8D3C

VWF tubule derived from monomeric D1-A1

  • Classification: BLOOD CLOTTING
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2022-06-01 Released: 2022-07-06 
  • Deposition Author(s): Anderson, J.R., Li, J., Springer, T.A., Brown, A.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structures of VWF tubules before and after concatemerization reveal a mechanism of disulfide bond exchange.

Anderson, J.R., Li, J., Springer, T.A., Brown, A.

(2022) Blood 140: 1419-1430

  • DOI: https://doi.org/10.1182/blood.2022016467
  • Primary Citation of Related Structures:  
    8D3C, 8D3D

  • PubMed Abstract: 

    von Willebrand factor (VWF) is an adhesive glycoprotein that circulates in the blood as disulfide-linked concatemers and functions in primary hemostasis. The loss of long VWF concatemers is associated with the excessive bleeding of type 2A von Willebrand disease (VWD). Formation of the disulfide bonds that concatemerize VWF requires VWF to self-associate into helical tubules, yet how the helical tubules template intermolecular disulfide bonds is not known. Here, we report electron cryomicroscopy (cryo-EM) structures of VWF tubules before and after intermolecular disulfide bond formation. The structures provide evidence that VWF tubulates through a charge-neutralization mechanism and that the A1 domain enhances tubule length by crosslinking successive helical turns. In addition, the structures reveal disulfide states before and after disulfide bond-mediated concatemerization. The structures and proposed assembly mechanism provide a foundation to rationalize VWD-causing mutations.

    • Organizational Affiliation: 

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
von Willebrand factor
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
1,469Homo sapiensMutation(s): 6 
Gene Names: VWF, F8VWF
UniProt & NIH Common Fund Data Resources
Find proteins for P04275 (Homo sapiens)
Explore P04275 
Go to UniProtKB:  P04275
PHAROS:  P04275
GTEx:  ENSG00000110799 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04275
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AB [auth E]
AC [auth H]
BA [auth B]
BB [auth E]
BC [auth H]
AB [auth E],
AC [auth H],
BA [auth B],
BB [auth E],
BC [auth H],
BE [auth O],
CA [auth B],
CB [auth E],
CE [auth O],
DA [auth B],
DB [auth E],
DD [auth L],
DE [auth O],
EA [auth B],
ED [auth L],
EE [auth O],
FA [auth B],
FC [auth I],
FD [auth L],
FE [auth O],
GC [auth I],
GD [auth L],
HB [auth F],
HC [auth I],
HD [auth L],
IB [auth F],
IC [auth I],
JA [auth C],
JB [auth F],
JC [auth I],
JE [auth P],
KA [auth C],
KB [auth F],
KE [auth P],
LA [auth C],
LB [auth F],
LD [auth M],
LE [auth P],
MA [auth C],
MD [auth M],
ME [auth P],
NA [auth C],
NC [auth J],
ND [auth M],
NE [auth P],
OC [auth J],
OD [auth M],
PB [auth G],
PC [auth J],
PD [auth M],
QB [auth G],
QC [auth J],
RA [auth D],
RB [auth G],
RC [auth J],
SA [auth D],
SB [auth G],
T [auth A],
TA [auth D],
TB [auth G],
TD [auth N],
U [auth A],
UA [auth D],
UD [auth N],
V [auth A],
VA [auth D],
VC [auth K],
VD [auth N],
W [auth A],
WC [auth K],
WD [auth N],
X [auth A],
XB [auth H],
XC [auth K],
XD [auth N],
YB [auth H],
YC [auth K],
ZA [auth E],
ZB [auth H],
ZC [auth K]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
AA [auth B]
AD [auth L]
AE [auth O]
BD [auth L]
CC [auth I]
AA [auth B],
AD [auth L],
AE [auth O],
BD [auth L],
CC [auth I],
CD [auth L],
DC [auth I],
EB [auth F],
EC [auth I],
FB [auth F],
GA [auth C],
GB [auth F],
GE [auth P],
HA [auth C],
HE [auth P],
IA [auth C],
ID [auth M],
IE [auth P],
JD [auth M],
KC [auth J],
KD [auth M],
LC [auth J],
MB [auth G],
MC [auth J],
NB [auth G],
OA [auth D],
OB [auth G],
PA [auth D],
Q [auth A],
QA [auth D],
QD [auth N],
R [auth A],
RD [auth N],
S [auth A],
SC [auth K],
SD [auth N],
TC [auth K],
UB [auth H],
UC [auth K],
VB [auth H],
WA [auth E],
WB [auth H],
XA [auth E],
Y [auth B],
YA [auth E],
YD [auth O],
Z [auth B],
ZD [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.3

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States1F30HL162128
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01-HL148755
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM141109

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2022-10-05
    Changes: Database references