6OQ3 | pdb_00006oq3

Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2

• PDB DOI: https://doi.org/10.2210/pdb6OQ3/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-25 Released: 2020-06-24 
• Deposition Author(s): Gingras, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.292 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.244 (DCC) 

Starting Model: experimental

Literature

Inhibition of the HEG1-KRIT1 interaction increases KLF4 and KLF2 expression in endothelial cells

Lopez-Ramirez, M.A., McCurdy, S., Li, W., Haynes, M.K., Hale, P., Francisco, K., Oukoloff, K., Bautista, M., Choi, C.H., Sun, H., Gongol, B., Shyy, J.Y., Ballatore, C., Sklar, L.A., Gingras, A.R.

(2021) FASEB Bioadv 

• DOI: https://doi.org/10.1096/fba.2020-00141

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 57.11 kDa 
• Atom Count: 3,936 
• Modeled Residue Count: 474 
• Deposited Residue Count: 489 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Krev interaction trapped protein 1	A	322	Homo sapiens	Mutation(s): 0  Gene Names: KRIT1, CCM1
UniProt & NIH Common Fund Data Resources
Find proteins for O00522 (Homo sapiens) Explore O00522  Go to UniProtKB:  O00522
PHAROS:  O00522 GTEx:  ENSG00000001631

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rap-1b	B	167	Homo sapiens	Mutation(s): 0  Gene Names: RAP1B, OK/SW-cl.11 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61224 (Homo sapiens) Explore P61224  Go to UniProtKB:  P61224
PHAROS:  P61224 GTEx:  ENSG00000127314

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
7WO (Subject of Investigation/LOI)	C [auth A]	2-hydroxynaphthalene-1-carbaldehyde C11 H8 O2 NTCCNERMXRIPTR-UHFFFAOYSA-N
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.292 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.244 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.11	α = 90
b = 76.83	β = 92.281
c = 58.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Gingras, A.R.

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references, Derived calculations
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description