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- EMDB-18951: CryoEM structure of wheat 40S ribosomal subunit, body domain -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-18951

Title

CryoEM structure of wheat 40S ribosomal subunit, body domain

Map data

Sample

Complex: small ribosomal subunit from Triticum aestivum (common wheat)
- Protein or peptide: x 20 types
- RNA: x 1 types
Ligand: x 4 types

Keywords

small ribosomal subunit / wheat / eukaryotes / 40S / ribosome

Function / homology

Function and homology information

plastid / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation ...
Similarity search - Function

: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S5, eukaryotic/archaeal ...: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S7e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / : / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 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 S4/S9 N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11
Similarity search - Domain/homology

Biological species

Triticum aestivum (bread wheat)

Method

single particle reconstruction / cryo EM / Resolution: 2.34 Å

Authors

Kravchenko OV / Baymukhametov TN / Afonina ZA / Vasilenko KS

Funding support

Russian Federation, 1 items

Citation

Journal: Int J Mol Sci / Year: 2023
Title: High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit.
Authors: Olesya V Kravchenko / Timur N Baymukhametov / Zhanna A Afonina / Konstantin S Vassilenko /

Abstract: Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has ...

History

Deposition	Nov 22, 2023	-
Header (metadata) release	Dec 27, 2023	-
Map release	Dec 27, 2023	-
Update	Apr 24, 2024	-
Current status	Apr 24, 2024	Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images	emd_18951.png

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Downloads & links

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EMDB archive

Map data	emd_18951.map.gz	11.9 MB		EMDB map data format
Header (meta data)	emd-18951-v30.xml emd-18951.xml	40.7 KB 40.7 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_18951_fsc.xml	15.7 KB	Display	FSC data file
Images	emd_18951.png	21.5 KB
Filedesc metadata	emd-18951.cif.gz	10.4 KB
Others	emd_18951_additional_1.map.gz emd_18951_half_map_1.map.gz emd_18951_half_map_2.map.gz	398.3 MB 391.6 MB 391.6 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-18951 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18951	HTTPS FTP

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Validation report

Summary document	emd_18951_validation.pdf.gz	758 KB	Display	EMDB validaton report
Full document	emd_18951_full_validation.pdf.gz	757.6 KB	Display
Data in XML	emd_18951_validation.xml.gz	25.4 KB	Display
Data in CIF	emd_18951_validation.cif.gz	33.2 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18951 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18951	HTTPS FTP

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Related structure data

Related structure data	8r6fMC 18903C 18911C 8r57C M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	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	#161 - May 2013 Ricin similarity (67) #266 - Feb 2022 Oligosaccharyltransferase similarity (2)

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Map

File

Download / File: emd_18951.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Voxel size

X=Y=Z: 0.86 Å

Density

Contour Level	By AUTHOR: 0.4
Minimum - Maximum	-6.5206194 - 9.899759
Average (Standard dev.)	0.006769936 (±0.13441591)

Symmetry

Space group: 1

Details

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Supplemental data

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Additional map: sharp

File

emd_18951_additional_1.map

Annotation

sharp

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

File

emd_18951_half_map_1.map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

File

emd_18951_half_map_2.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 : small ribosomal subunit from Triticum aestivum (common wheat)

Entire	Name: small ribosomal subunit from Triticum aestivum (common wheat)
Components	Complex: small ribosomal subunit from Triticum aestivum (common wheat) Protein or peptide: 40S ribosomal protein S24 Protein or peptide: 40S ribosomal protein S23 Protein or peptide: 40S ribosomal protein S4 Protein or peptide: 30S ribosomal protein S11, chloroplastic Protein or peptide: Small ribosomal subunit protein uS8c Protein or peptide: 40S ribosomal protein S27 Protein or peptide: 40S ribosomal protein S30 Protein or peptide: Small ribosomal subunit protein uS2 Protein or peptide: Small ribosomal subunit protein eS1 Protein or peptide: Genome assembly, chromosome: II Protein or peptide: 40S ribosomal protein S26 Protein or peptide: 30S ribosomal protein S4, chloroplastic Protein or peptide: S5 DRBM domain-containing protein Protein or peptide: 40S ribosomal protein S6 Protein or peptide: 40S ribosomal protein S7 Protein or peptide: 40S ribosomal protein S17 Protein or peptide: Small ribosomal subunit protein uS17 N-terminal domain-containing protein Protein or peptide: Small ribosomal subunit protein uS15 N-terminal domain-containing protein Protein or peptide: Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v Protein or peptide: 40S ribosomal protein S8 RNA: RNA (1177-MER) Ligand: ZINC ION Ligand: MAGNESIUM ION Ligand: POTASSIUM ION Ligand: water

Entire

Name: small ribosomal subunit from Triticum aestivum (common wheat)

Components

Complex: small ribosomal subunit from Triticum aestivum (common wheat)
- Protein or peptide: 40S ribosomal protein S24
- Protein or peptide: 40S ribosomal protein S23
- Protein or peptide: 40S ribosomal protein S4
- Protein or peptide: 30S ribosomal protein S11, chloroplastic
- Protein or peptide: Small ribosomal subunit protein uS8c
- Protein or peptide: 40S ribosomal protein S27
- Protein or peptide: 40S ribosomal protein S30
- Protein or peptide: Small ribosomal subunit protein uS2
- Protein or peptide: Small ribosomal subunit protein eS1
- Protein or peptide: Genome assembly, chromosome: II
- Protein or peptide: 40S ribosomal protein S26
- Protein or peptide: 30S ribosomal protein S4, chloroplastic
- Protein or peptide: S5 DRBM domain-containing protein
- Protein or peptide: 40S ribosomal protein S6
- Protein or peptide: 40S ribosomal protein S7
- Protein or peptide: 40S ribosomal protein S17
- Protein or peptide: Small ribosomal subunit protein uS17 N-terminal domain-containing protein
- Protein or peptide: Small ribosomal subunit protein uS15 N-terminal domain-containing protein
- Protein or peptide: Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v
- Protein or peptide: 40S ribosomal protein S8
- RNA: RNA (1177-MER)
Ligand: ZINC ION
Ligand: MAGNESIUM ION
Ligand: POTASSIUM ION
Ligand: water

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Supramolecule #1: small ribosomal subunit from Triticum aestivum (common wheat)

Supramolecule	Name: small ribosomal subunit from Triticum aestivum (common wheat) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)	Organism: Triticum aestivum (bread wheat)

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Macromolecule #1: 40S ribosomal protein S24

Macromolecule	Name: 40S ribosomal protein S24 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 15.76971 KDa
Sequence	String: MADAKTTTAV TLRTRKFMTN RLLARKQFVL EVIHPGRANV SKAELKERLA KVYEVKDPNC IFVFKFRTHF GGGKSSGFGL IYDNLESAK KFEPKYRLIR NGLATKVEKS RKQIKERKNR TKKIRGVKKT KAGDAKKK UniProtKB: 40S ribosomal protein S24

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Macromolecule #2: 40S ribosomal protein S23

Macromolecule	Name: 40S ribosomal protein S23 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 15.696476 KDa
Sequence	String: MGKTRGMGAG RKLKTHRRNQ RWADKAYKKS HLGNEWKKPF AGSSHAKGIV LEKIGIEAKQ PNSAIRKCAR VQLVKNGKKI AAFVPNDGC LNFIEENDEV LIAGFGRKGH AVGDIPGVRF KVVKVSGVSL LALFKEKKEK PRS UniProtKB: 40S ribosomal protein S23

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Macromolecule #3: 40S ribosomal protein S4

Macromolecule	Name: 40S ribosomal protein S4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 30.008111 KDa
Sequence	String: MARGLKKHLK RLNAPSHWML DKLGGAFAPK PSSGPHKARE CLPLILILRN RLKYALTYRE VQSILMQRHI MVDGKVRTDK TYPAGFMDI ISIPKTGENY RLLYDTKGRF RLHSVRDEDA KFKLCKVRSV QFGQKGIPYL NTYDGRTIRY PDPLIKANDT I KLDLETNK ...String: MARGLKKHLK RLNAPSHWML DKLGGAFAPK PSSGPHKARE CLPLILILRN RLKYALTYRE VQSILMQRHI MVDGKVRTDK TYPAGFMDI ISIPKTGENY RLLYDTKGRF RLHSVRDEDA KFKLCKVRSV QFGQKGIPYL NTYDGRTIRY PDPLIKANDT I KLDLETNK IVDFIKFDVG NVVMVTGGRN TGRVGVIKNR EKHKGTFETI HVEDAQGHQF ATRLGNVFTI GKGTKPWVSL PK GKGIKLT IIEEQRKRDA AAQAAAKA UniProtKB: 40S ribosomal protein S4

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Macromolecule #4: 30S ribosomal protein S11, chloroplastic

Macromolecule	Name: 30S ribosomal protein S11, chloroplastic / type: protein_or_peptide / ID: 4 Details: IAS - BETA-L-ASPARTIC ACID post-translational modification in the protein Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 16.398818 KDa
Sequence	String: MSSKRKTREP KEENVTLGPA VREGEHVFGV AHIFASFNDT FIHVTDLSGR ETLVRITGGM KVKADRDESS PYAAMLASQD VATRCKELG ITALHIKLRA TGGNKTKTPG PGAQSALRAL ARSGMKIGRI EDVTPVPT(IAS)S TRRKGGRRGR RL UniProtKB: 30S ribosomal protein S11, chloroplastic

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Macromolecule #5: Small ribosomal subunit protein uS8c

Macromolecule	Name: Small ribosomal subunit protein uS8c / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 14.815363 KDa
Sequence	String: MVRVSVLNDA LKSMYNAEKR GKRQVMIRPS SKVIIKFLIV MQKHGYIGEF EYVDDHRSGK IVVELNGRLN KCGVISPRFD VGVKEIEGW TARLLPSRQF GYIVLTTSAG IMDHEEARRK NVGGKVLGFF Y UniProtKB: Small ribosomal subunit protein uS8c

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Macromolecule #6: 40S ribosomal protein S27

Macromolecule	Name: 40S ribosomal protein S27 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 9.583195 KDa
Sequence	String: MVLQNDIDLL NPPAELEKLK HKKKRLVQSP NSFFMDVKCQ GCFNITTVFS HSQTVVVCPG CQTVLCQPTG GKARLTEGCS FRRKGD UniProtKB: 40S ribosomal protein S27

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Macromolecule #7: 40S ribosomal protein S30

Macromolecule	Name: 40S ribosomal protein S30 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 6.934164 KDa
Sequence	String: MGKVHGSLAR AGKVRGQTPK VAKQDKKKQP RGRAHKRIQY NRRFVTAVVG FGKKRGPNSS EK UniProtKB: 40S ribosomal protein S30

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Macromolecule #8: Small ribosomal subunit protein uS2

Macromolecule	Name: Small ribosomal subunit protein uS2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 33.300438 KDa
Sequence	String: MAAAAGEAPR ALSQKEQDIQ MMLAADVHLG TKNCDFQMER YAYKRRSDGI YIINLGKTWE KLQLAARVIV AIENPQDIIV QSARPYGQR AVLKFAQHTG ANAIAGRHTP GTFTNQMQTS FSEPRLLILT DPRTDHQPIK ESALGNIPTI AFCDTDSPMR Y VDIGIPAN ...String: MAAAAGEAPR ALSQKEQDIQ MMLAADVHLG TKNCDFQMER YAYKRRSDGI YIINLGKTWE KLQLAARVIV AIENPQDIIV QSARPYGQR AVLKFAQHTG ANAIAGRHTP GTFTNQMQTS FSEPRLLILT DPRTDHQPIK ESALGNIPTI AFCDTDSPMR Y VDIGIPAN NKGRNSIGCL YWLLARMVLQ MRGTILPGHK WDVMVDLFFY RDPEEAKEQE DEAAGAPEYA AITDYGAAAG QW GGDQWTS DAPAPPPVTG GEWPMAEAPV AGGDGWDAAG APVAVEGAVP APVVAATGWD AAVQPPAQGW E UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #9: Small ribosomal subunit protein eS1

Macromolecule	Name: Small ribosomal subunit protein eS1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 30.043955 KDa
Sequence	String: MAVGKNKRIS KGRKGSKKKA VDPFTKKQWY DIKAPLLFTS RNVGKTLVSR TQGTKIASEG LKHRVFEVSL ADLQNDEDQA YRKIRLRAE DVQGMNVLTN FWGMDFTTDK LRSLVRKWQT LIEAHVDVKT TDNYMLRMFA IGFTKRRPNQ VKRTCYAQAS Q IRQIRRKM ...String: MAVGKNKRIS KGRKGSKKKA VDPFTKKQWY DIKAPLLFTS RNVGKTLVSR TQGTKIASEG LKHRVFEVSL ADLQNDEDQA YRKIRLRAE DVQGMNVLTN FWGMDFTTDK LRSLVRKWQT LIEAHVDVKT TDNYMLRMFA IGFTKRRPNQ VKRTCYAQAS Q IRQIRRKM VEIMVNQAAS CDLKELVNKF IPEVIGKEIE KATSSIFPLQ NVYVRKVKIL KAPKFDLGKL MEVHGDYKED VG VKLDRPA DGDEVIPGAE EVAAAE UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #10: Genome assembly, chromosome: II

Macromolecule	Name: Genome assembly, chromosome: II / type: protein_or_peptide / ID: 10 Details: AME -N-ACETYLMETHIONINE post translational modification Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 8.99304 KDa
Sequence	String: (AME)QNEVGDMVD LYVPRKCSAT NRIITAKDHA SVQINIGHVD ANGLYNGSFT TFALSGFVRA QGDADGSLDR LWQQKR AEI KQ UniProtKB: Genome assembly, chromosome: II

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Macromolecule #11: 40S ribosomal protein S26

Macromolecule	Name: 40S ribosomal protein S26 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 15.319789 KDa
Sequence	String: MTFKRRNGGR NKHGRGHVKY IRCSNCAKCC PKDKAIKRFL VRNIVEQAAV RDVQEACVHD GYVLPKLYAK VHHCVSCAIH AHIVRVRSR ENRRNREPPQ RFRRRDDGPR PGQGGPPRAG GPGGAPAGAG AVPGAPAPRV UniProtKB: 40S ribosomal protein S26

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Macromolecule #12: 30S ribosomal protein S4, chloroplastic

Macromolecule	Name: 30S ribosomal protein S4, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 22.534111 KDa
Sequence	String: MVHVNFYRNY GKTFKKPRRP YEKERLDAEL KLVGEYGLRC KRELWRVQYA LSRIRNAARH LLTLDEKNPR RIFEGAALLR RMNRYGLLA EGQDKLDYVL ALTAENFLAR RLQTLVFKAG MAKSIHHARV LIRQRHIRVG RQIVNVPSFM VRVESEKHID F SLTSPFGG ...String: MVHVNFYRNY GKTFKKPRRP YEKERLDAEL KLVGEYGLRC KRELWRVQYA LSRIRNAARH LLTLDEKNPR RIFEGAALLR RMNRYGLLA EGQDKLDYVL ALTAENFLAR RLQTLVFKAG MAKSIHHARV LIRQRHIRVG RQIVNVPSFM VRVESEKHID F SLTSPFGG GPAGRVKRKN QKKASGGGDA GGDEEEE UniProtKB: 30S ribosomal protein S4, chloroplastic

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Macromolecule #13: S5 DRBM domain-containing protein

Macromolecule	Name: S5 DRBM domain-containing protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 30.081082 KDa
Sequence	String: MADRGGERGV GERGGFGRGF GRGGRGDRGG RRGGRRGPRQ EEEKWVPVTK LGRLVKEGRF TKMEEIYLHS LPVKEHQIVE TLCPGLKDE VMKITPVQKQ TRAGQRTRFK AFVVVGDSNG HVGLGVKCAK EVATAIRGAI ILAKLSIVPV RRGYWGNKIG L PHTVPCKV ...String: MADRGGERGV GERGGFGRGF GRGGRGDRGG RRGGRRGPRQ EEEKWVPVTK LGRLVKEGRF TKMEEIYLHS LPVKEHQIVE TLCPGLKDE VMKITPVQKQ TRAGQRTRFK AFVVVGDSNG HVGLGVKCAK EVATAIRGAI ILAKLSIVPV RRGYWGNKIG L PHTVPCKV TGKCGSVTVR MVPAPRGSGI VAARVPKKVL QFAGIDDVFT SSRGSTKTLG NFVKATFDCL MKTYGFLTPD FW RETTFTK APYQEFTDIL AKPTKALMLD APAEKIEA UniProtKB: S5 DRBM domain-containing protein

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Macromolecule #14: 40S ribosomal protein S6

Macromolecule	Name: 40S ribosomal protein S6 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 28.522609 KDa
Sequence	String: MKLNIANPTT GCQKKVEIDD DQKLRNLYDK RISQEVVGDL LGEEFKGYIF KIMGGCDKQG FPMKQGVLTS GRVRLLLHRG TPCFRGFGR RNGERRRKSV RGCIVSQDLS VINLVIVKKG ENDLPGLTDT EKPRMRGPKR ASKIKKLFNL GKDDDVRSYV N TYRRTFLN ...String: MKLNIANPTT GCQKKVEIDD DQKLRNLYDK RISQEVVGDL LGEEFKGYIF KIMGGCDKQG FPMKQGVLTS GRVRLLLHRG TPCFRGFGR RNGERRRKSV RGCIVSQDLS VINLVIVKKG ENDLPGLTDT EKPRMRGPKR ASKIKKLFNL GKDDDVRSYV N TYRRTFLN KKGKKVSKAP KIQRLVTPLT LQRKRARIAD KKKRIAKKKS EAAEYQKLLA QRLKEQRDRR SESMAKRRSK LS AATKAPA ASA UniProtKB: 40S ribosomal protein S6

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Macromolecule #15: 40S ribosomal protein S7

Macromolecule	Name: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 22.297891 KDa
Sequence	String: MYTARKKIQK DKGVEPSEFE DTVAQAFFDL ENGNQELKSD LKDLYINTAI QMDVVGNRKA VVIHVPYRLR KPFRKIHVRL VRELEKKFS GKDVVFVATR RIVRPPKKGS AVQRPRTRTL TAVHDGILED VVYPAEIVGK RVRYRLDGAK VIKIYLDPKE R NNTEYKLE ...String: MYTARKKIQK DKGVEPSEFE DTVAQAFFDL ENGNQELKSD LKDLYINTAI QMDVVGNRKA VVIHVPYRLR KPFRKIHVRL VRELEKKFS GKDVVFVATR RIVRPPKKGS AVQRPRTRTL TAVHDGILED VVYPAEIVGK RVRYRLDGAK VIKIYLDPKE R NNTEYKLE TFSAVYRRLC GKDVVFEYPV TETA UniProtKB: 40S ribosomal protein S7

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Macromolecule #16: 40S ribosomal protein S17

Macromolecule	Name: 40S ribosomal protein S17 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 16.47909 KDa
Sequence	String: MGRVRTKTVK KTSRQVIEKY YSRMTLDFHT NKKVLEEVSI LQSKRLRNKV AGFTTHLMRR IQRGPVRGIS LKLQEEERER RMDFVPEKS ALEVDEIRVD KETMDMLAFL GMADLPGVER APEATSAAAP YRQPFNGPRG GNRA UniProtKB: 40S ribosomal protein S17

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Macromolecule #17: Small ribosomal subunit protein uS17 N-terminal domain-containing...

Macromolecule	Name: Small ribosomal subunit protein uS17 N-terminal domain-containing protein type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 17.841061 KDa
Sequence	String: MAEQTEKSFL KQPKVFLSTK KADKAKRPGK AGNRFWKSVG LGFKTPREAI DGTYIDKKCP FTGTVAIRGR IIAGTCHSAK MNRTIIVRR NYLHFVKKYQ RYEKRHSNIP AHISPCFRVK EGDHVIIGQC RPLSKTVRFN VLKVVPAGTT GGGKKAFIAA UniProtKB: Small ribosomal subunit protein uS17 N-terminal domain-containing protein

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Macromolecule #18: Small ribosomal subunit protein uS15 N-terminal domain-containing...

Macromolecule	Name: Small ribosomal subunit protein uS15 N-terminal domain-containing protein type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 17.132303 KDa
Sequence	String: MGRMHSRGKG ISSSALPYKR TPPSWVKTAV ADVDELITKA AKKGQMPSQI GVLLRDQHGI PLVKSVTGSK ILRILKAHGL APEIPEDLY FLIKKAVAIR KHLERNRKDK DSKFRLILVE SRIHRLARYY KRTKKLPPTW KYESTTASTL VA UniProtKB: Small ribosomal subunit protein uS15 N-terminal domain-containing protein

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Macromolecule #19: Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v

Macromolecule	Name: Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 3.445437 KDa
Sequence	String: MRAKWKKKRM RRLKRKRRKM RQRSK UniProtKB: Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v

+
Macromolecule #20: 40S ribosomal protein S8

Macromolecule	Name: 40S ribosomal protein S8 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 25.183863 KDa
Sequence	String: GISRDSMHKR RATGGKQKAW RKKRKYELGR QPANTKLSSN KTVRRVRVRG GNVKWRALRL DTGNFSWGSE AVTRKTRLLD VVYNSSNNE LVRTQTLVKN AIVQVDAAPF KQWYLTHYGV EIGRKKKAAA AAKKEAAEGQ EAEVAAAATE EAKKSNNVQR K LEKRQQGR ...String: GISRDSMHKR RATGGKQKAW RKKRKYELGR QPANTKLSSN KTVRRVRVRG GNVKWRALRL DTGNFSWGSE AVTRKTRLLD VVYNSSNNE LVRTQTLVKN AIVQVDAAPF KQWYLTHYGV EIGRKKKAAA AAKKEAAEGQ EAEVAAAATE EAKKSNNVQR K LEKRQQGR TLDSHIEEQF SGGRLLACIS SRPGQCGRAD GYILEGKELE FYMRKLQKKK GKGATA UniProtKB: 40S ribosomal protein S8

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Macromolecule #21: RNA (1177-MER)

Macromolecule	Name: RNA (1177-MER) / type: rna / ID: 21 / Number of copies: 1
Source (natural)	Organism: Triticum aestivum (bread wheat)
Molecular weight	Theoretical: 584.382812 KDa
Sequence	String: UACCUGGUUG AUCCUGCCAG UAGUCAU(A2M)UG CUUG(PSU)CU(OMC)AA AGAUUAAGCC AUGCAUGUGC AAGUAUGA A CCAAUUUGAA CUGUGAAACU GCGAAUGGCU CAU(PSU)AAAUCA G(PSU)UAUAGUUU G(PSU)U(OMU)GAUGGU ACG UGCUAC ...String: UACCUGGUUG AUCCUGCCAG UAGUCAU(A2M)UG CUUG(PSU)CU(OMC)AA AGAUUAAGCC AUGCAUGUGC AAGUAUGA A CCAAUUUGAA CUGUGAAACU GCGAAUGGCU CAU(PSU)AAAUCA G(PSU)UAUAGUUU G(PSU)U(OMU)GAUGGU ACG UGCUAC UCGGAUAACC GUAGUAAUUC UAG(A2M)GCUAA(OMU) ACGUGCAACA AACCCCGACU UCUGGGAGGG GCGCAU UUA (PSU)UAGAUAAAA GGCUGACGCG GGCUCUGCUC GCUGAUCC(OMG)A UGAUUCA(PSU)GA (PSU)AACUCGACG G AUCGCACG GCCUUCGUGC CGGCGACGCA UCA(PSU)UCAAA(PSU) U(PSU)CUGCCCUA UCAACUUUCG AUGGUAGGAU AGGGGCCUA CCAUGGUGGU GACGGG(PSU)GAC GGAGAAUUAG GGUUCGAUUC CGGAGA(OMG)GGA GCCUGAGAAA CGG CUACCA CAU(OMC)CAAGG(A2M) AGGCAGCAG(OMG) CGCGC(A2M)AAUU ACCCAAUCCU GACACGGGGA GGU(A2M) GUGAC AAUAAAUAAC AAUACCGGGC GCAUUAGUGU CUGGUAAUUG GAAUGAGUAC AAUCUAAAUC CCUUAACGAG G (A2M)UCCAUUG GAGGGCAAGU CUGGUGCCAG CAGCCGCGGU AAUUCCAGCU CCAAUA(OMG)CGU A(UY1)A(PSU) (PSU)UAAG UUG(OMU)UGCAGU U(A2M)AAAAGCUC GUAG(PSU)UGGAC CUUGGGCCGG GUCGGCCGGU CCGCCUCAC GGCGAGCACC GACCUACUCG ACCCUUCGGC CGGCAUCGCG CUCCUAGCCU UAAUUGGCCG GGUCGUGUUU CCGGCAUCGU UACUUUGAA GAAA(PSU)(PSU)AGAG UGCUCAAAGC AAGCCAUCGC UCUGGAUACA UU(A2M)GCA(PSU)GGG A (PSU)AACAUCA UAGGAUUCCG GUCCUAUUGU GUUGGCCUUC GGGAUCGGAG UAAUGAUUAA UAGGGACAGU CGGGGGCA U UCGUAUUUCA UAGUCAGAGG UGAAAUUCUU GGAUUUAUGA AAGACGAACA ACUGCGAAAG CAUUUGCCAA GGAUGUUUU CAUUAAUCAA GA(A2M)CGAAAGU UGGGGGCUCG AAGACGA(PSU)CA GAUACCG(OMU)CC UAGUCUCAAC CAUAAACG A UGCCGACCAG GGAUCGGCGG AUGUUGCUUA UAGGACUCCG CCGGCACC(PSU)U AUGAGAAAUC AAAG(PSU)CUUUG G G(PSU)UCCGGG GGGAGUA(PSU)GG UCGCAA(OMG)GCU GAAACUUAAA GGAAUUGACG GAAGGCACCA CCAGGCGUGG AGCC(PSU)GCGG CUUAAUU(PSU)GA CUCAACACGG GGAAACUUAC CAGG(PSU)(OMC)CAGA CAUAGCAAGG A (OMU)UGACAGA CUGAGAGCUC UUUCUUGAUU C(OMU)A(OMU)GGGUGG (OMU)G(OMG)UGCAUGG C(4AC)GUUCUU A GU(PSU)GGUG(OMG)AG CGA(PSU)UUG(PSU)CU GG(PSU)UAAUUCC GUUAACGA(A2M)C GAGA(OMC)CUCAG C CUGCUAAC UAGCUAUGCG GAGCCAUCC(OMC) (PSU)CCGCAGCUA GCU(OMU)CUUAGA GGGACUAUCG CCGUU(PSU) AGG CGACGGAAGU UUGAGGCAAU AACA(OMG)GUCUG (PSU)GAUGCCC(OMU)U AGAUGUUCUG GGCCGCACGC GCGCU ACAC (PSU)GAUGUAUUC AACGAGUAUA UAGCCUUGGC CGACAGGCCC GGGUAAUCUU GGGAAA(PSU)U(PSU)C AUCG UGAUG GGGAUAGAUC AUUGCAAUUG U(PSU)GGUCUUCA ACG(A2M)G(7MG)AAUG CCUAGUAAGC GCGAGUCA(PSU) CAGC(PSU)CGCGU (PSU)GACUACGUC CCUGCCCUU(PSU) GUACACACCG (OMC)CCGUCGCUC CUACCGAUUG AAUG GUCCG GUGAAGUGUU CGGAUCGCGG CGACGGGGGC GGUUCGCCGC CCCCGACGUC GCGAGAAGUC CAUUGAACCU UAUCA UUUA GAGGA(A2M)GGAG AAGUCGUA(6MZ)C AAGGUUUC(4AC)G UAGGUG(MA6)(MA6)CC UGCGGAAGGA UCAUUG

+
Macromolecule #22: ZINC ION

Macromolecule	Name: ZINC ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: ZN
Molecular weight	Theoretical: 65.409 Da

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Macromolecule #23: MAGNESIUM ION

Macromolecule	Name: MAGNESIUM ION / type: ligand / ID: 23 / Number of copies: 32 / Formula: MG
Molecular weight	Theoretical: 24.305 Da

+
Macromolecule #24: POTASSIUM ION

Macromolecule	Name: POTASSIUM ION / type: ligand / ID: 24 / Number of copies: 14 / Formula: K
Molecular weight	Theoretical: 39.098 Da

+
Macromolecule #25: water

Macromolecule	Name: water / type: ligand / ID: 25 / Number of copies: 1067 / Formula: HOH
Molecular weight	Theoretical: 18.015 Da
Chemical component information	ChemComp-HOH: WATER

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Experimental details

-
Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

-
Sample preparation

Buffer	pH: 7.5
Vitrification	Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy

Microscope	FEI TITAN KRIOS
Image recording	Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 0-32 / Number grids imaged: 1 / Number real images: 6201 / Average exposure time: 1.6 sec. / Average electron dose: 84.0 e/Å²
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
Sample stage	Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selection	Number selected: 982063
Startup model	Type of model: OTHER
Final reconstruction	Resolution.type: BY AUTHOR / Resolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 256000
Initial angle assignment	Type: OTHER / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model	PDB ID: 7qix Chain - Source name: PDB / Chain - Initial model type: experimental model
Refinement	Protocol: RIGID BODY FIT
Output model	PDB-8r6f: CryoEM structure of wheat 40S ribosomal subunit, body domain

+
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+Entire : small ribosomal subunit from Triticum aestivum (common wheat)

+Supramolecule #1: small ribosomal subunit from Triticum aestivum (common wheat)

+Macromolecule #1: 40S ribosomal protein S24

+Macromolecule #2: 40S ribosomal protein S23

+Macromolecule #3: 40S ribosomal protein S4

+Macromolecule #4: 30S ribosomal protein S11, chloroplastic

+Macromolecule #5: Small ribosomal subunit protein uS8c

+Macromolecule #6: 40S ribosomal protein S27

+Macromolecule #7: 40S ribosomal protein S30

+Macromolecule #8: Small ribosomal subunit protein uS2

+Macromolecule #9: Small ribosomal subunit protein eS1

+Macromolecule #10: Genome assembly, chromosome: II

+Macromolecule #11: 40S ribosomal protein S26

+Macromolecule #12: 30S ribosomal protein S4, chloroplastic

+Macromolecule #13: S5 DRBM domain-containing protein

+Macromolecule #14: 40S ribosomal protein S6

+Macromolecule #15: 40S ribosomal protein S7

+Macromolecule #16: 40S ribosomal protein S17

+Macromolecule #17: Small ribosomal subunit protein uS17 N-terminal domain-containing...

+Macromolecule #18: Small ribosomal subunit protein uS15 N-terminal domain-containing...

+Macromolecule #19: Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v

+Macromolecule #20: 40S ribosomal protein S8

+Macromolecule #21: RNA (1177-MER)

+Macromolecule #22: ZINC ION

+Macromolecule #23: MAGNESIUM ION

+Macromolecule #24: POTASSIUM ION

+Macromolecule #25: water

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

+Image processing

-Atomic model buiding 1

+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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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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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

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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

-
Additional map: sharp

-
Half map: #2

-
Half map: #1

-
Sample components

+
Entire : small ribosomal subunit from Triticum aestivum (common wheat)

+
Supramolecule #1: small ribosomal subunit from Triticum aestivum (common wheat)

+
Macromolecule #1: 40S ribosomal protein S24

+
Macromolecule #2: 40S ribosomal protein S23

+
Macromolecule #3: 40S ribosomal protein S4

+
Macromolecule #4: 30S ribosomal protein S11, chloroplastic

+
Macromolecule #5: Small ribosomal subunit protein uS8c

+
Macromolecule #6: 40S ribosomal protein S27

+
Macromolecule #7: 40S ribosomal protein S30

+
Macromolecule #8: Small ribosomal subunit protein uS2

+
Macromolecule #9: Small ribosomal subunit protein eS1

+
Macromolecule #10: Genome assembly, chromosome: II

+
Macromolecule #11: 40S ribosomal protein S26

+
Macromolecule #12: 30S ribosomal protein S4, chloroplastic

+
Macromolecule #13: S5 DRBM domain-containing protein

+
Macromolecule #14: 40S ribosomal protein S6

+
Macromolecule #15: 40S ribosomal protein S7

+
Macromolecule #16: 40S ribosomal protein S17

+
Macromolecule #17: Small ribosomal subunit protein uS17 N-terminal domain-containing...

+
Macromolecule #18: Small ribosomal subunit protein uS15 N-terminal domain-containing...

+
Macromolecule #19: Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v

+
Macromolecule #20: 40S ribosomal protein S8

+
Macromolecule #21: RNA (1177-MER)

+
Macromolecule #22: ZINC ION

+
Macromolecule #23: MAGNESIUM ION

+
Macromolecule #24: POTASSIUM ION

+
Macromolecule #25: water

-
Experimental details

-
Structure determination

-
Sample preparation

-
Electron microscopy

+
Image processing

-
Atomic model buiding 1

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Yorodumi