5JST | pdb_00005jst

MBP fused MDV1 coiled coil

• PDB DOI: https://doi.org/10.2210/pdb5JST/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12, Saccharomyces cerevisiae YJM789
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-05-09 Released: 2017-03-22 
• Deposition Author(s): Kim, B.-W., Song, H.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Models: experimental

Literature

ACCORD: an assessment tool to determine the orientation of homodimeric coiled-coils.

Kim, B.W., Jung, Y.O., Kim, M.K., Kwon, D.H., Park, S.H., Kim, J.H., Kuk, Y.B., Oh, S.J., Kim, L., Kim, B.H., Yang, W.S., Song, H.K.

(2017) Sci Rep 7: 43318-43318

• PubMed: 28266564 
• DOI: https://doi.org/10.1038/srep43318
• Primary Citation Related Structures: 
  5JST


• PubMed Abstract: 
  

  The coiled-coil (CC) domain is a very important structural unit of proteins that plays critical roles in various biological functions. The major oligomeric state of CCs is a dimer, which can be either parallel or antiparallel. The orientation of each α-helix in a CC domain is critical for the molecular function of CC-containing proteins, but cannot be determined easily by sequence-based prediction. We developed a biochemical method for assessing differences between parallel and antiparallel CC homodimers and named it ACCORD (Assessment tool for homodimeric Coiled-Coil ORientation Decision). To validate this technique, we applied it to 15 different CC proteins with known structures, and the ACCORD results identified these proteins well, especially with long CCs. Furthermore, ACCORD was able to accurately determine the orientation of a CC domain of unknown directionality that was subsequently confirmed by X-ray crystallography and small angle X-ray scattering. Thus, ACCORD can be used as a tool to determine CC directionality to supplement the results of in silico prediction.

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Organizational Affiliation: 
• Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea.
Center for Molecular Dynamics and Spectroscopy, Institute of Basic Science, Seoul 02841, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 98.61 kDa 
• Atom Count: 6,822 
• Modeled Residue Count: 860 
• Deposited Residue Count: 886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Mitochondrial division protein 1	A, B	443	Escherichia coli K-12, Saccharomyces cerevisiae YJM789 This entity is chimeric	Mutation(s): 6  Gene Names: malE, b4034, JW3994, MDV1, FIS2, GAG3, NET2, SCY_3176
UniProt
Find proteins for A6ZQL5 (Saccharomyces cerevisiae (strain YJM789)) Explore A6ZQL5  Go to UniProtKB:  A6ZQL5
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
UniProt Groups	A6ZQL5P0AEX9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.515	α = 90
b = 102.942	β = 102.51
c = 79.267	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Kim, B.-W., Song, H.K.

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary