3T34 | pdb_00003t34

Arabidopsis thaliana dynamin-related protein 1A (AtDRP1A) in prefission state

PDB DOI: https://doi.org/10.2210/pdb3T34/pdb

Classification: MOTOR PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-24 Released: 2012-06-06
Deposition Author(s): Yan, L.M., Ma, Y.Y., Sun, Y.N., Lou, Z.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.284 (Depositor), 0.291 (DCC)
R-Value Work:
0.236 (Depositor), 0.256 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for mechanochemical role of Arabidopsis thaliana dynamin-related protein in membrane fission

Yan, L.M., Ma, Y.Y., Sun, Y.N., Gao, J., Chen, X., Liu, J., Wang, C., Rao, Z., Lou, Z.Y.

(2011) J Mol Cell Biol 3: 378-381

PubMed: 22107825 Search on PubMed
DOI: https://doi.org/10.1093/jmcb/mjr032
Primary Citation Related Structures:
3T34, 3T35

Macromolecule Content

Total Structure Weight: 81.01 kDa
Atom Count: 5,705
Modeled Residue Count: 676
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A	A, B	360	Arabidopsis thaliana	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P42697 (Arabidopsis thaliana) Explore P42697 Go to UniProtKB: P42697
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42697
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
ALF Query on ALF Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.284 (Depositor), 0.291 (DCC)
R-Value Work: 0.236 (Depositor), 0.256 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.471	α = 90
b = 86.407	β = 90.55
c = 88.485	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2017-06-28
Changes: Source and taxonomy
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

3T34 | pdb_00003t34

Arabidopsis thaliana dynamin-related protein 1A (AtDRP1A) in prefission state

Literature

Structural basis for mechanochemical role of Arabidopsis thaliana dynamin-related protein in membrane fission

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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