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- PDB-3qof: Crystal structure of the cytosolic domain of human atlastin-1 in ... -

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Basic information

Entry
Database: PDB / ID: 3qof
TitleCrystal structure of the cytosolic domain of human atlastin-1 in complex with GDP, orthorhombic form
ComponentsAtlastin-1
KeywordsHYDROLASE / GTPase / homotypic fusion / fusion of ER membranes / GDP / GTP / endoplasmic reticulum
Function / homology
Function and homology information


endoplasmic reticulum tubular network membrane / endoplasmic reticulum tubular network membrane organization / Golgi cis cisterna membrane / GTPase-dependent fusogenic activity / endoplasmic reticulum tubular network / endoplasmic reticulum membrane fusion / endoplasmic reticulum organization / axonogenesis / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...endoplasmic reticulum tubular network membrane / endoplasmic reticulum tubular network membrane organization / Golgi cis cisterna membrane / GTPase-dependent fusogenic activity / endoplasmic reticulum tubular network / endoplasmic reticulum membrane fusion / endoplasmic reticulum organization / axonogenesis / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Golgi membrane / axon / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / Golgi apparatus / identical protein binding
Similarity search - Function
AHSP / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / 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 / Rossmann fold ...AHSP / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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: 2.802 Å
AuthorsLiu, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structures of the atlastin GTPase provide insight into homotypic fusion of endoplasmic reticulum membranes.
Authors: Bian, X. / Klemm, R.W. / Liu, T.Y. / Zhang, M. / Sun, S. / Sui, X. / Liu, X. / Rapoport, T.A. / Hu, J.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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.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 / _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_label_asym_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)212,74412
Polymers210,8744
Non-polymers1,8708
Water2,270126
1
A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1863
Polymers52,7191
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1863
Polymers52,7191
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1863
Polymers52,7191
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1863
Polymers52,7191
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.742, 133.445, 176.266
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: 52718.609 Da / Num. of mol.: 4 / Fragment: atlastin ecto-domain (UNP RESIDUES 18-447)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Plasmid: pet30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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.: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M Tris-HCl, pH8.3, 25%(w/v) PEG 3350, 0.1M (NH4)2HPO4, 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: MAR CCD 165 mm / Detector: CCD / Date: Jul 14, 2010 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→48.751 Å / Num. all: 61398 / Num. obs: 60656 / % possible obs: 98.79 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 57.4 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.8-2.966.30.3013.676740.30191.6
2.96-3.156.90.2876.988630.28798.8
3.15-3.427.10.15115.493560.151100
3.42-3.977.40.08221.7104830.082100
3.97-4.797.80.07625.8111870.076100
4.79-507.60.05334.6120630.05399.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QNU

3qnu


Resolution: 2.802→40 Å / SU ML: 0.4 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 1 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 3074 5.07 %random
Rwork0.2253 ---
all0.241 60793 --
obs0.2274 60656 98.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.413 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 65.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.2373 Å2-0 Å20 Å2
2---17.1156 Å2-0 Å2
3---25.3528 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.032 Å
Luzzati d res low-7 Å
Luzzati sigma a0.52 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.802→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12332 0 116 126 12574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812707
X-RAY DIFFRACTIONf_angle_d1.31417243
X-RAY DIFFRACTIONf_dihedral_angle_d21.0334500
X-RAY DIFFRACTIONf_chiral_restr0.0891947
X-RAY DIFFRACTIONf_plane_restr0.0052192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.8021-2.84590.38441010.274322120.013221283
2.8459-2.89250.34191460.264424460.012244695
2.8925-2.94240.31941440.248825720.012257298
2.9424-2.99590.31191370.246226100.0132610100
2.9959-3.05350.35041560.250125880.0112588100
3.0535-3.11580.36391320.249726130.0122613100
3.1158-3.18350.30411280.257626300.0122630100
3.1835-3.25760.30931240.254726580.0112658100
3.2576-3.3390.31371690.249625690.0112569100
3.339-3.42930.32581350.248126100.0122610100
3.4293-3.53020.30871320.24626480.0132648100
3.5302-3.64410.27461570.227126190.012619100
3.6441-3.77430.25411330.219826410.0132641100
3.7743-3.92530.29041340.213526500.0122650100
3.9253-4.10390.25421430.207626320.0122632100
4.1039-4.32010.21821530.183426380.0122638100
4.3201-4.59060.21481620.170326450.0132645100
4.5906-4.94470.19891490.170126490.0122649100
4.9447-5.44180.21661380.19126810.0112681100
5.4418-6.22780.24161310.206727100.0112710100
6.2278-7.84110.23541200.223427530.0122753100
7.8411-48.75840.21711500.201928080.013280899

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