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- PDB-6n84: MBP-fusion protein of transducin-alpha residues 327-350 -

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Entry
Database: PDB / ID: 6n84
TitleMBP-fusion protein of transducin-alpha residues 327-350
ComponentsMaltose/maltodextrin-binding periplasmic protein,Guanine nucleotide-binding protein G(t) subunit alpha-2
KeywordsCHAPERONE / G alpha / MBP
Function / homology
Function and homology information


detection of light stimulus involved in visual perception / retinal cone cell development / G protein-coupled photoreceptor activity / response to light intensity / detection of chemical stimulus involved in sensory perception of bitter taste / photoreceptor outer segment membrane / detection of maltose stimulus / maltose transport complex / carbohydrate transport / phototransduction ...detection of light stimulus involved in visual perception / retinal cone cell development / G protein-coupled photoreceptor activity / response to light intensity / detection of chemical stimulus involved in sensory perception of bitter taste / photoreceptor outer segment membrane / detection of maltose stimulus / maltose transport complex / carbohydrate transport / phototransduction / carbohydrate transmembrane transporter activity / maltose binding / photoreceptor outer segment / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / visual perception / photoreceptor inner segment / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / heterotrimeric G-protein complex / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / outer membrane-bounded periplasmic space / periplasmic space / G protein-coupled receptor signaling pathway / GTPase activity / DNA damage response / GTP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / G-protein alpha subunit, group I / Bacterial extracellular solute-binding protein / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit ...Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / G-protein alpha subunit, group I / Bacterial extracellular solute-binding protein / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / Guanine nucleotide-binding protein G(t) subunit alpha-2
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSrivastava, D. / Gakhar, L. / Artemyev, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)NIH R01 EY12682 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor.
Authors: Dhiraj Srivastava / Lokesh Gakhar / Nikolai O Artemyev /
Abstract: Resistance to inhibitors of cholinesterase 8A (Ric8A) is an essential regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor and a chaperone. We report two crystal ...Resistance to inhibitors of cholinesterase 8A (Ric8A) is an essential regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor and a chaperone. We report two crystal structures of Ric8A, one in the apo form and the other in complex with a tagged C-terminal fragment of Gα. These structures reveal two principal domains of Ric8A: an armadillo-fold core and a flexible C-terminal tail. Additionally, they show that the Gα C-terminus binds to a highly-conserved patch on the concave surface of the Ric8A armadillo-domain, with selectivity determinants residing in the Gα sequence. Biochemical analysis shows that the Ric8A C-terminal tail is critical for its stability and function. A model of the Ric8A/Gα complex derived from crosslinking mass spectrometry and molecular dynamics simulations suggests that the Ric8A C-terminal tail helps organize the GTP-binding site of Gα. This study lays the groundwork for understanding Ric8A function at the molecular level.
History
DepositionNov 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0Jan 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_mutation / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Guanine nucleotide-binding protein G(t) subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,55910
Polymers45,4481
Non-polymers1,1119
Water8,611478
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.070, 83.070, 109.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-506-

SO4

21A-506-

SO4

31A-507-

SO4

41A-507-

SO4

51A-608-

HOH

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Guanine nucleotide-binding protein G(t) subunit alpha-2 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Transducin alpha-2 chain


Mass: 45448.391 Da / Num. of mol.: 1 / Mutation: D83A, K84A, E173A, N174A, A216H, K220H, K240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, GNAT2, GNATC / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: P19087, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2 M Ammonium Sulphate, 0.1 M sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→60.08 Å / Num. obs: 43096 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.021 / Rrim(I) all: 0.069 / Net I/σ(I): 29
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6311 / CC1/2: 0.809 / Rpim(I) all: 0.277 / Rrim(I) all: 0.849 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 1.75→60.08 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1849 2076 4.82 %
Rwork0.1565 --
obs0.1579 43059 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→60.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 63 478 3569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063194
X-RAY DIFFRACTIONf_angle_d0.7944356
X-RAY DIFFRACTIONf_dihedral_angle_d13.5111894
X-RAY DIFFRACTIONf_chiral_restr0.051478
X-RAY DIFFRACTIONf_plane_restr0.005556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79070.28261430.22242742X-RAY DIFFRACTION100
1.7907-1.83550.24511450.19842697X-RAY DIFFRACTION100
1.8355-1.88520.23441250.18172762X-RAY DIFFRACTION100
1.8852-1.94060.22461080.17792732X-RAY DIFFRACTION100
1.9406-2.00330.19381330.15962706X-RAY DIFFRACTION100
2.0033-2.07490.2061280.15522768X-RAY DIFFRACTION100
2.0749-2.1580.20211670.14592673X-RAY DIFFRACTION100
2.158-2.25620.19121330.14792732X-RAY DIFFRACTION100
2.2562-2.37510.18151390.14432743X-RAY DIFFRACTION100
2.3751-2.52390.19741450.15992714X-RAY DIFFRACTION100
2.5239-2.71880.22051290.15762736X-RAY DIFFRACTION100
2.7188-2.99240.17521510.17292723X-RAY DIFFRACTION100
2.9924-3.42540.18931450.15672734X-RAY DIFFRACTION100
3.4254-4.31550.1471520.12892737X-RAY DIFFRACTION100
4.3155-60.11580.16351330.162784X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 99.8971 Å / Origin y: 25.7937 Å / Origin z: 2.6083 Å
111213212223313233
T0.0934 Å20.0002 Å20.0164 Å2-0.1136 Å2-0.0037 Å2--0.1289 Å2
L0.5211 °2-0.2297 °2-0.2687 °2-0.5879 °20.2348 °2--0.9248 °2
S-0.0332 Å °0.0564 Å °-0.0558 Å °0.0409 Å °-0.0119 Å °0.0938 Å °0.0279 Å °-0.1079 Å °-0.0027 Å °
Refinement TLS groupSelection details: all

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