2A26 | pdb_00002a26

Crystal structure of the N-terminal, dimerization domain of Siah Interacting Protein

PDB DOI: https://doi.org/10.2210/pdb2A26/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-06-21 Released: 2005-08-09
Deposition Author(s): Santelli, E., Leone, M., Li, C., Fukushima, T., Preece, N.E., Olson, A.J., Ely, K.R., Reed, J.C., Pellecchia, M., Liddington, R.C., Matsuzawa, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.198 (Depositor), 0.199 (DCC)
R-Value Work:
0.174 (Depositor), 0.172 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural Analysis of Siah1-Siah-interacting Protein Interactions and Insights into the Assembly of an E3 Ligase Multiprotein Complex

Santelli, E., Leone, M., Li, C., Fukushima, T., Preece, N.E., Olson, A.J., Ely, K.R., Reed, J.C., Pellecchia, M., Liddington, R.C., Matsuzawa, S.

(2005) J Biological Chem 280: 34278-34287

PubMed: 16085652 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M506707200
Primary Citation Related Structures:
2A25, 2A26

PubMed Abstract:
Siah1 is the central component of a multiprotein E3 ubiquitin ligase complex that targets beta-catenin for destruction in response to p53 activation. The E3 complex comprises, in addition to Siah1, Siah-interacting protein (SIP), the adaptor protein Skp1, and the F-box protein Ebi. Here we show that SIP engages Siah1 by means of two elements, both of which are required for mediating beta-catenin destruction in cells. An N-terminal dimerization domain of SIP sits across the saddle-shaped upper surface of Siah1, with two extended legs packing against the sides of Siah1 by means of a consensus PXAXVXP motif that is common to a family of Siah-binding proteins. The C-terminal domain of SIP, which binds to Skp1, protrudes from the lower surface of Siah1, and we propose that this surface provides the scaffold for bringing substrate and the E2 enzyme into apposition in the functional complex.

Organizational Affiliation

The Burnham Institute, La Jolla, California 92037, USA.

Macromolecule Content

Total Structure Weight: 17.75 kDa
Atom Count: 1,493
Modeled Residue Count: 140
Deposited Residue Count: 150
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcyclin-binding protein	A, B, C	50	Homo sapiens	Mutation(s): 0 Gene Names: CACYBP, S100A6BP, SIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HB71 (Homo sapiens) Explore Q9HB71 Go to UniProtKB: Q9HB71
PHAROS: Q9HB71 GTEx: ENSG00000116161
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HB71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXS Query on CXS Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.198 (Depositor), 0.199 (DCC)
R-Value Work: 0.174 (Depositor), 0.172 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.793	α = 90
b = 152.609	β = 90
c = 36.988	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-08-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-08-09
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations