4GIW | pdb_00004giw

Crystal structure of the RUN domain of human NESCA

• PDB DOI: https://doi.org/10.2210/pdb4GIW/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-08-09 Released: 2012-08-29 
• Deposition Author(s): Bai, L., Sun, Q., Jiang, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.212 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.204 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure and functional implication of the RUN domain of human NESCA

Sun, Q., Han, C., Liu, L., Wang, Y., Deng, H., Bai, L., Jiang, T.

(2012) Protein Cell 3: 609-617

• PubMed: 22821014 
• DOI: https://doi.org/10.1007/s13238-012-2052-3
• Primary Citation Related Structures: 
  4GIW


• PubMed Abstract: 
  

  NESCA, a newly discovered signaling adapter protein in the NGF-pathway, contains a RUN domain at its N-terminus. Here we report the crystal structure of the NESCA RUN domain determined at 2.0-Å resolution. The overall fold of the NESCA RUN domain comprises nine helices, resembling the RUN domain of RPIPx and the RUN1 domain of Rab6IP1. However, compared to the other RUN domains, the RUN domain of NESCA has significantly different surface electrostatic distributions at the putative GTPase-interacting interface. We demonstrate that the RUN domain of NESCA can bind H-Ras, a downstream signaling molecule of TrkA, with high affinity. Moreover, NESCA RUN can directly interact with TrkA. These results provide new insights into how NESCA participates in the NGF-TrkA signaling pathway.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 43.66 kDa 
• Atom Count: 2,830 
• Modeled Residue Count: 349 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUN and SH3 domain-containing protein 1	A, B	198	Homo sapiens	Mutation(s): 2  Gene Names: NESCA
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVN2 (Homo sapiens) Explore Q9BVN2  Go to UniProtKB:  Q9BVN2
PHAROS:  Q9BVN2 GTEx:  ENSG00000160753

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.212 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.204 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.116	α = 90
b = 94.201	β = 99.54
c = 44.602	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Bai, L., Sun, Q., Jiang, T.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary