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- PDB-3r9x: Crystal structure of Era in complex with MgGDPNP, nucleotides 150... -

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Basic information

Entry
Database: PDB / ID: 3r9x
TitleCrystal structure of Era in complex with MgGDPNP, nucleotides 1506-1542 of 16S ribosomal RNA, and KsgA
Components
  • GTPase Era
  • RNA301
  • Ribosomal RNA small subunit methyltransferase A
KeywordsHYDROLASE/TRANSFERASE/RNA / GTPase / KH domain / ribosome / biogenesis / GTP / 16S ribosomal RNA / GTP hydrolysis / HYDROLASE-TRANSFERASE-RNA complex
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / ribosomal small subunit binding / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA binding / GTPase activity / GTP binding ...16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / ribosomal small subunit binding / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA binding / GTPase activity / GTP binding / RNA binding / plasma membrane / cytosol
Similarity search - Function
GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases ...GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Small GTP-binding protein domain / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / P-loop containing nucleotide triphosphate hydrolases / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / RNA / RNA (> 10) / Ribosomal RNA small subunit methyltransferase A / GTPase Era
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsTu, C. / Ji, X.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA.
Authors: Tu, C. / Zhou, X. / Tarasov, S.G. / Tropea, J.E. / Austin, B.P. / Waugh, D.S. / Court, D.L. / Ji, X.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of ERA in complex with the 3' end of 16S rRNA: Implications for ribosome biogenesis
Authors: Tu, C. / Zhou, X. / Tropea, J.E. / Austin, B.P. / Waugh, D.S. / Court, L.D. / Ji, X.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of ERA: A GTPase-dependent cell cycle regulator containing an RNA binding motif
Authors: Chen, X. / Court, L.D. / Ji, X.
History
DepositionMar 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase Era
B: Ribosomal RNA small subunit methyltransferase A
C: RNA301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2759
Polymers74,3743
Non-polymers9016
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-59 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.502, 68.094, 73.587
Angle α, β, γ (deg.)90.00, 100.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GTPase Era


Mass: 34765.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1994, era, era1 / Plasmid: pDONR201 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67800
#2: Protein Ribosomal RNA small subunit methyltransferase A / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine ...16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine transferase / 16S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 28397.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1816, ksgA, rsmA / Plasmid: pDONR201 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O67680, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase

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RNA chain , 1 types, 1 molecules C

#3: RNA chain RNA301


Mass: 11211.701 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Aquifex aeolicus except for U1506 that is replaced with C1506.

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Non-polymers , 5 types, 89 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium acetate, 20% (v/v) MPD, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 23217 / Num. obs: 23217 / % possible obs: 98.4 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.024 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.8-2.93.20.6141.6921141.00291
2.9-3.0240.4772.7222391.05596
3.02-3.154.60.3614.0422941.03798.2
3.15-3.324.90.2846.2923480.99199.5
3.32-3.534.90.226.6623411.04599.8
3.53-3.850.1499.5723441.02499.8
3.8-4.185.10.1112.9123621.01799.7
4.18-4.785.30.07219.9323620.972100
4.78-6.025.30.06223.9323721.058100
6.02-305.20.03731.8924411.03799.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IEV, 3FTF

3iev

3ftf


Resolution: 2.8→28.686 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 975 4.32 %random
Rwork0.171 ---
obs0.1735 22561 95.44 %-
all-22561 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.228 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 250.4 Å2 / Biso mean: 75.835 Å2 / Biso min: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1-4.9656 Å20 Å2-7.4092 Å2
2---8.1605 Å20 Å2
3----0.7229 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 744 57 83 5168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075293
X-RAY DIFFRACTIONf_angle_d1.247337
X-RAY DIFFRACTIONf_chiral_restr0.074873
X-RAY DIFFRACTIONf_plane_restr0.005796
X-RAY DIFFRACTIONf_dihedral_angle_d22.352229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.8-2.94740.30851170.265526462763276383
2.9474-3.13190.29951360.219329703106310693
3.1319-3.37340.27671390.200430973236323697
3.3734-3.71220.27111450.176631673312331298
3.7122-4.24790.20941430.156231693312331299
4.2479-5.34620.20061460.1338323133773377100
5.3462-28.68740.16941490.1503330634553455100

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