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- PDB-4v3p: The molecular structure of the left-handed supra-molecular helix ... -

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Basic information

Entry
Database: PDB / ID: 4v3p
TitleThe molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes
Components
  • (40S WHEAT GERM ...) x 2
  • (40S ribosomal protein ...) x 21
  • (60S acidic ribosomal protein ...) x 2
  • (60S ribosomal protein ...) x 27
  • (Ribosomal protein ...) x 12
  • (Unknown 40S wheat germ ribosome protein ...) x 4
  • (Unknown 60S wheat germ ribosome protein ...) x 5
  • 18S ribosomal RNA
  • 26S ribosomal RNA
  • 40S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • G protein beta subunit
  • Putative 40S ribosomal protein S3
  • Ribosomal L32
  • Ribosomal Pr 117
  • Ribosomal protein
  • Ubiquitin-60S ribosomal protein L40-1
KeywordsRIBOSOME
Function / homology
Function and homology information


protein kinase activator activity / translational elongation / ribonucleoprotein complex binding / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation ...protein kinase activator activity / translational elongation / ribonucleoprotein complex binding / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / signal transduction / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L19, eukaryotic / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L19/L19e conserved site ...Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L19, eukaryotic / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / 60S ribosomal protein L35 / Ribosomal Protein L6, KOW domain / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L6e / Ribosomal protein L18e / 60S ribosomal protein L6E / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L7, eukaryotic / Ribosomal_L19e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37ae/L37e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / K homology domain-like, alpha/beta / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14p/L23e
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L37a, expressed / Small ribosomal subunit protein uS14 / Ribosomal protein L17 / Ribosomal protein P1 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L37a, expressed / Small ribosomal subunit protein uS14 / Ribosomal protein L17 / Ribosomal protein P1 / Ribosomal protein L7 / Ribosomal protein L39 / Ribosomal protein l34 / Large ribosomal subunit protein eL30 / Ribosomal protein L18 / Ribosomal protein L13a / Ribosomal protein L11 / Ribosomal protein / 60S ribosomal protein L6 / 60S ribosomal protein L36 / Ribosomal protein L3 / Ribosomal Pr 117 / Ribosomal protein L19 / 30S ribosomal protein S3, chloroplastic / Large ribosomal subunit protein uL29 / G protein beta subunit / Uncharacterized protein / :
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 34 Å
AuthorsMyasnikov, A.G. / Afonina, Z.A. / Menetret, J.F. / Shirokov, V.A. / Spirin, A.S. / Klaholz, B.P.
CitationJournal: Nat Commun / Year: 2014
Title: The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.
Authors: Alexander G Myasnikov / Zhanna A Afonina / Jean-François Ménétret / Vladimir A Shirokov / Alexander S Spirin / Bruno P Klaholz /
Abstract: During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a ...During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.
History
DepositionOct 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Atomic model
Revision 1.2Jun 28, 2017Group: Data collection / Refinement description / Structure summary
Category: diffrn / entity / refine / Item: _entity.pdbx_description / _refine.pdbx_diffrn_id
Revision 1.3Jul 26, 2017Group: Database references / Structure summary / Category: audit_author / citation / Item: _audit_author.name / _citation.journal_abbrev
Revision 1.4Aug 23, 2017Group: Data collection / Derived calculations / Category: em_software / struct_conn
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.5Jun 20, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_PDB_caveat / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation_author.name
Revision 1.6Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Revision 1.7Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Revision 1.8Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
Sa: G protein beta subunit
SA: 40S ribosomal protein SA
SB: Putative 40S ribosomal protein S3
SD: 40S ribosomal protein S4
SE: 40S ribosomal protein S2
SF: 40S ribosomal protein S5
SI: 40S ribosomal protein S16
SJ: 40S ribosomal protein S20
SK: 40S ribosomal protein S14
SL: 40S ribosomal protein S23
SM: 40S ribosomal protein S18
SO: 40S ribosomal protein S13-1
SQ: 40S ribosomal protein S17-4
SP: 40S ribosomal protein S11
SS: 40S ribosomal protein S19
SR: 40S ribosomal protein S15
SV: 40S ribosomal protein S25
SW: 40S WHEAT GERM RIBOSOME1
SY: 40S ribosomal protein S28
SZ: 40S ribosomal protein S30
Sc: Unknown 40S wheat germ ribosome protein 2
Sb: Unknown 40S wheat germ ribosome protein 3
SU: Unknown 40S wheat germ ribosome protein 3
SX: 40S ribosomal protein S27
SC: 40S ribosomal protein S9
SG: Unknown 40S wheat germ ribosome protein 4
SH: Ribosomal protein S15
SN: 40S ribosomal protein S29
ST: 40S ribosomal protein S21
S3: 40S WHEAT GERM RIBOSOME protein 4
S2: 40S ribosomal RNA
S1: 18S ribosomal RNA
L1: 26S ribosomal RNA
L3: 5S ribosomal RNA
L2: 5.8S ribosomal RNA
LA: Ribosomal protein
LB: 60S ribosomal protein L2
LE: Ribosomal protein L11
LF: 60S ribosomal protein L9
LH: 60S ribosomal protein L7a
LM: Ribosomal Pr 117
LP: Ribosomal protein L15
LO: 60S ribosomal protein L27a-3
LR: 60S ribosomal protein L18
LQ: 60S ribosomal protein L5
LT: Ribosomal protein L19
LU: 60S ribosomal protein L21
LV: 60S ribosomal protein L17
LX: 60S ribosomal protein L23a
LZ: 60S ribosomal protein L24
LY: 60S ribosomal protein L26
Lb: 60S ribosomal protein l28
Ld: 60S ribosomal protein L29
Lf: 60S ribosomal protein L30
Lg: 60S ribosomal protein L31
Lh: Ribosomal L32
Ll: Ribosomal protein L37
Ln: 60S ribosomal protein L38
Lo: Ribosomal protein L39
Lr: 60S ribosomal protein L44
Lq: Unknown 60S wheat germ ribosome protein 1
Ly: Unknown 60S wheat germ ribosome protein 2
Lz: Unknown 60S wheat germ ribosome protein 3
LG: 60S ribosomal protein L6
LL: Unknown 60S wheat germ ribosome protein 5
LN: Unknown 60S wheat germ ribosome protein 6
LS: 60S ribosomal protein L18a
LW: 60S ribosomal protein L22
La: 60S ribosomal protein L27
Li: Ribosomal protein l34
Lj: ribosomal protein L35A
Lk: 60S ribosomal protein L36
Lp: Ubiquitin-60S ribosomal protein L40-1
Lx: Unknown 60S wheat germ ribosome protein 2
LJ: 60S ribosomal protein L12
Lt: Ribosomal protein P1
Lu: Ribosomal protein P1
Lv: 60S acidic ribosomal protein P2A
Lw: 60S acidic ribosomal protein P2A
Lc: 60S ribosomal protein L35
Le: Ribosomal protein L7
Ls: 60S acidic ribosomal protein P0
LC: Ribosomal protein L3
LD: 60S ribosomal protein L4/L1
LK: Ribosomal protein L13a
Lm: 60S ribosomal protein L37a, expressed
LI: 60S ribosomal protein L10-1


Theoretical massNumber of molelcules
Total (without water)3,001,44587
Polymers3,001,44587
Non-polymers00
Water00
1
Sa: G protein beta subunit
SA: 40S ribosomal protein SA
SB: Putative 40S ribosomal protein S3
SD: 40S ribosomal protein S4
SE: 40S ribosomal protein S2
SF: 40S ribosomal protein S5
SI: 40S ribosomal protein S16
SJ: 40S ribosomal protein S20
SK: 40S ribosomal protein S14
SL: 40S ribosomal protein S23
SM: 40S ribosomal protein S18
SO: 40S ribosomal protein S13-1
SQ: 40S ribosomal protein S17-4
SP: 40S ribosomal protein S11
SS: 40S ribosomal protein S19
SR: 40S ribosomal protein S15
SV: 40S ribosomal protein S25
SW: 40S WHEAT GERM RIBOSOME1
SY: 40S ribosomal protein S28
SZ: 40S ribosomal protein S30
Sc: Unknown 40S wheat germ ribosome protein 2
Sb: Unknown 40S wheat germ ribosome protein 3
SU: Unknown 40S wheat germ ribosome protein 3
SX: 40S ribosomal protein S27
SC: 40S ribosomal protein S9
SG: Unknown 40S wheat germ ribosome protein 4
SH: Ribosomal protein S15
SN: 40S ribosomal protein S29
ST: 40S ribosomal protein S21
S3: 40S WHEAT GERM RIBOSOME protein 4
S2: 40S ribosomal RNA
S1: 18S ribosomal RNA
L1: 26S ribosomal RNA
L3: 5S ribosomal RNA
L2: 5.8S ribosomal RNA
LA: Ribosomal protein
LB: 60S ribosomal protein L2
LE: Ribosomal protein L11
LF: 60S ribosomal protein L9
LH: 60S ribosomal protein L7a
LM: Ribosomal Pr 117
LP: Ribosomal protein L15
LO: 60S ribosomal protein L27a-3
LR: 60S ribosomal protein L18
LQ: 60S ribosomal protein L5
LT: Ribosomal protein L19
LU: 60S ribosomal protein L21
LV: 60S ribosomal protein L17
LX: 60S ribosomal protein L23a
LZ: 60S ribosomal protein L24
LY: 60S ribosomal protein L26
Lb: 60S ribosomal protein l28
Ld: 60S ribosomal protein L29
Lf: 60S ribosomal protein L30
Lg: 60S ribosomal protein L31
Lh: Ribosomal L32
Ll: Ribosomal protein L37
Ln: 60S ribosomal protein L38
Lo: Ribosomal protein L39
Lr: 60S ribosomal protein L44
Lq: Unknown 60S wheat germ ribosome protein 1
Ly: Unknown 60S wheat germ ribosome protein 2
Lz: Unknown 60S wheat germ ribosome protein 3
LG: 60S ribosomal protein L6
LL: Unknown 60S wheat germ ribosome protein 5
LN: Unknown 60S wheat germ ribosome protein 6
LS: 60S ribosomal protein L18a
LW: 60S ribosomal protein L22
La: 60S ribosomal protein L27
Li: Ribosomal protein l34
Lj: ribosomal protein L35A
Lk: 60S ribosomal protein L36
Lp: Ubiquitin-60S ribosomal protein L40-1
Lx: Unknown 60S wheat germ ribosome protein 2
LJ: 60S ribosomal protein L12
Lt: Ribosomal protein P1
Lu: Ribosomal protein P1
Lv: 60S acidic ribosomal protein P2A
Lw: 60S acidic ribosomal protein P2A
Lc: 60S ribosomal protein L35
Le: Ribosomal protein L7
Ls: 60S acidic ribosomal protein P0
LC: Ribosomal protein L3
LD: 60S ribosomal protein L4/L1
LK: Ribosomal protein L13a
Lm: 60S ribosomal protein L37a, expressed
LI: 60S ribosomal protein L10-1
x 23


Theoretical massNumber of molelcules
Total (without water)69,033,2262001
Polymers69,033,2262001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation22
MethodPISA

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Components

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Protein , 5 types, 5 molecules SaSBLALMLh

#1: Protein G protein beta subunit


Mass: 41794.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8LNY6
#3: Protein Putative 40S ribosomal protein S3


Mass: 23255.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L804
#36: Protein Ribosomal protein


Mass: 24604.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L3
#41: Protein Ribosomal Pr 117


Mass: 15040.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7X9K1, UniProt: Q5I7K4*PLUS
#56: Protein Ribosomal L32


Mass: 15740.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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40S ribosomal protein ... , 21 types, 21 molecules SASDSESFSISJSKSLSMSOSQSPSSSRSVSYSZSXSCSNST

#2: Protein 40S ribosomal protein SA


Mass: 28723.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#4: Protein 40S ribosomal protein S4


Mass: 22822.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#5: Protein 40S ribosomal protein S2


Mass: 28859.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#6: Protein 40S ribosomal protein S5


Mass: 21249.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#7: Protein 40S ribosomal protein S16


Mass: 14466.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#8: Protein 40S ribosomal protein S20


Mass: 14070.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#9: Protein 40S ribosomal protein S14


Mass: 12858.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#10: Protein 40S ribosomal protein S23


Mass: 15696.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#11: Protein 40S ribosomal protein S18


Mass: 17702.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#12: Protein 40S ribosomal protein S13-1


Mass: 13904.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#13: Protein 40S ribosomal protein S17-4


Mass: 16461.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#14: Protein 40S ribosomal protein S11


Mass: 9809.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#15: Protein 40S ribosomal protein S19


Mass: 16414.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#16: Protein 40S ribosomal protein S15


Mass: 10153.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#17: Protein 40S ribosomal protein S25


Mass: 11071.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#19: Protein 40S ribosomal protein S28


Mass: 6535.663 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#20: Protein 40S ribosomal protein S30


Mass: 6953.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#24: Protein/peptide 40S ribosomal protein S27


Mass: 5438.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#25: Protein 40S ribosomal protein S9


Mass: 22629.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#28: Protein/peptide 40S ribosomal protein S29


Mass: 5465.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K3
#29: Protein 40S ribosomal protein S21


Mass: 9266.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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40S WHEAT GERM ... , 2 types, 2 molecules SWS3

#18: Protein 40S WHEAT GERM RIBOSOME1


Mass: 7847.665 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#30: RNA chain 40S WHEAT GERM RIBOSOME protein 4


Mass: 3498.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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Unknown 40S wheat germ ribosome protein ... , 4 types, 4 molecules ScSbSUSG

#21: Protein/peptide Unknown 40S wheat germ ribosome protein 2


Mass: 2145.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#22: Protein/peptide Unknown 40S wheat germ ribosome protein 3


Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#23: Protein Unknown 40S wheat germ ribosome protein 3


Mass: 11259.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#26: Protein Unknown 40S wheat germ ribosome protein 4


Mass: 12188.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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Ribosomal protein ... , 12 types, 13 molecules SHLELPLTLlLoLiLjLtLuLeLCLK

#27: Protein Ribosomal protein S15


Mass: 14825.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#38: Protein Ribosomal protein L11


Mass: 19717.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L2
#42: Protein Ribosomal protein L15


Mass: 23118.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#46: Protein Ribosomal protein L19


Mass: 22478.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7XY20
#57: Protein Ribosomal protein L37


Mass: 10823.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#59: Protein Ribosomal protein L39


Mass: 6528.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K7
#70: Protein Ribosomal protein l34


Mass: 13808.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K8
#71: Protein ribosomal protein L35A


Mass: 11858.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#75: Protein Ribosomal protein P1 / Uncharacterized protein


Mass: 6155.269 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K5
#78: Protein Ribosomal protein L7


Mass: 28175.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K6
#80: Protein Ribosomal protein L3 / Ribosomal protein L3-A1 / Ribosomal protein L3A-1 / Uncharacterized protein


Mass: 44720.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7X744
#82: Protein Ribosomal protein L13a / Uncharacterized protein


Mass: 23581.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L1

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RNA chain , 5 types, 5 molecules S2S1L1L3L2

#31: RNA chain 40S ribosomal RNA


Mass: 24135.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#32: RNA chain 18S ribosomal RNA


Mass: 562064.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#33: RNA chain 26S ribosomal RNA


Mass: 1084820.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#34: RNA chain 5S ribosomal RNA


Mass: 38716.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: 21661
#35: RNA chain 5.8S ribosomal RNA


Mass: 51270.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: 17016972

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60S ribosomal protein ... , 27 types, 27 molecules LBLFLHLOLRLQLULVLXLZLYLbLdLfLgLnLrLGLSLWLaLkLJLcLDLmLI

#37: Protein 60S ribosomal protein L2


Mass: 27692.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#39: Protein 60S ribosomal protein L9


Mass: 21382.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#40: Protein 60S ribosomal protein L7a


Mass: 22910.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#43: Protein 60S ribosomal protein L27a-3


Mass: 15834.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#44: Protein 60S ribosomal protein L18


Mass: 18349.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L0
#45: Protein 60S ribosomal protein L5


Mass: 34723.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#47: Protein 60S ribosomal protein L21


Mass: 18691.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5EIT2
#48: Protein 60S ribosomal protein L17


Mass: 19536.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#49: Protein 60S ribosomal protein L23a


Mass: 14047.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#50: Protein 60S ribosomal protein L24


Mass: 9050.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#51: Protein 60S ribosomal protein L26


Mass: 14966.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#52: Protein 60S ribosomal protein l28


Mass: 8227.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#53: Protein/peptide 60S ribosomal protein L29


Mass: 2830.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#54: Protein 60S ribosomal protein L30


Mass: 12294.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K9
#55: Protein 60S ribosomal protein L31


Mass: 13719.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#58: Protein 60S ribosomal protein L38


Mass: 8053.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#60: Protein 60S ribosomal protein L44


Mass: 12174.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#64: Protein 60S ribosomal protein L6


Mass: 24589.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L4
#67: Protein 60S ribosomal protein L18a


Mass: 20148.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#68: Protein 60S ribosomal protein L22


Mass: 12298.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#69: Protein 60S ribosomal protein L27


Mass: 11154.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#72: Protein 60S ribosomal protein L36


Mass: 8758.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L5
#74: Protein 60S ribosomal protein L12


Mass: 13754.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#77: Protein 60S ribosomal protein L35


Mass: 14401.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L805
#81: Protein 60S ribosomal protein L4/L1


Mass: 41218.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#83: Protein 60S ribosomal protein L37a, expressed / Chromosome 3B / genomic scaffold / cultivar Chinese Spring / Uncharacterized protein


Mass: 10266.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: D8L9P6
#84: Protein 60S ribosomal protein L10-1


Mass: 21290.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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Unknown 60S wheat germ ribosome protein ... , 5 types, 6 molecules LqLyLxLzLLLN

#61: Protein/peptide Unknown 60S wheat germ ribosome protein 1


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#62: Protein/peptide Unknown 60S wheat germ ribosome protein 2


Mass: 1720.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#63: Protein/peptide Unknown 60S wheat germ ribosome protein 3


Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#65: Protein Unknown 60S wheat germ ribosome protein 5


Mass: 15507.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#66: Protein Unknown 60S wheat germ ribosome protein 6


Mass: 15418.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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Protein/peptide , 1 types, 1 molecules Lp

#73: Protein/peptide Ubiquitin-60S ribosomal protein L40-1


Mass: 4973.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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60S acidic ribosomal protein ... , 2 types, 3 molecules LvLwLs

#76: Protein 60S acidic ribosomal protein P2A


Mass: 6355.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5AP46
#79: Protein 60S acidic ribosomal protein P0


Mass: 28410.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: POLY-RIBOSOME FROM IN VITRO WHEAT GERM SYSTEM / Type: RIBOSOME
Buffer solutionName: 25MM HEPES-KOH, 3MM MG(OAC)2, 85MM KOAC,1.6MM DTT, 0.25MM SPERMIDINE
pH: 7.6
Details: 25MM HEPES-KOH, 3MM MG(OAC)2, 85MM KOAC,1.6MM DTT, 0.25MM SPERMIDINE
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 --CRYOGEN- ETHANE, HUMIDITY-95, TEMPERATURE- 120,INSTRUMENT- FEI VITROBOT MARK IV, METHOD- 3UL OF SAMPLE APPLIED ON 300 MESH HOLY CARBON QUANTIFOIL GRID. BLOTTING WAS DONE IN ...Details: VITRIFICATION 1 --CRYOGEN- ETHANE, HUMIDITY-95, TEMPERATURE- 120,INSTRUMENT- FEI VITROBOT MARK IV, METHOD- 3UL OF SAMPLE APPLIED ON 300 MESH HOLY CARBON QUANTIFOIL GRID. BLOTTING WAS DONE IN VITROBOT MARK IV, BLOT TIME 0.5 SEC, BLOT FORCE 5

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jan 1, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 150 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 41176 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 90 K / Tilt angle max: 70 ° / Tilt angle min: -70 °
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2IMAGIC3D reconstruction
3IMOD3D reconstruction
4Xmipp3D reconstruction
3D reconstructionMethod: MAXIMUM LIKELIHOOD / Resolution: 34 Å / Num. of particles: 106 / Actual pixel size: 6.8 Å / Details: SUBMISSION BASED ON EXPERIMENTAL DATA / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3IZ6

3iz6
PDB Unreleased entry

RefinementHighest resolution: 34 Å

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