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- PDB-6s9a: Artificial GTPase-BSE dimer of human Dynamin1 -

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Basic information

Entry
Database: PDB / ID: 6s9a
TitleArtificial GTPase-BSE dimer of human Dynamin1
ComponentsDynamin-1,Dynamin-1
KeywordsENDOCYTOSIS / GTPase / artificial dimer / GTP hydrolysis / membrane fission
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 / endosome organization ...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 / endosome organization / Formation of annular gap junctions / photoreceptor ribbon synapse / Gap junction degradation / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsGanichkin, O.M. / Vancraenenbroeck, R. / Rosenblum, G. / Hofmann, H. / Daumke, O. / Noel, J.K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchSFB 740, project C7 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Quantification and demonstration of the collective constriction-by-ratchet mechanism in the dynamin molecular motor.
Authors: Ganichkin, O.M. / Vancraenenbroeck, R. / Rosenblum, G. / Hofmann, H. / Mikhailov, A.S. / Daumke, O. / Noel, J.K.
History
DepositionJul 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / chem_comp / diffrn_radiation_wavelength / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all / _software.name / _software.version / _struct_sheet.number_strands
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Sep 8, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jan 24, 2024Group: 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

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)79,5138
Polymers79,1802
Non-polymers3336
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-144 kcal/mol
Surface area28900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.693, 69.546, 74.277
Angle α, β, γ (deg.)90.000, 113.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dynamin-1,Dynamin-1


Mass: 39590.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1, DNM / Plasmid: pET-M11 / Details (production host): Kn-resistance / Cell (production host): bacterial / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q05193, dynamin GTPase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Tris-HCl, 0.25M KBr, 30% (w/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.2825 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
ReflectionResolution: 1.86→48.73 Å / Num. obs: 55429 / % possible obs: 98.5 % / Redundancy: 3.49 % / CC1/2: 0.999 / Net I/σ(I): 9.02
Reflection shellResolution: 1.86→1.97 Å / Redundancy: 3.47 % / Num. unique obs: 17351 / CC1/2: 0.216 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3Q

5d3q


Resolution: 1.86→48.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.572 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 1078 1.9 %RANDOM
Rwork0.2187 ---
obs0.2194 54325 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.41 Å2 / Biso mean: 66.289 Å2 / Biso min: 20.36 Å2
Baniso -1Baniso -2Baniso -3
1-4.65 Å2-0 Å21.08 Å2
2---2.14 Å2-0 Å2
3----2.51 Å2
Refinement stepCycle: final / Resolution: 1.86→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 6 165 5145
Biso mean--52.49 57.5 -
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194923
X-RAY DIFFRACTIONr_bond_other_d0.0030.024784
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9816683
X-RAY DIFFRACTIONr_angle_other_deg1.237310902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95524.495218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87815819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3041536
X-RAY DIFFRACTIONr_chiral_restr0.0770.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215588
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021059
LS refinement shellResolution: 1.86→1.907 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.457 79 -
Rwork0.442 3952 -
obs--98.56 %
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)
14.0972.2448-2.02374.79190.27556.73160.13540.09280.1448-0.30960.0651-0.6093-0.58811.2655-0.20040.1114-0.1109-0.01440.62520.02850.32864.40611.11-29.172
22.551-3.6318-2.77449.10920.410711.07770.1691-0.22660.1378-0.1284-0.1155-0.44230.07960.4759-0.05370.1719-0.115-0.14050.7469-0.06740.579716.2248.052-23.61
33.4651.8371-1.55045.0156-1.06995.60390.1628-0.020.21030.162-0.0291-0.1625-0.28870.4667-0.13380.0465-0.0005-0.05110.32260.01970.169-6.1665.53-22.642
44.8961-0.3179-0.39137.6707-0.01973.501-0.14510.6969-0.4866-0.59210.044100.57340.01880.1010.27080.0019-0.0640.4655-0.02490.1967-9.552-6.989-35.695
52.73711.10240.81368.22222.73914.6205-0.35730.26390.6136-0.90860.41650.2591-1.08940.3911-0.05930.3643-0.05540.00340.44570.12130.3142-3.55519.019-35.856
60.972-1.6503-0.81883.52673.39558.28090.0826-0.00550.2836-0.5890.3448-0.3909-0.70020.1069-0.42750.6737-0.33690.02690.76330.08790.63817.05634.083-21.81
73.88330.4723-1.68133.80770.35162.2904-0.18150.1295-0.28350.0075-0.12530.20220.3887-0.11340.30690.0970.0033-0.01560.1877-0.01320.2181-29.508-22.409-4.24
84.24110.1334-0.97834.23791.68552.5856-0.11710.352-0.1205-0.494-0.12640.52890.2701-0.38650.24340.1817-0.0317-0.05540.2548-0.01330.2748-34.737-23.721-10.041
92.8506-0.0134-1.66113.7794-0.32633.38970.1166-0.11890.13310.2296-0.181-0.0548-0.19520.24550.06440.0538-0.0225-0.07120.19280.00970.1641-19.149-8.808-7.195
105.1127-0.9189-3.07732.48450.38593.6166-0.2145-0.596-0.33240.2786-0.0911-0.25190.32610.74430.30560.11370.0532-0.10110.29710.1030.2334-17.031-21.0480.581
119.173-3.29161.42017.7254-0.57534.8279-0.01780.13110.1507-0.1931-0.09560.6833-0.0231-0.37270.11330.1635-0.0750.09080.2858-0.07160.3615-47.26-15.1269.648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 83
2X-RAY DIFFRACTION2A84 - 105
3X-RAY DIFFRACTION3A106 - 220
4X-RAY DIFFRACTION4A221 - 273
5X-RAY DIFFRACTION5A274 - 311
6X-RAY DIFFRACTION6A312 - 743
7X-RAY DIFFRACTION7B5 - 83
8X-RAY DIFFRACTION8B84 - 136
9X-RAY DIFFRACTION9B137 - 221
10X-RAY DIFFRACTION10B222 - 311
11X-RAY DIFFRACTION11B312 - 744

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