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- PDB-5ngm: 2.9S structure of the 70S ribosome composing the S. aureus 100S c... -

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Entry
Database: PDB / ID: 5ngm
Title2.9S structure of the 70S ribosome composing the S. aureus 100S complex
DescriptorRibosomal subunit interface protein
(30S ribosomal protein ...) x 20
(50S ribosomal protein ...) x 28
KeywordsRIBOSOME / Ribosome Cryo-EM Structural Biology Hibernation / Ribosome
Specimen sourceStaphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌
MethodElectron microscopy (2.9 Å resolution / Particle / Single particle)
AuthorsMatzov, D. / Aibara, S. / Zimmerman, E. / Bashan, A. / Amunts, A. / Yonath, A.
CitationNat Commun, 2017, 8, 723-723

Nat Commun, 2017, 8, 723-723 Yorodumi Papers
The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.
Donna Matzov / Shintaro Aibara / Arnab Basu / Ella Zimmerman / Anat Bashan / Mee-Ngan F Yap / Alexey Amunts / Ada E Yonath

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 18, 2017 / Release: Oct 4, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 4, 2017Structure modelrepositoryInitial release
1.1Oct 11, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Assembly

Deposited unit
Aa: 16S ribosomal RNA
Ab: 30S ribosomal protein S2
Ac: 30S ribosomal protein S3
Ad: 30S ribosomal protein S4
Ae: 30S ribosomal protein S5
Af: 30S ribosomal protein S6
Ag: 30S ribosomal protein S7
Ah: 30S ribosomal protein S8
Ai: 30S ribosomal protein S9
Aj: 30S ribosomal protein S10
Ak: 30S ribosomal protein S11
Al: 30S ribosomal protein S12
Am: 30S ribosomal protein S13
An: 30S ribosomal protein S14 type Z
Ao: 30S ribosomal protein S15
Ap: 30S ribosomal protein S16
Aq: 30S ribosomal protein S17
Ar: 30S ribosomal protein S18
As: 30S ribosomal protein S19
At: 30S ribosomal protein S20
Au: 30S ribosomal protein S21
Av: Ribosome hibernation promoting factor
AA: 23S Ribosomal RNA
AB: 5S Ribosomal RNA
AC: 50S ribosomal protein L2
AD: 50S ribosomal protein L3
AE: 50S ribosomal protein L4
AF: 50S ribosomal protein L5
AG: 50S ribosomal protein L6
AH: 50S ribosomal protein L13
AI: 50S ribosomal protein L14
AJ: 50S ribosomal protein L15
AK: 50S ribosomal protein L16
AL: 50S ribosomal protein L17
AM: 50S ribosomal protein L18
AN: 50S ribosomal protein L19
AO: 50S ribosomal protein L20
AP: 50S ribosomal protein L21
AQ: 50S ribosomal protein L22
AR: 50S ribosomal protein L23
AS: 50S ribosomal protein L24
AT: 50S ribosomal protein L25
AU: 50S ribosomal protein L27
AV: 50S ribosomal protein L28
AW: 50S ribosomal protein L29
AX: 50S ribosomal protein L30
AY: 50S ribosomal protein L31 type B
AZ: 50S ribosomal protein L32
A1: 50S ribosomal protein L33
A2: 50S ribosomal protein L34
A3: 50S ribosomal protein L35
A4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,170,506257
Polyers2,165,52452
Non-polymers4,983205
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules AaAAAB

#1: RNA chain16S ribosomal RNA


Mass: 502975.906 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: GenBank: 1133392934
#23: RNA chain23S Ribosomal RNA


Mass: 946697.625 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: GenBank: 610395799
#24: RNA chain5S Ribosomal RNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: GenBank: 1130374198

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30S ribosomal protein ... , 20 types, 20 molecules AbAcAdAeAfAgAhAiAjAk...

#2: Polypeptide(L)30S ribosomal protein S2


Mass: 29136.369 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UDU1

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)30S ribosomal protein S3


Mass: 24143.867 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UU26

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)30S ribosomal protein S4


Mass: 23051.416 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TVK2

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)30S ribosomal protein S5


Mass: 17770.512 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TUC9

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein S6


Mass: 11613.146 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TPC6

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)30S ribosomal protein S7


Mass: 17826.555 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077VHU6

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)30S ribosomal protein S8


Mass: 14854.315 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8U8T8

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)30S ribosomal protein S9


Mass: 14856.987 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A0K7UQP6

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)30S ribosomal protein S10


Mass: 11598.503 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A0H2K0A0

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)30S ribosomal protein S11


Mass: 13907.978 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UKD6

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)30S ribosomal protein S12


Mass: 15320.870 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8U1C6

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein S13


Mass: 13747.919 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8U8U6

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S14 type Z


Mass: 7317.769 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UGW7

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)30S ribosomal protein S15


Mass: 10634.330 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8U6H8

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)30S ribosomal protein S16


Mass: 10253.886 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8U6K4

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)30S ribosomal protein S17


Mass: 10196.888 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077VLD5

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)30S ribosomal protein S18


Mass: 9332.018 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UZF4

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)30S ribosomal protein S19


Mass: 10639.309 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077V0P8

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein S20


Mass: 9039.472 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8UXC3

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)30S ribosomal protein S21


Mass: 6994.267 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UHS1

Cellular component

Molecular function

Biological process

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50S ribosomal protein ... , 28 types, 28 molecules ACADAEAFAGAHAIAJAKAL...

#25: Polypeptide(L)50S ribosomal protein L2


Mass: 30217.164 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077W1J0

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L3


Mass: 23760.256 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8U3W0

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L4


Mass: 22495.697 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TRC7

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L5


Mass: 20296.637 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TUC3

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L6


Mass: 19818.580 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8U3X2

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TUE6

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UUA0

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S ribosomal protein L15


Mass: 15628.890 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UGA7

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)50S ribosomal protein L16


Mass: 16274.049 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077V4G0

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)50S ribosomal protein L17


Mass: 13771.773 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UG91

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TRE0

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UVB6

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)50S ribosomal protein L20


Mass: 13720.295 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077VMP6

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: D7URR3

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UKF9

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)50S ribosomal protein L23


Mass: 10625.398 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TUB4

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)50S ribosomal protein L24


Mass: 11561.504 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TRD5

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)50S ribosomal protein L25 / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A133Q8Z9

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)50S ribosomal protein L27


Mass: 10334.798 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A0U1N012

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)50S ribosomal protein L28


Mass: 6995.289 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077URJ8

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)50S ribosomal protein L29


Mass: 8592.900 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A0H3KED7

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)50S ribosomal protein L30


Mass: 6565.683 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8UVN7

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)50S ribosomal protein L31 type B


Mass: 9737.912 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TRP5

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)50S ribosomal protein L32


Mass: 6500.609 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UWR7

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)50S ribosomal protein L33


Mass: 5944.937 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077V2P0

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)50S ribosomal protein L34


Mass: 5454.642 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YZB6

Cellular component

Molecular function

Biological process

#51: Polypeptide(L)50S ribosomal protein L35


Mass: 7722.368 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UL47

Cellular component

Molecular function

Biological process

#52: Polypeptide(L)50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UGV8

Cellular component

Molecular function

Biological process

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Polypeptide(L) / Non-polymers , 2 types, 206 molecules Av

#22: Polypeptide(L)Ribosome hibernation promoting factor / HPF


Mass: 22244.914 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus / References: UniProt: W8USK0

Cellular component

Biological process

#53: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 205 / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
170S ribosome of the S. aureus 100S complexRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 520NATURAL
230S subunitCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 221NATURAL
316S rRNACOMPLEX12NATURAL
430S ribosomal proteinsCOMPLEX2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 212NATURAL
550S subunitCOMPLEX23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 521NATURAL
623S and 5S rRNACOMPLEX23, 245NATURAL
750S ribosomal proteinsCOMPLEX25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 525NATURAL
Molecular weight
IDEntity assembly IDExperimental value
11NO
12
13
14
15
16
17
Source (natural)
IDEntity assembly IDNcbi tax IDOrganismStrain
211280Staphylococcus aureusUSA300_FPR3757
321280Staphylococcus aureusUSA300_FPR3757
431280Staphylococcus aureusUSA300_FPR3757
541280Staphylococcus aureusUSA300_FPR3757
651280Staphylococcus aureusUSA300_FPR3757
761280Staphylococcus aureusUSA300_FPR3757
871280Staphylococcus aureusUSA300_FPR3757
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2.3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 224554 / Symmetry type: POINT

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