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- PDB-4ido: human atlastin-1 1-446, C-his6, GDPAlF4- -

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Basic information

Entry
Database: PDB / ID: 4ido
Titlehuman atlastin-1 1-446, C-his6, 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: 2.091 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1448
Polymers105,0032
Non-polymers1,1416
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-72 kcal/mol
Surface area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.610, 116.430, 185.400
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: 52501.383 Da / Num. of mol.: 2 / Fragment: cytoplasmic domain (UNP residues 1-446)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Plasmid: pET21 / 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
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M ammonium phosphate dibasic, 20% PEG3350, 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: Mar 3, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.091→50 Å / Num. all: 64491 / Num. obs: 63782 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8 % / Rsym value: 0.081 / Net I/σ(I): 23.3
Reflection shellResolution: 2.091→2.18 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.474 / % possible all: 96.8

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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 4IDQ

4idq


Resolution: 2.091→43.74 Å / SU ML: 0.23 / σ(F): 1.3 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 1927 3.13 %RANDOM
Rwork0.1988 ---
obs0.2004 61511 95.25 %-
all-64491 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.091→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6704 0 68 661 7433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086945
X-RAY DIFFRACTIONf_angle_d1.2299392
X-RAY DIFFRACTIONf_dihedral_angle_d15.9142604
X-RAY DIFFRACTIONf_chiral_restr0.0811021
X-RAY DIFFRACTIONf_plane_restr0.0061203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.091-2.14310.29121330.23824079X-RAY DIFFRACTION93
2.1431-2.2010.36571290.33143986X-RAY DIFFRACTION91
2.201-2.26580.52861160.42273598X-RAY DIFFRACTION83
2.2658-2.33890.52841030.38983300X-RAY DIFFRACTION75
2.3389-2.42250.2611410.21034333X-RAY DIFFRACTION98
2.4225-2.51950.25091430.19434383X-RAY DIFFRACTION99
2.5195-2.63410.23091430.19534404X-RAY DIFFRACTION99
2.6341-2.7730.27941430.2024420X-RAY DIFFRACTION100
2.773-2.94670.25811430.19914441X-RAY DIFFRACTION100
2.9467-3.17410.24571430.19344425X-RAY DIFFRACTION100
3.1741-3.49340.23141440.18184492X-RAY DIFFRACTION100
3.4934-3.99860.18881450.1664412X-RAY DIFFRACTION98
3.9986-5.03670.17821480.13174569X-RAY DIFFRACTION100
5.0367-43.74970.1911530.16024742X-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)
11.66460.71360.33241.8975-0.00572.166-0.13390.3038-0.143-0.35380.0941-0.10.0551-0.0180.02730.1646-0.02210.0490.1403-0.03190.1523-27.9459-12.110534.5382
20.95520.36230.1941.4682-0.02551.0639-0.06810.0452-0.1784-0.04740.0811-0.17840.0773-0.0002-0.01430.11530.00030.05530.111-0.01990.1779-19.5145-16.371646.3179
33.11412.107-2.83051.8638-1.83754.8305-0.03630.21950.5076-0.03560.19320.2598-0.1627-0.1261-0.12960.1605-0.0179-0.04890.31040.15830.3261-46.3863-24.988384.7818
41.86940.2641-0.04041.6399-0.0371.780.0401-0.19760.01960.28570.0075-0.2441-0.06630.1369-0.03830.14440.0137-0.03950.1290.00320.1346-14.4754.900972.0356
50.99450.2805-0.32381.0365-0.19661.480.0198-0.09810.04380.17350.0417-0.0621-0.1148-0.0538-0.0580.13390.01790.00080.1070.00060.1268-23.277.243665.1348
61.72552.9282-1.79965.2552-3.72683.7937-0.26430.1765-0.0743-0.35180.1955-0.22230.415-0.07040.07540.2847-0.02240.030.25760.03930.1724-41.922-40.983575.4499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 31:163)
2X-RAY DIFFRACTION2(chain A and resid 164:346)
3X-RAY DIFFRACTION3(chain A and resid 347:442)
4X-RAY DIFFRACTION4(chain B and resid 31:205)
5X-RAY DIFFRACTION5(chain B and resid 206:344)
6X-RAY DIFFRACTION6(chain B and resid 345:452)

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