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- PDB-4a2i: Cryo-electron Microscopy Structure of the 30S Subunit in Complex ... -

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Entry
Database: PDB / ID: 4a2i
TitleCryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RIBOSOMAL RNA
  • PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA
KeywordsRIBOSOME/HYDROLASE / RIBOSOME-HYDROLASE COMPLEX / RIBOSOME ASSEMBLY
Function / homologyRibosomal protein S6, plastid/chloroplast / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site ...Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S9/S16 / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, N-terminal / Nucleic acid-binding, OB-fold / Ribosomal protein S13-like, H2TH / RsgA GTPase domain / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S7, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S4, bacterial-type / Ribosomal protein S7 domain superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S21 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S19 conserved site / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S5, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S17 / Ribosomal protein S14 signature. / Ribosomal protein S20 / RsgA GTPase / Ribosomal protein S5, C-terminal domain / KH domain / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ribosomal protein S18 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S15 signature. / Ribosomal protein S3 signature. / Ribosomal protein S6 / Ribosomal protein S5 signature. / Ribosomal protein S4 signature. / Ribosomal protein S13 signature. / Ribosomal protein S16 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S6 signature. / Ribosomal protein S21 signature. / Ribosomal protein S13 family profile. / Type-2 KH domain profile. / S5 double stranded RNA-binding domain profile. / S4 RNA-binding domain profile. / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / S4 domain
Function and homology information
Specimen sourceSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
ESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 16.5 Å resolution
AuthorsJomaa, A. / Stewart, G. / Mears, J.A. / Kireeva, I. / Brown, E.D. / Ortega, J.
CitationJournal: RNA / Year: 2011
Title: Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor.
Authors: Ahmad Jomaa / Geordie Stewart / Jason A Mears / Inga Kireeva / Eric D Brown / Joaquin Ortega
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 27, 2011 / Release: Nov 2, 2011
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 2, 2011Structure modelrepositoryInitial release
1.1Jul 10, 2013Structure modelDerived calculations
1.2Aug 23, 2017Structure modelData collection / Derived calculations / Refinement description / Source and taxonomy / Structure summaryem_3d_fitting / em_software / entity / entity_src_nat / struct_conn_em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _entity.src_method / _entity_src_nat.common_name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "VA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "VA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
B: 30S RIBOSOMAL PROTEIN S2
C: 30S RIBOSOMAL PROTEIN S3
D: 30S RIBOSOMAL PROTEIN S4
E: 30S RIBOSOMAL PROTEIN S5
F: 30S RIBOSOMAL PROTEIN S6
G: 30S RIBOSOMAL PROTEIN S7
H: 30S RIBOSOMAL PROTEIN S8
I: 30S RIBOSOMAL PROTEIN S9
J: 30S RIBOSOMAL PROTEIN S10
K: 30S RIBOSOMAL PROTEIN S11
L: 30S RIBOSOMAL PROTEIN S12
M: 30S RIBOSOMAL PROTEIN S13
N: 30S RIBOSOMAL PROTEIN S14
O: 30S RIBOSOMAL PROTEIN S15
P: 30S RIBOSOMAL PROTEIN S16
Q: 30S RIBOSOMAL PROTEIN S17
R: 30S RIBOSOMAL PROTEIN S18
S: 30S RIBOSOMAL PROTEIN S19
T: 30S RIBOSOMAL PROTEIN S20
U: 30S RIBOSOMAL PROTEIN S21
V: PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA


Theoretical massNumber of molelcules
Total (without water)791,44822
Polyers791,44822
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein/peptide 30S RIBOSOMAL PROTEIN S2 /


Mass: 24253.943 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V0
#3: Protein/peptide 30S RIBOSOMAL PROTEIN S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V3
#4: Protein/peptide 30S RIBOSOMAL PROTEIN S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7V8
#5: Protein/peptide 30S RIBOSOMAL PROTEIN S5 /


Mass: 15804.282 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7W1
#6: Protein/peptide 30S RIBOSOMAL PROTEIN S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02358
#7: Protein/peptide 30S RIBOSOMAL PROTEIN S7 /


Mass: 16764.406 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02359
#8: Protein/peptide 30S RIBOSOMAL PROTEIN S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7W7
#9: Protein/peptide 30S RIBOSOMAL PROTEIN S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7X3
#10: Protein/peptide 30S RIBOSOMAL PROTEIN S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7R5
#11: Protein/peptide 30S RIBOSOMAL PROTEIN S11 /


Mass: 12487.200 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7R9
#12: Protein/peptide 30S RIBOSOMAL PROTEIN S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7S3
#13: Protein/peptide 30S RIBOSOMAL PROTEIN S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7S9
#14: Protein/peptide 30S RIBOSOMAL PROTEIN S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02370, UniProt: P0AG61*PLUS
#15: Protein/peptide 30S RIBOSOMAL PROTEIN S15 /


Mass: 10188.687 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02371, UniProt: P0ADZ5*PLUS
#16: Protein/peptide 30S RIBOSOMAL PROTEIN S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7T3
#17: Protein/peptide 30S RIBOSOMAL PROTEIN S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P02373, UniProt: P0AG66*PLUS
#18: Protein/peptide 30S RIBOSOMAL PROTEIN S18 /


Mass: 6466.477 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7T7
#19: Protein/peptide 30S RIBOSOMAL PROTEIN S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7U3
#20: Protein/peptide 30S RIBOSOMAL PROTEIN S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7U7
#21: Protein/peptide 30S RIBOSOMAL PROTEIN S21 /


Mass: 6067.081 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P68679

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RNA chain / Protein/peptide , 2 types, 2 molecules AV

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 495927.719 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / References: GenBank: 33357879
#22: Protein/peptide PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA / YJEQ


Mass: 30816.074 Da / Num. of mol.: 1
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Plasmid name: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: Q8ZKB0, UniProt: P39286*PLUS

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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: ESCHERICHIA COLI 30S RIBOSOMAL SUBUNIT WITH YJEQ PROTEIN BOUND IN THE PRESENCE OF GMP-PNP
Type: RIBOSOME
Buffer solutionName: 10 MM TRIS-HCL PH 7.5, 10 MM MAGNESIUM ACETATE, 60 MM NH4CL, 3 MM 2- MERCAPTOETHANOL AND 2 MM GMP-PNP
Details: 10 MM TRIS-HCL PH 7.5, 10 MM MAGNESIUM ACETATE, 60 MM NH4CL, 3 MM 2- MERCAPTOETHANOL AND 2 MM GMP-PNP
pH: 7.5
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: FORMVAR PLUS CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: BLOT FOR 7 SECONDS IN FEI VITROBOT III

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 2010F / Date: May 12, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 / Calibrated magnification: 50000 / Nominal defocus max: 3900 nm / Nominal defocus min: 650 nm / Cs: 1 mm
Specimen holderTemperature: 100 kelvins / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 150
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2Xmipp3D reconstruction
CTF correctionDetails: EACH MICROGRAPH
SymmetryPoint symmetry: C1
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 16.5 Å / Number of particles: 16228 / Nominal pixel size: 2.54 / Actual pixel size: 2.54
Details: THE COORDINATES IN THIS ENTRY WERE GENERATED BY MANUAL DOCKING OF THE STRUCTURE OF THE ESCHERICHIA COLI 30S RIBOSOMAL SUBUNIT (2AVY) AND SALMONELLA TYPHYMURIUM (2RCN) INTO THE DENSITY MAP OF THE ESCHERICHIA COLI 30S_YJEQ COMPLEX GENERATED BY CRYO-ELECTRON MICROSCOPY. THE YEJQ PROTEIN WAS FITTED AS THREE SEPARATE DOMAINS: THE OB-FOLD, THE GTPASE DOMAIN, AND THE ZINC-FINGER DOMAIN. THE PROTEIN DATA BANK CONVENTIONS REQUIRE TO ENTER INFORMATION ABOUT THE UNIT CELL, CRYSTAL DATA AND COORDINATE SYSTEM. THESE INFORMATION IS MEANINGLESS IN THIS ENTRY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1895.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--MANUAL REFINEMENT PROTOCOL--X-RAY / Ref protocol: OTHER / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting ID
12AVY1
22RCN1
Least-squares processHighest resolution: 16.5 Å
Refine hist #LASTHighest resolution: 16.5 Å
Number of atoms included #LASTProtein: 20702 / Nucleic acid: 32831 / Ligand: 0 / Solvent: 0 / Total: 53533

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