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- PDB-4idq: human atlastin-1 1-446, N440T, GDPAlF4- -

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Basic information

Entry
Database: PDB / ID: 4idq
Titlehuman atlastin-1 1-446, N440T, GDPAlF4-
ComponentsAtlastin-1
KeywordsHYDROLASE / GTPase / GTP/GDP 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 / 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
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Atlastin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsByrnes, L.J. / Singh, A. / Szeto, K. / Benvin, N.M. / O'Donnell, J.P. / Zipfel, W.R. / Sondermann, H.
CitationJournal: Embo J. / Year: 2013
Title: Structural basis for conformational switching and GTP loading of the large G protein atlastin.
Authors: Byrnes, L.J. / Singh, A. / Szeto, K. / Benvin, N.M. / O'Donnell, J.P. / Zipfel, W.R. / Sondermann, H.
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Sep 20, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_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: Atlastin-1
B: Atlastin-1
C: Atlastin-1
D: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,57620
Polymers205,1644
Non-polymers3,41116
Water12,683704
1
A: Atlastin-1
B: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,28810
Polymers102,5822
Non-polymers1,7068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-68 kcal/mol
Surface area34290 Å2
MethodPISA
2
C: Atlastin-1
D: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,28810
Polymers102,5822
Non-polymers1,7068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-73 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.993, 267.084, 62.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 51291.082 Da / Num. of mol.: 4 / Fragment: cytoplasmic domain (UNP residues 1-446) / Mutation: N440T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8WXF7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Non-polymers , 5 types, 720 molecules

#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-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.2 M lithium citrate tribasic tetrahydrate, 20% PEG3350, pH 8.4, 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: Mar 6, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.295→50 Å / Num. all: 96866 / Num. obs: 92313 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.6 % / Rsym value: 0.12 / Net I/σ(I): 35.6
Reflection shellResolution: 2.295→2.38 Å / Redundancy: 3 % / Mean I/σ(I) obs: 10.5 / Rsym value: 0.504 / % possible all: 81.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q5D

3q5d


Resolution: 2.295→41.139 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 37.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1919 2.18 %RANDOM
Rwork0.2061 ---
obs0.2071 88117 90.89 %-
all-96866 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.295→41.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13440 0 212 704 14356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813986
X-RAY DIFFRACTIONf_angle_d1.18718874
X-RAY DIFFRACTIONf_dihedral_angle_d16.3045298
X-RAY DIFFRACTIONf_chiral_restr0.0822040
X-RAY DIFFRACTIONf_plane_restr0.0052408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.295-2.35210.39231110.28544959X-RAY DIFFRACTION75
2.3521-2.41570.30461340.26056027X-RAY DIFFRACTION90
2.4157-2.48680.2921340.24076009X-RAY DIFFRACTION90
2.4868-2.5670.26951330.22286037X-RAY DIFFRACTION90
2.567-2.65870.27771360.22836074X-RAY DIFFRACTION91
2.6587-2.76520.25851350.22456083X-RAY DIFFRACTION91
2.7652-2.8910.29361380.23126169X-RAY DIFFRACTION92
2.891-3.04340.28291370.236313X-RAY DIFFRACTION94
3.0434-3.2340.27691440.22236422X-RAY DIFFRACTION95
3.234-3.48350.25481440.20756516X-RAY DIFFRACTION96
3.4835-3.83390.24581390.18766352X-RAY DIFFRACTION94
3.8339-4.38810.21061420.17026226X-RAY DIFFRACTION91
4.3881-5.52640.21061400.17176365X-RAY DIFFRACTION92
5.5264-41.14590.24011520.19486646X-RAY DIFFRACTION93
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)
12.13490.52170.1711.6874-0.21951.9707-0.0184-0.20430.0550.1070.04220.3624-0.132-0.3718-0.0140.18540.0250.01140.2161-0.02710.2153-57.471751.864-12.3319
23.13452.83291.00347.3622.74533.49670.040.12510.2846-0.56060.16431.0343-0.3259-0.5676-0.10610.5240.1207-0.09210.24230.04110.4502-56.208472.6524-19.9771
31.0807-0.2927-0.45750.95710.08251.08570.04420.0827-0.017-0.1402-0.00280.0962-0.0635-0.1307-0.04090.19920.0184-0.07190.1585-0.0020.1679-44.81352.7129-21.9723
42.8447-0.84041.09831.8137-0.7562.60360.07430.0099-0.2268-0.1750.02830.30910.2708-0.3064-0.05980.1477-0.0215-0.0450.1885-0.04270.2291-56.900338.9143-18.975
50.8023-0.80970.06475.0507-1.03130.6126-0.08-0.09650.12980.33880.0278-0.3119-0.08370.06520.05190.19470.0057-0.03380.18250.00950.1439-24.11216.5908-11.3153
61.4438-0.3139-0.45621.95710.01681.9465-0.02090.08850.0761-0.02480.0143-0.3199-0.09010.4091-0.02030.1929-0.0105-0.0140.233-0.02110.206-7.286751.251-20.9105
74.2655-2.5099-2.83937.26826.13145.3230.1991-0.50270.97820.5244-0.0316-0.4-0.95350.3623-0.15350.5839-0.107-0.22640.4543-0.04150.6691-3.620468.2545-10.1736
80.930.0891-0.32021.0078-0.03330.80130.0567-0.09450.05720.0247-0.0105-0.1352-0.03950.1496-0.05790.2158-0.02-0.06410.1897-0.00980.1561-19.41653.564-11.1658
93.34951.17780.99972.34840.50922.4928-0.1385-0.2247-0.06460.02010.0641-0.465-0.02330.29330.02250.23330.0456-0.02450.23010.0250.2036-6.724939.2051-13.5083
100.34940.67970.20935.10351.02670.413-0.10850.04890.0889-0.4389-0.04850.3598-0.0385-0.11410.19380.2310.0126-0.02350.2072-0.01110.1827-40.11216.9787-21.5513
111.8733-0.4820.35862.0339-0.38051.42410.03210.1575-0.0788-0.1908-0.00170.2781-0.0074-0.2283-0.01670.1895-0.03550.00330.2120.01670.1496-57.3496-26.7632-51.732
122.5769-1.668-0.74954.73060.42463.0835-0.05460.0677-0.89050.45080.02250.63620.7845-0.60870.02850.4382-0.1257-0.01210.24530.04070.304-55.5016-47.0517-45.2699
130.9861-0.09550.23250.80430.07160.84960.0097-0.0591-0.0035-0.00150.02280.04740.0129-0.0753-0.02140.1361-0.02390.0480.14680.01780.1522-44.7377-27.2379-42.0022
142.10221.2374-0.79771.8911-0.59242.02810.0156-0.20970.27790.04930.00140.4073-0.2137-0.27560.00090.10740.02270.04870.2440.00470.294-56.7487-13.7168-45.0805
150.91260.27510.19985.2982-0.8180.6037-0.05930.0644-0.0718-0.37070.0035-0.1838-0.01890.06560.05980.18190.01150.01330.1650.0080.1134-24.207518.84-52.5505
161.34230.3013-0.11151.69350.34821.30940.028-0.1307-0.01370.18360.0951-0.28080.14880.2549-0.10760.15560.01980.0280.2081-0.00250.1119-7.0505-26.9197-43.4707
174.8986-5.1889-4.78935.58875.62367.9331-0.11740.5023-0.90220.03470.0029-0.06060.54370.42230.08660.46640.06680.1120.29710.03360.4467-5.6167-46.084-55.2772
180.9133-0.22540.11530.8023-0.00491.09350.04670.11170.0348-0.1273-0.0057-0.09540.04050.0887-0.0420.16440.0170.04690.13970.00110.1028-19.3979-28.0389-52.695
193.261-0.8646-1.10972.08310.43322.28690.05070.24270.4027-0.0604-0.0188-0.2375-0.23180.1914-0.04360.1772-0.02440.00760.18580.070.2226-7.6792-13.6161-49.895
201.1059-0.49220.06264.7691.00230.6744-0.0692-0.0985-0.11350.3155-0.00410.2122-0.018-0.09240.08150.21050.02030.00870.15320.01270.139-40.407818.8317-42.3874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 30:93)
2X-RAY DIFFRACTION2(chain A and resid 94:105)
3X-RAY DIFFRACTION3(chain A and resid 106:307)
4X-RAY DIFFRACTION4(chain A and resid 308:346)
5X-RAY DIFFRACTION5(chain A and resid 347:446)
6X-RAY DIFFRACTION6(chain B and resid 30:90)
7X-RAY DIFFRACTION7(chain B and resid 91:98)
8X-RAY DIFFRACTION8(chain B and resid 99:307)
9X-RAY DIFFRACTION9(chain B and resid 308:344)
10X-RAY DIFFRACTION10(chain B and resid 345:446)
11X-RAY DIFFRACTION11(chain C and resid 30:93)
12X-RAY DIFFRACTION12(chain C and resid 94:107)
13X-RAY DIFFRACTION13(chain C and resid 108:307)
14X-RAY DIFFRACTION14(chain C and resid 308:346)
15X-RAY DIFFRACTION15(chain C and resid 347:446)
16X-RAY DIFFRACTION16(chain D and resid 30:94)
17X-RAY DIFFRACTION17(chain D and resid 95:99)
18X-RAY DIFFRACTION18(chain D and resid 100:307)
19X-RAY DIFFRACTION19(chain D and resid 308:346)
20X-RAY DIFFRACTION20(chain D and resid 347:446)

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