7WQT

Cryo-EM structure of VWF D'D3 dimer complexed with D1D2 at 4.3 angstron resolution (VWF tube)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of von Willebrand factor multimerization and tubular storage.

Zeng, J.Shu, Z.Liang, Q.Zhang, J.Wu, W.Wang, X.Zhou, A.

(2022) Blood 139: 3314-3324

  • DOI: https://doi.org/10.1182/blood.2021014729
  • Primary Citation of Related Structures:  
    7WPP, 7WPQ, 7WPR, 7WPS, 7WQT

  • PubMed Abstract: 

    The von Willebrand factor (VWF) propeptide (domains D1D2) is essential for the assembly of VWF multimers and its tubular storage in Weibel-Palade bodies. However, detailed molecular mechanism underlying this propeptide dependence is unclear. Here, we prepared Weibel-Palade body-like tubules using the N-terminal fragment of VWF and solved the cryo-electron microscopy structures of the tubule at atomic resolution. Detailed structural and biochemical analysis indicate that the propeptide forms a homodimer at acidic pH through the D2:D2 binding interface and then recruits 2 D'D3 domains, forming an intertwined D1D2D'D3 homodimer in essence. Stacking of these homodimers by the intermolecular D1:D2 interfaces brings 2 D3 domains face-to-face and facilitates their disulfide linkages and multimerization of VWF. Sequential stacking of these homodimers leads to a right-hand helical tubule for VWF storage. The clinically identified VWF mutations in the propeptide disrupted different steps of the assembling process, leading to diminished VWF multimers in von Willebrand diseases (VWD). Overall, these results indicate that the propeptide serves as a pH-sensing template for VWF multimerization and tubular storage. This sheds light on delivering normal propeptide as a template to rectify the defects in multimerization of VWD mutants.


  • Organizational Affiliation

    Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
von Willebrand antigen 2741Homo sapiensMutation(s): 0 
Gene Names: VWFF8VWF
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
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P04275-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
von Willebrand factor490Homo sapiensMutation(s): 0 
Gene Names: VWFF8VWF
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
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P04275-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth D]
AD [auth S]
BD [auth S]
CB [auth d]
CC [auth L]
AB [auth D],
AD [auth S],
BD [auth S],
CB [auth d],
CC [auth L],
DC [auth L],
EB [auth E],
ED [auth T],
FB [auth E],
FD [auth T],
GA [auth A],
GC [auth M],
HA [auth A],
HC [auth M],
JB [auth F],
JD [auth U],
KA [auth a],
KB [auth F],
KC [auth N],
KD [auth U],
LA [auth a],
MD [auth V],
NA [auth B],
NC [auth N],
OA [auth B],
OB [auth G],
OC [auth O],
PB [auth G],
PC [auth O],
PD [auth W],
QD [auth W],
RA [auth b],
SA [auth b],
SC [auth P],
TC [auth P],
UA [auth C],
UB [auth I],
VA [auth C],
VB [auth I],
XD [auth Z],
YD [auth Z],
ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
AC [auth K]
BB [auth D]
BC [auth K]
CD [auth S]
DB [auth d]
AC [auth K],
BB [auth D],
BC [auth K],
CD [auth S],
DB [auth d],
DD [auth S],
EC [auth L],
FC [auth L],
GB [auth E],
GD [auth T],
HB [auth E],
HD [auth T],
IA [auth A],
IB [auth e],
IC [auth M],
ID [auth U],
JA [auth A],
JC [auth M],
LB [auth F],
LC [auth N],
LD [auth U],
MA [auth a],
MB [auth F],
MC [auth N],
NB [auth f],
ND [auth V],
OD [auth V],
PA [auth B],
QA [auth B],
QB [auth G],
QC [auth O],
RB [auth G],
RC [auth O],
RD [auth W],
SB [auth H],
SD [auth W],
TA [auth b],
TB [auth H],
TD [auth X],
UC [auth P],
UD [auth X],
VC [auth P],
VD [auth Y],
WA [auth C],
WB [auth I],
WC [auth Q],
WD [auth Y],
XA [auth C],
XB [auth I],
XC [auth Q],
YA [auth c],
YB [auth J],
YC [auth R],
ZB [auth J],
ZC [auth R],
ZD [auth Z]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0501103

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary