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- PDB-6ne6: Crystal Structure of heterotrimeric G-protein alpha subunit Galph... -

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Basic information

Entry
Database: PDB / ID: 6ne6
TitleCrystal Structure of heterotrimeric G-protein alpha subunit Galpha7 from Naegleria fowleri
ComponentsG-protein alpha subunit Galpha7
KeywordsCELL CYCLE / SSGCID / guanine nucleotide binding / G protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal Structure of heterotrimeric G-protein alpha subunit Galpha7 from Naegleria fowleri
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-protein alpha subunit Galpha7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,87610
Polymers38,3961
Non-polymers4809
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint5 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.690, 68.310, 79.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein G-protein alpha subunit Galpha7


Mass: 38395.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Gene: NF0037180 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NafoA.01088.e.B1 and NafoA.19531.b.B2 were co-purified (PW38434) to 20.24 mg/ml in a buffer containing 25 mM HEPES pH 7.5, 500 mM NaCl, 5% Glycerol , 2 mM DTT, 0.025% Azide, 10mM MgCl2, 10mM ...Details: NafoA.01088.e.B1 and NafoA.19531.b.B2 were co-purified (PW38434) to 20.24 mg/ml in a buffer containing 25 mM HEPES pH 7.5, 500 mM NaCl, 5% Glycerol , 2 mM DTT, 0.025% Azide, 10mM MgCl2, 10mM NaF, 30uM AlCl3, 5uM GDP, was mixed 1:1 with Wiz3/4(c8): 16% (w/v) PEG-800, 40 mM potassium phosphate monobasic, 20% (v/v) glycerol, cryoprotected with 20% ethylene glycol. Tray 299259c8, puck: rhn8-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 5, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→48.256 Å / Num. obs: 37029 / % possible obs: 99.8 % / Redundancy: 6.003 % / Biso Wilson estimate: 19.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.05 / Χ2: 1.039 / Net I/σ(I): 23.09 / Num. measured all: 222267
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.744.9960.5122.9913464270126950.8580.57299.8
1.74-1.795.90.4194.2215624264826480.9340.459100
1.79-1.846.1570.3315.5115774256225620.9580.361100
1.84-1.96.1650.2517.3815425250325020.9740.274100
1.9-1.966.1210.1869.8314775241424140.9850.203100
1.96-2.036.1710.14812.2114365232923280.990.162100
2.03-2.116.1480.11615.0413894226022600.9940.127100
2.11-2.196.1680.09418.2513490218921870.9950.10399.9
2.19-2.296.1390.07522.3512874209820970.9970.082100
2.29-2.46.1410.06525.0812344201220100.9970.07199.9
2.4-2.536.1520.05827.911751191219100.9980.06399.9
2.53-2.696.1270.0531.7711152182118200.9980.05599.9
2.69-2.876.1010.04236.5510396170517040.9990.04599.9
2.87-3.16.0760.03640.919715160015990.9990.0499.9
3.1-3.46.0820.03146.648923147814670.9990.03499.3
3.4-3.86.0230.02553.228089135213430.9990.02899.3
3.8-4.395.9550.02357.817092119411910.9990.02599.7
4.39-5.385.9260.02258.756033102210180.9990.02499.6
5.38-7.65.7450.02455.7446888218160.9990.02699.4
7.6-48.2565.2380.02258.8823994764580.9990.02596.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5do9

5do9


Resolution: 1.7→48.256 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.73
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 2146 5.99 %0
Rwork0.1609 ---
obs0.163 35817 96.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.9 Å2 / Biso mean: 24.1924 Å2 / Biso min: 5.23 Å2
Refinement stepCycle: final / Resolution: 1.7→48.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 30 334 3000
Biso mean--41.38 34.74 -
Num. residues----327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6999-1.73950.2485960.2252033212988
1.7395-1.7830.27821270.20842107223491
1.783-1.83120.24181380.18872133227194
1.8312-1.88510.20651520.17432155230795
1.8851-1.94590.20991490.16072218236797
1.9459-2.01550.18931620.15982209237197
2.0155-2.09620.19491470.16022217236497
2.0962-2.19160.21071290.15712268239798
2.1916-2.30710.17321460.1572262240898
2.3071-2.45170.1841450.15252286243198
2.4517-2.6410.18971530.15862307246099
2.641-2.90670.21211530.15522302245599
2.9067-3.32720.20121490.15872341249099
3.3272-4.19160.16121450.14512367251299
4.1916-48.27510.20031550.16862466262199
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)
11.1439-0.7207-0.2271.6130.36261.4431-0.03630.2402-0.0247-0.06470.01040.10650.0518-0.02690.0240.1151-0.01130.00120.130.02040.12140.138738.3353-3.812
21.93663.01253.71124.69645.79627.1347-0.09280.08060.1061-0.1280.01190.0276-0.2410.15840.0680.13450.02330.020.14750.02960.147823.575839.32628.4888
31.1835-0.38761.20351.4549-1.20113.0056-0.01560.10550.12320.0154-0.2771-0.31010.04030.47370.17150.1523-0.01420.0020.21230.0290.23634.065441.928117.5709
41.2315-0.07610.51771.6254-0.08631.66620.0138-0.0206-0.07250.0263-0.03-0.0140.10440.1244-0.00780.11780.0072-0.00690.13110.02680.12924.306336.046815.7465
53.5932-0.24061.88260.532-0.09861.74890.02420.1226-0.0884-0.0171-0.02420.05490.06250.03410.01890.1623-0.01040.01290.15250.0060.14676.585635.3267-0.7778
61.94210.48081.01261.12671.24221.6095-0.1630.487-0.0515-0.25670.1103-0.0122-0.30010.40150.04270.2232-0.01950.00770.24630.03560.20634.111649.1482.302
71.1857-0.13890.87861.8375-0.67492.379-0.0237-0.07510.02870.14020.00510.1209-0.1359-0.12520.02070.10190.01580.02720.09930.00050.1272-2.635148.958716.6186
89.4354-8.58885.56648.8982-4.65754.58180.1197-0.13210.0497-0.022-0.03110.18810.1003-0.2289-0.11040.1428-0.03570.03940.14420.01970.2368-11.99538.24883.6828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 62 )A27 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 90 )A63 - 90
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 116 )A91 - 116
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 165 )A117 - 165
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 203 )A166 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 244 )A204 - 244
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 331 )A245 - 331
8X-RAY DIFFRACTION8chain 'A' and (resid 332 through 353 )A332 - 353

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