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- PDB-5a9w: Structure of GDPCP BipA -

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Basic information

Entry
Database: PDB / ID: 5a9w
TitleStructure of GDPCP BipA
ComponentsGTP-BINDING PROTEING protein
KeywordsRIBOSOMAL PROTEIN / RIBOSOME / TRANSLATIONAL GTPASE FACTORS
Function / homology
Function and homology information


guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / ribosome biogenesis / tRNA binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / TypA/BipA C-terminal domain / GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / Elongation factor EFG, domain V-like / Elongation factor G C-terminus ...: / : / : / : / TypA/BipA C-terminal domain / GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Large ribosomal subunit assembly factor BipA / Large ribosomal subunit assembly factor BipA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsKumar, V. / Chen, Y. / Ero, R. / Li, Z. / Gao, Y.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structure of BipA in GTP form bound to the ratcheted ribosome.
Authors: Veerendra Kumar / Yun Chen / Rya Ero / Tofayel Ahmed / Jackie Tan / Zhe Li / Andrew See Weng Wong / Shashi Bhushan / Yong-Gui Gao /
Abstract: BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly ...BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation.
History
DepositionJul 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9612
Polymers67,4391
Non-polymers5211
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)237.554, 237.554, 237.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein GTP-BINDING PROTEIN / G protein / BIPA


Mass: 67439.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA T1R / References: UniProt: B7MHF0, UniProt: P0DTT0*PLUS
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM

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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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.66→48.49 Å / Num. obs: 12870 / % possible obs: 99.5 % / Observed criterion σ(I): 2.1 / Redundancy: 18.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.3
Reflection shellResolution: 3.66→3.86 Å / Redundancy: 17.3 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 2.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E3X

3e3x


Resolution: 3.7→48.49 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / SU B: 47.304 / SU ML: 0.66 / Cross valid method: THROUGHOUT / ESU R Free: 0.718 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30863 940 7.5 %RANDOM
Rwork0.24367 ---
obs0.24869 11598 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 152.456 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.7→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4313 0 32 0 4345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194402
X-RAY DIFFRACTIONr_bond_other_d0.0020.024266
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9795968
X-RAY DIFFRACTIONr_angle_other_deg1.11439794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5445560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59324.824199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06315752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.481534
X-RAY DIFFRACTIONr_chiral_restr0.0910.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214994
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02935
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.9115.0322261
X-RAY DIFFRACTIONr_mcbond_other9.89515.0322260
X-RAY DIFFRACTIONr_mcangle_it15.93522.5232814
X-RAY DIFFRACTIONr_mcangle_other15.93422.5252815
X-RAY DIFFRACTIONr_scbond_it8.86615.6482141
X-RAY DIFFRACTIONr_scbond_other8.86415.6392138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.04923.2343152
X-RAY DIFFRACTIONr_long_range_B_refined23.7424937
X-RAY DIFFRACTIONr_long_range_B_other23.7444936
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 68 -
Rwork0.393 845 -
obs--100 %

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