5C2J: Rac GTPase-activating protein 1

Complex structure of the GAP domain of MgcRacGAP and Cdc42. Determined by X-ray diffraction at 2.5 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Mus musculus
Chains: 2
Atoms: 3,216
Mol. weight: 45.55 kDa
Ligands: MG, GDP, AF3
Released: 22 Jun 2016

Explore 5C2J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C2J contains 26 α-helices and 8 β-strands across 2 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: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	351-354	4
β-strand	355	1	1
β-strand	363	1	1
α-helix	364-375	12
α-helix	390-403	14
α-helix	406-408	3
α-helix	416-427	12
α-helix	439-446	8
α-helix	451-462	12
α-helix	467-484	18
α-helix	487-489	3
α-helix	493-500	8
α-helix	501-505	5
α-helix	514-533	20
α-helix	536-540	5
α-helix	541-543	3

Chain B: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	2
α-helix	16-25	10
β-strand	37-46	10	2
β-strand	49-58	10	2
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	2
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	2
α-helix	117-121	5
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	2
α-helix	165-177	13
α-helix	183-186	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rac GTPase-activating protein 1	A	protein	208	Homo sapiens	Q9H0H5 (AlphaFold model)
Cell division control protein 42 homolog	B	protein	198	Mus musculus	P60766 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5C2J_1 Rac GTPase-activating protein 1 (chains A)
GSSGSSGIGEGMLADFVSQTSPMIPSIVVHCVNEIEQRGLTETGLYRISGCDRTVKELKE
KFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKEPLLTFRLNRAFMEAAEITDEDNSIAAM
YQAVGELPQANRDTLAFLMIHLQRVAQSPHTKMDVANLAKVFGPTIVAHAVPNPDPVTMS
QDIKRQPKVVERLLSLPLEYWSQFMMVE

Sequence of entity 2 (B), FASTA

>5C2J_2 Cell division control protein 42 homolog (chains B)
GSSGSSGMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTL
GLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLV
GTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAI
LAALEPPEPKKSRRCVLL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
AF3	Aluminum fluoride	Al F3	1

Primary citation

Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA. Murayama, K., Kato-Murayama, M., Hosaka, T. et al. J Struct Biol (2024) 216:108151-108151. DOI 10.1016/j.jsb.2024.108151 · PubMed

Other PDB entries of the same protein (UniProt Q9H0H5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5C2K 1.42 Å, Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP
2OVJ 1.49 Å, The crystal structure of the human Rac GTPase activating protein 1 (RACGAP1) MgcRacGAP.
3WPQ 1.84 Å, crystal structure of the GAP domain of MgcRacGAP(S387A)
3W6R 1.9 Å, Crystal structure of the GAP domain of human MgcRacGAP
4B6D 2.2 Å, Structure of the atypical C1 domain of MgcRacGAP
3WPS 2.7 Å, crystal structure of the GAP domain of MgcRacGAP(S387D)

Browse structure collections

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