4KVG: RIAM RA-PH domains

Crystal structure of RIAM RA-PH domains in complex with GTP bound Rap1. Determined by X-ray diffraction at 1.65 Å resolution. Released 5 Mar 2014.

Method: X-ray diffraction
Resolution: 1.65 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 7,731
Mol. weight: 101.5 kDa
Ligands: GTP, MG
Released: 5 Mar 2014

Explore 4KVG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KVG contains 41 α-helices and 44 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1	1
β-strand	2-9	8	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	66-74	9
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	1
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	1
β-strand	147	1	2
β-strand	152	1	2
α-helix	154-166	13

Chain B: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	180-187	8	1
β-strand	192-198	7	1
β-strand	202	1	3
α-helix	203-214	12
β-strand	222-228	7	1
β-strand	233-236	4	1
α-helix	237-238	2
β-strand	242	1	3
α-helix	243-247	5
β-strand	257-262	6	1
α-helix	268-271	4
α-helix	273-275	3
α-helix	295-306	12
β-strand	317-323	7	1
α-helix	324	1
β-strand	330-337	8	1
β-strand	341-344	4	1
α-helix	345-346	2
α-helix	356	1
β-strand	357-361	5	1
α-helix	362-364	3
β-strand	366-370	5	1
α-helix	373-377	5
β-strand	384-388	5	1
β-strand	400-403	4	1
α-helix	407-422	16
α-helix	424-434	11

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	4
α-helix	16-25	10
β-strand	37-46	10	4
β-strand	49-58	10	4
α-helix	69-74	6
β-strand	77-83	7	4
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	4
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	4
β-strand	147	1	5
β-strand	152	1	5
α-helix	154-165	12

Chain D: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	180-186	7	4
α-helix	187	1
β-strand	192-198	7	4
β-strand	202	1	6
α-helix	203-214	12
β-strand	222-228	7	4
β-strand	233-236	4	4
α-helix	237-238	2
β-strand	242	1	6
α-helix	243-247	5
β-strand	257-262	6	4
α-helix	268-271	4
α-helix	273-275	3
α-helix	295-306	12
β-strand	317-323	7	4
α-helix	324	1
β-strand	330-337	8	4
β-strand	341-345	5	4
α-helix	356-357	2
β-strand	358-361	4	4
α-helix	362-364	3
β-strand	366-370	5	4
α-helix	373-377	5
β-strand	384-388	5	4
β-strand	400-403	4	4
α-helix	407-422	16
α-helix	424-434	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rap-1A	A, C	protein	168	Homo sapiens	P62834 (AlphaFold model)
Amyloid beta A4 precursor protein-binding family B member 1-interacting protein	B, D	protein	260	Mus musculus	Q8R5A3 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4KVG_1 Ras-related protein Rap-1A (chains A, C)
HMREYKLVVLGSVGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDCQQCMLEILDTA
GTEEFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCD
LEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINR

Sequence of entity 2 (B, D), FASTA

>4KVG_2 Amyloid beta A4 precursor protein-binding family B member 1-interacting protein (chains B, D)
MKKLVVKVHMDDSSTKSLMVDERQLARDVLDNLFEKTHCDCNVDWCLYEIYPELQIERVF
EDHENVVEVLSDWTRDTENKVLFLEKEERYAVFKNPQNFYLDNKGKKENKETNEKMNAKN
KEYLLEESFCGTSIIVPELEGALYLKEDGKKSWKRRYFLLRASGIYYVPKGKTKTSRDLA
CFIQFENVNIYYGIQCKMKYKAPTDHCFVLKHPQIQKESQYIKYLCCDDARTLSQWVMGI
RIAKYGKTLYDNYQRAVARA

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2

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

Primary citation

The structure of Rap1 in complex with RIAM reveals specificity determinants and recruitment mechanism. Zhang, H., Chang, Y.C., Brennan, M.L. et al. J Mol Cell Biol (2014) 6:128-139. DOI 10.1093/jmcb/mjt044 · PubMed

Other PDB entries of the same protein (UniProt P62834 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1C1Y 1.9 Å, Crystal structure of rap.gmppnp in complex with the ras-binding-domain of C-RAF1 kinase…
3KUC 1.92 Å, Complex of Rap1A(E30D/K31E)GDP with RafRBD(A85K/N71R)
1GUA 2.0 Å, Human RAP1A, residues 1-167, double mutant (E30D,K31E) complexed with gppnhp and the…

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