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- PDB-3l43: Crystal structure of the dynamin 3 GTPase domain bound with GDP -

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Basic information

Entry
Database: PDB / ID: 3l43
TitleCrystal structure of the dynamin 3 GTPase domain bound with GDP
ComponentsDynamin-3
KeywordsHYDROLASE / structural genomics consortium / sgc / Cytoskeleton / Endocytosis / GTP-binding / Microtubule / Motor protein / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


type 1 metabotropic glutamate receptor binding / basal tubulobulbar complex / postsynaptic endocytic zone membrane / apical tubulobulbar complex / positive regulation of synaptic vesicle recycling / structural constituent of postsynapse / negative regulation of dendritic spine morphogenesis / dynamin GTPase / postsynaptic neurotransmitter receptor internalization / Toll Like Receptor 4 (TLR4) Cascade ...type 1 metabotropic glutamate receptor binding / basal tubulobulbar complex / postsynaptic endocytic zone membrane / apical tubulobulbar complex / positive regulation of synaptic vesicle recycling / structural constituent of postsynapse / negative regulation of dendritic spine morphogenesis / dynamin GTPase / postsynaptic neurotransmitter receptor internalization / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / filopodium assembly / type 5 metabotropic glutamate receptor binding / positive regulation of filopodium assembly / dendritic spine head / nitric-oxide synthase binding / Recycling pathway of L1 / synaptic vesicle endocytosis / synaptic cleft / protein serine/threonine kinase binding / synapse assembly / MHC class II antigen presentation / receptor internalization / endocytosis / presynapse / Clathrin-mediated endocytosis / microtubule binding / microtubule / dendritic spine / postsynaptic density / axon / GTPase activity / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / 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-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsYang, S. / Tempel, W. / Tong, Y. / Nedyalkova, L. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Yang, S. / Tempel, W. / Tong, Y. / Nedyalkova, L. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the dynamin 3 GTPase domain bound with GDP
Authors: Yang, S. / Tempel, W. / Tong, Y. / Nedyalkova, L. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 11, 2014Group: Refinement description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 13, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynamin-3
B: Dynamin-3
C: Dynamin-3
D: Dynamin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,14614
Polymers143,3734
Non-polymers1,77310
Water1,40578
1
A: Dynamin-3
D: Dynamin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5738
Polymers71,6872
Non-polymers8866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-23 kcal/mol
Surface area20270 Å2
MethodPISA
2
B: Dynamin-3
C: Dynamin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5736
Polymers71,6872
Non-polymers8864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-24 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.286, 166.500, 74.985
Angle α, β, γ (deg.)90.00, 109.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dynamin-3 / Dynamin / T-dynamin


Mass: 35843.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM3, KIAA0820 / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9UQ16, dynamin GTPase
#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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.029 Å3/Da / Density % sol: 39.372 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2M sodium chloride, 0.1M HEPES. 1:100 w/w subtilisin., pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→20 Å / Num. obs: 52532 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Χ2: 1.806 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.27-2.313.40.58325781.7831100
2.31-2.353.50.51626841.8381100
2.35-2.43.50.46825531.781100
2.4-2.443.50.41426571.8081100
2.44-2.53.50.37626501.831100
2.5-2.563.50.32425571.8411100
2.56-2.623.50.28726361.8321100
2.62-2.693.50.25426331.911100
2.69-2.773.50.21726431.9121100
2.77-2.863.50.18725891.9051100
2.86-2.963.60.14926141.9211100
2.96-3.083.60.12326581.9631100
3.08-3.223.60.09726061.9531100
3.22-3.393.70.07426321.981100
3.39-3.63.70.05526111.8761100
3.6-3.873.80.04426241.8071100
3.87-4.263.80.03526361.6261100
4.26-4.873.80.0326581.5751100
4.87-6.113.80.03126391.5631100
6.11-203.80.02526741.5051100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2aka

2aka


Resolution: 2.27→19.97 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0
Details: Phenix.xtriage indicated pseudomerohedral twinning with twin law "h,-k,-h-l". Non-merged reflection intensities are included in the structure factor file. The programs chainsaw, phenix, ...Details: Phenix.xtriage indicated pseudomerohedral twinning with twin law "h,-k,-h-l". Non-merged reflection intensities are included in the structure factor file. The programs chainsaw, phenix, coot, molprobity were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1514 2.88 %thin shells (sftools)
Rwork0.229 ---
obs0.23 52485 --
Displacement parametersBiso mean: 40.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.293 Å20 Å21.377 Å2
2---2.807 Å20 Å2
3---2.514 Å2
Refine analyzeLuzzati coordinate error obs: 0.363 Å
Refinement stepCycle: LAST / Resolution: 2.27→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7339 0 118 78 7535
LS refinement shellResolution: 2.27→2.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.237 3867
all0.237 -

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