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- PDB-6g5h: Cryo-EM structure of a late human pre-40S ribosomal subunit - Mature -

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Entry
Database: PDB / ID: 6g5h
TitleCryo-EM structure of a late human pre-40S ribosomal subunit - Mature
Components
  • (40S ribosomal protein ...) x 31
  • 18S ribosomal RNA
  • 60S ribosomal protein L41
  • Receptor of activated protein C kinase 1
  • Ribosomal protein S27aRibosome
KeywordsRIBOSOME / 40S / pre-40S / ribosome biogenesis
Function / homologyUbiquitin conserved site / Ribosomal protein S5, C-terminal / KOW / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal ...Ubiquitin conserved site / Ribosomal protein S5, C-terminal / KOW / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Plectin/S10, N-terminal / Ribosomal protein S25 / Ribosomal protein S30 / K Homology domain, type 2 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / RNA-binding S4 domain / Ribosomal protein S27a / Ribosomal protein S19/S15 / Ribosomal protein S24e / Ribosomal protein S11 / Ribosomal protein S21e / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S12/S23 / Ribosomal protein L41 / Ribosomal protein S10 / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / K homology domain-like, alpha/beta / Ribosomal protein L2, domain 2 / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / Ribosomal protein S2 / WD40 repeat / Ribosomal protein S17e, conserved site / Ubiquitin domain profile. / Ribosomal protein S26e signature. / Ribosomal protein S7e signature. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S21e signature. / Ribosomal protein S27e signature. / Ribosomal protein S12e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S8e signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats signature. / Ribosomal protein S13 family profile. / Trp-Asp (WD) repeats circular profile. / Type-2 KH domain profile. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S4e signature. / S4 RNA-binding domain profile. / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Ribosomal protein S17e signature. / Ribosomal protein S13 signature. / Ribosomal protein S3Ae / Ribosomal protein S8 / Ribosomal protein S6e / Ribosomal protein S3, C-terminal / Ribosomal protein S19e / Ribosomal protein S17e / Ribosomal protein S14 / Ribosomal protein S8e / Ribosomal protein S26e / Ribosomal protein S4e / Ribosomal protein S5 / Ribosomal protein S9 / Ubiquitin domain / Ribosomal protein S4 signature. / Ribosomal protein S27e / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S12e / Ribosomal protein S28e / Ribosomal protein S17/S11 / Ribosomal protein S5/S7
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsAmeismeier, M. / Cheng, J. / Berninghausen, O. / Beckmann, R.
CitationJournal: Nature / Year: 2018
Title: Visualizing late states of human 40S ribosomal subunit maturation.
Authors: Michael Ameismeier / Jingdong Cheng / Otto Berninghausen / Roland Beckmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 29, 2018 / Release: Jun 6, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 6, 2018Structure modelrepositoryInitial release
1.1Jun 20, 2018Structure modelData collection / Database referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Jun 27, 2018Structure modelData collection / Database referencescitation_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
2: 18S ribosomal RNA
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein S2
E: 40S ribosomal protein S4, X isoform
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
L: 40S ribosomal protein S11
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14
V: 40S ribosomal protein S21
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: 40S ribosomal protein S24
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
h: 60S ribosomal protein L41
D: 40S ribosomal protein S3
F: 40S ribosomal protein S5
K: 40S ribosomal protein S10
M: 40S ribosomal protein S12
P: 40S ribosomal protein S15
Q: 40S ribosomal protein S16
R: 40S ribosomal protein S17
S: 40S ribosomal protein S18
T: 40S ribosomal protein S19
U: 40S ribosomal protein S20
Z: 40S ribosomal protein S25
c: 40S ribosomal protein S28
f: Ribosomal protein S27a
g: Receptor of activated protein C kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,225,25038
Polyers1,225,05435
Non-polymers1963
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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40S ribosomal protein ... , 31 types, 31 molecules ABCEGHIJLNOVWXYabdeDFKMPQRSTUZc

#2: Protein/peptide 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P08865
#3: Protein/peptide 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P61247
#4: Protein/peptide 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P15880
#5: Protein/peptide 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62701
#6: Protein/peptide 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62753
#7: Protein/peptide 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62081
#8: Protein/peptide 40S ribosomal protein S8 / / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62241
#9: Protein/peptide 40S ribosomal protein S9 / / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P46781
#10: Protein/peptide 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62280
#11: Protein/peptide 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62277
#12: Protein/peptide 40S ribosomal protein S14 / / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62263
#13: Protein/peptide 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P63220
#14: Protein/peptide 40S ribosomal protein S15a / / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62244
#15: Protein/peptide 40S ribosomal protein S23 / / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62266
#16: Protein/peptide 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62847
#17: Protein/peptide 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62854
#18: Protein/peptide 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P42677
#19: Protein/peptide 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62273
#20: Protein/peptide 40S ribosomal protein S30 / / Small ribosomal subunit protein eS30


Mass: 6668.938 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62861
#22: Protein/peptide 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#23: Protein/peptide 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P46782
#24: Protein/peptide 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P46783
#25: Protein/peptide 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P25398
#26: Protein/peptide 40S ribosomal protein S15 / / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62841
#27: Protein/peptide 40S ribosomal protein S16 / / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62249
#28: Protein/peptide 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P08708
#29: Protein/peptide 40S ribosomal protein S18 / / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62269
#30: Protein/peptide 40S ribosomal protein S19 / / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P39019
#31: Protein/peptide 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P60866
#32: Protein/peptide 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62851
#33: Protein/peptide 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62857

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Protein/peptide , 3 types, 3 molecules hfg

#21: Protein/peptide 60S ribosomal protein L41 / / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62945
#34: Protein/peptide Ribosomal protein S27a / Ribosome


Mass: 17944.008 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q5RKT7, UniProt: P62979*PLUS
#35: Protein/peptide Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P63244

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RNA chain / Non-polymers , 2 types, 4 molecules 2

#1: RNA chain 18S ribosomal RNA /


Mass: 602432.625 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: GenBank: 337376
#36: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of a late human pre-40S ribosomal subunit - Mature
Type: RIBOSOME
Entity ID: 1, 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
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
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 FIELDBright-field microscopy
Image recordingElectron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 70822 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01179410
ELECTRON MICROSCOPYf_angle_d1.265115136
ELECTRON MICROSCOPYf_dihedral_angle_d14.31644582
ELECTRON MICROSCOPYf_chiral_restr0.06414223
ELECTRON MICROSCOPYf_plane_restr0.0088426

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