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- PDB-9azm: In situ human ribosome (Focused on 40S with SERBP1 CTD) -

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Basic information

Entry
Database: PDB / ID: 9azm
TitleIn situ human ribosome (Focused on 40S with SERBP1 CTD)
Components
  • (40S ribosomal protein ...) x 7
  • (Small ribosomal subunit protein ...) x 5
  • 18S rRNA
  • Receptor of activated protein C kinase 1
  • Serbp1
  • Ubiquitin-40S ribosomal protein S27a
KeywordsRIBOSOME / In situ
Function / homology
Function and homology information


negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / IRE1-RACK1-PP2A complex ...negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / IRE1-RACK1-PP2A complex / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / supercoiled DNA binding / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / protein kinase A binding / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / pigmentation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / monocyte chemotaxis / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / regulation of cell division / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / positive regulation of GTPase activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / protein serine/threonine kinase inhibitor activity / positive regulation of signal transduction by p53 class mediator / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / phagocytic cup / regulation of translational fidelity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of protein binding / positive regulation of intrinsic apoptotic signaling pathway / spindle assembly / ribosomal small subunit export from nucleus / translation regulator activity / gastrulation / DNA-(apurinic or apyrimidinic site) endonuclease activity / Maturation of protein E / Maturation of protein E / signaling adaptor activity / MDM2/MDM4 family protein binding / positive regulation of microtubule polymerization / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / negative regulation of protein ubiquitination / FLT3 signaling by CBL mutants / Hsp70 protein binding / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / liver regeneration / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of interleukin-2 production / cytosolic ribosome / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / TICAM1-dependent activation of IRF3/IRF7
Similarity search - Function
: / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain ...: / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 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 / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ubiquitin family / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ubiquitin homologues / K homology domain-like, alpha/beta / Ubiquitin domain profile. / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ubiquitin-like domain / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Zinc-binding ribosomal protein / Ribosomal protein S5 domain 2-type fold, subgroup / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / Ribosomal protein S5 domain 2-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsWei, Z. / Yong, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: In situ human ribosome (Focused on 40S with SERBP1 CTD)
Authors: Wei, Z. / Yong, Z.
History
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
CD: Serbp1
SD: Small ribosomal subunit protein uS3
SF: 40S ribosomal protein S5
SK: 40S ribosomal protein S10
SP: Small ribosomal subunit protein uS19
SQ: Small ribosomal subunit protein uS9
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
Sc: 40S ribosomal protein S28
Sd: 40S ribosomal protein S29
Sg: Receptor of activated protein C kinase 1
SM: Small ribosomal subunit protein eS12
SZ: Small ribosomal subunit protein eS25
Sf: Ubiquitin-40S ribosomal protein S27a
S2: 18S rRNA


Theoretical massNumber of molelcules
Total (without water)782,68716
Polymers782,68716
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules CDSgSf

#1: Protein Serbp1


Mass: 9566.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#12: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...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: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#15: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 7884.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979

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Small ribosomal subunit protein ... , 5 types, 5 molecules SDSPSQSMSZ

#2: Protein Small ribosomal subunit protein uS3


Mass: 25172.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P23396
#5: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 14092.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#6: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16249.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#13: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 13652.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#14: Protein Small ribosomal subunit protein eS25 / 40S ribosomal protein S25


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851

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40S ribosomal protein ... , 7 types, 7 molecules SFSKSSSTSUScSd

#3: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 21327.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#4: Protein 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#7: Protein 40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17029.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#8: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 15822.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#9: Protein 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 11765.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#10: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7263.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#11: Protein 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273

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RNA chain , 1 types, 1 molecules S2

#16: RNA chain 18S rRNA


Mass: 561332.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: In situ human ribosome (Focused on 40S with SERBP1 CTD)
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1754680 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00427254
ELECTRON MICROSCOPYf_angle_d0.8139102
ELECTRON MICROSCOPYf_dihedral_angle_d14.6357947
ELECTRON MICROSCOPYf_chiral_restr0.0424767
ELECTRON MICROSCOPYf_plane_restr0.0073185

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