5O33: A structure of the GEF Kalirin DH1 domain

A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1. Determined by X-ray diffraction at 1.64 Å resolution. Released 31 May 2017.

Method: X-ray diffraction
Resolution: 1.64 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 2
Atoms: 3,144
Mol. weight: 41.58 kDa
Ligands: GDP
Released: 31 May 2017

Explore 5O33 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O33 contains 26 α-helices and 6 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	16-25	10
β-strand	40-46	7	1
β-strand	49-56	8	1
α-helix	68-71	4
β-strand	77-83	7	1
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	1
α-helix	117-119	3
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-149	11
β-strand	153-156	4	1
α-helix	165-176	12

Chain B: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	1233-1255	23
α-helix	1256-1260	5
α-helix	1261-1265	5
α-helix	1278-1282	5
α-helix	1285-1291	7
α-helix	1292-1296	5
α-helix	1297-1302	6
α-helix	1307-1309	3
α-helix	1311-1316	6
α-helix	1318-1322	5
α-helix	1323-1341	19
α-helix	1345-1353	9
α-helix	1359-1363	5
α-helix	1365-1370	6
α-helix	1373-1381	9
α-helix	1388-1407	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related C3 botulinum toxin substrate 1	A	protein	177	Homo sapiens	P63000 (AlphaFold model)
Kalirin	B	protein	180	Rattus norvegicus	P97924 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5O33_1 Ras-related C3 botulinum toxin substrate 1 (chains A)
MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAG
QEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLR
DDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL

Sequence of entity 2 (B), FASTA

>5O33_2 Kalirin (chains B)
RKKEFIMAELLQTEKAYVRDLHECLETYLWEMTSGVEEIPPGILNKEHIIFGNIQEIYDF
HNNIFLKELEKYEQLPEDVGHCFVTWADKFQMYVTYCKNKPDSNQLILEHAGTFFDEIQQ
RHGLANSISSYLIKPVQRVTKYQLLLKELLTCCEEGKGELKDGLEVMLSVPKKANDAMHV

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

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

Primary citation

A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1. Gray, J., Krojer, T., Talon, R. et al. To be published.

Other PDB entries of the same protein (UniProt P63000 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RFF 1.25 Å, Crystal Structure of Human Rac1 Fused with the Scaffold Protein POSH (residues 319-371)
9IFK 1.34 Å, Crystal structure of Kalirin/Rac1 in complex with DK-2
1MH1 1.38 Å, Small G-protein
9HU8 1.48 Å, Crystal structure of Kalirin/Rac1 in complex with MC-278.
2WKQ 1.6 Å, Structure of a photoactivatable Rac1 containing the Lov2 C450A Mutant
6X1G 1.6 Å, Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in…
9IG1 1.65 Å, Crystal structure of Kalirin/Rac1 in complex with DK-652
9I1L 1.68 Å, Crystal structure of Kalirin/Rac1 in complex with RS-009
8I5V 1.73 Å, DOCK10 mutant L1903Y complexed with Rac1
1RYF 1.75 Å, Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
1RYH 1.75 Å, Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
9TJY 1.77 Å, Crystal Structure of the Human Oncogenic Splice Variant Rac1b Fused with the Scaffold…

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