8XF6 | pdb_00008xf6

Cryo-EM structure of integrin ITGAV, ITGB3 and Cilengitide TFA complex, conformation 2

PDB DOI: https://doi.org/10.2210/pdb8XF6/pdb
EM Map EMD-38299: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-12-13 Released: 2024-12-18
Deposition Author(s): Xi, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8XF6

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

Literature

Cryo-EM structure of integrin ITGAV, ITGB3 and Cilengitide TFA complex, conformation 2

Xi, Z.

To be published.

Macromolecule Content

Total Structure Weight: 203.89 kDa
Atom Count: 10,907
Modeled Residue Count: 1,401
Deposited Residue Count: 1,836
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V	A	1,048	Homo sapiens	Mutation(s): 0 Gene Names: ITGAV
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens) Explore P06756 Go to UniProtKB: P06756
PHAROS: P06756 GTEx: ENSG00000138448
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06756
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B	788	Homo sapiens	Mutation(s): 0 Gene Names: ITGB3
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens) Explore P05106 Go to UniProtKB: P05106
PHAROS: P05106 GTEx: ENSG00000259207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05106
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LU4 Query on A1LU4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2-[(2~{R},5~{R},8~{S},11~{S})-11-(3-carbamimidamidopropyl)-7-methyl-3,6,9,12,15-pentakis(oxidanylidene)-5-(phenylmethyl)-8-propan-2-yl-1,4,7,10,13-pentazacyclopentadec-2-yl]ethanoic acid C₂₇ H₄₀ N₈ O₇ AMLYAMJWYAIXIA-JYLXEMOASA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.