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- PDB-5d3q: Dynamin 1 GTPase-BSE fusion dimer complexed with GDP -

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Basic information

Entry
Database: PDB / ID: 5d3q
TitleDynamin 1 GTPase-BSE fusion dimer complexed with GDP
ComponentsDynamin-1,Dynamin-1
KeywordsHYDROLASE / Fusion protein / GTPase / Endocytosis
Function / homology
Function and homology information


clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions / endosome organization / Gap junction degradation / photoreceptor ribbon synapse / membrane coat / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / photoreceptor inner segment / receptor-mediated endocytosis / cell projection / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / endocytosis / : / GDP binding / presynapse / Clathrin-mediated endocytosis / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / synapse / GTP binding / protein kinase binding / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Dynamin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsAnand, R. / Eschenburg, S. / Reubold, T.F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of the GTPase domain and the bundle signalling element of dynamin in the GDP state.
Authors: Anand, R. / Eschenburg, S. / Reubold, T.F.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Mar 22, 2017Group: Data collection
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynamin-1,Dynamin-1
B: Dynamin-1,Dynamin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0656
Polymers77,0542
Non-polymers1,0114
Water10,971609
1
A: Dynamin-1,Dynamin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0323
Polymers38,5271
Non-polymers5052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dynamin-1,Dynamin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0323
Polymers38,5271
Non-polymers5052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.220, 49.960, 82.520
Angle α, β, γ (deg.)99.40, 87.18, 105.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Dynamin-1,Dynamin-1


Mass: 38527.035 Da / Num. of mol.: 2
Fragment: UNP residues 5-320, 726-746,UNP residues 5-320, 726-746
Source method: isolated from a genetically manipulated source
Details: The sequence contains residues 5-320 and 726-746 of human dynamin 1. The very N-terminus contains a glycine residue from the TEV cleavage step. The two dynamin fragments are connected by a ...Details: The sequence contains residues 5-320 and 726-746 of human dynamin 1. The very N-terminus contains a glycine residue from the TEV cleavage step. The two dynamin fragments are connected by a linker sequence of eight residues (KHGTDSRV).
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1, DNM / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q05193, dynamin GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Before crystallization set-ups, GG1 at a concentration of 10 mg/ml was supplemented with 2 mM GDP and 2 mM MgCl2 and incubated for 1 h on ice. GG1GDP was crystallized by hanging drop vapour ...Details: Before crystallization set-ups, GG1 at a concentration of 10 mg/ml was supplemented with 2 mM GDP and 2 mM MgCl2 and incubated for 1 h on ice. GG1GDP was crystallized by hanging drop vapour diffusion mixing 1.5 ul protein solution with 1.5 ul reservoir solution containing 0.1 M Tris (pH 8.0), 26 % PEG 3350 and 0.2 M NaSCN. The drops were equilibrated against 700 ul of reservoir.
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.7→47.626 Å / Num. obs: 72213 / % possible obs: 97.6 % / Redundancy: 4.63 % / Rmerge(I) obs: 0.118 / Rsym value: 0.108 / Net I/σ(I): 10.75
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 6.7 / % possible all: 96.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x2e

2x2e


Resolution: 1.7→47.626 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 3611 5 %Random selection
Rwork0.1727 ---
obs0.1744 72207 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 64 609 5807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155347
X-RAY DIFFRACTIONf_angle_d1.47259
X-RAY DIFFRACTIONf_dihedral_angle_d13.6583346
X-RAY DIFFRACTIONf_chiral_restr0.082844
X-RAY DIFFRACTIONf_plane_restr0.008945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72240.26571390.20692642X-RAY DIFFRACTION96
1.7224-1.7460.25881340.21052538X-RAY DIFFRACTION96
1.746-1.77090.24681370.20122603X-RAY DIFFRACTION96
1.7709-1.79730.24711360.19642599X-RAY DIFFRACTION96
1.7973-1.82540.23251380.19472616X-RAY DIFFRACTION96
1.8254-1.85540.25671380.18382620X-RAY DIFFRACTION96
1.8554-1.88740.21591340.1812552X-RAY DIFFRACTION97
1.8874-1.92170.23181420.18192690X-RAY DIFFRACTION97
1.9217-1.95860.18791330.17952538X-RAY DIFFRACTION96
1.9586-1.99860.23851400.17812657X-RAY DIFFRACTION97
1.9986-2.04210.23241360.18132579X-RAY DIFFRACTION97
2.0421-2.08960.2241390.18262644X-RAY DIFFRACTION97
2.0896-2.14180.21851370.17552596X-RAY DIFFRACTION97
2.1418-2.19970.20431400.17652653X-RAY DIFFRACTION97
2.1997-2.26450.22291370.17782608X-RAY DIFFRACTION98
2.2645-2.33760.21891400.17412661X-RAY DIFFRACTION97
2.3376-2.42110.21761380.17812620X-RAY DIFFRACTION97
2.4211-2.5180.22271390.17222639X-RAY DIFFRACTION98
2.518-2.63260.23321420.1742709X-RAY DIFFRACTION99
2.6326-2.77140.21291420.17712691X-RAY DIFFRACTION100
2.7714-2.9450.22091400.17822673X-RAY DIFFRACTION100
2.945-3.17240.22151430.18112702X-RAY DIFFRACTION100
3.1724-3.49150.18831400.17392658X-RAY DIFFRACTION100
3.4915-3.99650.16841430.15732720X-RAY DIFFRACTION100
3.9965-5.03430.16961410.14672683X-RAY DIFFRACTION100
5.0343-47.64470.17931430.16822705X-RAY DIFFRACTION100

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