4WJV

Crystal structure of Rsa4 in complex with the Nsa2 binding peptide

• PDB DOI: https://doi.org/10.2210/pdb4WJV/pdb

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae S288C, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-01 Released: 2014-11-19 
• Deposition Author(s): Holdermann, I., Paternoga, H., Bassler, J., Hurt, E., Sinning, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors and generated by (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors and generated by (software)

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors and generated by (software)

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 8 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 348.68 kDa 
• Atom Count: 23,675 
• Modelled Residue Count: 3,032 
• Deposited Residue Count: 3,136 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome assembly protein 4	A, B, C, D	381	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RSA4, YCR072C, YCR72C
UniProt
Find proteins for P25382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25382  Go to UniProtKB:  P25382

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein	E, F, G, H	381	Escherichia coli K-12	Mutation(s): 7  Gene Names: malE, b4034, JW3994
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome biogenesis protein NSA2	I, J, K, L	22	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NSA2, YER126C, SYGP-ORF47
UniProt
Find proteins for P40078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40078  Go to UniProtKB:  P40078

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	M, N, O, P	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	Q [auth A], R [auth A], S [auth A], T [auth B], U [auth B], V [auth C], W [auth C], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	M, N, O, P	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.578	α = 90
b = 96.493	β = 115.45
c = 196.445	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Holdermann, I., Paternoga, H., Bassler, J., Hurt, E., Sinning, I.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2014-12-03
  Changes: Database references
• Version 1.2: 2014-12-10
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary