5GQQ: ALG-2/HEBP2 Complex

Name: PDB 5GQQ: Structure of ALG-2/HEBP2 Complex
Published: 2016-11-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: apoptosis

Structure of ALG-2/HEBP2 Complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 2 Nov 2016.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,948
Mol. weight: 80.45 kDa
Ligands: CA
Released: 2 Nov 2016

Explore 5GQQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GQQ contains 34 α-helices and 38 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	1
β-strand	25-26	2	2
β-strand	39-43	5	2
α-helix	44-45	2
β-strand	46-55	10	2
α-helix	58-74	17
β-strand	77	1	3
β-strand	86	1	1
β-strand	89-94	6	2
α-helix	101-102	2
β-strand	103-110	8	2
α-helix	111-112	2
α-helix	113-116	4
α-helix	119-121	3
β-strand	122	1	3
β-strand	127-132	6	2
α-helix	133-134	2
β-strand	135-142	8	2
α-helix	148-164	17
β-strand	169	1	4
β-strand	174-178	5	2
β-strand	190-195	6	2
β-strand	196	1	4

Chain B: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	5
β-strand	39-43	5	5
α-helix	44-45	2
β-strand	46-55	10	5
α-helix	58-73	16
β-strand	77	1	6
β-strand	89-94	6	5
α-helix	101-102	2
β-strand	103-110	8	5
α-helix	111-112	2
α-helix	113-116	4
α-helix	119-121	3
β-strand	122	1	6
β-strand	127-132	6	5
α-helix	133-134	2
β-strand	135-142	8	5
α-helix	148-164	17
β-strand	169	1	7
β-strand	174-178	5	5
β-strand	190-195	6	5
β-strand	196	1	7

Chain C: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
β-strand	43-44	2	8
α-helix	45-51	7
α-helix	59-60	2
α-helix	62-72	11
β-strand	79-80	2	8
α-helix	82-102	21
β-strand	110	1	9
α-helix	112-122	11
α-helix	130-138	9
β-strand	146	1	9
α-helix	148-168	21
β-strand	175-179	5	10
α-helix	180-187	8

Chain D: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
β-strand	43-44	2	11
α-helix	45-51	7
α-helix	59-60	2
α-helix	62-72	11
β-strand	79-80	2	11
α-helix	82-102	21
β-strand	110	1	12
α-helix	112-122	11
α-helix	128-138	11
β-strand	146	1	12
α-helix	148-168	21
β-strand	175-179	5	10
α-helix	180-186	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heme-binding protein 2	A, B	protein	178	Homo sapiens	Q9Y5Z4 (AlphaFold model)
Programmed cell death protein 6	C, D	protein	170	Homo sapiens	O75340 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5GQQ_1 Heme-binding protein 2 (chains A, B)
VETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEK
EMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFV
RSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQK

Sequence of entity 2 (C, D), FASTA

>5GQQ_2 Programmed cell death protein 6 (chains C, D)
GSDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVN
FSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQ
GRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6

Water and common crystallization additives (CL) are not listed.

Primary citation

Structural and Functional Study of Apoptosis-linked Gene-2Heme-binding Protein 2 Interactions in HIV-1 Production. Ma, J., Zhang, X., Feng, Y. et al. J Biol Chem (2016) 291:26670-26685. DOI 10.1074/jbc.M116.752444 · PubMed

Other PDB entries of the same protein (UniProt Q9Y5Z4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3R8J 1.6 Å, Crystal structure of human SOUL protein (orthorhombic form)
3R85 1.95 Å, Crystal structure of human SOUL BH3 domain in complex with Bcl-xL
3R8K 2.85 Å, Crystal structure of human SOUL protein (hexagonal form)
4AYZ 3.5 Å, X-ray Structure of human SOUL
4B0Y 3.5 Å, Determination of X-ray Structure of human SOUL by Molecular Replacement

Browse structure collections

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