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- PDB-3rbq: Co-crystal structure of human UNC119 (retina gene 4) and an N-ter... -

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Basic information

Entry
Database: PDB / ID: 3rbq
TitleCo-crystal structure of human UNC119 (retina gene 4) and an N-terminal Transducin-alpha mimicking peptide
Components
  • Guanine nucleotide-binding protein G(t) subunit alpha-1
  • Protein unc-119 homolog A
KeywordsProtein Transport/Lipid Binding Protein / UNC(uncoordinated)119 homolog C. elegans / G protein trafficking / acyl binnding protein / light-induced translocation / UNC119 deletion / Protein Transport-Lipid Binding Protein complex
Function / homology
Function and homology information


negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / detection of light stimulus involved in visual perception / regulation of opsin-mediated signaling pathway / negative regulation of cyclic-nucleotide phosphodiesterase activity / cellular response to electrical stimulus / sensory perception of umami taste / photoreceptor connecting cilium / eye photoreceptor cell development / response to light intensity ...negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / detection of light stimulus involved in visual perception / regulation of opsin-mediated signaling pathway / negative regulation of cyclic-nucleotide phosphodiesterase activity / cellular response to electrical stimulus / sensory perception of umami taste / photoreceptor connecting cilium / eye photoreceptor cell development / response to light intensity / G protein-coupled opsin signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / G protein-coupled adenosine receptor signaling pathway / PLC beta mediated events / phototransduction, visible light / lipoprotein transport / photoreceptor outer segment membrane / positive regulation of cyclic-nucleotide phosphodiesterase activity / intercellular bridge / phototransduction / positive regulation of protein tyrosine kinase activity / mitotic cytokinesis / photoreceptor outer segment / response to light stimulus / acyl binding / spindle midzone / visual perception / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / photoreceptor inner segment / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein activation / photoreceptor disc membrane / spindle pole / endocytosis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GDP binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / protein folding / retina development in camera-type eye / nervous system development / G alpha (i) signalling events / chemical synaptic transmission / cell population proliferation / apical plasma membrane / GTPase activity / centrosome / neuronal cell body / lipid binding / synapse / GTP binding / protein kinase binding / signal transduction / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit ...GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / G-protein alpha subunit, group I / 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 / Distorted Sandwich / Immunoglobulin E-set / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(t) subunit alpha-1 / Protein unc-119 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsConstantine, R. / Whitby, F.G. / Hill, C.P. / Baehr, W.
CitationJournal: Nat.Neurosci. / Year: 2011
Title: UNC119 is required for G protein trafficking in sensory neurons.
Authors: Zhang, H. / Constantine, R. / Vorobiev, S. / Chen, Y. / Seetharaman, J. / Huang, Y.J. / Xiao, R. / Montelione, G.T. / Gerstner, C.D. / Davis, M.W. / Inana, G. / Whitby, F.G. / Jorgensen, E.M. ...Authors: Zhang, H. / Constantine, R. / Vorobiev, S. / Chen, Y. / Seetharaman, J. / Huang, Y.J. / Xiao, R. / Montelione, G.T. / Gerstner, C.D. / Davis, M.W. / Inana, G. / Whitby, F.G. / Jorgensen, E.M. / Hill, C.P. / Tong, L. / Baehr, W.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein unc-119 homolog A
B: Protein unc-119 homolog A
C: Protein unc-119 homolog A
D: Protein unc-119 homolog A
E: Protein unc-119 homolog A
F: Protein unc-119 homolog A
G: Guanine nucleotide-binding protein G(t) subunit alpha-1
H: Guanine nucleotide-binding protein G(t) subunit alpha-1
I: Guanine nucleotide-binding protein G(t) subunit alpha-1
J: Guanine nucleotide-binding protein G(t) subunit alpha-1
K: Guanine nucleotide-binding protein G(t) subunit alpha-1
L: Guanine nucleotide-binding protein G(t) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)145,19612
Polymers145,19612
Non-polymers00
Water14,286793
1
A: Protein unc-119 homolog A
G: Guanine nucleotide-binding protein G(t) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)24,1992
Polymers24,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein unc-119 homolog A
H: Guanine nucleotide-binding protein G(t) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)24,1992
Polymers24,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein unc-119 homolog A
I: Guanine nucleotide-binding protein G(t) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)24,1992
Polymers24,1992
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein unc-119 homolog A
J: Guanine nucleotide-binding protein G(t) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)24,1992
Polymers24,1992
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein unc-119 homolog A
K: Guanine nucleotide-binding protein G(t) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)24,1992
Polymers24,1992
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protein unc-119 homolog A
L: Guanine nucleotide-binding protein G(t) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)24,1992
Polymers24,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Guanine nucleotide-binding protein G(t) subunit alpha-1


  • defined by author&software
  • 1.14 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1401
Polymers1,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Guanine nucleotide-binding protein G(t) subunit alpha-1


  • defined by author&software
  • 1.14 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1401
Polymers1,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Guanine nucleotide-binding protein G(t) subunit alpha-1


  • defined by author&software
  • 1.14 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1401
Polymers1,1401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Guanine nucleotide-binding protein G(t) subunit alpha-1


  • defined by author&software
  • 1.14 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1401
Polymers1,1401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Guanine nucleotide-binding protein G(t) subunit alpha-1


  • defined by author&software
  • 1.14 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1401
Polymers1,1401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Guanine nucleotide-binding protein G(t) subunit alpha-1


  • defined by author&software
  • 1.14 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1401
Polymers1,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.546, 79.713, 189.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein unc-119 homolog A / Retinal protein 4 / hRG4


Mass: 23059.129 Da / Num. of mol.: 6 / Fragment: UNP Residues 56-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNC119, RG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13432
#2: Protein/peptide
Guanine nucleotide-binding protein G(t) subunit alpha-1 / Transducin alpha-1 chain


Mass: 1140.287 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P11488
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 277 K / Method: liquid diffusion / pH: 5
Details: 40% PEG 5000, 0.1 M sodium acetate, 0.1 M potassium acetate, 30% isopropanol, pH 5.0, LIQUID DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9749 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 4, 2010
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9749 Å / Relative weight: 1
ReflectionResolution: 1.988→30 Å / Num. obs: 82342 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Rsym value: 0.116 / Net I/σ(I): 11
Reflection shellResolution: 1.988→2.07 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.701 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GQQ

3gqq


Resolution: 2→29.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.036 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24557 4087 5 %RANDOM
Rwork0.18845 ---
obs0.19134 77030 99.96 %-
all-78089 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.7 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8494 0 0 793 9287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0228797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.95511834
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25251023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77822.966472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.773151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.781576
X-RAY DIFFRACTIONr_chiral_restr0.150.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216860
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3391.55155
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.32228355
X-RAY DIFFRACTIONr_scbond_it3.45233642
X-RAY DIFFRACTIONr_scangle_it5.4414.53479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 288 -
Rwork0.213 5583 -
obs--99.97 %

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