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- EMDB-10323: IC2 body cryo-EM structure of a full archaeal ribosomal translati... -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-10323

Title

IC2 body cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

Map data

IC2 body map

Sample

Complex: Archaeal translation initiation complex devoid of aIF1 - IC2 body
- Complex: ribosome
  - RNA: x 1 types
  - Protein or peptide: x 16 types
- Complex: mRNAMessenger RNA
  - RNA: x 1 types
- Complex: Translation initiation factor 1A
  - Protein or peptide: x 1 types
Ligand: x 3 types

Keywords

Translation initiation /

cryo-EM /

ribosome /

tRNA /

evolution /

archaea / rRNA modifications

Function / homology

Function and homology information

translation initiation factor activity / cytosolic ribosome / small ribosomal subunit /

rRNA binding /

ribosome / structural constituent of ribosome /

translation /

ribonucleoprotein complex /

RNA binding / zinc ion binding
Similarity search - Function

Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / : /

Ribosomal protein S17, archaeal /

Ribosomal protein S6e, archaeal /

Ribosomal protein S4, archaeal /

Ribosomal protein S12, archaea /

30S ribosomal protein S3Ae /

Ribosomal protein S11, archaeal ...Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / : /

Ribosomal protein S17, archaeal /

Ribosomal protein S6e, archaeal /

Ribosomal protein S4, archaeal /

Ribosomal protein S12, archaea /

30S ribosomal protein S3Ae /

Ribosomal protein S11, archaeal /

Ribosomal protein S2, archaeal /

Ribosomal protein S8e, archaeal / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) /

RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. /

Ribosomal protein S3Ae, conserved site /

Ribosomal protein S2, eukaryotic/archaeal /

Ribosomal protein S5, eukaryotic/archaeal /

Ribosomal protein S8e, conserved site /

Ribosomal protein S4e, N-terminal, conserved site /

Ribosomal protein S27, zinc-binding domain superfamily /

Ribosomal protein S17, archaeal/eukaryotic /

Ribosomal protein S27 /

Ribosomal protein S6/S6e/A/B/2, conserved site /

Ribosomal protein S4e, N-terminal /

Ribosomal protein S23, eukaryotic/archaeal /

Ribosomal protein S3Ae / Ribosomal S3Ae family /

Ribosomal protein S8e /

Ribosomal protein S4, KOW domain /

Ribosomal protein S4e /

Ribosomal protein S4e, central region /

Ribosomal protein S4e, central domain superfamily /

Ribosomal protein S6e /

Ribosomal protein S13/S15, N-terminal /

Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain /

Ribosomal protein S6e /

Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain /

Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain /

Ribosomal protein S6e /

Ribosomal protein S3Ae signature. /

Ribosomal protein S27e signature. /

Ribosomal protein S4e signature. /

Ribosomal protein S8e signature. / Ribosomal S24e conserved site /

Ribosomal protein S24e signature. /

Ribosomal protein S24e /

Ribosomal protein S6e signature. /

Ribosomal protein S8e/ribosomal biogenesis NSA2 /

Ribosomal protein S8e /

Ribosomal protein S2 signature 2. /

: /

Ribosomal protein S17, conserved site /

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 S4/S9 N-terminal domain /

Ribosomal protein S4/S9, N-terminal /

Ribosomal protein S4, conserved site /

Ribosomal protein S4/S9 /

Ribosomal protein S8 /

Ribosomal protein S8 superfamily /

Ribosomal protein S5, N-terminal, conserved site /

Ribosomal protein S5 signature. /

Ribosomal protein S5 /

Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / S5 double stranded RNA-binding domain profile. /

Ribosomal protein S5, C-terminal /

Ribosomal protein S5, N-terminal domain /

Ribosomal protein S8 /

Ribosomal protein S17 signature. /

Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain /

Ribosomal protein S11 / RNA-binding S4 domain / RNA-binding S4 domain superfamily /

Ribosomal protein S8 signature. /

Ribosomal protein S11 /

Ribosomal protein S17/S11 /

S4 domain /

Ribosomal protein S4 signature. / Ribosomal_S15 /

Ribosomal protein S15 signature. /

Ribosomal protein S15 /

Ribosomal protein S12/S23 / KOW (Kyprides, Ouzounis, Woese) motif. /

Ribosomal protein S17
Similarity search - Domain/homology

Biological species

Pyrococcus abyssi GE5 (archaea) /

Pyrococcus abyssi (strain GE5 / Orsay) (archaea)

Method

single particle reconstruction /

cryo EM / Resolution: 3.2 Å

Authors

Coureux P-D / Mechulam Y / Schmitt E

Funding support

France, 1 items

Citation

Journal: Commun Biol / Year: 2020
Title: Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt /

Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP: ...

History

Deposition	Sep 20, 2019	-
Header (metadata) release	Feb 19, 2020	-
Map release	Feb 19, 2020	-
Update	Apr 24, 2024	-
Current status	Apr 24, 2024	Processing site: PDBe / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.006 Imaged by UCSF Chimera Download Surface view colored by height Surface level: 0.006 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-6swd Surface level: 0.006 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_10323.png

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Downloads & links

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EMDB archive

Map data	emd_10323.map.gz	126 MB		EMDB map data format
Header (meta data)	emd-10323-v30.xml emd-10323.xml	39.3 KB 39.3 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_10323_fsc.xml	15.9 KB	Display	FSC data file
Images	emd_10323.png	95.9 KB
Masks	emd_10323_msk_1.map	160.8 MB		Mask map
Filedesc metadata	emd-10323.cif.gz	9 KB
Others	emd_10323_additional.map.gz emd_10323_half_map_1.map.gz emd_10323_half_map_2.map.gz	12.7 MB 126.7 MB 126.7 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-10323 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10323	HTTPS FTP

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Related structure data

Related structure data	6swdMC 10320C 10322C 10324C 6sw9C 6swcC 6sweC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	11567 22039 7cbp-d 6d6q-d 6xas-d 7chh-d 4zux-1 7l09-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource
Related items in Molecule of the Month	#10 - Oct 2000 Ribosome similarity (1) #161 - May 2013 Ricin similarity (41)

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Map

File

Download / File: emd_10323.map.gz / Format: CCP4 / Size: 160.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Annotation

IC2 body map

Voxel size

X=Y=Z: 1.09 Å

Density

Contour Level	By AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum	-0.018816726 - 0.0495441
Average (Standard dev.)	-0.00016238765 (±0.0019113938)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	348	348	348
Spacing	348	348	348

Cell

A=B=C: 379.32 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.09	1.09	1.09
M x/y/z	348	348	348
origin x/y/z	0.000	0.000	0.000
length x/y/z	379.320	379.320	379.320
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	348	348	348
D min/max/mean	-0.019	0.050	-0.000

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Supplemental data

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Mask #1

File

emd_10323_msk_1.map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Additional map: IC2 body postprocessed map

File

emd_10323_additional.map

Annotation

IC2 body postprocessed map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: IC2 body half1 map

File

emd_10323_half_map_1.map

Annotation

IC2 body half1 map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: IC2 body half2 map

File

emd_10323_half_map_2.map

Annotation

IC2 body half2 map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Archaeal translation initiation complex devoid of aIF1 - IC2 body

Entire	Name: Archaeal translation initiation complex devoid of aIF1 - IC2 body
Components	Complex: Archaeal translation initiation complex devoid of aIF1 - IC2 body Complex: ribosome RNA: 16S ribosomal RNA Protein or peptide: 30S ribosomal protein S3AeRibosome Protein or peptide: 30S ribosomal protein S2 Protein or peptide: Zn-ribbon RNA-binding protein involved in translation Protein or peptide: 30S ribosomal protein S4 Protein or peptide: 30S ribosomal protein S4eRibosome Protein or peptide: 30S ribosomal protein S5 Protein or peptide: 30S ribosomal protein S6eRibosome Protein or peptide: 30S ribosomal protein S8 Protein or peptide: 30S ribosomal protein S8eRibosome Protein or peptide: 30S ribosomal protein S11 Protein or peptide: 30S ribosomal protein S12 Protein or peptide: 30S ribosomal protein S15 Protein or peptide: 30S ribosomal protein S17 Protein or peptide: 30S ribosomal protein S24eRibosome Protein or peptide: 30S ribosomal protein S27eRibosome Protein or peptide: 30S ribosomal protein aL41 Complex: mRNAMessenger RNA RNA: mRNAMessenger RNA Complex: Translation initiation factor 1A Protein or peptide: Translation initiation factor 1A Ligand: MAGNESIUM ION Ligand: ZINC ION Ligand: water

Entire

Name: Archaeal translation initiation complex devoid of aIF1 - IC2 body

Components

Complex: Archaeal translation initiation complex devoid of aIF1 - IC2 body
- Complex: ribosome
  - RNA: 16S ribosomal RNA
  - Protein or peptide: 30S ribosomal protein S3AeRibosome
  - Protein or peptide: 30S ribosomal protein S2
  - Protein or peptide: Zn-ribbon RNA-binding protein involved in translation
  - Protein or peptide: 30S ribosomal protein S4
  - Protein or peptide: 30S ribosomal protein S4eRibosome
  - Protein or peptide: 30S ribosomal protein S5
  - Protein or peptide: 30S ribosomal protein S6eRibosome
  - Protein or peptide: 30S ribosomal protein S8
  - Protein or peptide: 30S ribosomal protein S8eRibosome
  - Protein or peptide: 30S ribosomal protein S11
  - Protein or peptide: 30S ribosomal protein S12
  - Protein or peptide: 30S ribosomal protein S15
  - Protein or peptide: 30S ribosomal protein S17
  - Protein or peptide: 30S ribosomal protein S24eRibosome
  - Protein or peptide: 30S ribosomal protein S27eRibosome
  - Protein or peptide: 30S ribosomal protein aL41
- Complex: mRNAMessenger RNA
  - RNA: mRNAMessenger RNA
- Complex: Translation initiation factor 1A
  - Protein or peptide: Translation initiation factor 1A
Ligand: MAGNESIUM ION
Ligand: ZINC ION
Ligand: water

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Supramolecule #1: Archaeal translation initiation complex devoid of aIF1 - IC2 body

Supramolecule	Name: Archaeal translation initiation complex devoid of aIF1 - IC2 body type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Molecular weight	Theoretical: 1.05 MDa

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Supramolecule #2: ribosome

Supramolecule	Name: ribosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#17
Source (natural)	Organism: Pyrococcus abyssi GE5 (archaea)

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Supramolecule #3: mRNA

Supramolecule	Name: mRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #18
Source (natural)	Organism: Pyrococcus abyssi GE5 (archaea)

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Supramolecule #4: Translation initiation factor 1A

Supramolecule	Name: Translation initiation factor 1A / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #19
Source (natural)	Organism: Pyrococcus abyssi GE5 (archaea)

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Macromolecule #1: 16S ribosomal RNA

Macromolecule	Name: 16S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)	Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weight	Theoretical: 340.430125 KDa
Sequence	String: AUUC(4AC)GGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC AUGCGAGUCA AGGGGGCGUC CC UUCUGGG ACGCCACCGG CGGACGGCUC AGUAACACGU CGGUAACCUA CCCUCGGGAG GGGGAUAACC CCGGGAAACU GGG GCUAAU ...String: AUUC(4AC)GGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC AUGCGAGUCA AGGGGGCGUC CC UUCUGGG ACGCCACCGG CGGACGGCUC AGUAACACGU CGGUAACCUA CCCUCGGGAG GGGGAUAACC CCGGGAAACU GGG GCUAAU CCCCCAUAGG CCUGGGGUAC UGGAAGGUCC CCAGGCCGAA AGGGAGCCGU AAGGCUCCGC CCGAGGAUGG GCCG GCGGC (LHH)GAUUAGGUA GUUGGUGGGG UAACGGCCCA CCAAGC(4AC)GAA GAUCGGUACG GGC(4AC)GUGAGA GCG GGAGCC (4AC)GGAGAUGGA CACUGAGACA CGGGUCCAGG CCCUACGGGG CGCAGCAGGC GCGA(A2M)ACCUC (4AC)G CAAUGCG GGAAAC(4AC)GCG ACGGGGGGAC CCCCAGUGCC GUGCCUCUGG CACGGCUUUU CCGGAGUGUA AAAAGCUCC GGGAAUAAGG GCUGGGCAAG GC(4AC)GGUGGCA GCCGCCGCGG UAAUACCGGC GGCC(4AC)GAGUG GUGGCCACUA UU AUUGGGC CUAAAGCGGC (4AC)GUAGCCGGG CCCGUAAGUC CCUGGCGAAA UCCCACGGCU CAAC(4AC)GUGGG GCUCG CUGG GGAUACUGCG GGCCUUGGGA C(4AC)GGGAGAGG C(4AC)GGGGGUAC CCC(4AC)GGGGUA GGGGUGAAAU CCUA UAAUC CCGGGGGGAC CGCCAGUGGC GAAGGCGCC(4AC) GGCUGGAACG GGUC(4AC)GACGG UGAGGGC(4AC)GA AGG CCAGGG GAGCGAAC(4AC)G GAUUAGAUAC CCGGGUAGUC CUGGCUGUAA AGGAUGCGGG CUAGGUGUCG GGCGAGCUUC GAGCUCGCC CGGUGC(4AC)GUA GGGAAGC(4AC)GU UAAGCC(4AC)GC(4AC) GCCUGGGGAG UACGGC(4AC)GCA A GGCUGAAA CUUAAAGGAA UUGGCGGGGG AGCCUGCUCC UUGCACACAC CG(OMC)C(5HM)GUCAC UCCACCCGAG CGGG GCCUA GGUGAGGCCC GAUCUCCUUC GGGAGGUCGG GUCGAGCCUA GGCUCCGUGA GGGGGGAGAA GUCG(UR3)A(6MZ) CA AGGUAGC(4AC)GU AGGGG(MA6)(MA6)CCU ACGGCUCGAU CACCUCCU

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Macromolecule #18: mRNA

Macromolecule	Name: mRNA / type: rna / ID: 18 / Number of copies: 1
Source (natural)	Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weight	Theoretical: 6.448871 KDa
Sequence	String: UGGAGGUGAU UUAAAUGCCA

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Macromolecule #2: 30S ribosomal protein S3Ae

Macromolecule	Name: 30S ribosomal protein S3Ae / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 22.888068 KDa
Sequence	String: MAAKRRVSAA KDKWKLKQWY VIYAPDFFGG VEVGLTPADD PEKVLNRVVE VTLKDITGDF LKGHVKLYFQ VYDVKGQNAY TKFKGMKLA RSYIRSLVRR RTTRIDGIFN ITTKDGYKLR VMAMVIAARR IQTSQERAIR KIMQEIIYKK AEELNFKDFV L EAVNGKIA ...String: MAAKRRVSAA KDKWKLKQWY VIYAPDFFGG VEVGLTPADD PEKVLNRVVE VTLKDITGDF LKGHVKLYFQ VYDVKGQNAY TKFKGMKLA RSYIRSLVRR RTTRIDGIFN ITTKDGYKLR VMAMVIAARR IQTSQERAIR KIMQEIIYKK AEELNFKDFV L EAVNGKIA AEIAKEAKKI YPLKKAEIRK IKVLGEPEVA A UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #3: 30S ribosomal protein S2

Macromolecule	Name: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 23.026865 KDa
Sequence	String: MADEYLVPLD QYLAAGVHIG TQQKTKDMKK FIYRVRQDGL YVLDVRKTDE RLKVAGKFLA RFDPQSILAV SVRLYGQKPV KKFGEVTGA RAIPGRFLPG TMTNPAVKNF FEPDVIIITD PRADHQAMKE AIEIGIPIVA LVDTENLLSY VDLAIPTNNK G RKALALIY ...String: MADEYLVPLD QYLAAGVHIG TQQKTKDMKK FIYRVRQDGL YVLDVRKTDE RLKVAGKFLA RFDPQSILAV SVRLYGQKPV KKFGEVTGA RAIPGRFLPG TMTNPAVKNF FEPDVIIITD PRADHQAMKE AIEIGIPIVA LVDTENLLSY VDLAIPTNNK G RKALALIY WILAREILYN RGEISSREEF KIPVEEFEMK IVRR UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #4: Zn-ribbon RNA-binding protein involved in translation

Macromolecule	Name: Zn-ribbon RNA-binding protein involved in translation / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 7.163395 KDa
Sequence	String: MAENVELKFE IPVCTSCGRE ITPREHATHF VCPNCGEAII WRCETCRLLA KPYKCPKCGW EGP UniProtKB: Zn-ribbon RNA-binding protein involved in translation

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Macromolecule #5: 30S ribosomal protein S4

Macromolecule	Name: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 21.38191 KDa
Sequence	String: MGDPKRQRKK YETPPHPWIK ERLDRERVLM DKYELKNKKE LWKHETQLKN FRRRARRLLA ARGKQAEIER EQLLARLKRL GLLPEDAVL DDVLSLTIED ILERRLQTIV YKKGLARTMR QARQLIVHGH IEVNGQIIRS PSYLVLKEEE DTITYARTSP F ANPQHPER MMIEKAKQGG EA UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #6: 30S ribosomal protein S4e

Macromolecule	Name: 30S ribosomal protein S4e / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 28.246119 KDa
Sequence	String: MARKGPKRHL KRLAAPTSWY IERKAYKWAV RPRPGPHNMR TSIPLLYIVR DYLGYAKTAR EARKILNEGK FLVDGRVRKD YKFPVGIMD VVSIPETGEH YRVLPNRIGK LILHPISEEE ANIKPLRIRN KRMVKGAKIQ LNFHDGTNHL IPLSEKDNYF T SYTVLMKV ...String: MARKGPKRHL KRLAAPTSWY IERKAYKWAV RPRPGPHNMR TSIPLLYIVR DYLGYAKTAR EARKILNEGK FLVDGRVRKD YKFPVGIMD VVSIPETGEH YRVLPNRIGK LILHPISEEE ANIKPLRIRN KRMVKGAKIQ LNFHDGTNHL IPLSEKDNYF T SYTVLMKV PEREILEVLP FEKGAYVFVT QGKNVARKGR IVEIKKFPMG WPDVVTIEDE EGELFDTLKE YAFVVGRDKP RI SLP UniProtKB: Small ribosomal subunit protein eS4

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Macromolecule #7: 30S ribosomal protein S5

Macromolecule	Name: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 26.523904 KDa
Sequence	String: MSQEWKEYAK RVLDEWQPKT KLGMLVKEGQ ITDIHEIFRK GYQIKEPEII DVLLPEVNAR ENQEILDIAL TVRMTDSGRR VRFRVLAAV GNRDGYVGLG IGHGREVGIA IRKAINYAKL NIIEIKRGCG SWECRCRRPH SVPFTVEGKE GSVRVKLIPG P RGLGLVIG ...String: MSQEWKEYAK RVLDEWQPKT KLGMLVKEGQ ITDIHEIFRK GYQIKEPEII DVLLPEVNAR ENQEILDIAL TVRMTDSGRR VRFRVLAAV GNRDGYVGLG IGHGREVGIA IRKAINYAKL NIIEIKRGCG SWECRCRRPH SVPFTVEGKE GSVRVKLIPG P RGLGLVIG DVGKKILRLA GIQDVWSQTL GETRTTVNFA KAVFNALYNT NKVVVTPEMI ERYGIVVGRA MPASFTLE UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #8: 30S ribosomal protein S6e

Macromolecule	Name: 30S ribosomal protein S6e / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 14.029461 KDa
Sequence	String: MATFKLVISD PKTGIAKQIE ITGPEAEKLI GKRIGDQIPV KELGINLNEL FGKEFPEDVK MEIRGGTDKD GFPMRPDIHG PRRVRILLS KGPGFRPKEK GERRKKTVRG NTISPEIVQV NVKLVY UniProtKB: Small ribosomal subunit protein eS6

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Macromolecule #9: 30S ribosomal protein S8

Macromolecule	Name: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 14.772246 KDa
Sequence	String: MTLLDPLANA LSHITNSERV GKREVYIKPA SKLIGEVLRV MQKYGYIGEF EFIDDGRAGV YRVQLLGKIN KAGAIKPRFP VKARDYERW EKRFLPAFEF GILIVSTSQG VMSHKEAREK GIGGRLIAYV Y UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #10: 30S ribosomal protein S8e

Macromolecule	Name: 30S ribosomal protein S8e / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 14.293733 KDa
Sequence	String: MAIWQGRSLR KPSGGRIVLA RKKRKRELGR EPSNTRVAEQ DKRKIIRTYG GNKKVRLTAA AYANVFDKSG KGRKVRIIRV IENPANRQF ARRNIITKGA IIETEIGKAK VTSRPGQDGV VNAILLEE UniProtKB: Small ribosomal subunit protein eS8

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Macromolecule #11: 30S ribosomal protein S11

Macromolecule	Name: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 14.77295 KDa
Sequence	String: MSEEQVNIKK KEKWGIAHIY SSYNNTIIHI TDITGAETIS RWSGGMVVKA DRDEPSPYAA MLAARRAAEE ALEKGIVGVH IRVRAPGGS KSKTPGPGAQ AAIRALARAG LKIGRVEDVT PIPHDGTRPK GGRRGRRV UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #12: 30S ribosomal protein S12

Macromolecule	Name: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 16.477621 KDa
Sequence	String: MPGKKAPNGE FAGRKLKLKR KKFRWSDIRY KRRVLRLKEK SDPLEGAPQA RGIVLEKIAV EAKQPNSGMR KAVRVQLIKN GKVVTAFCP GDGAIKFIDE HDEVIIEGIG GPKGGSMGDI PGIRYKVVKV NRVSLKELVK GRKEKPRR UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #13: 30S ribosomal protein S15

Macromolecule	Name: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 18.697143 KDa
Sequence	String: MARMHARKRG KSGSKRPPRT APPIWLEYTV EDIENLVVKL RKEGYSTAMI GTILRDQYGI PTVKLFRDPD NPNRKLTITR ILEKHGLAP EIPEDLMFLI KRAVNLRKHL EQHPKDLHSM RGLQLIESKI RRLVKYYKRK GKLPKDWRYD PEQAKLLVR UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #14: 30S ribosomal protein S17

Macromolecule	Name: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 13.364604 KDa
Sequence	String: MVRDIGLRIQ PPAEKCDDPK CPWHGHLKIH GRVFEGIVVS DKPRKTVTVE RQYYHYLKKY ERYELRRSRI HAHNPPCINA KVGDRVLIA ETRPLSKTKH FVVVAVLERA EERR UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #15: 30S ribosomal protein S24e

Macromolecule	Name: 30S ribosomal protein S24e / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 11.798637 KDa
Sequence	String: MEIKITEVKE NKLIGRKEIY FEIYHPGEPT PSRKDVKGKL VAMLDLNPET TVIQYIRSYF GSYKSKGYAK YYYDKDRMLY IEPEYILIR DGIIEKKEGE UniProtKB: Small ribosomal subunit protein eS24

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Macromolecule #16: 30S ribosomal protein S27e

Macromolecule	Name: 30S ribosomal protein S27e / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 7.186609 KDa
Sequence	String: MALPRNVIPM PRSRFLRVKC IDCGNEQIVF SHPATRVRCN VCGATLVEPT GGKGIIRAKI LEVLE UniProtKB: Small ribosomal subunit protein eS27

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Macromolecule #17: 30S ribosomal protein aL41

Macromolecule	Name: 30S ribosomal protein aL41 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weight	Theoretical: 4.910237 KDa
Sequence	String: MKRRPRKWKK KGRMRWKWIK KRIRRLKRQR KKERGL

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Macromolecule #19: Translation initiation factor 1A

Macromolecule	Name: Translation initiation factor 1A / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weight	Theoretical: 13.078265 KDa
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: MPKKERKVEG DEVIRVPLPE GNQLFGVVEQ ALGAGWMDVR CEDGKIRRCR IPGKLRRRVW IRVGDLVIVQ PWPVQSDKRG DIVYRYTQT QVDWLLRKGK ITQEFLTGGS LLVE UniProtKB: Translation initiation factor 1A

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Macromolecule #20: MAGNESIUM ION

Macromolecule	Name: MAGNESIUM ION / type: ligand / ID: 20 / Number of copies: 25 / Formula: MG
Molecular weight	Theoretical: 24.305 Da

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Macromolecule #21: ZINC ION

Macromolecule	Name: ZINC ION / type: ligand / ID: 21 / Number of copies: 5 / Formula: ZN
Molecular weight	Theoretical: 65.409 Da

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Macromolecule #22: water

Macromolecule	Name: water / type: ligand / ID: 22 / Number of copies: 26 / Formula: HOH
Molecular weight	Theoretical: 18.015 Da
Chemical component information	ChemComp-HOH: WATER / Water

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Experimental details

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Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

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Sample preparation

Buffer	pH: 6.7
Vitrification	Cryogen name: ETHANE

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Electron microscopy

Microscope	FEI TITAN KRIOS
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recording	Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å²
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup model	Type of model: PDB ENTRY
Initial angle assignment	Type: MAXIMUM LIKELIHOOD
Final angle assignment	Type: MAXIMUM LIKELIHOOD
Final reconstruction	Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142000
FSC plot (resolution estimation)

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-Mask #1

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-Sample components

+Entire : Archaeal translation initiation complex devoid of aIF1 - IC2 body

+Supramolecule #1: Archaeal translation initiation complex devoid of aIF1 - IC2 body

+Supramolecule #2: ribosome

+Supramolecule #3: mRNA

+Supramolecule #4: Translation initiation factor 1A

+Macromolecule #1: 16S ribosomal RNA

+Macromolecule #18: mRNA

+Macromolecule #2: 30S ribosomal protein S3Ae

+Macromolecule #3: 30S ribosomal protein S2

+Macromolecule #4: Zn-ribbon RNA-binding protein involved in translation

+Macromolecule #5: 30S ribosomal protein S4

+Macromolecule #6: 30S ribosomal protein S4e

+Macromolecule #7: 30S ribosomal protein S5

+Macromolecule #8: 30S ribosomal protein S6e

+Macromolecule #9: 30S ribosomal protein S8

+Macromolecule #10: 30S ribosomal protein S8e

+Macromolecule #11: 30S ribosomal protein S11

+Macromolecule #12: 30S ribosomal protein S12

+Macromolecule #13: 30S ribosomal protein S15

+Macromolecule #14: 30S ribosomal protein S17

+Macromolecule #15: 30S ribosomal protein S24e

+Macromolecule #16: 30S ribosomal protein S27e

+Macromolecule #17: 30S ribosomal protein aL41

+Macromolecule #19: Translation initiation factor 1A

+Macromolecule #20: MAGNESIUM ION

+Macromolecule #21: ZINC ION

+Macromolecule #22: water

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

-Image processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

-
Basic information

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Structure visualization

-
Downloads & links

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EMDB archive

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Related structure data

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Links

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Map

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Supplemental data

-
Mask #1

-
Additional map: IC2 body postprocessed map

-
Half map: IC2 body half1 map

-
Half map: IC2 body half2 map

-
Sample components

+
Entire : Archaeal translation initiation complex devoid of aIF1 - IC2 body

+
Supramolecule #1: Archaeal translation initiation complex devoid of aIF1 - IC2 body

+
Supramolecule #2: ribosome

+
Supramolecule #3: mRNA

+
Supramolecule #4: Translation initiation factor 1A

+
Macromolecule #1: 16S ribosomal RNA

+
Macromolecule #18: mRNA

+
Macromolecule #2: 30S ribosomal protein S3Ae

+
Macromolecule #3: 30S ribosomal protein S2

+
Macromolecule #4: Zn-ribbon RNA-binding protein involved in translation

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Macromolecule #5: 30S ribosomal protein S4

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Macromolecule #6: 30S ribosomal protein S4e

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Macromolecule #7: 30S ribosomal protein S5

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Macromolecule #8: 30S ribosomal protein S6e

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Macromolecule #9: 30S ribosomal protein S8

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Macromolecule #10: 30S ribosomal protein S8e

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Macromolecule #11: 30S ribosomal protein S11

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Macromolecule #12: 30S ribosomal protein S12

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Macromolecule #13: 30S ribosomal protein S15

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Macromolecule #14: 30S ribosomal protein S17

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Macromolecule #15: 30S ribosomal protein S24e

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Macromolecule #16: 30S ribosomal protein S27e

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Macromolecule #17: 30S ribosomal protein aL41

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Macromolecule #19: Translation initiation factor 1A

+
Macromolecule #20: MAGNESIUM ION

+
Macromolecule #21: ZINC ION

+
Macromolecule #22: water

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Experimental details

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Structure determination

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Electron microscopy

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Image processing

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About Yorodumi

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