3EJH

Crystal Structure of the Fibronectin 8-9FnI Domain Pair in Complex with a Type-I Collagen Peptide

• PDB DOI: https://doi.org/10.2210/pdb3EJH/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2008-09-18 Released: 2009-02-03 
• Deposition Author(s): Erat, M.C., Lowe, E.D., Campbell, I.D., Vakonakis, I.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.13 kDa 
• Atom Count: 1,956 
• Modelled Residue Count: 215 
• Deposited Residue Count: 232 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibronectin	A, C [auth B]	93	Homo sapiens	Mutation(s): 2  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen type-I a1 chain	B [auth E], D [auth F]	23	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02452 (Homo sapiens) Explore P02452  Go to UniProtKB:  P02452
PHAROS:  P02452 GTEx:  ENSG00000108821

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	B [auth E], D [auth F]	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.84	α = 90
b = 56.84	β = 90
c = 150.22	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Erat, M.C., Lowe, E.D., Campbell, I.D., Vakonakis, I.

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description