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- PDB-5ng8: The cryo-EM structure of hibernating 100S ribosome dimer from pat... -

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Entry
Database: PDB / ID: 5ng8
TitleThe cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus
DescriptorRibosome hibernation promotion factor
(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 (6.76 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 17, 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
1.2Oct 25, 2017Structure modelStructure summaryentity_entity.pdbx_description

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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 promotion 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
Ba: 16S ribosomal RNA
Bb: 30S ribosomal protein S2
Bc: 30S ribosomal protein S3
Bd: 30S ribosomal protein S4
Be: 30S ribosomal protein S5
Bf: 30S ribosomal protein S6
Bg: 30S ribosomal protein S7
Bh: 30S ribosomal protein S8
Bi: 30S ribosomal protein S9
Bj: 30S ribosomal protein S10
Bk: 30S ribosomal protein S11
Bl: 30S ribosomal protein S12
Bm: 30S ribosomal protein S13
Bn: 30S ribosomal protein S14 type Z
Bo: 30S ribosomal protein S15
Bp: 30S ribosomal protein S16
Bq: 30S ribosomal protein S17
Br: 30S ribosomal protein S18
Bs: 30S ribosomal protein S19
Bt: 30S ribosomal protein S20
Bu: 30S ribosomal protein S21
Bv: Ribosome hibernation promotion factor
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L13
BI: 50S ribosomal protein L14
BJ: 50S ribosomal protein L15
BK: 50S ribosomal protein L16
BL: 50S ribosomal protein L17
BM: 50S ribosomal protein L18
BN: 50S ribosomal protein L19
BO: 50S ribosomal protein L20
BP: 50S ribosomal protein L21
BQ: 50S ribosomal protein L22
BR: 50S ribosomal protein L23
BS: 50S ribosomal protein L24
BT: 50S ribosomal protein L25
BU: 50S ribosomal protein L27
BV: 50S ribosomal protein L28
BW: 50S ribosomal protein L29
BX: 50S ribosomal protein L30
BY: 50S ribosomal protein L31 type B
BZ: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36


Theoretical massNumber of molelcules
Total (without water)4,246,636104
Polyers4,246,636104
Non-polymers00
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, 6 molecules AaBaAABAABBB

#1: RNA chain16S ribosomal RNA


Mass: 502975.906 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: GenBank: 1133392934
#23: RNA chain23S ribosomal RNA


Mass: 946697.625 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: GenBank: 610395799
#24: RNA chain5S ribosomal RNA


Mass: 36974.945 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: GenBank: 1130374198

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30S ribosomal protein ... , 20 types, 40 molecules AbBbAcBcAdBdAeBeAfBf...

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


Mass: 25929.135 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YXL2

Cellular component

Molecular function

Biological process

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


Mass: 22684.201 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYQ2

Cellular component

Molecular function

Biological process

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


Mass: 22849.145 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YTH0

Cellular component

Molecular function

Biological process

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


Mass: 16522.119 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYL4

Cellular component

Molecular function

Biological process

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


Mass: 11239.766 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YVJ2

Cellular component

Molecular function

Biological process

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


Mass: 17181.830 Da / Num. of mol.: 2 / Details: Ribosomal protein uS7 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077VHU6

Cellular component

Molecular function

Biological process

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


Mass: 14723.118 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYL1

Cellular component

Molecular function

Biological process

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


Mass: 14312.321 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYM9

Cellular component

Molecular function

Biological process

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


Mass: 11009.742 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYP5

Cellular component

Molecular function

Biological process

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


Mass: 12047.609 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYM1

Cellular component

Molecular function

Biological process

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


Mass: 15075.570 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A133PZQ5

Cellular component

Molecular function

Biological process

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


Mass: 13747.919 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYM0

Cellular component

Molecular function

Biological process

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


Mass: 7186.573 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYL0

Cellular component

Molecular function

Biological process

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


Mass: 10503.135 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YXP3

Cellular component

Molecular function

Biological process

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


Mass: 9993.510 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YXH8

Cellular component

Molecular function

Biological process

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


Mass: 9366.860 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYK6

Cellular component

Molecular function

Biological process

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


Mass: 6404.623 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A1D4K9U8

Cellular component

Molecular function

Biological process

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


Mass: 9205.604 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A133PYC3

Cellular component

Molecular function

Biological process

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


Mass: 8779.096 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YT41

Cellular component

Molecular function

Biological process

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


Mass: 6241.280 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YT04

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 1 types, 2 molecules AvBv

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


Mass: 22244.914 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YSH7

Cellular component

Biological process

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50S ribosomal protein ... , 28 types, 56 molecules ACBCADBDAEBEAFBFAGBG...

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


Mass: 29827.607 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYP9

Cellular component

Molecular function

Biological process

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


Mass: 23199.545 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYP6

Cellular component

Molecular function

Biological process

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


Mass: 22364.504 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYP7

Cellular component

Molecular function

Biological process

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


Mass: 19731.893 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYK9

Cellular component

Molecular function

Biological process

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


Mass: 19501.154 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYL2

Cellular component

Molecular function

Biological process

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


Mass: 16359.427 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYM8

Cellular component

Molecular function

Biological process

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


Mass: 13157.342 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYK7

Cellular component

Molecular function

Biological process

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


Mass: 15628.890 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYL6

Cellular component

Molecular function

Biological process

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


Mass: 15599.435 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYQ3

Cellular component

Molecular function

Biological process

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


Mass: 13583.523 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYM3

Cellular component

Molecular function

Biological process

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


Mass: 13124.093 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: W8TRE0

Cellular component

Molecular function

Biological process

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


Mass: 13104.381 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YXM4

Cellular component

Molecular function

Biological process

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


Mass: 13459.919 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YTB1

Cellular component

Molecular function

Biological process

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


Mass: 11354.081 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YT83

Cellular component

Molecular function

Biological process

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


Mass: 12328.358 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYQ1

Cellular component

Molecular function

Biological process

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


Mass: 10380.100 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYP8

Cellular component

Molecular function

Biological process

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


Mass: 11316.205 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYK8

Cellular component

Molecular function

Biological process

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


Mass: 10462.200 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A133Q8Z9

Cellular component

Molecular function

Biological process

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


Mass: 8911.099 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A0U1N012

Cellular component

Molecular function

Biological process

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


Mass: 6550.716 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YXJ2

Cellular component

Molecular function

Biological process

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


Mass: 7845.942 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYN0

Cellular component

Molecular function

Biological process

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


Mass: 6434.487 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YYL5

Cellular component

Molecular function

Biological process

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


Mass: 6909.694 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YUN3

Cellular component

Molecular function

Biological process

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


Mass: 5569.565 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A1Q8DAT0

Cellular component

Molecular function

Biological process

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


Mass: 5684.561 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077V2P0

Cellular component

Molecular function

Biological process

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


Mass: 5252.369 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YZB6

Cellular component

Molecular function

Biological process

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


Mass: 7461.992 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: Q2YTB0

Cellular component

Molecular function

Biological process

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


Mass: 4318.422 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus / References: UniProt: A0A077UGV8

Cellular component

Molecular function

Biological process

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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
1100S complex of Staphylococcus aureusRIBOSOME1, 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
350S 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
423S and 5S rRNACOMPLEX23, 241NATURAL
550S 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, 521NATURAL
616S rRNACOMPLEX11NATURAL
730S ribosomal proteinsCOMPLEX2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 211NATURAL
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: 6.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 12570 / Number of class averages: 1 / Symmetry type: POINT

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