- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- Legacy PDB Format
- Legacy PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full (PDF - gz)
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 2 (CIF - gz)
- Biological Assembly 3 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
- Biological Assembly 2 (PDB - gz)
- Biological Assembly 3 (PDB - gz)
2AST | pdb_00002ast
Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide
- PDB DOI: https://doi.org/10.2210/pdb2AST/pdb
- Classification: LIGASE/LIGASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2005-08-24 Released: 2005-10-18
- Deposition Author(s): Hao, B., Zhang, N., Schulman, B.A., Wu, G., Pagano, M., Pavletich, N.P.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.221 (Depositor), 0.190 (DCC)
- R-Value Work: 0.202 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.203 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
- 👁 Image
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Structural Basis of the Cks1-Dependent Recognition of p27(Kip1) by the SCF(Skp2) Ubiquitin Ligase.
Hao, B., Zheng, N., Schulman, B.A., Wu, G., Miller, J.J., Pagano, M., Pavletich, N.P.(2005) Mol Cell 20: 9-19
- PubMed: 16209941 Search on PubMed
- DOI: https://doi.org/10.1016/j.molcel.2005.09.003
- Primary Citation Related Structures:
2ASS, 2AST - PubMed Abstract:
The ubiquitin-mediated proteolysis of the Cdk2 inhibitor p27(Kip1) plays a central role in cell cycle progression, and enhanced degradation of p27(Kip1) is associated with many common cancers. Proteolysis of p27(Kip1) is triggered by Thr187 phosphorylation, which leads to the binding of the SCF(Skp2) (Skp1-Cul1-Rbx1-Skp2) ubiquitin ligase complex. Unlike other known SCF substrates, p27(Kip1) ubiquitination also requires the accessory protein Cks1. The crystal structure of the Skp1-Skp2-Cks1 complex bound to a p27(Kip1) phosphopeptide shows that Cks1 binds to the leucine-rich repeat (LRR) domain and C-terminal tail of Skp2, whereas p27(Kip1) binds to both Cks1 and Skp2. The phosphorylated Thr187 side chain of p27(Kip1) is recognized by a Cks1 phosphate binding site, whereas the side chain of an invariant Glu185 inserts into the interface between Skp2 and Cks1, interacting with both. The structure and biochemical data support the proposed model that Cdk2-cyclin A contributes to the recruitment of p27(Kip1) to the SCF(Skp2)-Cks1 complex.
- Howard Hughes Medical Institute, New York, New York 10021, USA.
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (BEN)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (BEN)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 4-mer - A1B1C1D1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (BEN)
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2
Pseudo Symmetry: Asymmetric - C1
Pseudo Stoichiometry: Hetero 8-mer - A2B2C2D1E1
Find Similar Assemblies
Biological assembly 2 generated by PISA (software)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (BEN)
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2
Pseudo Symmetry: Asymmetric - C1
Pseudo Stoichiometry: Hetero 8-mer - A2B2C2D1E1
Find Similar Assemblies
Biological assembly 3 generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 65.91 kDa
- Atom Count: 4,660
- Modeled Residue Count: 546
- Deposited Residue Count: 574
- Unique protein chains: 4
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| S-phase kinase-associated protein 1A | 159 | Homo sapiens | Mutation(s): 1 Gene Names: SKP1A, EMC19, OCP2, SKP1, TCEB1L | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P63208 (Homo sapiens) Explore P63208 Go to UniProtKB: P63208 | |||||
PHAROS: P63208 GTEx: ENSG00000113558 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P63208 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| S-phase kinase-associated protein 2 | 336 | Homo sapiens | Mutation(s): 0 Gene Names: SKP2, FBXL1 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q13309 (Homo sapiens) Explore Q13309 Go to UniProtKB: Q13309 | |||||
PHAROS: Q13309 GTEx: ENSG00000145604 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q13309 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cyclin-dependent kinases regulatory subunit 1 | 69 | Homo sapiens | Mutation(s): 0 Gene Names: CKS1, CKS1B | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61024 (Homo sapiens) Explore P61024 Go to UniProtKB: P61024 | |||||
PHAROS: P61024 GTEx: ENSG00000173207 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61024 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cyclin-dependent kinase inhibitor 1B | 10 | N/A | Mutation(s): 0 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P46527 (Homo sapiens) Explore P46527 Go to UniProtKB: P46527 | |||||
PHAROS: P46527 GTEx: ENSG00000111276 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P46527 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BEN Query on BEN Download Ideal Coordinates CCD File | E [auth B], F [auth C] | BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N | 👁 Image | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TPO Query on TPO | D | L-PEPTIDE LINKING | C4 H10 N O6 P | 👁 Image | THR |
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.221 (Depositor), 0.190 (DCC)
- R-Value Work: 0.202 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.203 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 148.7 | α = 90 |
| b = 148.7 | β = 90 |
| c = 98.8 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
Deposition Data
- Released Date: 2005-10-18 Deposition Author(s): Hao, B., Zhang, N., Schulman, B.A., Wu, G., Pagano, M., Pavletich, N.P.
Revision History (Full details and data files)
- Version 1.0: 2005-10-18
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance - Version 1.3: 2021-10-20
Changes: Database references, Derived calculations - Version 1.4: 2023-08-23
Changes: Data collection, Refinement description - Version 1.5: 2024-10-30
Changes: Structure summary
