Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 28.34 kDa 
• Atom Count: 1886 
• Modelled Residue Count: 215 
• Deposited Residue Count: 242 
• Unique protein chains: 2

6UUI

Crystal structure of the heterocomplex between coil 2B domains of wild-type keratin 1 (KRT1) and keratin 10 (KRT10) containing mutation Cys401Ala

• PDB DOI: 10.2210/pdb6UUI/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-10-30 Released: 2019-11-13 
• Deposition Author(s): Lomakin, I.B., Bunick, C.G.
• Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.277 
• R-Value Work: 0.250 
• R-Value Observed: 0.252 

Literature

Crystal Structure of Keratin 1/10(C401A) 2B Heterodimer Demonstrates a Proclivity for the C-Terminus of Helix 2B to Form Higher Order Molecular Contacts.

Lomakin, I.B., Hinbest, A.J., Ho, M., Eldirany, S.A., Bunick, C.G.

(2020) Yale J Biol Med 93: 3-17

• PubMed: 32226330 
• Primary Citation of Related Structures:  
  6UUI


• PubMed Abstract: 
  

We previously determined the crystal structure of the wild-type keratin 1/10 helix 2B heterodimer at 3.3 Å resolution. We proposed that the resolution of the diffraction data was limited due to the crystal packing effect from keratin 10 (K10) residue Cys401. Cys401 ^K10 formed a disulfide-linkage with Cys401 from another K1/10 heterodimer, creating an "X-shaped" structure and a loose crystal packing arrangement. We hypothesized that mutation of Cys401 ^K10 to alanine would eliminate the disulfide-linkage and improve crystal packing thereby increasing resolution of diffraction and enabling a more accurate side chain electron density map. Indeed, when a K10 Cys401Ala 2B mutant was paired with its native keratin 1 (K1) 2B heterodimer partner its x-ray crystal structure was determined at 2.07 Å resolution; the structure does not contain a disulfide linkage. Superposition of the K1/K10(Cys401Ala) 2B structure onto the wild-type K1/10 2B heterodimer structure had a root-mean-square-deviation of 1.88 Å; the variability in the atomic positions reflects the dynamic motion expected in this filamentous coiled-coil complex. The electrostatic, hydrophobic, and contour features of the molecular surface are similar to the lower resolution wild-type structure. We postulated that elimination of the disulfide linkage in the K1/K10(Cys401Ala) 2B structure could allow for the 2B heterodimers to bind/pack in the A ₂₂ tetramer configuration associated with mature keratin intermediate filament assembly. Analysis of the crystal packing revealed a half-staggered anti-parallel tetrameric complex of 2B heterodimers; however, their register is not consistent with models of the A ₂₂ mode of tetrameric alignment or prior biochemical cross-linking studies.

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Organizational Affiliation: 

Department of Dermatology, Yale University, New Haven, CT.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Keratin, type II cytoskeletal 1	A [auth C]	120	Homo sapiens	Mutation(s): 0  Gene Names: KRT1, KRTA
UniProt & NIH Common Fund Data Resources
Find proteins for P04264 (Homo sapiens) Explore P04264  Go to UniProtKB:  P04264
PHAROS:  P04264

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Keratin, type I cytoskeletal 10	B [auth X]	122	Homo sapiens	Mutation(s): 1  Gene Names: KRT10, KPP
UniProt & NIH Common Fund Data Resources
Find proteins for P13645 (Homo sapiens) Explore P13645  Go to UniProtKB:  P13645
PHAROS:  P13645

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	C	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
GOL	D [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.277 
• R-Value Work: 0.250 
• R-Value Observed: 0.252 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.124	α = 90
b = 100.124	β = 90
c = 224.788	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-10-30 
• Released Date: 2019-11-13 
Deposition Author(s): Lomakin, I.B., Bunick, C.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	K08AR070290
Other private	United States	Foundation for Ichthyosis and Related Skin Types

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Author supporting evidence, Database references
• Version 1.2: 2020-04-08
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary