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- PDB-3q5d: crystal structure of human Atlastin-1 (residues 1-447) bound to G... -

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Basic information

Entry
Database: PDB / ID: 3q5d
Titlecrystal structure of human Atlastin-1 (residues 1-447) bound to GDP, crystal form 1
ComponentsAtlastin-1
KeywordsHYDROLASE / G protein / GTPase / GDP/GTP binding
Function / homology
Function and homology information


endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / axon / Golgi membrane ...endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / axon / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / identical protein binding / membrane
Similarity search - Function
AHSP / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase ...AHSP / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Atlastin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.699 Å
AuthorsByrnes, L.J. / Sondermann, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for the nucleotide-dependent dimerization of the large G protein atlastin-1/SPG3A.
Authors: Byrnes, L.J. / Sondermann, H.
History
DepositionDec 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2553
Polymers51,7871
Non-polymers4682
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Atlastin-1
hetero molecules

A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5096
Polymers103,5742
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area7590 Å2
ΔGint-60 kcal/mol
Surface area35560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.353, 145.353, 104.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Atlastin-1 / Brain-specific GTP-binding protein / GTP-binding protein 3 / GBP-3 / hGBP3 / Guanine nucleotide- ...Brain-specific GTP-binding protein / GTP-binding protein 3 / GBP-3 / hGBP3 / Guanine nucleotide-binding protein 3 / Spastic paraplegia 3 protein A


Mass: 51787.055 Da / Num. of mol.: 1 / Fragment: G and middle domain, UNP residues 1-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, atlastin-1 (residues 1-447), GBP3, SPG3A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: Q8WXF7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bicine pH 8.5, 30% PEG-MME550, 0.1 M succinic acid pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2010
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 33815 / Num. obs: 33815 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.7→2.8 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.699→48.127 Å / SU ML: 0.38 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 3154 10.01 %random
Rwork0.1877 ---
all0.1938 31518 --
obs0.1938 31518 93.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.439 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1768 Å20 Å2-0 Å2
2--4.1768 Å2-0 Å2
3----8.3536 Å2
Refinement stepCycle: LAST / Resolution: 2.699→48.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 29 5 3323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083387
X-RAY DIFFRACTIONf_angle_d1.2544576
X-RAY DIFFRACTIONf_dihedral_angle_d20.4331269
X-RAY DIFFRACTIONf_chiral_restr0.09499
X-RAY DIFFRACTIONf_plane_restr0.006586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6991-2.73940.4651160.33221037X-RAY DIFFRACTION78
2.7394-2.78220.38761090.30021087X-RAY DIFFRACTION82
2.7822-2.82780.39441170.28761078X-RAY DIFFRACTION81
2.8278-2.87660.31321280.24921095X-RAY DIFFRACTION84
2.8766-2.92890.29731410.23431178X-RAY DIFFRACTION89
2.9289-2.98520.31271300.27211176X-RAY DIFFRACTION89
2.9852-3.04610.33881370.23931161X-RAY DIFFRACTION89
3.0461-3.11230.36261310.23961192X-RAY DIFFRACTION90
3.1123-3.18470.34951340.22291219X-RAY DIFFRACTION91
3.1847-3.26440.29681310.20891254X-RAY DIFFRACTION93
3.2644-3.35260.26041440.18641259X-RAY DIFFRACTION96
3.3526-3.45120.2641480.20371258X-RAY DIFFRACTION96
3.4512-3.56260.23111420.19441274X-RAY DIFFRACTION96
3.5626-3.68990.30441410.20081290X-RAY DIFFRACTION97
3.6899-3.83750.22051470.19261298X-RAY DIFFRACTION97
3.8375-4.01210.2411480.17311285X-RAY DIFFRACTION98
4.0121-4.22350.23541380.17271295X-RAY DIFFRACTION98
4.2235-4.4880.21571460.14511313X-RAY DIFFRACTION99
4.488-4.83420.21091500.14331317X-RAY DIFFRACTION99
4.8342-5.32010.18791420.1631311X-RAY DIFFRACTION99
5.3201-6.08860.25681410.17681327X-RAY DIFFRACTION99
6.0886-7.6660.23151480.18291326X-RAY DIFFRACTION100
7.666-48.13470.23031450.191334X-RAY DIFFRACTION100
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)
11.36680.48590.57572.76150.21471.74530.17210.07430.2636-0.13630.06570.3448-0.0956-0.5026-0.19390.21040.0720.03660.31390.03770.24093.936742.54446.1842
21.89030.385-0.26291.1563-1.03321.14670.2799-0.40950.03180.5341-0.0722-0.07010.0387-0.1355-0.17430.3492-0.0246-0.0610.3377-0.02760.238414.262338.679250.0119
30.92990.2279-1.92251.8666-1.16563.5190.196-0.4504-0.03480.3752-0.34920.0483-0.89830.90130.07810.732-0.4046-0.00750.54130.01570.29746.87766.9125.1272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(resid 29:199)
2X-RAY DIFFRACTION2(resid 200:341)
3X-RAY DIFFRACTION3(resid 342:438)

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