4DXA: Co-crystal structure of Rap1

Co-crystal structure of Rap1 in complex with KRIT1. Determined by X-ray diffraction at 1.95 Å resolution. Released 16 May 2012.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,185
Mol. weight: 57.14 kDa
Ligands: GSP, MG
Released: 16 May 2012

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

Secondary structure: helices and β-sheets

4DXA contains 24 α-helices and 20 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1	1
β-strand	2-10	9	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	65-74	10
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: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	421-425	5	1
β-strand	431-435	5	1
α-helix	439-441	3
α-helix	444-448	5
α-helix	457-460	4
β-strand	461-466	6	1
β-strand	471-473	3	1
α-helix	474-475	2
α-helix	480-485	6
α-helix	487-494	8
α-helix	502-504	3
β-strand	505-510	6	1
α-helix	516-519	4
α-helix	525-541	17
α-helix	548-563	16
α-helix	568-571	4
α-helix	578-581	4
α-helix	594-596	3
α-helix	598-609	12
α-helix	618-630	13
β-strand	638-645	8	3
β-strand	655-662	8	3
β-strand	666-671	6	3
β-strand	677-682	6	3
β-strand	686-690	5	3
β-strand	696-701	6	3
β-strand	707-711	5	3
α-helix	715-727	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rap-1b	A	protein	169	Homo sapiens	P61224 (AlphaFold model)
Krev interaction trapped protein 1	B	protein	322	Homo sapiens	O00522 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DXA_1 Ras-related protein Rap-1b (chains A)
GSMREYKLVVLGSVGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDT
AGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKC
DLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR

Sequence of entity 2 (B), FASTA

>4DXA_2 Krev interaction trapped protein 1 (chains B)
GSPEFEKVRIYRMDGSYRSVELKHGNNTTVQQIMEGMRLSQETQQYFTIWICSENLSLQL
KPYHKPLQHVRDWPEILAELTNLDPQRETPQLFLRRDVRLPLEVEKQIEDPLAILILFDE
ARYNLLKGFYTAPDAKLITLASLLLQIVYGNYESKKHKQGFLNEENLKSIVPVTKLKSKA
PHWTNRILHEYKNLSTSEGVSKEMHHLQRMFLQNCWEIPTYGAAFFTGQIFTKASPSNHK
VIPVYVGVNIKGLHLLNMETKALLISLKYGCFMWQLGDTDTCFQIHSMENKMSFIVHTKQ
AGLVVKLLMKLNGQLMPTERNS

Ligands and cofactors

ID	Name	Formula	Copies
GSP	5'-guanosine-diphosphate-monothiophosphate	C10 H16 N5 O13 P3 S	1
MG	Magnesium ion	Mg	1

Primary citation

Structural Basis for Small G Protein Effector Interaction of Ras-related Protein 1 (Rap1) and Adaptor Protein Krev Interaction Trapped 1 (KRIT1). Li, X., Zhang, R., Draheim, K.M. et al. J Biol Chem (2012) 287:22317-22327. DOI 10.1074/jbc.M112.361295 · PubMed

Other PDB entries of the same protein (UniProt P61224 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HDO 1.67 Å, Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase
6OQ4 1.75 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi1
6OQ3 1.85 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2
6UZK 1.92 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6
4HDQ 1.95 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and the…
8SU8 2.01 Å, Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative…
8T09 2.15 Å, Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative…
3CF6 2.2 Å, Structure of Epac2 in complex with cyclic-AMP and Rap
8T7V 2.25 Å, Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative…
7C7I 2.28 Å, Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(E30D,K31E)
7C7J 2.39 Å, Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E)
4MH0 2.4 Å, Selective activation of Epac1 and Epac2

Browse structure collections

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