5YAN | pdb_00005yan

Deconstructing the Salt-Bridge Network of a Computationally Designed Collagen Heterotrimer

• PDB DOI: https://doi.org/10.2210/pdb5YAN/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-09-01 Released: 2018-06-13 
• Deposition Author(s): Fan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.288 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

How electrostatic networks modulate specificity and stability of collagen.

Zheng, H., Lu, C., Lan, J., Fan, S., Nanda, V., Xu, F.

(2018) Proc Natl Acad Sci U S A 115: 6207-6212

• PubMed: 29844169 
• DOI: https://doi.org/10.1073/pnas.1802171115
• Primary Citation Related Structures: 
  5YAN


• PubMed Abstract: 
  

  One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

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Organizational Affiliation: 
• Ministry of Education Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, 214122 Wuxi, China.
Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.
Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China; [e-mail] [e-mail] [e-mail].
Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854; [e-mail] [e-mail] [e-mail].
Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854.
Ministry of Education Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, 214122 Wuxi, China; [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Helical - H  (Explore in 3D)
Pseudo Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 18.49 kDa 
• Atom Count: 1,443 
• Modeled Residue Count: 183 
• Deposited Residue Count: 192 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen	A, D	32	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen	B, E	32	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen	C, F	32	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	A, D	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.288 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.597	α = 90
b = 51.391	β = 90
c = 128.522	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Fan, S.

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2018-12-26
  Changes: Data collection, Database references
• Version 1.2: 2025-04-09
  Changes: Data collection, Database references, Structure summary