[English] 日本語
Yorodumi
- EMDB-10769: Structure of a human 48S translational initiation complex - eIF3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10769
TitleStructure of a human 48S translational initiation complex - eIF3
Map data
Sample
  • Complex: 48S initiation complex
    • Protein or peptide: x 19 types
Function / homology
Function and homology information


positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / cytoplasmic translational initiation ...positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / metal-dependent deubiquitinase activity / negative regulation of RNA splicing / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / regulation of translational initiation / laminin receptor activity / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / ubiquitin ligase inhibitor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / fibroblast growth factor binding / SARS-CoV-1 modulates host translation machinery / protein deubiquitination / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / 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 / translation regulator activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / translation initiation factor binding / laminin binding / maturation of SSU-rRNA / Mitotic Prometaphase / negative regulation of translational initiation / EML4 and NUDC in mitotic spindle formation / negative regulation of ubiquitin-dependent protein catabolic process / translational initiation / Resolution of Sister Chromatid Cohesion / translation initiation factor activity / small-subunit processome / cytosolic ribosome / erythrocyte differentiation / : / positive regulation of translation / mRNA 3'-UTR binding / neural tube closure / RHO GTPases Activate Formins / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / PML body / small ribosomal subunit rRNA binding / fibrillar center / RMTs methylate histone arginines / rRNA processing / Regulation of expression of SLITs and ROBOs / ribosomal small subunit assembly / Separation of Sister Chromatids / metallopeptidase activity / cytosolic small ribosomal subunit / ribosome binding / virus receptor activity / small ribosomal subunit / cytoplasmic translation / SARS-CoV-2 modulates host translation machinery / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / postsynaptic density / cell differentiation / protein stabilization / ribosome / structural constituent of ribosome / cadherin binding / translation / ribonucleoprotein complex / focal adhesion / mRNA binding / centrosome
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain ...Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Eukaryotic translation initiation factor 3 subunit A / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / 40S ribosomal protein SA / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / : / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S7e / Ribosomal S17 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal S11, conserved site / Ribosomal_S15 / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal protein S11 / Ribosomal protein S11 / Ribosomal protein S15 / Ribosomal protein S11 signature. / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS27 / Eukaryotic translation initiation factor 3 subunit E / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 ...Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS27 / Eukaryotic translation initiation factor 3 subunit E / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS21 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit L
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBrito Querido J / Sokabe M / Kraatz S / Gordiyenko Y / Skehel M / Fraser C / Ramakrishnan V
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
History
DepositionMar 16, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ybd
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ybd
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10769.png

Downloads & links

-
Map

FileDownload / File: emd_10769.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.04
Minimum - Maximum-0.18092114 - 0.29472923
Average (Standard dev.)0.0009115565 (±0.00900954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 300.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z300.720300.720300.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1810.2950.001

-
Supplemental data

-
Mask #1

Fileemd_10769_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_10769_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_10769_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_10769_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : 48S initiation complex

EntireName: 48S initiation complex
Components
  • Complex: 48S initiation complex
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit MEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit FEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit AEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit EEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit CEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit HEukaryotic initiation factor 3
    • Protein or peptide: 40S ribosomal protein S7
    • Protein or peptide: 40S ribosomal protein S27
    • Protein or peptide: 40S ribosomal protein S21
    • Protein or peptide: 40S ribosomal protein S17
    • Protein or peptide: 40S ribosomal protein S2
    • Protein or peptide: 40S ribosomal protein S3a
    • Protein or peptide: 40S ribosomal protein SA
    • Protein or peptide: 40S ribosomal protein S26
    • Protein or peptide: 40S ribosomal protein S14
    • Protein or peptide: 40S ribosomal protein S13
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit DEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit KEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit LEukaryotic initiation factor 3

+
Supramolecule #1: 48S initiation complex

SupramoleculeName: 48S initiation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Eukaryotic translation initiation factor 3 subunit M

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit M / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 42.555832 KDa
SequenceString: MSVPAFIDIS EEDQAAELRA YLKSKGAEIS EENSEGGLHV DLAQIIEACD VCLKEDDKDV ESVMNSVVSL LLILEPDKQE ALIESLCEK LVKFREGERP SLRLQLLSNL FHGMDKNTPV RYTVYCSLIK VAASCGAIQY IPTELDQVRK WISDWNLTTE K KHTLLRLL ...String:
MSVPAFIDIS EEDQAAELRA YLKSKGAEIS EENSEGGLHV DLAQIIEACD VCLKEDDKDV ESVMNSVVSL LLILEPDKQE ALIESLCEK LVKFREGERP SLRLQLLSNL FHGMDKNTPV RYTVYCSLIK VAASCGAIQY IPTELDQVRK WISDWNLTTE K KHTLLRLL YEALVDCKKS DAASKVMVEL LGSYTEDNAS QARVDAHRCI VRALKDPNAF LFDHLLTLKP VKFLEGELIH DL LTIFVSA KLASYVKFYQ NNKDFIDSLG LLHEQNMAKM RLLTFMGMAV ENKEISFDTM QQELQIGADD VEAFVIDAVR TKM VYCKID QTQRKVVVSH STHRTFGKQQ WQQLYDTLNA WKQNLNKVKN SLLSLSDT

+
Macromolecule #2: Eukaryotic translation initiation factor 3 subunit F

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit F / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 37.593645 KDa
SequenceString: MATPAVPVSA PPATPTPVPA AAPASVPAPT PAPAAAPVPA AAPASSSDPA AAAAATAAPG QTPASAQAPA QTPAPALPGP ALPGPFPGG RVVRLHPVIL ASIVDSYERR NEGAARVIGT LLGTVDKHSV EVTNCFSVPH NESEDEVAVD MEFAKNMYEL H KKVSPNEL ...String:
MATPAVPVSA PPATPTPVPA AAPASVPAPT PAPAAAPVPA AAPASSSDPA AAAAATAAPG QTPASAQAPA QTPAPALPGP ALPGPFPGG RVVRLHPVIL ASIVDSYERR NEGAARVIGT LLGTVDKHSV EVTNCFSVPH NESEDEVAVD MEFAKNMYEL H KKVSPNEL ILGWYATGHD ITEHSVLIHE YYSREAPNPI HLTVDTSLQN GRMSIKAYVS TLMGVPGRTM GVMFTPLTVK YA YYDTERI GVDLIMKTCF SPNRVIGLSS DLQQVGGASA RIQDALSTVL QYAEDVLSGK VSADNTVGRF LMSLVNQVPK IVP DDFETM LNSNINDLLM VTYLANLTQS QIALNEKLVN L

+
Macromolecule #3: Eukaryotic translation initiation factor 3 subunit A

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 166.903781 KDa
SequenceString: MPAYFQRPEN ALKRANEFLE VGKKQPALDV LYDVMKSKKH RTWQKIHEPI MLKYLELCVD LRKSHLAKEG LYQYKNICQQ VNIKSLEDV VRAYLKMAEE KTEAAKEESQ QMVLDIEDLD NIQTPESVLL SAVSGEDTQD RTDRLLLTPW VKFLWESYRQ C LDLLRNNS ...String:
MPAYFQRPEN ALKRANEFLE VGKKQPALDV LYDVMKSKKH RTWQKIHEPI MLKYLELCVD LRKSHLAKEG LYQYKNICQQ VNIKSLEDV VRAYLKMAEE KTEAAKEESQ QMVLDIEDLD NIQTPESVLL SAVSGEDTQD RTDRLLLTPW VKFLWESYRQ C LDLLRNNS RVERLYHDIA QQAFKFCLQY TRKAEFRKLC DNLRMHLSQI QRHHNQSTAI NLNNPESQSM HLETRLVQLD SA ISMELWQ EAFKAVEDIH GLFSLSKKPP KPQLMANYYN KVSTVFWKSG NALFHASTLH RLYHLSREMR KNLTQDEMQR MST RVLLAT LSIPITPERT DIARLLDMDG IIVEKQRRLA TLLGLQAPPT RIGLINDMVR FNVLQYVVPE VKDLYNWLEV EFNP LKLCE RVTKVLNWVR EQPEKEPELQ QYVPQLQNNT ILRLLQQVSQ IYQSIEFSRL TSLVPFVDAF QLERAIVDAA RHCDL QVRI DHTSRTLSFG SDLNYATRED APIGPHLQSM PSEQIRNQLT AMSSVLAKAL EVIKPAHILQ EKEEQHQLAV TAYLKN SRK EHQRILARRQ TIEERKERLE SLNIQREKEE LEQREAELQK VRKAEEERLR QEAKEREKER ILQEHEQIKK KTVRERL EQ IKKTELGAKA FKDIDIEDLE ELDPDFIMAK QVEQLEKEKK ELQERLKNQE KKIDYFERAK RLEEIPLIKS AYEEQRIK D MDLWEQQEEE RITTMQLERE KALEHKNRMS RMLEDRDLFV MRLKAARQSV YEEKLKQFEE RLAEERHNRL EERKRQRKE ERRITYYREK EEEEQRRAEE QMLKEREERE RAERAKREEE LREYQERVKK LEEVERKKRQ RELEIEERER RREEERRLGD SSLSRKDSR WGDRDSEGTW RKGPEADSEW RRGPPEKEWR RGEGRDEDRS HRRDEERPRR LGDDEDREPS LRPDDDRVPR R GMDDDRGP RRGPEEDRFS RRGADDDRPS WRNTDDDRPP RRIADEDRGN WRHADDDRPP RRGLDEDRGS WRTADEDRGP RR GMDDDRG PRRGGADDER SSWRNADDDR GPRRGLDDDR GPRRGMDDDR GPRRGMDDDR GPRRGMDDDR GPRRGLDDDR GPW RNADDD RIPRRGAEDD RGPWRNMDDD RLSRRADDDR FPRRGDDSRP GPWRPLVKPG GWREKEKARE ESWGPPRESR PSEE REWDR EKERDRDNQD REENDKDPER ERDRERDVDR EDRFRRPRDE GGWRRGPAEE SSSWRDSSRR DDRDRDDRRR ERDDR RDLR ERRDLRDDRD RRGPPLRSER EEVSSWRRAD DRKDDRVEER DPPRRVPPPA LSRDRERDRD REREGEKEKA SWRAEK DRE SLRRTKNETD EDGWTTVRR

+
Macromolecule #4: Eukaryotic translation initiation factor 3 subunit E

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit E / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 52.281633 KDa
SequenceString: MAEYDLTTRI AHFLDRHLVF PLLEFLSVKE IYNEKELLQG KLDLLSDTNM VDFAMDVYKN LYSDDIPHAL REKRTTVVAQ LKQLQAETE PIVKMFEDPE TTRQMQSTRD GRMLFDYLAD KHGFRQEYLD TLYRYAKFQY ECGNYSGAAE YLYFFRVLVP A TDRNALSS ...String:
MAEYDLTTRI AHFLDRHLVF PLLEFLSVKE IYNEKELLQG KLDLLSDTNM VDFAMDVYKN LYSDDIPHAL REKRTTVVAQ LKQLQAETE PIVKMFEDPE TTRQMQSTRD GRMLFDYLAD KHGFRQEYLD TLYRYAKFQY ECGNYSGAAE YLYFFRVLVP A TDRNALSS LWGKLASEIL MQNWDAAMED LTRLKETIDN NSVSSPLQSL QQRTWLIHWS LFVFFNHPKG RDNIIDLFLY QP QYLNAIQ TMCPHILRYL TTAVITNKDV RKRRQVLKDL VKVIQQESYT YKDPITEFVE CLYVNFDFDG AQKKLRECES VLV NDFFLV ACLEDFIENA RLFIFETFCR IHQCISINML ADKLNMTPEE AERWIVNLIR NARLDAKIDS KLGHVVMGNN AVSP YQQVI EKTKSLSFRS QMLAMNIEKK LNQNSRSEAP NWATQDSGFY

+
Macromolecule #5: Eukaryotic translation initiation factor 3 subunit C

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 105.503945 KDa
SequenceString: MSRFFTTGSD SESESSLSGE ELVTKPVGGN YGKQPLLLSE DEEDTKRVVR SAKDKRFEEL TNLIRTIRNA MKIRDVTKCL EEFELLGKA YGKAKSIVDK EGVPRFYIRI LADLEDYLNE LWEDKEGKKK MNKNNAKALS TLRQKIRKYN RDFESHITSY K QNPEQSAD ...String:
MSRFFTTGSD SESESSLSGE ELVTKPVGGN YGKQPLLLSE DEEDTKRVVR SAKDKRFEEL TNLIRTIRNA MKIRDVTKCL EEFELLGKA YGKAKSIVDK EGVPRFYIRI LADLEDYLNE LWEDKEGKKK MNKNNAKALS TLRQKIRKYN RDFESHITSY K QNPEQSAD EDAEKNEEDS EGSSDEDEDE DGVSAATFLK KKSEAPSGES RKFLKKMDDE DEDSEDSEDD EDWDTGSTSS DS DSEEEEG KQTALASRFL KKAPTTDEDK KAAEKKREDK AKKKHDRKSK RLDEEEEDNE GGEWERVRGG VPLVKEKPKM FAK GTEITH AVVIKKLNEI LQARGKKGTD RAAQIELLQL LVQIAAENNL GEGVIVKIKF NIIASLYDYN PNLATYMKPE MWGK CLDCI NELMDILFAN PNIFVGENIL EESENLHNAD QPLRVRGCIL TLVERMDEEF TKIMQNTDPH SQEYVEHLKD EAQVC AIIE RVQRYLEEKG TTEEVCRIYL LRILHTYYKF DYKAHQRQLT PPEGSSKSEQ DQAENEGEDS AVLMERLCKY IYAKDR TDR IRTCAILCHI YHHALHSRWY QARDLMLMSH LQDNIQHADP PVQILYNRTM VQLGICAFRQ GLTKDAHNAL LDIQSSG RA KELLGQGLLL RSLQERNQEQ EKVERRRQVP FHLHINLELL ECVYLVSAML LEIPYMAAHE SDARRRMISK QFHHQLRV G ERQPLLGPPE SMREHVVAAS KAMKMGDWKT CHSFIINEKM NGKVWDLFPE ADKVRTMLVR KIQEESLRTY LFTYSSVYD SISMETLSDM FELDLPTVHS IISKMIINEE LMASLDQPTQ TVVMHRTEPT AQQNLALQLA EKLGSLVENN ERVFDHKQGT YGGYFRDQK DGYRKNEGYM RRGGYRQQQS QTAY

+
Macromolecule #6: Eukaryotic translation initiation factor 3 subunit H

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit H / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 39.979277 KDa
SequenceString: MASRKEGTGS TATSSSSTAG AAGKGKGKGG SGDSAVKQVQ IDGLVVLKII KHYQEEGQGT EVVQGVLLGL VVEDRLEITN CFPFPQHTE DDADFDEVQY QMEMMRSLRH VNIDHLHVGW YQSTYYGSFV TRALLDSQFS YQHAIEESVV LIYDPIKTAQ G SLSLKAYR ...String:
MASRKEGTGS TATSSSSTAG AAGKGKGKGG SGDSAVKQVQ IDGLVVLKII KHYQEEGQGT EVVQGVLLGL VVEDRLEITN CFPFPQHTE DDADFDEVQY QMEMMRSLRH VNIDHLHVGW YQSTYYGSFV TRALLDSQFS YQHAIEESVV LIYDPIKTAQ G SLSLKAYR LTPKLMEVCK EKDFSPEALK KANITFEYMF EEVPIVIKNS HLINVLMWEL EKKSAVADKH ELLSLASSNH LG KNLQLLM DRVDEMSQDI VKYNTYMRNT SKQQQQKHQY QQRRQQENMQ RQSRGEPPLP EEDLSKLFKP PQPPARMDSL LIA GQINTY CQNIKEFTAQ NLGKLFMAQA LQEYNN

+
Macromolecule #7: 40S ribosomal protein S7

MacromoleculeName: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 22.168914 KDa
SequenceString: MFSSSAKIVK PNGEKPDEFE SGISQALLEL EMNSDLKAQL RELNITAAKE IEVGGGRKAI IIFVPVPQLK SFQKIQVRLV RELEKKFSG KHVVFIAQRR ILPKPTRKSR TKNKQKRPRS RTLTAVHDAI LEDLVFPSEI VGKRIRVKLD GSRLIKVHLD K AQQNNVEH ...String:
MFSSSAKIVK PNGEKPDEFE SGISQALLEL EMNSDLKAQL RELNITAAKE IEVGGGRKAI IIFVPVPQLK SFQKIQVRLV RELEKKFSG KHVVFIAQRR ILPKPTRKSR TKNKQKRPRS RTLTAVHDAI LEDLVFPSEI VGKRIRVKLD GSRLIKVHLD K AQQNNVEH KVETFSGVYK KLTGKDVNFE FPEFQL

+
Macromolecule #8: 40S ribosomal protein S27

MacromoleculeName: 40S ribosomal protein S27 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 9.480186 KDa
SequenceString:
MPLAKDLLHP SPEEEKRKHK KKRLVQSPNS YFMDVKCPGC YKITTVFSHA QTVVLCVGCS TVLCQPTGGK ARLTEGCSFR RKQH

+
Macromolecule #9: 40S ribosomal protein S21

MacromoleculeName: 40S ribosomal protein S21 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 9.124389 KDa
SequenceString:
MQNDAGEFVD LYVPRKCSAS NRIIGAKDHA SIQMNVAEVD KVTGRFNGQF KTYAICGAIR RMGESDDSIL RLAKADGIVS KNF

+
Macromolecule #10: 40S ribosomal protein S17

MacromoleculeName: 40S ribosomal protein S17 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.578156 KDa
SequenceString:
MGRVRTKTVK KAARVIIEKY YTRLGNDFHT NKRVCEEIAI IPSKKLRNKI AGYVTHLMKR IQRGPVRGIS IKLQEEERER RDNYVPEVS ALDQEIIEVD PDTKEMLKLL DFGSLSNLQV TQPTVGMNFK TPRGPV

+
Macromolecule #11: 40S ribosomal protein S2

MacromoleculeName: 40S ribosomal protein S2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 31.376516 KDa
SequenceString: MADDAGAAGG PGGPGGPGMG NRGGFRGGFG SGIRGRGRGR GRGRGRGRGA RGGKAEDKEW MPVTKLGRLV KDMKIKSLEE IYLFSLPIK ESEIIDFFLG ASLKDEVLKI MPVQKQTRAG QRTRFKAFVA IGDYNGHVGL GVKCSKEVAT AIRGAIILAK L SIVPVRRG ...String:
MADDAGAAGG PGGPGGPGMG NRGGFRGGFG SGIRGRGRGR GRGRGRGRGA RGGKAEDKEW MPVTKLGRLV KDMKIKSLEE IYLFSLPIK ESEIIDFFLG ASLKDEVLKI MPVQKQTRAG QRTRFKAFVA IGDYNGHVGL GVKCSKEVAT AIRGAIILAK L SIVPVRRG YWGNKIGKPH TVPCKVTGRC GSVLVRLIPA PRGTGIVSAP VPKKLLMMAG IDDCYTSARG CTATLGNFAK AT FDAISKT YSYLTPDLWK ETVFTKSPYQ EFTDHLVKTH TRVSVQRTQA PAVATT

+
Macromolecule #12: 40S ribosomal protein S3a

MacromoleculeName: 40S ribosomal protein S3a / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 30.002061 KDa
SequenceString: MAVGKNKRLT KGGKKGAKKK VVDPFSKKDW YDVKAPAMFN IRNIGKTLVT RTQGTKIASD GLKGRVFEVS LADLQNDEVA FRKFKLITE DVQGKNCLTN FHGMDLTRDK MCSMVKKWQT MIEAHVDVKT TDGYLLRLFC VGFTKKRNNQ IRKTSYAQHQ Q VRQIRKKM ...String:
MAVGKNKRLT KGGKKGAKKK VVDPFSKKDW YDVKAPAMFN IRNIGKTLVT RTQGTKIASD GLKGRVFEVS LADLQNDEVA FRKFKLITE DVQGKNCLTN FHGMDLTRDK MCSMVKKWQT MIEAHVDVKT TDGYLLRLFC VGFTKKRNNQ IRKTSYAQHQ Q VRQIRKKM MEIMTREVQT NDLKEVVNKL IPDSIGKDIE KACQSIYPLH DVFVRKVKML KKPKFELGKL MELHGEGSSS GK ATGDETG AKVERADGYE PPVQESV

+
Macromolecule #13: 40S ribosomal protein SA

MacromoleculeName: 40S ribosomal protein SA / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 32.883938 KDa
SequenceString: MSGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSVISSR NTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQAAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRYVDI A IPCNNKGA ...String:
MSGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSVISSR NTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQAAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRYVDI A IPCNNKGA HSVGLMWWML AREVLRMRGT ISREHPWEVM PDLYFYRDPE EIEKEEQAAA EKAVTKEEFQ GEWTAPAPEF TA TQPEVAD WSEGVQVPSV PIQQFPTEDW SAQPATEDWS AAPTAQATEW VGATTDWS

+
Macromolecule #14: 40S ribosomal protein S26

MacromoleculeName: 40S ribosomal protein S26 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 13.047532 KDa
SequenceString:
MTKKRRNNGR AKKGRGHVQP IRCTNCARCV PKDKAIKKFV IRNIVEAAAV RDISEASVFD AYVLPKLYVK LHYCVSCAIH SKVVRNRSR EARKDRTPPP RFRPAGAAPR PPPKPM

+
Macromolecule #15: 40S ribosomal protein S14

MacromoleculeName: 40S ribosomal protein S14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 16.302772 KDa
SequenceString:
MAPRKGKEKK EEQVISLGPQ VAEGENVFGV CHIFASFNDT FVHVTDLSGK ETICRVTGGM KVKADRDESS PYAAMLAAQD VAQRCKELG ITALHIKLRA TGGNRTKTPG PGAQSALRAL ARSGMKIGRI EDVTPIPSDS TRRKGGRRGR RL

+
Macromolecule #16: 40S ribosomal protein S13

MacromoleculeName: 40S ribosomal protein S13 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.259389 KDa
SequenceString:
MGRMHAPGKG LSQSALPYRR SVPTWLKLTS DDVKEQIYKL AKKGLTPSQI GVILRDSHGV AQVRFVTGNK ILRILKSKGL APDLPEDLY HLIKKAVAVR KHLERNRKDK DAKFRLILIE SRIHRLARYY KTKRVLPPNW KYESSTASAL VA

+
Macromolecule #17: Eukaryotic translation initiation factor 3 subunit D

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit D / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 64.060758 KDa
SequenceString: MAKFMTPVIQ DNPSGWGPCA VPEQFRDMPY QPFSKGDRLG KVADWTGATY QDKRYTNKYS SQFGGGSQYA YFHEEDESSF QLVDTARTQ KTAYQRNRMR FAQRNLRRDK DRRNMLQFNL QILPKSAKQK ERERIRLQKK FQKQFGVRQK WDQKSQKPRD S SVEVRSDW ...String:
MAKFMTPVIQ DNPSGWGPCA VPEQFRDMPY QPFSKGDRLG KVADWTGATY QDKRYTNKYS SQFGGGSQYA YFHEEDESSF QLVDTARTQ KTAYQRNRMR FAQRNLRRDK DRRNMLQFNL QILPKSAKQK ERERIRLQKK FQKQFGVRQK WDQKSQKPRD S SVEVRSDW EVKEEMDFPQ LMKMRYLEVS EPQDIECCGA LEYYDKAFDR ITTRSEKPLR SIKRIFHTVT TTDDPVIRKL AK TQGNVFA TDAILATLMS CTRSVYSWDI VVQRVGSKLF FDKRDNSDFD LLTVSETANE PPQDEGNSFN SPRNLAMEAT YIN HNFSQQ CLRMGKERYN FPNPNPFVED DMDKNEIASV AYRYRRWKLG DDIDLIVRCE HDGVMTGANG EVSFINIKTL NEWD SRHCN GVDWRQKLDS QRGAVIATEL KNNSYKLARW TCCALLAGSE YLKLGYVSRY HVKDSSRHVI LGTQQFKPNE FASQI NLSV ENAWGILRCV IDICMKLEEG KYLILKDPNK QVIRVYSLPD GTFSSDEDEE EEEEEEEEEE EEET

+
Macromolecule #18: Eukaryotic translation initiation factor 3 subunit K

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit K / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 25.083619 KDa
SequenceString: MAMFEQMRAN VGKLLKGIDR YNPENLATLE RYVETQAKEN AYDLEANLAV LKLYQFNPAF FQTTVTAQIL LKALTNLPHT DFTLCKCMI DQAHQEERPI RQILYLGDLL ETCHFQAFWQ ALDENMDLLE GITGFEDSVR KFICHVVGIT YQHIDRWLLA E MLGDLSDS ...String:
MAMFEQMRAN VGKLLKGIDR YNPENLATLE RYVETQAKEN AYDLEANLAV LKLYQFNPAF FQTTVTAQIL LKALTNLPHT DFTLCKCMI DQAHQEERPI RQILYLGDLL ETCHFQAFWQ ALDENMDLLE GITGFEDSVR KFICHVVGIT YQHIDRWLLA E MLGDLSDS QLKVWMSKYG WSADESGQIF ICSQEESIKP KNIVEKIDFD SVSSIMASSQ

+
Macromolecule #19: Eukaryotic translation initiation factor 3 subunit L

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit L / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 66.803734 KDa
SequenceString: MSYPADDYES EAAYDPYAYP SDYDMHTGDP KQDLAYERQY EQQTYQVIPE VIKNFIQYFH KTVSDLIDQK VYELQASRVS SDVIDQKVY EIQDIYENSW TKLTERFFKN TPWPEAEAIA PQVGNDAVFL ILYKELYYRH IYAKVSGGPS LEQRFESYYN Y CNLFNYIL ...String:
MSYPADDYES EAAYDPYAYP SDYDMHTGDP KQDLAYERQY EQQTYQVIPE VIKNFIQYFH KTVSDLIDQK VYELQASRVS SDVIDQKVY EIQDIYENSW TKLTERFFKN TPWPEAEAIA PQVGNDAVFL ILYKELYYRH IYAKVSGGPS LEQRFESYYN Y CNLFNYIL NADGPAPLEL PNQWLWDIID EFIYQFQSFS QYRCKTAKKS EEEIDFLRSN PKIWNVHSVL NVLHSLVDKS NI NRQLEVY TSGGDPESVA GEYGRHSLYK MLGYFSLVGL LRLHSLLGDY YQAIKVLENI ELNKKSMYSR VPECQVTTYY YVG FAYLMM RRYQDAIRVF ANILLYIQRT KSMFQRTTYK YEMINKQNEQ MHALLAIALT MYPMRIDESI HLQLREKYGD KMLR MQKGD PQVYEELFSY SCPKFLSPVV PNYDNVHPNY HKEPFLQQLK VFSDEVQQQA QLSTIRSFLK LYTTMPVAKL AGFLD LTEQ EFRIQLLVFK HKMKNLVWTS GISALDGEFQ SASEVDFYID KDMIHIADTK VARRYGDFFI RQIHKFEELN RTLKKM GQR P

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 107.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

4kzy

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11882
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