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- Structure Factors (CIF - gz)
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- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 2 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
- Biological Assembly 2 (PDB - gz)
4ZZJ|pdb_00004zzj
SIRT1/Activator/Substrate Complex
- PDB DOI: https://doi.org/10.2210/pdb4ZZJ/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-05-22 Released: 2015-07-15
- Deposition Author(s): Dai, H.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.74 Å
- R-Value Free: 0.221 (Depositor), 0.220 (DCC)
- R-Value Work: 0.182 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.184 (Depositor)
Starting Models:experimental
View more details
Download MendeleyCrystallographic structure of a small molecule SIRT1 activator-enzyme complex.
Dai, H., Case, A.W., Riera, T.V., Considine, T., Lee, J.E., Hamuro, Y., Zhao, H., Jiang, Y., Sweitzer, S.M., Pietrak, B., Schwartz, B., Blum, C.A., Disch, J.S., Caldwell, R., Szczepankiewicz, B., Oalmann, C., Yee Ng, P., White, B.H., Casaubon, R., Narayan, R., Koppetsch, K., Bourbonais, F., Wu, B., Wang, J., Qian, D., Jiang, F., Mao, C., Wang, M., Hu, E., Wu, J.C., Perni, R.B., Vlasuk, G.P., Ellis, J.L.(2015) Nat Commun 6: 7645-7645
- PubMed: 26134520 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1038/ncomms8645
- Primary Citation of Related Structures:
4ZZH,4ZZI,4ZZJ - PubMed Abstract:
SIRT1, the founding member of the mammalian family of seven NAD(+)-dependent sirtuins, is composed of 747 amino acids forming a catalytic domain and extended N- and C-terminal regions. We report the design and characterization of an engineered human SIRT1 construct (mini-hSIRT1) containing the minimal structural elements required for lysine deacetylation and catalytic activation by small molecule sirtuin-activating compounds (STACs). Using this construct, we solved the crystal structure of a mini-hSIRT1-STAC complex, which revealed the STAC-binding site within the N-terminal domain of hSIRT1. Together with hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis using full-length hSIRT1, these data establish a specific STAC-binding site and identify key intermolecular interactions with hSIRT1. The determination of the interface governing the binding of STACs with human SIRT1 facilitates greater understanding of STAC activation of this enzyme, which holds significant promise as a therapeutic target for multiple human diseases.
- 1] Sirtris, a GlaxoSmithKline Company, 200 Technology Square, Suite 300, Cambridge, Massachusetts 02139, USA [2] GlaxoSmithKline, 1250S. Collegeville Road, Collegeville, Pennsylvania 19426, USA.
- Sirtris, a GlaxoSmithKline Company, 200 Technology Square, Suite 300, Cambridge, Massachusetts 02139, USA.
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, USA.
- GlaxoSmithKline, 1250S. Collegeville Road, Collegeville, Pennsylvania 19426, USA.
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 350 Shushanhu Road, Hefei, Anhui Province 230031, China.
- Viva Biotech, 334 Aidisheng Road, Zhangjiang High-tech Park, Shanghai 201203, China.
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (CNA)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
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 (CNA)
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2
Pseudo Symmetry: Asymmetric - C1
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1
Find Similar Assemblies
Biological assembly 2 generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 42.52 kDa
- Atom Count: 2,961
- Modeled Residue Count: 351
- Deposited Residue Count: 363
- Unique protein chains: 2
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NAD-dependent protein deacetylase sirtuin-1 | 356 | Homo sapiens | Mutation(s): 0 Gene Names: SIRT1, SIR2L1 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q96EB6 (Homo sapiens) Explore Q96EB6 Go to UniProtKB: Q96EB6 | |||||
PHAROS: Q96EB6 GTEx: ENSG00000096717 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96EB6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ac-p53 | 7 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04637 (Homo sapiens) Explore P04637 Go to UniProtKB: P04637 | |||||
PHAROS: P04637 GTEx: ENSG00000141510 | |||||
Entity Groups | |||||
| UniProt Group | P04637 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CNA Query on CNA Download Ideal Coordinates CCD File | D [auth A] | CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE C22 H30 N7 O13 P2 DGPLSUKWXXSBCU-VGXGLJSLSA-O |  | ||
| 4TQ Query on 4TQ Download Ideal Coordinates CCD File | E [auth A] | (3S)-1,3-dimethyl-N-[3-(1,3-oxazol-5-yl)phenyl]-6-[3-(trifluoromethyl)phenyl]-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide C26 H22 F3 N5 O2 NWNBKQCPAUNKSG-INIZCTEOSA-N |  | ||
| GOL Query on GOL Download Ideal Coordinates CCD File | F [auth A], G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN Download Ideal Coordinates CCD File | C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| ALY Query on ALY | B | L-PEPTIDE LINKING | C8 H16 N2 O3 |  | LYS |
| NLE Query on NLE | B | L-PEPTIDE LINKING | C6 H13 N O2 |  | LEU |
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.74 Å
- R-Value Free: 0.221 (Depositor), 0.220 (DCC)
- R-Value Work: 0.182 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.184 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 94.51 | α = 90 |
| b = 94.51 | β = 90 |
| c = 356.84 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PHASER | phasing |
| xia2 | data reduction |
| xia2 | data scaling |
Deposition Data
- Released Date: 2015-07-15 Deposition Author(s): Dai, H.
Revision History (Full details and data files)
- Version 1.0: 2015-07-15
Type: Initial release - Version 1.1: 2015-09-23
Changes: Data collection - Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2023-11-15
Changes: Data collection - Version 1.4: 2024-11-13
Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational 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.