2QRA | pdb_00002qra

Crystal structure of XIAP BIR1 domain (P21 form)

PDB DOI: https://doi.org/10.2210/pdb2QRA/pdb

Classification: Apoptosis, Signaling protein
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2007-07-27 Released: 2007-09-18
Deposition Author(s): Lin, S.-C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the BIR1 domain of XIAP in two crystal forms

Lin, S.C., Huang, Y., Lo, Y.C., Lu, M., Wu, H.

(2007) J Mol Biology 372: 847-854

PubMed: 17698078 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jmb.2007.07.019
Primary Citation Related Structures:
2QRA

PubMed Abstract:
X-linked inhibitor of apoptosis (XIAP) is a potent negative regulator of apoptosis. It also plays a role in BMP signaling, TGF-beta signaling, and copper homeostasis. Previous structural studies have shown that the baculoviral IAP repeat (BIR2 and BIR3) domains of XIAP interact with the IAP-binding-motifs (IBM) in several apoptosis proteins such as Smac and caspase-9 via the conserved IBM-binding groove. Here, we report the crystal structure in two crystal forms of the BIR1 domain of XIAP, which does not possess this IBM-binding groove and cannot interact with Smac or caspase-9. Instead, the BIR1 domain forms a conserved dimer through the region corresponding to the IBM-binding groove. Structural and sequence analyses suggest that this dimerization of BIR1 in XIAP may be conserved in other IAP family members such as cIAP1 and cIAP2 and may be important for the action of XIAP in TGF-beta and BMP signaling and the action of cIAP1 and cIAP2 in TNF receptor signaling.

Organizational Affiliation

Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA.

Macromolecule Content

Total Structure Weight: 50.09 kDa
Atom Count: 2,595
Modeled Residue Count: 316
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing protein 4	A [auth D], B [auth C], C [auth B], D [auth A]	111	Homo sapiens	Mutation(s): 0 Gene Names: BIRC4, API3, IAP3, XIAP EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens) Explore P98170 Go to UniProtKB: P98170
PHAROS: P98170 GTEx: ENSG00000101966
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P98170
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain L [auth A] SDF format, chain K [auth B] SDF format, chain G [auth C] MOL2 format, chain E [auth D] MOL2 format, chain L [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth C] mmCIF format, chain E [auth D] mmCIF format, chain L [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth C]	E [auth D], G [auth C], K [auth B], L [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain G [auth C] Focus chain K [auth B] Focus chain L [auth A] Interactions & Density Focus chain E [auth D] Focus chain G [auth C] Focus chain K [auth B] Focus chain L [auth A]
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain H [auth C] SDF format, chain J [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain I [auth C] MOL2 format, chain F [auth D] MOL2 format, chain H [auth C] MOL2 format, chain J [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain I [auth C] mmCIF format, chain F [auth D] mmCIF format, chain H [auth C] mmCIF format, chain J [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain I [auth C]	F [auth D] H [auth C] I [auth C] J [auth C] M [auth A] F [auth D], H [auth C], I [auth C], J [auth C], M [auth A], N [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain F [auth D] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth A] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.563	α = 90
b = 72.983	β = 95.69
c = 68.904	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-09-18

Deposition Author(s):

Lin, S.-C.

Revision History (Full details and data files)

Version 1.0: 2007-09-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-29
Changes: Database references