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- EMDB-50641: Human NatA-MAP2 80S ribosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-50641
TitleHuman NatA-MAP2 80S ribosome complex
Map data
Sample
  • Complex: human NatA and MAP2 bound to the PTE of the 80S ribosome
    • Protein or peptide: x 11 types
    • RNA: x 2 types
  • Ligand: x 2 types
Keywordsco-translational processing / ribosome associated factor (RAF) / methionine aminopeptidase 2 (MAP2) / N-terminal methionine excision (NME) / N-acetyl-transferase A (NatA) / N-termional acetylation (NTA) / UBA domain / a-solenoid / protein-protein and protein-RNA interactions / TRANSLATION
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / eukaryotic 80S initiation complex / axial mesoderm development / metalloexopeptidase activity / 90S preribosome assembly / N-acetyltransferase activity / TORC2 complex binding / middle ear morphogenesis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / internal protein amino acid acetylation / protein acetylation / Peptide chain elongation / Selenocysteine synthesis / metalloaminopeptidase activity / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / chromosome organization / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / aminopeptidase activity / rough endoplasmic reticulum / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / ribosomal large subunit biogenesis / skeletal system development / positive regulation of translation / sensory perception of sound / protein processing / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to UV / ribosome binding / regulation of translation / cell body / angiogenesis / transcription regulator complex / cytosolic large ribosomal subunit / cytoplasmic translation / postsynaptic density / cell differentiation / nuclear body / protein stabilization / rRNA binding / structural constituent of ribosome / ribonucleoprotein complex / cadherin binding / translation / intracellular membrane-bounded organelle / focal adhesion / mRNA binding / synapse / dendrite / regulation of DNA-templated transcription / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Peptidase M24A, methionine aminopeptidase, subfamily 2 / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain ...N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Peptidase M24A, methionine aminopeptidase, subfamily 2 / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Metallopeptidase family M24 / Tetratricopeptide repeat / Creatinase/aminopeptidase-like / Acetyltransferase (GNAT) family / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / 60S ribosomal protein L19 / 60S ribosomal protein L35 / Ribosomal Protein L6, KOW domain / Ribosomal protein L6e / TPR repeat region circular profile. / 60S ribosomal protein L6E / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / TPR repeat profile. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Tetratricopeptide repeat / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 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 / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Ribosomal protein L23/L15e core domain superfamily / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 / Methionine aminopeptidase 2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / 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: 2.69 Å
AuthorsKlein MA / Wild K / Sinning I
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Multi-protein assemblies orchestrate enzymatic processing of the nascent chain on the 80S ribosome
Authors: Klein MA / Wild K / Sinning I
History
DepositionJun 14, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50641.png

Downloads & links

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Map

FileDownload / File: emd_50641.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.16646926 - 0.4570433
Average (Standard dev.)0.000121019955 (±0.020057173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 604.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50641_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50641_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human NatA and MAP2 bound to the PTE of the 80S ribosome

EntireName: human NatA and MAP2 bound to the PTE of the 80S ribosome
Components
  • Complex: human NatA and MAP2 bound to the PTE of the 80S ribosome
    • Protein or peptide: N-alpha-acetyltransferase 10
    • RNA: 5.8S rRNA (58-MER)
    • Protein or peptide: Methionine aminopeptidase 2
    • Protein or peptide: N-alpha-acetyltransferase 15, NatA auxiliary subunit
    • RNA: 28S rRNA (300-MER, fragments)
    • 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
  • Ligand: COBALT (II) ION
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: human NatA and MAP2 bound to the PTE of the 80S ribosome

SupramoleculeName: human NatA and MAP2 bound to the PTE of the 80S ribosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: N-alpha-acetyltransferase 10

MacromoleculeName: N-alpha-acetyltransferase 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal amino-acid Nalpha-acetyltransferase NatA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.003795 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MGNIRNARPE DLMNMQHCNL LCLPENYQMK YYFYHGLSWP QLSYIAEDEN GKIVGYVLAK MEEDPDDVPH GHITSLAVKR SHRRLGLAQ KLMDQASRAM IENFNAKYVS LHVRKSNRAA LHLYSNTLNF QISEVEPKYY ADGEDAYAMK RDLTQMADEL R RHLELKEK GRH

UniProtKB: N-alpha-acetyltransferase 10

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Macromolecule #3: Methionine aminopeptidase 2

MacromoleculeName: Methionine aminopeptidase 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: methionyl aminopeptidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.413945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSGSMAGV EEVAASGSHL NGDLDPDDRE EGAASTAEEA AKKKRRKKKK SKGPSAAGEQ EPDKESGASV DEVARQLERS ALEDKERDE DDEDGDGDGD GATGKKKKKK KKKRGPKVQT DPPSVPICDL YPNGVFPKGQ ECEYPPTQDG RTAAWRTTSE E KKALDQAS ...String:
GPGSGSMAGV EEVAASGSHL NGDLDPDDRE EGAASTAEEA AKKKRRKKKK SKGPSAAGEQ EPDKESGASV DEVARQLERS ALEDKERDE DDEDGDGDGD GATGKKKKKK KKKRGPKVQT DPPSVPICDL YPNGVFPKGQ ECEYPPTQDG RTAAWRTTSE E KKALDQAS EEIWNDFREA AEAHRQVRKY VMSWIKPGMT MIEICEKLED CSRKLIKENG LNAGLAFPTG CSLNNCAAHY TP NAGDTTV LQYDDICKID FGTHISGRII DCAFTVTFNP KYDTLLKAVK DATNTGIKCA GIDVRLCDVG EAIQEVMESY EVE IDGKTY QVKPIRNLNG HSIGQYRIHA GKTVPIVKGG EATRMEEGEV YAIETFGSTG KGVVHDDMEC SHYMKNFDVG HVPI RLPRT KHLLNVINEN FGTLAFCRRW LDRLGESKYL MALKNLCDLG IVDPYPPLCD IKGSYTAQFE HTILLRPTCK EVVSR GDDY

UniProtKB: Methionine aminopeptidase 2

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Macromolecule #4: N-alpha-acetyltransferase 15, NatA auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 15, NatA auxiliary subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.658648 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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Macromolecule #6: 60S ribosomal protein L4

MacromoleculeName: 60S ribosomal protein L4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.804621 KDa
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

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Macromolecule #7: Large ribosomal subunit protein eL6

MacromoleculeName: Large ribosomal subunit protein eL6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.810176 KDa
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

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Macromolecule #8: 60S ribosomal protein L38

MacromoleculeName: 60S ribosomal protein L38 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.238948 KDa
SequenceString:
MPRKIEEIKD FLLTARRKDA KSVKIKKNKD NVKFKVRCSR YLYTLVITDK EKAEKLKQSL PPGLAVKELK

UniProtKB: Large ribosomal subunit protein eL38

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Macromolecule #9: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.174184 KDa
SequenceString:
MKFNPFVTSD RSKNRKRHFN APSHIRRKIM SSPLSKELRQ KYNVRSMPIR KDDEVQVVRG HYKGQQIGKV VQVYRKKYVI YIERVQREK ANGTTVHVGI HPSKVVITRL KLDKDRKKIL ERKAKSRQVG EKGKYKEETI EKMQE

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #10: 60S ribosomal protein L35

MacromoleculeName: 60S ribosomal protein L35 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.462429 KDa
SequenceString:
AKIKARDLRG KKKEELLKQL DDLKVELSQL RVAKVTGGAA SKLSKIRVVR KSIARVLTVI NQTQKENLRK FYKGKKYKPL DLRPKKTRA MRRRLNKHEE NLKTKKQQRK ERLYPLRKYA VKA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #11: 60S ribosomal protein L23a

MacromoleculeName: 60S ribosomal protein L23a / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.740193 KDa
SequenceString:
MAPKAKKEAP APPKAEAKAK ALKAKKAVLK GVHSHKKKKI RTSPTFRRPK TLRLRRQPKY PRKSAPRRNK LDHYAIIKFP LTTESAMKK IEDNNTLVFI VDVKANKHQI KQAVKKLYDI DVAKVNTLIR PDGEKKAYVR LAPDYDALDV ANKIGII

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #12: 60S ribosomal protein L19

MacromoleculeName: 60S ribosomal protein L19 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.535281 KDa
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

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Macromolecule #13: 60S ribosomal protein L28

MacromoleculeName: 60S ribosomal protein L28 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.784622 KDa
SequenceString:
MSAHLQWMVV RNCSSFLIKR NKQTYSTEPN NLKARNSFRY NGLIHRKTVG VEPAADGKGV VVVIKRRSGQ RKPATSYVRT TINKNARAT LSSIRHMIRK NKYRPDLRMA AIRRASAILR SQKPVMVKRK RTRPTKSS

UniProtKB: Large ribosomal subunit protein eL28

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Macromolecule #2: 5.8S rRNA (58-MER)

MacromoleculeName: 5.8S rRNA (58-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.646127 KDa
SequenceString:
AACGCAGCUA GCUGCGAGAA UUAAUGUGAA UUGCAGGACA CAUUGAUCAU CGACACUU

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Macromolecule #5: 28S rRNA (300-MER, fragments)

MacromoleculeName: 28S rRNA (300-MER, fragments) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.089398 KDa
SequenceString: CAAGUCCUUC UGAUCGAGGC CCAGCCCGUG GACGGUGUGA GGCCGGUAGU UGAAAAGAAC UUUGAAGAGA GAGUUCAAGA GGGCGCCGC CCGGAGGAUU CAACCCGGCG GCGGGUCCGG CCGUGUCGGC GGCCCGGCGG AUCUUUCCCG CGCGGGGGAC C GUCCCCCG ...String:
CAAGUCCUUC UGAUCGAGGC CCAGCCCGUG GACGGUGUGA GGCCGGUAGU UGAAAAGAAC UUUGAAGAGA GAGUUCAAGA GGGCGCCGC CCGGAGGAUU CAACCCGGCG GCGGGUCCGG CCGUGUCGGC GGCCCGGCGG AUCUUUCCCG CGCGGGGGAC C GUCCCCCG ACCGGCGACC GGCCGCCGCC GGGCGCAUUU CCACCGCGGC GGUUCAAACG AGAACUUUGA AUCGGGUUCA GA UCCCCGA AUCUUGGAAA GCGUCGCGGU UCCGGCGGCG UAAGGGCUGG UAGCAGCCGA CUU

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Macromolecule #14: COBALT (II) ION

MacromoleculeName: COBALT (II) ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: CO
Molecular weightTheoretical: 58.933 Da

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Macromolecule #15: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 15 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.28 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ek0
PDB Unreleased entry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25404
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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  • 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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