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- PDB-3r9w: Crystal structure of Era in complex with MgGDPNP and nucleotides ... -

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Basic information

Entry
Database: PDB / ID: 3r9w
TitleCrystal structure of Era in complex with MgGDPNP and nucleotides 1506-1542 of 16S ribosomal RNA
Components
  • GTPase Era
  • RNA301
KeywordsHYDROLASE/RNA / GTPase / KH domain / ribosome / biogenesis / GTP / 16S ribosomal RNA / GTP hydrolysis / HYDROLASE-RNA complex
Function / homology
Function and homology information


ribosomal small subunit binding / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA binding / GTPase activity / GTP 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. / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 ...GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / RNA / RNA (> 10) / GTPase Era
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 U S A / Year: 1999
Title: Crystal structure of ERA: a GTPase-dependent cell cycle regulator containing an RNA binding motif.
Authors: X Chen / D L Court / X Ji /
Abstract: ERA forms a unique family of GTPase. It is widely conserved and essential in bacteria. ERA functions in cell cycle control by coupling cell division with growth rate. ERA homologues also are found in ...ERA forms a unique family of GTPase. It is widely conserved and essential in bacteria. ERA functions in cell cycle control by coupling cell division with growth rate. ERA homologues also are found in eukaryotes. Here we report the crystal structure of ERA from Escherichia coli. The structure has been determined at 2.4-A resolution. It reveals a two-domain arrangement of the molecule: an N-terminal domain that resembles p21 Ras and a C-terminal domain that is unique. Structure-based topological search of the C domain fails to reveal any meaningful match, although sequence analysis suggests that it contains a KH domain. KH domains are RNA binding motifs that usually occur in tandem repeats and exhibit low sequence similarity except for the well-conserved segment VIGxxGxxIK. We have identified a betaalphaalphabeta fold that contains the VIGxxGxxIK sequence and is shared by the C domain of ERA and the KH domain. We propose that this betaalphaalphabeta fold is the RNA binding motif, the minimum structural requirement for RNA binding. ERA dimerizes in crystal. The dimer formation involves a significantly distorted switch II region, which may shed light on how ERA protein regulates downstream events.
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_conn.ptnr2_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase Era
B: RNA301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,78912
Polymers45,6712
Non-polymers1,11810
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-52 kcal/mol
Surface area19720 Å2
MethodPISA
2
A: GTPase Era
B: RNA301
hetero molecules

A: GTPase Era
B: RNA301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,57724
Polymers91,3414
Non-polymers2,23620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area14060 Å2
ΔGint-122 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.946, 85.604, 67.184
Angle α, β, γ (deg.)90.00, 111.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain , 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: RNA chain RNA301


Mass: 10905.535 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 , 6 types, 101 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M calcium acetate, 40% (v/v) MPD, pH 7.2, 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: 2.05→30 Å / Num. obs: 27524 / % possible obs: 93.7 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.078 / Χ2: 0.981 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.05-2.1230.6652.1821430.97572.9
2.12-2.213.50.5451.4324400.96284.1
2.21-2.314.20.432.5625300.96686.5
2.31-2.435.20.3334.127580.9894.9
2.43-2.585.90.2845.7429230.96199.3
2.58-2.786.20.2058.7129251.01100
2.78-3.066.40.12314.1829290.954100
3.06-3.56.30.09418.0629311.008100
3.5-4.416.30.07519.7329670.97100
4.41-306.20.05425.6229661.00299.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IEV

3iev


Resolution: 2.05→25.913 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 1404 5.1 %random
Rwork0.1881 ---
obs0.1908 27524 93.35 %-
all-27524 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.738 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 148.07 Å2 / Biso mean: 62.1928 Å2 / Biso min: 30.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→25.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 724 70 91 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083351
X-RAY DIFFRACTIONf_angle_d1.1674711
X-RAY DIFFRACTIONf_chiral_restr0.072571
X-RAY DIFFRACTIONf_plane_restr0.005467
X-RAY DIFFRACTIONf_dihedral_angle_d16.0031418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.05-2.12320.50781100.472920022112211271
2.1232-2.20820.4481370.398122862423242384
2.2082-2.30870.39191260.329423892515251585
2.3087-2.43030.3411370.299826292766276695
2.4303-2.58240.32911590.271527592918291899
2.5824-2.78160.34911460.2505279129372937100
2.7816-3.06110.32421450.2279280629512951100
3.0611-3.50320.24471270.1929281329402940100
3.5032-4.41010.19981710.148281029812981100
4.4101-25.91530.18021460.143428352981298199

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