9LT3 | pdb_00009lt3

Integrin alpha-v beta-3 in complex with Trimucrin

PDB DOI: https://doi.org/10.2210/pdb9LT3/pdb
EM Map EMD-63364: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Protobothrops mucrosquamatus
Expression System: Cricetulus griseus, Komagataella pastoris
Mutation(s): No

Deposited: 2025-02-05 Released: 2026-02-18
Deposition Author(s): Wang, Y.T., Chuang, W.J.
Funding Organization(s): National Science Council (NSC, Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for the differential recognition of integrin alpha v beta 3 by rhodostomin and trimucrin.

Wang, Y.T., Chang, Y.T., Huang, C.H., Liau, C.T., Chen, C.Y., Chuang, W.J.

(2026) Commun Biol 9

PubMed: 42045602 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-026-10139-6
Primary Citation Related Structures:
9IUJ, 9LT3, 9UAL

PubMed Abstract:
Rhodostomin (Rho) and Trimucrin (Tmu) are RGD-containing disintegrins that inhibit integrins more effectively than short RGD peptides. They differ in their linker, RGD loop, and C-terminal sequences. We determined the X-ray structure of Tmu and the cryo-EM structures of integrin αvβ3 in complex with both disintegrins. Structural analysis revealed subtle differences in binding, with both adopting a rigid backbone conformation and interacting with integrin through three cooperative binding sites. Besides the conserved RGD interface, Tmu features a cluster of basic residues in its linker, while Rho has distinct C-terminal interactions. Disintegrin binding stabilizes αvβ3 in an extended-open conformation, while the β3-Y110 residue is essential for maintaining the bent state without ligands. These findings enhance our understanding of integrin recognition and inform the development of integrin-targeted therapeutics for anti-angiogenic, anti-tumor, and anti-inflammatory applications.

Organizational Affiliation

Institute of Basic Medical Sciences, National Cheng Kung University College of Medicine, Tainan, Taiwan, ROC.

Macromolecule Content

Total Structure Weight: 245.97 kDa
Atom Count: 10,075
Modeled Residue Count: 1,270
Deposited Residue Count: 2,176
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V,Integrin alpha-v	A	1,184	Homo sapiens	Mutation(s): 0 Gene Names: ITGAV, MSK8, VNRA, VTNR, DKFZp686C11235
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens) Explore P06756 Go to UniProtKB: P06756
PHAROS: P06756 GTEx: ENSG00000138448
Find proteins for Q6MZV7 (Homo sapiens) Explore Q6MZV7 Go to UniProtKB: Q6MZV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P06756 Q6MZV7
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A	Go to GlyGen: P06756-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B	919	Homo sapiens	Mutation(s): 0 Gene Names: ITGB3, GP3A, DKFZp686C11235
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens) Explore P05106 Go to UniProtKB: P05106
PHAROS: P05106 GTEx: ENSG00000259207
Find proteins for Q6MZV7 (Homo sapiens) Explore Q6MZV7 Go to UniProtKB: Q6MZV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P05106 Q6MZV7
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B	Go to GlyGen: P05106-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc metalloproteinase/disintegrin PMMP-2	C	73	Protobothrops mucrosquamatus	Mutation(s): 0
UniProt
Find proteins for E9NW27 (Protobothrops mucrosquamatus) Explore E9NW27 Go to UniProtKB: E9NW27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E9NW27
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G	3		N-Glycosylation	Interactions Focus chain D Focus chain G Interactions & Density Focus chain D Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H [auth J], I [auth K]	2		N-Glycosylation	Interactions Focus chain E Focus chain H [auth J] Focus chain I [auth K] Interactions & Density Focus chain E Focus chain H [auth J] Focus chain I [auth K]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	6		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G93290PO GlyCosmos: G93290PO GlyGen: G93290PO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain T [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain T [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]