6EC0 | pdb_00006ec0

Crystal structure of the wild-type heterocomplex between coil 1B domains of human intermediate filament proteins keratin 1 (KRT1) and keratin 10 (KRT10)

• PDB DOI: https://doi.org/10.2210/pdb6EC0/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-07 Released: 2019-05-15 
• Deposition Author(s): Eldirany, S.A., 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: 2.98 Å
• R-Value Free: 
  0.300 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.281 (Depositor), 0.285 (DCC) 
• R-Value Observed: 
  0.282 (Depositor) 

Starting Model: experimental

Literature

Human keratin 1/10-1B tetramer structures reveal a knob-pocket mechanism in intermediate filament assembly.

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

(2019) EMBO J 38

• PubMed: 31036554 
• DOI: https://doi.org/10.15252/embj.2018100741
• Primary Citation Related Structures: 
  6E2J, 6EC0


• PubMed Abstract: 
  

  To characterize keratin intermediate filament assembly mechanisms at atomic resolution, we determined the crystal structure of wild-type human keratin-1/keratin-10 helix 1B heterotetramer at 3.0 Å resolution. It revealed biochemical determinants for the A ₁₁ mode of axial alignment in keratin filaments. Four regions on a hydrophobic face of the K1/K10-1B heterodimer dictated tetramer assembly: the N-terminal hydrophobic pocket (defined by L227 ^K1 , Y230 ^K1 , F231 ^K1 , and F234 ^K1 ), the K10 hydrophobic stripe, K1 interaction residues, and the C-terminal anchoring knob (formed by F314 ^K1 and L318 ^K1 ). Mutation of both knob residues to alanine disrupted keratin 1B tetramer and full-length filament assembly. Individual knob residue mutant F314A ^K1 , but not L318A ^K1 , abolished 1B tetramer formation. The K1-1B knob/pocket mechanism is conserved across keratins and many non-keratin intermediate filaments. To demonstrate how pathogenic mutations cause skin disease by altering filament assembly, we additionally determined the 2.39 Å structure of K1/10-1B containing a S233L ^K1 mutation linked to epidermolytic palmoplantar keratoderma. Light scattering and circular dichroism measurements demonstrated enhanced aggregation of K1 ^S233L /K10-1B in solution without affecting secondary structure. The K1 ^S233L /K10-1B octamer structure revealed S233L ^K1 causes aberrant hydrophobic interactions between 1B tetramers.

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Organizational Affiliation: 
• Department of Dermatology, Yale University, New Haven, CT, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Department of Dermatology, Yale University, New Haven, CT, USA [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration, light scattering, homology

Macromolecule Content 

• Total Structure Weight: 25.57 kDa 
• Atom Count: 1,774 
• Modeled Residue Count: 209 
• Deposited Residue Count: 211 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Keratin 1	A	107	Homo sapiens	Mutation(s): 0  Gene Names: KRT1
UniProt
Find proteins for H6VRG1 (Homo sapiens) Explore H6VRG1  Go to UniProtKB:  H6VRG1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Keratin, type I cytoskeletal 10	B	104	Homo sapiens	Mutation(s): 0  Gene Names: KRT10, KPP
UniProt & NIH Common Fund Data Resources
Find proteins for P13645 (Homo sapiens) Explore P13645  Go to UniProtKB:  P13645
PHAROS:  P13645 GTEx:  ENSG00000186395

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	C [auth A], D [auth A], E [auth A], G [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CO	F [auth A], H [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NI	I [auth B], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free:  0.300 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.281 (Depositor), 0.285 (DCC) 
• R-Value Observed: 0.282 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.685	α = 90
b = 106.685	β = 90
c = 70.321	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

• Released Date: 2019-05-15 
Deposition Author(s): Eldirany, S.A., 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	K08-AR070290
Other private	United States	Foundation for Ichthyosis & Related Skin Types

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description