Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.46 kDa 
• Atom Count: 1668 
• Residue Count: 189 
• Unique protein chains: 1

2UVL

Human BIR3 domain of Baculoviral Inhibitor of Apoptosis Repeat- Containing 3 (BIRC3)

• DOI: 10.2210/pdb2UVL/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-12 Released: 2007-03-27 
• Deposition Author(s): Moche, M., Lehtio, L., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Karlberg, T., Kotenyova, T., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Upsten, M., Van Den Berg, S., Weigelt, J., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.240 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structures of Bir Domains from Human Naip and Ciap2.

Herman, M.D., Moche, M., Flodin, S., Welin, M., Tresaugues, L., Johansson, I., Nilsson, M., Nordlund, P., Nyman, T.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1091

• PubMed: 19923725 
• DOI: 10.1107/S1744309109038597
• Primary Citation of Related Structures:  
  2UVL, 2VM5


• PubMed Abstract: 
  

The inhibitor of apoptosis (IAP) family of proteins contains key modulators of apoptosis and inflammation that interact with caspases through baculovirus IAP-repeat (BIR) domains. Overexpression of IAP proteins frequently occurs in cancer cells, thus counteracting the activated apoptotic program. The IAP proteins have therefore emerged as promising targets for cancer therapy. In this work, X-ray crystallography was used to determine the first structures of BIR domains from human NAIP and cIAP2. Both structures harbour an N-terminal tetrapeptide in the conserved peptide-binding groove. The structures reveal that these two proteins bind the tetrapeptides in a similar mode as do other BIR domains. Detailed interactions are described for the P1'-P4' side chains of the peptide, providing a structural basis for peptide-specific recognition. An arginine side chain in the P3' position reveals favourable interactions with its hydrophobic moiety in the binding pocket, while hydrophobic residues in the P2' and P4' pockets make similar interactions to those seen in other BIR domain-peptide complexes. The structures also reveal how a serine in the P1' position is accommodated in the binding pockets of NAIP and cIAP2. In addition to shedding light on the specificity determinants of these two proteins, the structures should now also provide a framework for future structure-based work targeting these proteins.

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Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 3	A, B	96	Homo sapiens	Mutation(s): 0  Gene Names: BIRC3, API2, MIHC, RNF49 EC: 2.3.2.27
Find proteins for Q13489 (Homo sapiens) Explore Q13489  Go to UniProtKB:  Q13489
NIH Common Fund Data Resources
PHAROS:  Q13489 GTEx:  ENSG00000023445

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.240 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.41	α = 90
b = 53.72	β = 90
c = 85.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-12 
• Released Date: 2007-03-27 
Deposition Author(s): Moche, M., Lehtio, L., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Karlberg, T., Kotenyova, T., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Upsten, M., Van Den Berg, S., Weigelt, J., Nordlund, P.

Revision History 

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2011-12-28
  Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2020-03-04
  Changes: Derived calculations, Other