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- PDB-3q5e: crystal structure of human Atlastin-1 (residues 1-447) bound to G... -

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Basic information

Entry
Database: PDB / ID: 3q5e
Titlecrystal structure of human Atlastin-1 (residues 1-447) bound to GDP, crystal form 2
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 / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane / identical protein binding
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 / MOLECULAR REPLACEMENT / Resolution: 3.013 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Atlastin-1
C: Atlastin-1
E: Atlastin-1
G: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,14212
Polymers205,2724
Non-polymers1,8708
Water0
1
A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7863
Polymers51,3181
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7863
Polymers51,3181
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7863
Polymers51,3181
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7863
Polymers51,3181
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.394, 133.549, 175.835
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
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: 51318.109 Da / Num. of mol.: 4 / 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, 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 / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350 and 0.15 M ammonium phosphate dibasic, pH 8.0, 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: 3→50 Å / Num. all: 49019 / Num. obs: 48872 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3→3.11 Å / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.013→42.544 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 1890 4.07 %random
Rwork0.1971 ---
all0.2003 48786 --
obs0.2003 46452 94.24 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.669 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.9973 Å2-0 Å20 Å2
2---18.7807 Å20 Å2
3---25.778 Å2
Refinement stepCycle: LAST / Resolution: 3.013→42.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12820 0 116 0 12936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913207
X-RAY DIFFRACTIONf_angle_d1.24817829
X-RAY DIFFRACTIONf_dihedral_angle_d19.6994956
X-RAY DIFFRACTIONf_chiral_restr0.0861943
X-RAY DIFFRACTIONf_plane_restr0.0052268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0131-3.09460.39871110.28942659X-RAY DIFFRACTION74
3.0946-3.18560.36791310.24333085X-RAY DIFFRACTION87
3.1856-3.28840.3211400.24213342X-RAY DIFFRACTION93
3.2884-3.40590.31411470.23073459X-RAY DIFFRACTION96
3.4059-3.54220.29411470.21993493X-RAY DIFFRACTION97
3.5422-3.70330.27561480.20643497X-RAY DIFFRACTION97
3.7033-3.89840.30111430.19863425X-RAY DIFFRACTION95
3.8984-4.14250.24111520.18243462X-RAY DIFFRACTION96
4.1425-4.4620.24821500.15763496X-RAY DIFFRACTION97
4.462-4.91040.22931530.1613545X-RAY DIFFRACTION97
4.9104-5.61960.2621530.17583608X-RAY DIFFRACTION98
5.6196-7.07480.27611510.20933677X-RAY DIFFRACTION99
7.0748-42.54860.24911640.19563814X-RAY DIFFRACTION99
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)
11.3019-0.5731-0.8321.60820.33690.53440.27060.80780.2596-0.7414-0.0147-0.2659-0.1073-0.3849-0.18890.3248-0.0285-0.03840.5478-0.00180.0168-4.340814.8844-25.2303
21.5362-0.10480.84442.5124-1.42851.17730.15660.73840.2676-0.72560.18670.16820.06520.1737-0.21890.14370.0165-0.0870.46350.02630.0003-10.947515.2109-20.9315
31.83250.1242-0.59040.4078-0.24060.8250.38370.47090.8478-0.088-0.0490.204-0.0854-0.3197-0.15210.15570.0324-0.13660.0626-0.0226-0.1915-11.407613.4836-9.1245
40.33860.43-0.85880.489-0.95532.3157-0.36830.0215-0.3513-0.5972-0.1017-0.48271.38520.9384-0.02620.6604-0.0026-0.35740.6257-0.0246-0.0646-24.79-11.2263-37.0808
50.70960.1761-0.0460.23080.55941.8128-0.11640.15180.0885-0.35980.0958-0.3162-0.55960.2016-0.1230.1942-0.05010.19650.0521-0.09250.1909-52.629822.2348-17.1666
61.60840.7519-0.05140.55250.26780.9609-0.1606-0.0884-0.21680.22450.44060.0797-0.1094-0.32850.0060.20.14410.04930.3383-0.10640.2319-58.530123.6117-15.2074
70.25090.168-0.04530.2903-0.280.83310.0803-0.08470.19840.1054-0.0470.1215-0.1506-0.1615-0.05830.0957-0.00270.11480.0862-0.05240.3301-61.737220.4072-2.483
80.20220.1949-0.23340.75050.05591.22090.0731-0.01470.194-0.21120.14740.5317-0.1905-0.2801-0.05940.0584-0.0945-0.24820.0179-0.24370.2098-72.49843.0402-32.7787
91.680.75531.03832.29460.73620.6592-0.1069-0.192-0.38840.90460.2154-0.30190.16720.1644-0.1750.2410.0556-0.10860.1180.02080.1206-2.0674-14.519910.3232
100.3946-0.15290.05941.12890.22950.68240.04510.0694-0.76770.0791-0.26520.10860.1221-0.2235-0.04180.0293-0.0198-0.17270.0040.0205-0.166-12.8816-17.3971.1071
110.17080.1816-0.06842.59261.52354.8677-0.14780.07060.02090.69490.18190.53-0.76081.0504-0.16840.6164-0.04030.16630.23620.0268-0.1192-22.34611.878623.7202
121.5429-0.7114-0.60822.199-0.24680.3508-0.4595-0.5258-0.2671-0.21610.35240.29960.01850.13420.04570.4097-0.04050.2680.1465-0.02490.3132-67.3173-5.45324.3474
130.4137-0.06190.37971.71940.08020.61850.1697-0.054-0.0090.0061-0.09590.29680.1424-0.0742-0.05910.1103-0.04970.0080.0857-0.0240.2139-59.254-12.92056.7305
140.7465-0.5675-0.05040.34410.08850.76110.7142-0.3373-0.44430.669-0.00650.76220.7424-0.5185-0.1894-0.1790.23340.7355-0.2578-0.35380.1901-78.402910.723720.9571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 30:111)
2X-RAY DIFFRACTION2(chain A and resid 112:175)
3X-RAY DIFFRACTION3(chain A and resid 176:348)
4X-RAY DIFFRACTION4(chain A and resid 349:441)
5X-RAY DIFFRACTION5(chain C and resid 30:111)
6X-RAY DIFFRACTION6(chain C and resid 112:162)
7X-RAY DIFFRACTION7(chain C and resid 163:335)
8X-RAY DIFFRACTION8(chain C and resid 336:438)
9X-RAY DIFFRACTION9(chain E and resid 29:144)
10X-RAY DIFFRACTION10(chain E and resid 145:371)
11X-RAY DIFFRACTION11(chain E and resid 372:438)
12X-RAY DIFFRACTION12(chain G and resid 29:67)
13X-RAY DIFFRACTION13(chain G and resid 68:307)
14X-RAY DIFFRACTION14(chain G and resid 308:438)

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