7AX3

CryoEM structure of the super-constricted two-start dynamin 1 filament

PDB DOI: https://doi.org/10.2210/pdb7AX3/pdb
EM Map EMD-11932: EMDB EMDataResource

Classification: CYTOSOLIC PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2020-11-09 Released: 2021-11-10
Deposition Author(s): Liu, J.W., Zhang, P.J.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.74 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structure of the super-constricted two-start dynamin 1 filament.

Liu, J., Alvarez, F.J.D., Clare, D.K., Noel, J.K., Zhang, P.

(2021) Nat Commun 12: 5393-5393

PubMed: 34518553 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-25741-x
Primary Citation of Related Structures:
7AX3

PubMed Abstract:
Dynamin belongs to the large GTPase superfamily, and mediates the fission of vesicles during endocytosis. Dynamin molecules are recruited to the neck of budding vesicles to assemble into a helical collar and to constrict the underlying membrane. Two helical forms were observed: the one-start helix in the constricted state and the two-start helix in the super-constricted state. Here we report the cryoEM structure of a super-constricted two-start dynamin 1 filament at 3.74 Å resolution. The two strands are joined by the conserved GTPase dimeric interface. In comparison with the one-start structure, a rotation around Hinge 1 is observed, essential for communicating the chemical power of the GTPase domain and the mechanical force of the Stalk and PH domain onto the underlying membrane. The Stalk interfaces are well conserved and serve as fulcrums for adapting to changing curvatures. Relative to one-start, small rotations per interface accumulate to bring a drastic change in the helical pitch. Elasticity theory rationalizes the diversity of dynamin helical symmetries and suggests corresponding functional significance.

Organizational Affiliation

Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.

Macromolecule Content

Total Structure Weight: 3,530.95 kDa
Atom Count: 169,717
Modelled Residue Count: 21,037
Deposited Residue Count: 31,104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynamin-1	A [auth C2] AA [auth W] B [auth D2] BA [auth X] C [auth A2] A [auth C2], AA [auth W], B [auth D2], BA [auth X], C [auth A2], CA [auth Y], D [auth B2], DA [auth Z], E [auth A], EA [auth E2], F [auth B], FA [auth F2], G [auth C], GA [auth G2], H [auth D], HA [auth H2], I [auth E], IA [auth I2], J [auth F], JA [auth J2], K [auth G], L [auth H], M [auth I], N [auth J], O [auth K], P [auth L], Q [auth M], R [auth N], S [auth O], T [auth P], U [auth Q], V [auth R], W [auth S], X [auth T], Y [auth U], Z [auth V]	864	Homo sapiens	Mutation(s): 1 Gene Names: DNM1, DNM EC: 3.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q05193 (Homo sapiens) Explore Q05193 Go to UniProtKB: Q05193
PHAROS: Q05193 GTEx: ENSG00000106976
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05193
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCP (Subject of Investigation/LOI) Query on GCP Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain AC [auth R] SDF format, chain AD [auth I2] SDF format, chain CB [auth F] SDF format, chain CC [auth S] SDF format, chain CD [auth J2] SDF format, chain EB [auth G] SDF format, chain EC [auth T] SDF format, chain GB [auth H] SDF format, chain GC [auth U] SDF format, chain IB [auth I] SDF format, chain IC [auth V] SDF format, chain KA [auth C2] SDF format, chain KB [auth J] SDF format, chain KC [auth W] SDF format, chain MA [auth D2] SDF format, chain MB [auth K] SDF format, chain MC [auth X] SDF format, chain OA [auth A2] SDF format, chain OB [auth L] SDF format, chain OC [auth Y] SDF format, chain QA [auth B2] SDF format, chain QB [auth M] SDF format, chain QC [auth Z] SDF format, chain SA [auth A] SDF format, chain SB [auth N] SDF format, chain SC [auth E2] SDF format, chain UA [auth B] SDF format, chain UB [auth O] SDF format, chain UC [auth F2] SDF format, chain WA [auth C] SDF format, chain WB [auth P] SDF format, chain WC [auth G2] SDF format, chain YA [auth D] SDF format, chain YB [auth Q] SDF format, chain YC [auth H2] MOL2 format, chain AB [auth E] MOL2 format, chain AC [auth R] MOL2 format, chain AD [auth I2] MOL2 format, chain CB [auth F] MOL2 format, chain CC [auth S] MOL2 format, chain CD [auth J2] MOL2 format, chain EB [auth G] MOL2 format, chain EC [auth T] MOL2 format, chain GB [auth H] MOL2 format, chain GC [auth U] MOL2 format, chain IB [auth I] MOL2 format, chain IC [auth V] MOL2 format, chain KA [auth C2] MOL2 format, chain KB [auth J] MOL2 format, chain KC [auth W] MOL2 format, chain MA [auth D2] MOL2 format, chain MB [auth K] MOL2 format, chain MC [auth X] MOL2 format, chain OA [auth A2] MOL2 format, chain OB [auth L] MOL2 format, chain OC [auth Y] MOL2 format, chain QA [auth B2] MOL2 format, chain QB [auth M] MOL2 format, chain QC [auth Z] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth N] MOL2 format, chain SC [auth E2] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth O] MOL2 format, chain UC [auth F2] MOL2 format, chain WA [auth C] MOL2 format, chain WB [auth P] MOL2 format, chain WC [auth G2] MOL2 format, chain YA [auth D] MOL2 format, chain YB [auth Q] MOL2 format, chain YC [auth H2]	AB [auth E] AC [auth R] AD [auth I2] CB [auth F] CC [auth S] AB [auth E], AC [auth R], AD [auth I2], CB [auth F], CC [auth S], CD [auth J2], EB [auth G], EC [auth T], GB [auth H], GC [auth U], IB [auth I], IC [auth V], KA [auth C2], KB [auth J], KC [auth W], MA [auth D2], MB [auth K], MC [auth X], OA [auth A2], OB [auth L], OC [auth Y], QA [auth B2], QB [auth M], QC [auth Z], SA [auth A], SB [auth N], SC [auth E2], UA [auth B], UB [auth O], UC [auth F2], WA [auth C], WB [auth P], WC [auth G2], YA [auth D], YB [auth Q], YC [auth H2]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ PHBDHXOBFUBCJD-KQYNXXCUSA-N		Interactions Focus chain AB [auth E] Focus chain AC [auth R] Focus chain AD [auth I2] Focus chain CB [auth F] Focus chain CC [auth S] Focus chain CD [auth J2] Focus chain EB [auth G] Focus chain EC [auth T] Focus chain GB [auth H] Focus chain GC [auth U] Focus chain IB [auth I] Focus chain IC [auth V] Focus chain KA [auth C2] Focus chain KB [auth J] Focus chain KC [auth W] Focus chain MA [auth D2] Focus chain MB [auth K] Focus chain MC [auth X] Focus chain OA [auth A2] Focus chain OB [auth L] Focus chain OC [auth Y] Focus chain QA [auth B2] Focus chain QB [auth M] Focus chain QC [auth Z] Focus chain SA [auth A] Focus chain SB [auth N] Focus chain SC [auth E2] Focus chain UA [auth B] Focus chain UB [auth O] Focus chain UC [auth F2] Focus chain WA [auth C] Focus chain WB [auth P] Focus chain WC [auth G2] Focus chain YA [auth D] Focus chain YB [auth Q] Focus chain YC [auth H2] Interactions & Density Focus chain AB [auth E] Focus chain AC [auth R] Focus chain AD [auth I2] Focus chain CB [auth F] Focus chain CC [auth S] Focus chain CD [auth J2] Focus chain EB [auth G] Focus chain EC [auth T] Focus chain GB [auth H] Focus chain GC [auth U] Focus chain IB [auth I] Focus chain IC [auth V] Focus chain KA [auth C2] Focus chain KB [auth J] Focus chain KC [auth W] Focus chain MA [auth D2] Focus chain MB [auth K] Focus chain MC [auth X] Focus chain OA [auth A2] Focus chain OB [auth L] Focus chain OC [auth Y] Focus chain QA [auth B2] Focus chain QB [auth M] Focus chain QC [auth Z] Focus chain SA [auth A] Focus chain SB [auth N] Focus chain SC [auth E2] Focus chain UA [auth B] Focus chain UB [auth O] Focus chain UC [auth F2] Focus chain WA [auth C] Focus chain WB [auth P] Focus chain WC [auth G2] Focus chain YA [auth D] Focus chain YB [auth Q] Focus chain YC [auth H2]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BB [auth E] SDF format, chain BC [auth R] SDF format, chain BD [auth I2] SDF format, chain DB [auth F] SDF format, chain DC [auth S] SDF format, chain DD [auth J2] SDF format, chain FB [auth G] SDF format, chain FC [auth T] SDF format, chain HB [auth H] SDF format, chain HC [auth U] SDF format, chain JB [auth I] SDF format, chain JC [auth V] SDF format, chain LA [auth C2] SDF format, chain LB [auth J] SDF format, chain LC [auth W] SDF format, chain NA [auth D2] SDF format, chain NB [auth K] SDF format, chain NC [auth X] SDF format, chain PA [auth A2] SDF format, chain PB [auth L] SDF format, chain PC [auth Y] SDF format, chain RA [auth B2] SDF format, chain RB [auth M] SDF format, chain RC [auth Z] SDF format, chain TA [auth A] SDF format, chain TB [auth N] SDF format, chain TC [auth E2] SDF format, chain VA [auth B] SDF format, chain VB [auth O] SDF format, chain VC [auth F2] SDF format, chain XA [auth C] SDF format, chain XB [auth P] SDF format, chain XC [auth G2] SDF format, chain ZA [auth D] SDF format, chain ZB [auth Q] SDF format, chain ZC [auth H2] MOL2 format, chain BB [auth E] MOL2 format, chain BC [auth R] MOL2 format, chain BD [auth I2] MOL2 format, chain DB [auth F] MOL2 format, chain DC [auth S] MOL2 format, chain DD [auth J2] MOL2 format, chain FB [auth G] MOL2 format, chain FC [auth T] MOL2 format, chain HB [auth H] MOL2 format, chain HC [auth U] MOL2 format, chain JB [auth I] MOL2 format, chain JC [auth V] MOL2 format, chain LA [auth C2] MOL2 format, chain LB [auth J] MOL2 format, chain LC [auth W] MOL2 format, chain NA [auth D2] MOL2 format, chain NB [auth K] MOL2 format, chain NC [auth X] MOL2 format, chain PA [auth A2] MOL2 format, chain PB [auth L] MOL2 format, chain PC [auth Y] MOL2 format, chain RA [auth B2] MOL2 format, chain RB [auth M] MOL2 format, chain RC [auth Z] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth N] MOL2 format, chain TC [auth E2] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth O] MOL2 format, chain VC [auth F2] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth P] MOL2 format, chain XC [auth G2] MOL2 format, chain ZA [auth D] MOL2 format, chain ZB [auth Q] MOL2 format, chain ZC [auth H2]	BB [auth E] BC [auth R] BD [auth I2] DB [auth F] DC [auth S] BB [auth E], BC [auth R], BD [auth I2], DB [auth F], DC [auth S], DD [auth J2], FB [auth G], FC [auth T], HB [auth H], HC [auth U], JB [auth I], JC [auth V], LA [auth C2], LB [auth J], LC [auth W], NA [auth D2], NB [auth K], NC [auth X], PA [auth A2], PB [auth L], PC [auth Y], RA [auth B2], RB [auth M], RC [auth Z], TA [auth A], TB [auth N], TC [auth E2], VA [auth B], VB [auth O], VC [auth F2], XA [auth C], XB [auth P], XC [auth G2], ZA [auth D], ZB [auth Q], ZC [auth H2]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth E] Focus chain BC [auth R] Focus chain BD [auth I2] Focus chain DB [auth F] Focus chain DC [auth S] Focus chain DD [auth J2] Focus chain FB [auth G] Focus chain FC [auth T] Focus chain HB [auth H] Focus chain HC [auth U] Focus chain JB [auth I] Focus chain JC [auth V] Focus chain LA [auth C2] Focus chain LB [auth J] Focus chain LC [auth W] Focus chain NA [auth D2] Focus chain NB [auth K] Focus chain NC [auth X] Focus chain PA [auth A2] Focus chain PB [auth L] Focus chain PC [auth Y] Focus chain RA [auth B2] Focus chain RB [auth M] Focus chain RC [auth Z] Focus chain TA [auth A] Focus chain TB [auth N] Focus chain TC [auth E2] Focus chain VA [auth B] Focus chain VB [auth O] Focus chain VC [auth F2] Focus chain XA [auth C] Focus chain XB [auth P] Focus chain XC [auth G2] Focus chain ZA [auth D] Focus chain ZB [auth Q] Focus chain ZC [auth H2] Interactions & Density Focus chain BB [auth E] Focus chain BC [auth R] Focus chain BD [auth I2] Focus chain DB [auth F] Focus chain DC [auth S] Focus chain DD [auth J2] Focus chain FB [auth G] Focus chain FC [auth T] Focus chain HB [auth H] Focus chain HC [auth U] Focus chain JB [auth I] Focus chain JC [auth V] Focus chain LA [auth C2] Focus chain LB [auth J] Focus chain LC [auth W] Focus chain NA [auth D2] Focus chain NB [auth K] Focus chain NC [auth X] Focus chain PA [auth A2] Focus chain PB [auth L] Focus chain PC [auth Y] Focus chain RA [auth B2] Focus chain RB [auth M] Focus chain RC [auth Z] Focus chain TA [auth A] Focus chain TB [auth N] Focus chain TC [auth E2] Focus chain VA [auth B] Focus chain VB [auth O] Focus chain VC [auth F2] Focus chain XA [auth C] Focus chain XB [auth P] Focus chain XC [auth G2] Focus chain ZA [auth D] Focus chain ZB [auth Q] Focus chain ZC [auth H2]