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- PDB-4jhr: An auto-inhibited conformation of LGN reveals a distinct interact... -

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Basic information

Entry
Database: PDB / ID: 4jhr
TitleAn auto-inhibited conformation of LGN reveals a distinct interaction mode between GoLoco motifs and TPR motifs
ComponentsG-protein-signaling modulator 2
KeywordsSIGNALING PROTEIN / TPR motifs / GoLoco tandem motifs / Asymmetric cell division / LGN / GoLoco
Function / homology
Function and homology information


Ran protein signal transduction / lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / G alpha (i) signalling events / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation ...Ran protein signal transduction / lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / G alpha (i) signalling events / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / positive regulation of protein localization to cell cortex / G-protein alpha-subunit binding / lateral plasma membrane / regulation of mitotic spindle organization / mitotic spindle organization / : / cell cortex / cell division / protein domain specific binding / nucleotide binding / centrosome / protein-containing complex / identical protein binding / cytosol / cytoplasm
Similarity search - Function
GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. ...GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
G-protein-signaling modulator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPan, Z. / Zhu, J. / Shang, Y. / Wei, Z. / Jia, M. / Xia, C. / Wen, W. / Wang, W. / Zhang, M.
CitationJournal: Structure / Year: 2013
Title: An autoinhibited conformation of LGN reveals a distinct interaction mode between GoLoco motifs and TPR motifs
Authors: Pan, Z. / Zhu, J. / Shang, Y. / Wei, Z. / Jia, M. / Xia, C. / Wen, W. / Wang, W. / Zhang, M.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-protein-signaling modulator 2
B: G-protein-signaling modulator 2


Theoretical massNumber of molelcules
Total (without water)73,7582
Polymers73,7582
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-24 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.213, 81.803, 106.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 110:151 or resseq 165:353 or resseq 358:414 )
211chain 'B' and (resseq 110:151 or resseq 165:353 or resseq 358:414 )

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Components

#1: Protein G-protein-signaling modulator 2 / Pins homolog


Mass: 36879.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpsm2, Lgn, Pins / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDU0
Sequence detailsThis SEQUENCE HAS BEEN BUILT BY DELETION MUTATION.

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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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5.5
Details: 0.2M NaCl, 0.1M Bis-Tris, 25% Polyethylene Glycol 3350, pH 5.5, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97939
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16221

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RO3

3ro3


Resolution: 2.8→38.043 Å / SU ML: 0.35 / σ(F): 2.01 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3113 798 5.04 %RANDOM
Rwork0.2498 ---
obs0.2527 15822 97.22 %-
all-16216 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.612 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---1.9503 Å2-0 Å2
3---0.6404 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4249 0 0 0 4249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084325
X-RAY DIFFRACTIONf_angle_d1.1125885
X-RAY DIFFRACTIONf_dihedral_angle_d16.151455
X-RAY DIFFRACTIONf_chiral_restr0.08667
X-RAY DIFFRACTIONf_plane_restr0.004791
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2058X-RAY DIFFRACTIONPOSITIONAL
12B2058X-RAY DIFFRACTIONPOSITIONAL0.06
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.96840.32211260.2327236194
2.9684-3.19750.3261210.2478245697
3.1975-3.5190.33191450.2708246097
3.519-4.02780.30631380.2646250898
4.0278-5.07270.31291390.2475254598
5.0727-38.04650.29851290.2404269499

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