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- PDB-3zys: Human dynamin 1 deltaPRD polymer stabilized with GMPPCP -

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Basic information

Entry
Database: PDB / ID: 3zys
TitleHuman dynamin 1 deltaPRD polymer stabilized with GMPPCP
Components
  • (DYNAMIN-1) x 2
  • INTERFERON-INDUCED GTP-BINDING PROTEIN MX1
KeywordsHYDROLASE/GTP-BINDING PROTEIN / HYDROLASE-GTP-BINDING PROTEIN COMPLEX / ENDOCYTOSIS / GTP HYDROLYSIS / MEMBRANE REMODELING
Function / homology
Function and homology information


clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / interleukin-27-mediated signaling pathway / dynamin GTPase / chromaffin granule / regulation of vesicle size / Retrograde neurotrophin signalling / Toll Like Receptor 4 (TLR4) Cascade / Formation of annular gap junctions ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / interleukin-27-mediated signaling pathway / dynamin GTPase / chromaffin granule / regulation of vesicle size / Retrograde neurotrophin signalling / Toll Like Receptor 4 (TLR4) Cascade / Formation of annular gap junctions / endosome organization / Gap junction degradation / response to type I interferon / negative regulation of viral genome replication / phosphatidylinositol-3,4,5-trisphosphate binding / Recycling pathway of L1 / EPH-ephrin mediated repulsion of cells / endocytic vesicle / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / antiviral innate immune response / MHC class II antigen presentation / receptor-mediated endocytosis / cell projection / defense response / protein homooligomerization / receptor internalization / ISG15 antiviral mechanism / response to virus / endocytosis / Interferon alpha/beta signaling / GDP binding / presynapse / Clathrin-mediated endocytosis / nuclear membrane / protein homotetramerization / microtubule binding / defense response to virus / microtubule / innate immune response / GTPase activity / apoptotic process / synapse / protein kinase binding / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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
Interferon-induced GTP-binding protein Mx1 / Dynamin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 12.2 Å
AuthorsChappie, J.S. / Mears, J.A. / Fang, S. / Leonard, M. / Schmid, S.L. / Milligan, R.A. / Hinshaw, J.E. / Dyda, F.
CitationJournal: Cell / Year: 2011
Title: A pseudoatomic model of the dynamin polymer identifies a hydrolysis-dependent powerstroke.
Authors: Joshua S Chappie / Jason A Mears / Shunming Fang / Marilyn Leonard / Sandra L Schmid / Ronald A Milligan / Jenny E Hinshaw / Fred Dyda /
Abstract: The GTPase dynamin catalyzes membrane fission by forming a collar around the necks of clathrin-coated pits, but the specific structural interactions and conformational changes that drive this process ...The GTPase dynamin catalyzes membrane fission by forming a collar around the necks of clathrin-coated pits, but the specific structural interactions and conformational changes that drive this process remain a mystery. We present the GMPPCP-bound structures of the truncated human dynamin 1 helical polymer at 12.2 Å and a fusion protein, GG, linking human dynamin 1's catalytic G domain to its GTPase effector domain (GED) at 2.2 Å. The structures reveal the position and connectivity of dynamin fragments in the assembled structure, showing that G domain dimers only form between tetramers in sequential rungs of the dynamin helix. Using chemical crosslinking, we demonstrate that dynamin tetramers are made of two dimers, in which the G domain of one molecule interacts in trans with the GED of another. Structural comparison of GG(GMPPCP) to the GG transition-state complex identifies a hydrolysis-dependent powerstroke that may play a role in membrane-remodeling events necessary for fission.
History
DepositionAug 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other
Revision 1.2Sep 18, 2013Group: Derived calculations / Source and taxonomy
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.5May 8, 2024Group: 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 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1949
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  • Superimposition on EM map
  • EMDB-1949
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DYNAMIN-1
B: INTERFERON-INDUCED GTP-BINDING PROTEIN MX1
C: DYNAMIN-1
D: DYNAMIN-1
E: INTERFERON-INDUCED GTP-BINDING PROTEIN MX1
F: DYNAMIN-1


Theoretical massNumber of molelcules
Total (without water)256,9056
Polymers256,9056
Non-polymers00
Water00
1
A: DYNAMIN-1
B: INTERFERON-INDUCED GTP-BINDING PROTEIN MX1
C: DYNAMIN-1
D: DYNAMIN-1
E: INTERFERON-INDUCED GTP-BINDING PROTEIN MX1
F: DYNAMIN-1
x 12


Theoretical massNumber of molelcules
Total (without water)3,082,86072
Polymers3,082,86072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation11
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 12 / Rise per n subunits: 15.045 Å / Rotation per n subunits: 54.545 °)

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Components

#1: Protein DYNAMIN-1


Mass: 39388.961 Da / Num. of mol.: 2
Fragment: G DOMAIN, RESIDUES 1-320, GTPASE EFFECTOR DOMAIN, RESIDUES 726-750
Source method: isolated from a genetically manipulated source
Details: EIGHT AMINO ACID POLYPEPTIDE LINKER BETWEEN G DOMAIN AND GTPASE EFFECTOR DOMAIN, RESIDUES 321-328
Source: (gene. exp.) HOMO SAPIENS (human) / Variant: ISOFORM 1 / Plasmid: PMALC2XP5D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05193, dynamin GTPase
#2: Protein INTERFERON-INDUCED GTP-BINDING PROTEIN MX1 / INTERFERON-INDUCED PROTEIN P78 / IFI-78K / INTERFERON-REGULATED RESISTANCE GTP-BINDING PROTEIN MXA ...INTERFERON-INDUCED PROTEIN P78 / IFI-78K / INTERFERON-REGULATED RESISTANCE GTP-BINDING PROTEIN MXA / MYXOMA RESISTANCE PROTEIN 1 / MYXOVIRUS RESISTANCE PROTEIN 1


Mass: 75623.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSKB-LNB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P20591
#3: Protein DYNAMIN-1


Mass: 13440.362 Da / Num. of mol.: 2 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 518-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q05193, dynamin GTPase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: GMPPCP STABILIZED HUMAN DYNAMIN 1 DELTA PRD HELICAL POLYMER
Type: COMPLEX
Details: DELTA PRD DYNAMIN HELICAL TUBES GENERATED IN THE PRESENCE OF GMPPCP AND DOPS LIPOSOMES
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: PLUNGE FROZEN IN LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Yup.scxmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: INDIVIDUAL IMAGES USING ACE2
3D reconstructionMethod: IHRSR / Resolution: 12.2 Å / Num. of particles: 4814 / Nominal pixel size: 2.26 Å
Details: THIS MODEL INCORPORATES COORDINATES FROM 3ZYC AND 1DYN, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS A AND D OF THE MODEL SHOW RESIDUES 6-311 OF HUMAN DYNAMIN 1'S G DOMAIN AND ...Details: THIS MODEL INCORPORATES COORDINATES FROM 3ZYC AND 1DYN, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS A AND D OF THE MODEL SHOW RESIDUES 6-311 OF HUMAN DYNAMIN 1'S G DOMAIN AND RESIDUES 726-748 OF ITS GTPASE EFFECTOR DOMAIN. CHAINS C AND F INCLUDE RESIDUES 518-630 OF DYNAMIN'S PH DOMAIN. RESIDUE 5 SER IN CHAINS A AND D IS A CLONING ARTIFACT THAT WAS VISIBLE IN THE CRYSTAL STRUCTURE OF 3ZYC. INCORPORATES COORDINATES FROM 3LJB, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS B AND E INCLUDE RESIDUES 367-435 AND 451-531 OF HUMAN MXA'S MIDDLE DOMAIN AND RESIDUES 576-636 OF IF GTPASE EFFECTOR DOMAIN. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1949. (DEPOSITION ID: 10194).
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: REFINEMENT PROTOCOL--YUP ALGORITHM
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12X2E

2x2e

12X2E1PDBexperimental model
23LJB

3ljb

13LJB2PDBexperimental model
31DYN

1dyn

11DYN3PDBexperimental model
RefinementHighest resolution: 12.2 Å
Refinement stepCycle: LAST / Highest resolution: 12.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10677 0 0 0 10677

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