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- PDB-2ykr: 30S ribosomal subunit with RsgA bound in the presence of GMPPNP -

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Entry
Database: PDB / ID: 2ykr
Title30S ribosomal subunit with RsgA bound in the presence of GMPPNP
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RRNA
  • PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA
KeywordsRIBOSOME/HYDROLASE / RIBOSOME-HYDROLASE COMPLEX / RIBOSOME BIOGENESIS / YJEQ / CIRCULARLY PERMUTATED GTPASE
Function / homologyRibosomal protein S2, flavodoxin-like domain superfamily / Ribosomal S11, 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 S2, flavodoxin-like domain superfamily / Ribosomal S11, 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 S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein S16, 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 S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S3, bacterial / Ribosomal protein S3, C-terminal domain superfamily / 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 S7 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6, plastid/chloroplast / 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 S10p/S20e / Ribosomal protein S19, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, N-terminal domain / 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 sourceESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.8 Å resolution
AuthorsGuo, Q. / Yuan, Y. / Xu, Y. / Feng, B. / Liu, L. / Chen, K. / Lei, J. / Gao, N.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy.
Authors: Qiang Guo / Yi Yuan / Yanji Xu / Boya Feng / Liang Liu / Kai Chen / Ming Sun / Zhixiu Yang / Jianlin Lei / Ning Gao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 30, 2011 / Release: Aug 24, 2011
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 24, 2011Structure modelrepositoryInitial release
1.1Mar 20, 2013Structure modelOther / Refinement description
1.2Aug 30, 2017Structure modelData collection / Derived calculations / Refinement description / Structure summaryem_3d_fitting / em_image_scans / em_software / entity / struct_conn_em_3d_fitting.target_criteria / _em_software.image_processing_id / _entity.src_method

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1884
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 16S RRNA
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
W: PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA


Theoretical massNumber of molelcules
Total (without water)800,89822
Polyers800,89822
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 / Fragment: RESIDUES 9-226 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7NID0, UniProt: P0A7V0*PLUS
#3: Protein/peptide 30S RIBOSOMAL PROTEIN S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-207 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGK2, UniProt: P0A7V3*PLUS
#4: Protein/peptide 30S RIBOSOMAL PROTEIN S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-206 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGI7, UniProt: P0A7V8*PLUS
#5: Protein/peptide 30S RIBOSOMAL PROTEIN S5 /


Mass: 15804.282 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-159 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: D6JG86, UniProt: P0A7W1*PLUS
#6: Protein/peptide 30S RIBOSOMAL PROTEIN S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-100 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I2A6, UniProt: P02358*PLUS
#7: Protein/peptide 30S RIBOSOMAL PROTEIN S7 /


Mass: 16861.523 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-152 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: E3XT25, UniProt: P02359*PLUS
#8: Protein/peptide 30S RIBOSOMAL PROTEIN S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-130 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I220, UniProt: P0A7W7*PLUS
#9: Protein/peptide 30S RIBOSOMAL PROTEIN S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-130 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: Q0TCN6, UniProt: P0A7X3*PLUS
#10: Protein/peptide 30S RIBOSOMAL PROTEIN S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-102 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A7ZSL0, UniProt: P0A7R5*PLUS
#11: Protein/peptide 30S RIBOSOMAL PROTEIN S11 /


Mass: 12487.200 Da / Num. of mol.: 1 / Fragment: RESIDUES 13-129 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7M103, UniProt: P0A7R9*PLUS
#12: Protein/peptide 30S RIBOSOMAL PROTEIN S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-124 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: P0A7S4, UniProt: P0A7S3*PLUS
#13: Protein/peptide 30S RIBOSOMAL PROTEIN S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-115 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGI9, UniProt: P0A7S9*PLUS
#14: Protein/peptide 30S RIBOSOMAL PROTEIN S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-101 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7M1M1, UniProt: P0AG59*PLUS
#15: Protein/peptide 30S RIBOSOMAL PROTEIN S15 /


Mass: 10159.621 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-89 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B3HGB0, UniProt: P0ADZ4*PLUS
#16: Protein/peptide 30S RIBOSOMAL PROTEIN S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7N6J5, UniProt: P0A7T3*PLUS
#17: Protein/peptide 30S RIBOSOMAL PROTEIN S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-83 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: P0AG65, UniProt: P0AG63*PLUS
#18: Protein/peptide 30S RIBOSOMAL PROTEIN S18 /


Mass: 6466.477 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-74 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: E3PE70, UniProt: P0A7T7*PLUS
#19: Protein/peptide 30S RIBOSOMAL PROTEIN S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-81 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I230, UniProt: P0A7U3*PLUS
#20: Protein/peptide 30S RIBOSOMAL PROTEIN S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-87 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7L4E5, UniProt: P0A7U7*PLUS
#21: Protein/peptide 30S RIBOSOMAL PROTEIN S21 /


Mass: 6067.081 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-54 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B1LF57, UniProt: P68679*PLUS

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

#1: RNA chain 16S RRNA


Mass: 496892.375 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: GenBank: 54791136
#22: Protein/peptide PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA


Mass: 39233.246 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E3PE32, UniProt: P39286*PLUS, Hydrolases, Acting on acid anhydrides, In phosphorus-containing anhydrides

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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: 30S RIBOSOMAL SUBUNIT WITH RSGA BOUND IN THE PRESENCE OF GMPPNP
Type: RIBOSOME
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen 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 / Nominal magnification: 59000 / Nominal defocus max: 3850 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: MAPS FROM EACH DEFOCUS GROUP
SymmetryPoint symmetry: C1
3D reconstructionMethod: REFERENCE BASED / Resolution: 9.8 Å / Number of particles: 77483 / Nominal pixel size: 2.9 / Actual pixel size: 2.9
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -1884. (DEPOSITION ID: 7882).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--MDFF REFINEMENT PROTOCOL--X-RAY / Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting ID
13OFA1
22RCN1
Least-squares processHighest resolution: 9.8 Å
Refine hist #LASTHighest resolution: 9.8 Å
Number of atoms included #LASTProtein: 20741 / Nucleic acid: 32892 / Ligand: 0 / Solvent: 0 / Total: 53633

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