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- PDB-4g2v: Structure complex of LGN binding with FRMPD1 -

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Basic information

Entry
Database: PDB / ID: 4g2v
TitleStructure complex of LGN binding with FRMPD1
Components
  • G-protein-signaling modulator 2
  • peptide from FERM and PDZ domain-containing protein 1
KeywordsPROTEIN BINDING / TPR repeat / LGN / Cell polarity
Function / homology
Function and homology information


lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / G alpha (i) signalling events / regulation of G protein-coupled receptor signaling pathway / establishment of protein localization to membrane / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole ...lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / G alpha (i) signalling events / regulation of G protein-coupled receptor signaling pathway / establishment of protein localization to membrane / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / regulation of mitotic spindle organization / mitotic spindle organization / : / cell cortex / cytoskeleton / protein domain specific binding / cell division / nucleotide binding / centrosome / protein-containing complex / identical protein binding / plasma membrane / cytosol
Similarity search - Function
FERM and PDZ domain-containing protein 1/3/4, FERM domain C-lobe / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / : / FAK1/PYK2, FERM domain C-lobe / Tetratricopeptide repeat ...FERM and PDZ domain-containing protein 1/3/4, FERM domain C-lobe / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / : / FAK1/PYK2, FERM domain C-lobe / Tetratricopeptide repeat / Tetratricopeptide repeat domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Tetratricopeptide repeat / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
FERM and PDZ domain-containing protein 1 / G-protein-signaling modulator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShang, Y. / Pan, Z. / Wen, W. / Wang, W. / Zhang, M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural and biochemical characterization of the interaction between LGN and Frmpd1
Authors: Pan, Z. / Shang, Y. / Jia, M. / Zhang, L. / Xia, C. / Zhang, M. / Wang, W. / Wen, W.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: G-protein-signaling modulator 2
B: peptide from FERM and PDZ domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,67312
Polymers41,6922
Non-polymers98110
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-18 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.835, 93.835, 172.863
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-152-

PHE

21A-552-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 37497.836 Da / Num. of mol.: 1 / Fragment: TPR domain, UNP residues 22-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDU0
#2: Protein/peptide peptide from FERM and PDZ domain-containing protein 1 / FERM domain-containing protein 2


Mass: 4193.839 Da / Num. of mol.: 1 / Fragment: UNP residues 901-938
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SYB0

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Non-polymers , 4 types, 94 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.63 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium Chloride, 0.1M BISTIS PH6.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 18332 / Num. obs: 18332 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Biso Wilson estimate: 38.68 Å2 / Rmerge(I) obs: 0.103

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→41.234 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8427 / SU ML: 0.57 / σ(F): 1.33 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 929 5.09 %RANDOM
Rwork0.1895 ---
obs0.1916 18248 99.83 %-
all-18248 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.516 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 158.74 Å2 / Biso mean: 59.7121 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1-6.7753 Å2-0 Å2-0 Å2
2--6.7753 Å20 Å2
3----13.5506 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 63 84 2724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042683
X-RAY DIFFRACTIONf_angle_d0.7123601
X-RAY DIFFRACTIONf_dihedral_angle_d17.369969
X-RAY DIFFRACTIONf_chiral_restr0.056389
X-RAY DIFFRACTIONf_plane_restr0.003469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4004-2.52690.27541310.2052388
2.5269-2.68520.23711520.19772388
2.6852-2.89250.27631210.19512441
2.8925-3.18350.251330.1912437
3.1835-3.64390.22811300.18332476
3.6439-4.58990.20961430.17382491
4.5899-41.24020.22631190.1992698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.33731.3692-1.51314.0064-1.18582.0455-0.1546-0.1157-0.37730.30020.13620.1920.8008-0.65180.04740.5717-0.23-0.03230.42080.07230.2452-13.6124-33.2786-14.5726
26.9469-1.4017-0.26151.53630.44972.9191-0.12390.22130.4202-0.08960.0027-0.0988-0.1139-0.12360.1030.3289-0.0484-0.09220.12810.05930.2162.1418-20.6593-15.9253
32.8583-0.45910.00512.06680.11561.5117-0.1361-0.0657-0.22580.32620.0699-0.23630.37270.30860.10290.41450.0853-0.1520.1727-0.00120.250419.4924-30.8447-6.0363
41.5441-1.579-0.0024.54991.80953.6714-0.08790.3519-0.0398-0.2635-0.2539-0.26421.5790.53470.1281.16870.3247-0.00020.4814-0.03390.618528.4777-54.3777-15.9361
55.9209-5.7312-5.03775.55424.87824.28680.32250.9498-0.8834-0.6764-0.23070.1440.994-0.1451-0.18870.69530.0425-0.04030.3508-0.06250.488511.7095-33.5535-11.4174
66.0460.9815-4.77777.2369-3.10835.260.2445-0.9951-0.19440.9063-0.2728-0.0827-0.2768-0.49920.01550.3509-0.048-0.01980.3550.00310.1027-6.9158-27.324-8.9575
75.16284.69773.17464.27462.88861.9520.9972-1.13460.80813.1368-1.63581.32892.3167-2.40140.69411.0041-0.38460.31390.99150.06790.9617-16.9801-27.431-2.7707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 13:87)A13 - 87
2X-RAY DIFFRACTION2chain 'A' and (resseq 88:164)A88 - 164
3X-RAY DIFFRACTION3chain 'A' and (resseq 165:268)A165 - 268
4X-RAY DIFFRACTION4chain 'A' and (resseq 269:344)A269 - 344
5X-RAY DIFFRACTION5chain 'B' and (resseq 4:11)B4 - 11
6X-RAY DIFFRACTION6chain 'B' and (resseq 12:16)B12 - 16
7X-RAY DIFFRACTION7chain 'B' and (resseq 17:19)B17 - 19

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