[English] 日本語
Yorodumi
- PDB-6zn3: Plasmodium facliparum glideosome trimeric sub-complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zn3
TitlePlasmodium facliparum glideosome trimeric sub-complex
Components
  • Myosin A tail domain interacting protein
  • Myosin essential light chain ELC
  • Myosin-A
KeywordsMOTOR PROTEIN / motility / glideosome / myosin / essential light chain
Function / homology
Function and homology information


pellicle / inner membrane pellicle complex / glideosome / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton ...pellicle / inner membrane pellicle complex / glideosome / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / : / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily ...: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / : / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin A tail domain interacting protein / Myosin-A / Myosin essential light chain ELC
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsPazicky, S. / Loew, C.
Funding support Sweden, Germany, 2items
OrganizationGrant numberCountry
Swedish Research Council621-2013-5905 Sweden
Joachim Herz Stiftung800026 Germany
CitationJournal: Commun Biol / Year: 2020
Title: Structural role of essential light chains in the apicomplexan glideosome.
Authors: Pazicky, S. / Dhamotharan, K. / Kaszuba, K. / Mertens, H.D.T. / Gilberger, T. / Svergun, D. / Kosinski, J. / Weininger, U. / Low, C.
History
DepositionJul 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin essential light chain ELC
B: Myosin A tail domain interacting protein
C: Myosin-A
D: Myosin essential light chain ELC
E: Myosin A tail domain interacting protein
F: Myosin-A
G: Myosin essential light chain ELC
H: Myosin A tail domain interacting protein
I: Myosin-A
J: Myosin essential light chain ELC
K: Myosin A tail domain interacting protein
L: Myosin-A
M: Myosin essential light chain ELC
N: Myosin A tail domain interacting protein
O: Myosin-A


Theoretical massNumber of molelcules
Total (without water)188,04815
Polymers188,04815
Non-polymers00
Water543
1
A: Myosin essential light chain ELC
B: Myosin A tail domain interacting protein
C: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-44 kcal/mol
Surface area16350 Å2
MethodPISA
2
D: Myosin essential light chain ELC
E: Myosin A tail domain interacting protein
F: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-47 kcal/mol
Surface area16440 Å2
MethodPISA
3
G: Myosin essential light chain ELC
H: Myosin A tail domain interacting protein
I: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-47 kcal/mol
Surface area16210 Å2
MethodPISA
4
J: Myosin essential light chain ELC
K: Myosin A tail domain interacting protein
L: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-47 kcal/mol
Surface area16800 Å2
MethodPISA
5
M: Myosin essential light chain ELC
N: Myosin A tail domain interacting protein
O: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-47 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.880, 211.880, 75.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein
Myosin essential light chain ELC


Mass: 15779.875 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1017500 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IJM4
#2: Protein
Myosin A tail domain interacting protein


Mass: 16788.572 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1246400 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8I4W8
#3: Protein/peptide
Myosin-A / PfM-A


Mass: 5041.055 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF13_0233 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IDR3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.58 Å3/Da / Density % sol: 73.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, ethylene glycol, di-ethyleneglycol, tri-ethyleneglycol, tetra-ethyleneglycol, penta-ethyleneglycol, imidazole, MES

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.51→47.42 Å / Num. obs: 114354 / % possible obs: 83.53 % / Redundancy: 6.7 % / Biso Wilson estimate: 81.46 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0874 / Rpim(I) all: 0.03701 / Rrim(I) all: 0.09505 / Net I/σ(I): 12.69
Reflection shellResolution: 2.51→2.604 Å / Redundancy: 6.6 % / Rmerge(I) obs: 3.79 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 911 / CC1/2: 0.111 / CC star: 0.448 / Rpim(I) all: 1.602 / Rrim(I) all: 4.118 / % possible all: 7.97

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.17.1.3660refinement
STARANISOdata scaling
PHASER1.17.1.3660phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6jt4, 4aom

6jt4

4aom


Resolution: 2.51→47.42 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.812 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 2.51 / ESU R: 0.314 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23756 4756 5 %RANDOM
Rwork0.20027 ---
obs0.20216 90855 83.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 2.51→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12965 0 0 3 12968
Refine LS restraintsType: r_bond_refined_d / Dev ideal: 0.009 / Dev ideal target: 0.013 / Number: 13175
LS refinement shellResolution: 2.514→2.579 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 19 -
Rwork0.373 341 -
obs--4.27 %

+
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