Biological Assembly 1  

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

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 72.81 kDa 
• Atom Count: 5669 
• Modelled Residue Count: 594 
• Deposited Residue Count: 627 
• Unique protein chains: 1

6I44

Allosteric activation of human prekallikrein by apple domain disc rotation

• PDB DOI: 10.2210/pdb6I44/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2018-11-09 Released: 2019-03-06 
• Deposition Author(s): Li, C., Pathak, M., MaCrae, K., Dreveny, I., Emsley, J.
• Funding Organization(s): British Heart Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Plasma kallikrein structure reveals apple domain disc rotated conformation compared to factor XI.

Li, C., Voos, K.M., Pathak, M., Hall, G., McCrae, K.R., Dreveny, I., Li, R., Emsley, J.

(2019) J Thromb Haemost 17: 759-770

• PubMed: 30801944 
• DOI: 10.1111/jth.14418
• Primary Citation of Related Structures:  
  6I44, 6I58


• PubMed Abstract: 
  

Essentials Zymogen PK is activated to PKa and cleaves substrates kininogen and FXII contributing to bradykinin generation. Monomeric PKa and dimeric homologue FXI utilize the N-terminal apple domains to recruit substrates. A high-resolution 1.3 Å structure of full-length PKa reveals an active conformation of the protease and apple domains. The PKa protease and four-apple domain disc organization is 180° rotated compared to FXI. SUMMARY: Background Plasma prekallikrein (PK) and factor XI (FXI) are apple domain-containing serine proteases that when activated to PKa and FXIa cleave substrates kininogen, factor XII, and factor IX, respectively, directing plasma coagulation, bradykinin release, inflammation, and thrombosis pathways. Objective To investigate the three-dimensional structure of full-length PKa and perform a comparison with FXI. Methods A series of recombinant full-length PKa and FXI constructs and variants were developed and the crystal structures determined. Results and conclusions A 1.3 Å structure of full-length PKa reveals the protease domain positioned above a disc-shaped assemblage of four apple domains in an active conformation. A comparison with the homologous FXI structure reveals the intramolecular disulfide and structural differences in the apple 4 domain that prevents dimer formation in PK as opposed to FXI. Two latchlike loops (LL1 and LL2) extend from the PKa protease domain to form interactions with the apple 1 and apple 3 domains, respectively. A major unexpected difference in the PKa structure compared to FXI is the 180° disc rotation of the apple domains relative to the protease domain. This results in a switched configuration of the latch loops such that LL2 interacts and buries portions of the apple 3 domain in the FXI zymogen whereas in PKa LL2 interacts with the apple 1 domain. Hydrogen-deuterium exchange mass spectrometry on plasma purified human PK and PKa determined that regions of the apple 3 domain have increased surface exposure in PKa compared to the zymogen PK, suggesting conformational change upon activation.

---

Related Citations: 

• Crystal structure of the factor XI zymogen reveals a pathway for transactivation.
  Papagrigoriou, E., McEwan, P.A., Walsh, P.N., Emsley, J.
  (2006) Nat Struct Mol Biol 13: 557

---

Organizational Affiliation: 

Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasma kallikrein	A	627	Homo sapiens	Mutation(s): 0  Gene Names: KLKB1, KLK3 EC: 3.4.21.34
UniProt & NIH Common Fund Data Resources
Find proteins for P03952 (Homo sapiens) Explore P03952  Go to UniProtKB:  P03952
PHAROS:  P03952 GTEx:  ENSG00000164344

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	E [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
BEN	C [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG	I [auth A], J [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SER	DA [auth A]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth A], L [auth A], M [auth A], N [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY	CA [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
ACT	AA [auth A], BA [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.611	α = 90
b = 129.633	β = 90
c = 55.84	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-09 
• Released Date: 2019-03-06 
Deposition Author(s): Li, C., Pathak, M., MaCrae, K., Dreveny, I., Emsley, J.

---

Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	RG/12/9/29775

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Database references
• Version 1.2: 2020-07-08
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 3.0: 2021-08-04
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary