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- PDB-5a9v: Structure of apo BipA -

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Basic information

Entry
Database: PDB / ID: 5a9v
TitleStructure of apo 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 / ribosomal large subunit assembly / tRNA binding / rRNA binding / GTPase activity / GTP binding / 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
Large ribosomal subunit assembly factor BipA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-BINDING PROTEIN
B: GTP-BINDING PROTEIN
C: GTP-BINDING PROTEIN
D: GTP-BINDING PROTEIN
E: GTP-BINDING PROTEIN
F: GTP-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)404,6366
Polymers404,6366
Non-polymers00
Water0
1
A: GTP-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)67,4391
Polymers67,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTP-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)67,4391
Polymers67,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GTP-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)67,4391
Polymers67,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GTP-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)67,4391
Polymers67,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: GTP-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)67,4391
Polymers67,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: GTP-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)67,4391
Polymers67,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)241.946, 241.946, 241.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 1 - 601 / Label seq-ID: 1 - 601

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 67439.312 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: TRANSLATIONAL GTPASE / 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

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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: 4.2 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growDetails: 20% (W/V) PEG3350, 0.2 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2014 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 86230 / % possible obs: 96.1 % / Observed criterion σ(I): 1 / Redundancy: 17.3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 17.1
Reflection shellResolution: 3.3→3.51 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 1.1 / % possible all: 90.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
MOLREPphasing
REFMAC5.8.0107refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3E3X, 3CB4
Resolution: 3.31→49.39 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.895 / SU B: 38.394 / SU ML: 0.531 / Cross valid method: THROUGHOUT / ESU R Free: 0.555 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28781 9472 10 %RANDOM
Rwork0.26257 ---
obs0.26512 85198 91.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 132.757 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 3.31→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25398 0 0 0 25398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01925752
X-RAY DIFFRACTIONr_bond_other_d0.0040.0224864
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.96734716
X-RAY DIFFRACTIONr_angle_other_deg1.399357138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.19253294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60324.3321122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.259154500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.19515204
X-RAY DIFFRACTIONr_chiral_restr0.1110.24008
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02129046
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025508
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_it10.08613.09313284
X-RAY DIFFRACTIONr_mcbond_other10.08513.09313283
X-RAY DIFFRACTIONr_mcangle_it15.8619.61816542
X-RAY DIFFRACTIONr_mcangle_other15.8619.61716543
X-RAY DIFFRACTIONr_scbond_it9.87313.89112468
X-RAY DIFFRACTIONr_scbond_other9.87113.89112468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.15520.55218175
X-RAY DIFFRACTIONr_long_range_B_refined22.98728154
X-RAY DIFFRACTIONr_long_range_B_other22.98828155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A684540.03
12B684540.03
21A683960.04
22C683960.04
31A684200.04
32D684200.04
41A682140.05
42E682140.05
51A684340.04
52F684340.04
61B683840.04
62C683840.04
71B684160.04
72D684160.04
81B682700.05
82E682700.05
91B685140.04
92F685140.04
101C684040.05
102D684040.05
111C682640.05
112E682640.05
121C685420.03
122F685420.03
131D682340.05
132E682340.05
141D684840.04
142F684840.04
151E683680.04
152F683680.04
LS refinement shellResolution: 3.313→3.399 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 687 -
Rwork0.481 6164 -
obs--91.41 %

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