1L5G | pdb_00001l5g
CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN AVB3 IN COMPLEX WITH AN ARG-GLY-ASP LIGAND
- PDB DOI: https://doi.org/10.2210/pdb1L5G/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2002-03-06 Released: 2002-04-17
- Deposition Author(s): Xiong, J.-P., Stehle, T., Zhang, R., Joachimiak, A., Frech, M., Goodman, S.L., Arnaout, M.A.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.328 (Depositor)
- R-Value Work: 0.248 (Depositor)
Starting Model: experimental
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wwPDB Validation3D Report Full Report
Literature
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Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand.
Xiong, J.P., Stehle, T., Zhang, R., Joachimiak, A., Frech, M., Goodman, S.L., Arnaout, M.A.(2002) Science 296: 151-155
- PubMed: 11884718 Search on PubMed
- DOI: https://doi.org/10.1126/science.1069040
- Primary Citation Related Structures:
1L5G, 1M1X - PubMed Abstract:
The structural basis for the divalent cation-dependent binding of heterodimeric alphabeta integrins to their ligands, which contain the prototypical Arg-Gly-Asp sequence, is unknown. Interaction with ligands triggers tertiary and quaternary structural rearrangements in integrins that are needed for cell signaling. Here we report the crystal structure of the extracellular segment of integrin alphaVbeta3 in complex with a cyclic peptide presenting the Arg-Gly-Asp sequence. The ligand binds at the major interface between the alphaV and beta3 subunits and makes extensive contacts with both. Both tertiary and quaternary changes are observed in the presence of ligand. The tertiary rearrangements take place in betaA, the ligand-binding domain of beta3; in the complex, betaA acquires two cations, one of which contacts the ligand Asp directly and the other stabilizes the ligand-binding surface. Ligand binding induces small changes in the orientation of alphaV relative to beta3.
- Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA.
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (NAG)
Biological Assembly 1
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (NAG)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 3-mer - A1B1C1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 187.43 kDa
- Atom Count: 11,700
- Modeled Residue Count: 1,471
- Deposited Residue Count: 1,654
- Unique protein chains: 3
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| INTEGRIN ALPHA V | 957 | Homo sapiens | Mutation(s): 0 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P06756 GTEx: ENSG00000138448 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06756 | ||||
Glycosylation | |||||
| Glycosylation Sites: 7 | Go to GlyGen: P06756-1 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| INTEGRIN BETA-3 | 692 | Homo sapiens | Mutation(s): 0 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P05106 GTEx: ENSG00000259207 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P05106 | ||||
Glycosylation | |||||
| Glycosylation Sites: 4 | Go to GlyGen: P05106-1 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Oligosaccharides
HelpEntity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, E, F, H | 2 | 👁 Image | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Small Molecules
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MVA Query on MVA | C | L-PEPTIDE LINKING | C6 H13 N O2 | 👁 Image | VAL |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.328 (Depositor)
- R-Value Work: 0.248 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 129.79 | α = 90 |
| b = 129.79 | β = 90 |
| c = 308.78 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| X-PLOR | model building |
| X-PLOR | refinement |
| X-PLOR | phasing |
Entry History
Deposition Data
- Released Date: 2002-04-17 Deposition Author(s): Xiong, J.-P., Stehle, T., Zhang, R., Joachimiak, A., Frech, M., Goodman, S.L., Arnaout, M.A.
Revision History (Full details and data files)
- Version 1.0: 2002-04-17
Type: Initial release - Version 1.1: 2008-04-28
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary - Version 2.2: 2024-11-06
Changes: Structure summary
