6MSV | pdb_00006msv

Structure of the 6th type III domain from human fibronectin

• PDB DOI: https://doi.org/10.2210/pdb6MSV/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-18 Released: 2019-10-23 
• Deposition Author(s): Loa, S., Mou, T.C., Sprang, S.R., Briknarova, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Structure of the 6th type III domain from human fibronectin

Loa, S., Mou, T.C., Sprang, S.R., Briknarova, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Biological Assembly 9  

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

Biological assembly 9 assigned by authors.

Biological Assembly 10  

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

Biological assembly 10 assigned by authors.

Biological Assembly 11  

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

Biological assembly 11 assigned by authors.

Biological Assembly 12  

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

Biological assembly 12 assigned by authors.

Biological Assembly 13  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 13 generated by PISA (software)

Biological Assembly 14  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 14 generated by PISA (software)

Biological Assembly 15  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 15 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.58 kDa 
• Atom Count: 7,827 
• Modeled Residue Count: 1,015 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibronectin	A, B, C, D, E, F, G, H, I, J, K, L	92	Homo sapiens	Mutation(s): 0  Gene Names: FN1, FN
UniProt & NIH Common Fund Data Resources
Find proteins for P02751 (Homo sapiens) Explore P02751  Go to UniProtKB:  P02751
PHAROS:  P02751 GTEx:  ENSG00000115414

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	M [auth B], N [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.52	α = 112.33
b = 79.46	β = 95.88
c = 80.886	γ = 94.48

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Loa, S., Mou, T.C., Sprang, S.R., Briknarova, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM114657
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103546

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description