[English] 日本語
Yorodumi
- PDB-3t35: Arabidopsis thaliana dynamin-related protein 1A in postfission state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t35
TitleArabidopsis thaliana dynamin-related protein 1A in postfission state
ComponentsDynamin-related protein 1A, LINKER, Dynamin-related protein 1A
KeywordsMOTOR PROTEIN / dynamin-like protein 1A / GTPase / membrane fission
Function / homology
Function and homology information


cell plate formation involved in plant-type cell wall biogenesis / stigma development / regulation of plant-type cell wall organization or biogenesis / regulation of lipid localization / regulation of phragmoplast microtubule organization / cell plate / response to boron-containing substance / cellular response to boron-containing substance levels / cytokinesis by cell plate formation / trichome branching ...cell plate formation involved in plant-type cell wall biogenesis / stigma development / regulation of plant-type cell wall organization or biogenesis / regulation of lipid localization / regulation of phragmoplast microtubule organization / cell plate / response to boron-containing substance / cellular response to boron-containing substance levels / cytokinesis by cell plate formation / trichome branching / root hair initiation / xylem and phloem pattern formation / phragmoplast / protein histidine kinase binding / embryo development ending in seed dormancy / plasmodesma / clathrin-coated endocytic vesicle / plant-type vacuole / clathrin-dependent endocytosis / regulation of establishment of cell polarity / clathrin-coated vesicle / plastid / clathrin binding / chloroplast thylakoid membrane / regulation of endocytosis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / cell cortex / microtubule / cytoskeleton / GTPase activity / GTP 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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Phragmoplastin DRP1A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.592 Å
AuthorsYan, L.M. / Ma, Y.Y. / Sun, Y.N. / Lou, Z.Y.
CitationJournal: J Mol Cell Biol / Year: 2011
Title: Structural basis for mechanochemical role of Arabidopsis thaliana dynamin-related protein in membrane fission
Authors: Yan, L.M. / Ma, Y.Y. / Sun, Y.N. / Gao, J. / Chen, X. / Liu, J. / Wang, C. / Rao, Z. / Lou, Z.Y.
History
DepositionJul 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 1, 2023Group: 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
B: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
C: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
D: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4208
Polymers159,6474
Non-polymers1,7734
Water6,864381
1
A: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
B: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7104
Polymers79,8232
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-25 kcal/mol
Surface area30660 Å2
MethodPISA
2
C: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
D: Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7104
Polymers79,8232
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-20 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.157, 146.157, 204.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A


Mass: 39911.703 Da / Num. of mol.: 4 / Fragment: UNP residues 1-325, 579-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P42697
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 160mM sodium formate, 16%(w/v) polyethylene glycol 3350, 40mM magnesium chloride, 6%(w/v) 2-Propanol, 20mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.592→50 Å / Num. obs: 28872 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X2E

2x2e


Resolution: 3.592→43.323 Å / SU ML: 0.6 / σ(F): 0.05 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2907 1276 5.08 %random
Rwork0.238 ---
obs0.2407 25139 87.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.2 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0361 Å2-0 Å20 Å2
2--4.0361 Å2-0 Å2
3---6.8555 Å2
Refinement stepCycle: LAST / Resolution: 3.592→43.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10544 0 112 381 11037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210808
X-RAY DIFFRACTIONf_angle_d1.73514616
X-RAY DIFFRACTIONf_dihedral_angle_d20.8794148
X-RAY DIFFRACTIONf_chiral_restr0.1041712
X-RAY DIFFRACTIONf_plane_restr0.0071864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.592-3.73570.33131390.2461266988
3.7357-3.90570.31731220.279234077
3.9057-4.11140.34041030.2383169056
4.1114-4.36880.2891260.1961255084
4.3688-4.70570.26651340.163282192
4.7057-5.17860.20741800.1692280594
5.1786-5.92630.28061530.1921293396
5.9263-7.46040.27891590.2158297698
7.4604-43.32630.20031600.2013079100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more