Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

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

Macromolecule Content

• Total Structure Weight: 42203.14 
• Atom Count: 2496 
• Residue Count: 428 
• Unique protein chains: 3

5CVA

Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment a1a2a1 of type I collagen

• DOI: 10.2210/pdb5CVA/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2015-07-25 Released: 2016-08-10 
• Deposition Author(s): Boudko, S.P., Bachinger, H.P.
• Funding Organization(s): Shriners Hospitals for Children 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.098 Å
• R-Value Free: 0.279 
• R-Value Work: 0.234 

Literature

Structural insight for chain selection and stagger control in collagen.

Boudko, S.P., Bachinger, H.P.

(2016) Sci Rep 6: 37831-37831

• PubMed: 27897211 
• DOI: 10.1038/srep37831
• Primary Citation of Related Structures:  
  5CVB, 5CTI, 5CTD


• PubMed Abstract: 
  

Collagen plays a fundamental role in all known metazoans. In collagens three polypeptides form a unique triple-helical structure with a one-residue stagger to fit every third glycine residue in the inner core without disturbing the poly-proline type II helical conformation of each chain. There are homo- and hetero-trimeric types of collagen consisting of one, two or three distinct chains. Thus there must be mechanisms that control composition and stagger during collagen folding. Here, we uncover the structural basis for both chain selection and stagger formation of a collagen molecule. Three distinct chains (α1, α2 and α3) of the non-collagenous domain 2 (NC2) of type IX collagen are assembled to guide triple-helical sequences in the leading, middle and trailing positions. This unique domain opens the door for generating any fragment of collagen in its native composition and stagger.

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Organizational Affiliation: 

Research Department, Shriners Hospital for Children, Portland, Oregon 97239, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Collagen alpha-2(I) chain,Collagen alpha-1(IX) chain	A, D	71	Homo sapiens	Mutation(s): 0  Gene Names: COL1A2, COL9A1
Find proteins for P08123 (Homo sapiens) Go to Gene View: COL1A2 Go to UniProtKB:  P08123
Find proteins for P20849 (Homo sapiens) Go to Gene View: COL9A1 Go to UniProtKB:  P20849

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain	B, E	71	Homo sapiens	Mutation(s): 0  Gene Names: COL9A2, COL1A1
Find proteins for Q14055 (Homo sapiens) Go to Gene View: COL9A2 Go to UniProtKB:  Q14055
Find proteins for P02452 (Homo sapiens) Go to Gene View: COL1A1 Go to UniProtKB:  P02452

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain	C, F	72	Homo sapiens	Mutation(s): 0  Gene Names: COL9A3, COL1A1
Find proteins for Q14050 (Homo sapiens) Go to Gene View: COL9A3 Go to UniProtKB:  Q14050
Find proteins for P02452 (Homo sapiens) Go to Gene View: COL1A1 Go to UniProtKB:  P02452

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, F	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.098 Å
• R-Value Free: 0.279 
• R-Value Work: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 52.410	α = 90.00
b = 63.980	β = 112.75
c = 65.370	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-07-25 
• Released Date: 2016-08-10 
• Deposition Author(s): Boudko, S.P., Bachinger, H.P.

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Funding Organization	Location	Grant Number
Shriners Hospitals for Children	United States	--

Revision History 

• Version 1.0: 2016-08-10
  Type: Initial release
• Version 1.1: 2017-07-12
  Type: Database references, Derived calculations