7WN6

Cryo-EM structure of VWF D'D3 dimer (R1136M/E1143M mutant) complexed with D1D2 at 3.29 angstron resolution (2 units)

PDB DOI: https://doi.org/10.2210/pdb7WN6/pdb
EM Map EMD-32622: EMDB EMDataResource

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

Deposited: 2022-01-17 Released: 2022-05-18
Deposition Author(s): Zeng, J.W., Shu, Z.M., Zhou, A.W.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural mechanism of VWF D'D3 dimer formation.

Shu, Z., Zeng, J., Xia, L., Cai, H., Zhou, A.

(2022) Cell Discov 8: 14-14

PubMed: 35169124 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-022-00378-2
Primary Citation of Related Structures:
7WN3, 7WN4, 7WN6

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.

Macromolecule Content

Total Structure Weight: 547.61 kDa
Atom Count: 36,584
Modelled Residue Count: 4,756
Deposited Residue Count: 4,924
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Willebrand antigen 2	A, C [auth B], E, F [auth G]	741	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04275
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
von Willebrand factor	B [auth F], D [auth H], G [auth C], H [auth D]	490	Homo sapiens	Mutation(s): 2 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04275
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain IA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth F] SDF format, chain MA [auth C] SDF format, chain NA [auth D] SDF format, chain P [auth F] SDF format, chain Q [auth F] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth H] SDF format, chain Y [auth H] SDF format, chain Z [auth H] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth F] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth H]	CA [auth E] DA [auth E] GA [auth G] HA [auth G] IA [auth C] CA [auth E], DA [auth E], GA [auth G], HA [auth G], IA [auth C], K [auth A], L [auth A], LA [auth C], M [auth F], MA [auth C], NA [auth D], P [auth F], Q [auth F], QA [auth D], RA [auth D], T [auth B], U [auth B], V [auth H], Y [auth H], Z [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth F] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain P [auth F] Focus chain Q [auth F] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth H] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth F] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain P [auth F] Focus chain Q [auth F] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth H] Focus chain Y [auth H] Focus chain Z [auth H]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain N [auth F] SDF format, chain O [auth F] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain W [auth H] SDF format, chain X [auth H] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain N [auth F] MOL2 format, chain O [auth F] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H]	AA [auth E] BA [auth E] EA [auth G] FA [auth G] I [auth A] AA [auth E], BA [auth E], EA [auth G], FA [auth G], I [auth A], J [auth A], JA [auth C], KA [auth C], N [auth F], O [auth F], OA [auth D], PA [auth D], R [auth B], S [auth B], W [auth H], X [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain N [auth F] Focus chain O [auth F] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain N [auth F] Focus chain O [auth F] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth H] Focus chain X [auth H]