCGG CGCCCCCCCG GUGUCCCCG CGAGGGGCCC GGGGCGGGGU CCGCCGGCCC UGCGGGCCGC CGGUGAAAUA CCACUACUCU GAUCGUUUUU UCACUGACCC GGUGAGGCG GGGGGGCGAG CCCCGAGGGG CUCUCGCUUC UGGCGCCAAG CGCCCGGCCG CGCGCCGGCC GGGCGCGACC C GCUCCGGG GACAGUGCCA GGUGGGGAGU UUGACUGGGG CGGUACACCU GUCAAACGGU AACGCAGGUG UCCUAAGGCG AG CUCAGGG AGGACAGAAA CCUCCCGUGG AGCAGAAGGG CAAAAGCUCG CUUGAUCUUG AUUUUCAGUA CGAAUACAGA CCG UGAAAG CGGGGCCUCA CGAUCCUUCU GACCUUUUGG GUUUUAAGCA GGAGGUGUCA GAAAAGUUAC CACAGGGAUA ACUG GCUUG UGGCGGCCAA GCGUUCAUAG CGACGUCGCU UUUUGAUCCU UCGAUGUCGG CUCUUCCUAU CAUUGUGAAG CAGAA UUCA CCAAGCGUUG GAUUGUUCAC CCACUAAUAG GGAACGUGAG CUGGGUUUAG ACCGUCGUGA GACAGGUUAG UUUUAC CCU ACUGAUGAUG UGUUGUUGCC AUGGUAAUCC UGCUCAGUAC GAGAGGAACC GCAGGUUCAG ACAUUUGGUG UAUGUGC UU GGCUGAGGAG CCAAUGGGGC GAAGCUACCA UCUGUGGGAU UAUGACUGAA CGCCUCUAAG UCAGAAUCCC GCCCAGGC G GAACGAUACG GCAGCGCCGC GGAGCCUCGG UUGGCCUCGG AUAGCCGGUC CCCCGCCUGU CCCCGCCGGC GGGCCGCCC CCCCCCUCCA CGCGCCCCGC GCGCGCGGGA GGGCGCGUGC CCCGCCGCGC GCCGGGACCG GGGUCCGGUG CGGAGUGCCC UUCGUCCUG GGAAACGGGG CGCGGCCGGA GAGGCGGCCG CCCCCUCGCC CGUCACGCAC CGCACGUUCG UGGGGAACCU G GCGCUAAA CCAUUCGUAG ACGACCUGCU UCUGGGUCGG GGUUUCGUAC GUAGCAGAGC AGCUCCCUCG CUGCGAUCUA UU GAAAGUC AGCCCUCGAC ACAAGGGUUU GUC

+
Macromolecule #4: 5.8S rRNA

MacromoleculeName: 5.8S rRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.449812 KDa
SequenceString:
CGACUCUUAG CGGUGGAUCA CUCGGCUCGU GCGUCGAUGA AGAACGCAGC UAGCUGCGAG AAUUAAUGUG AAUUGCAGGA CACAUUGAU CAUCGACACU UCGAACGCAC UUGCGGCCCC GGGUUCCUCC CGGGGCUACG CCUGUCUGAG CGUCGCUU

GENBANK: GENBANK: NR_145819.1

+
Macromolecule #16: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 16 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 27.51 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6sxo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17765
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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