6AMB: Afadin RA1 domain

Crystal Structure of the Afadin RA1 domain in complex with HRAS. Determined by X-ray diffraction at 2.5 Å resolution. Released 1 Nov 2017.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Mus musculus
Chains: 2
Atoms: 2,016
Mol. weight: 31.46 kDa
Ligands: MG, GNP
Released: 1 Nov 2017

Explore 6AMB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AMB contains 9 α-helices and 13 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	1
α-helix	16-25	10
β-strand	37-45	9	1
β-strand	50-58	9	1
α-helix	62-64	3
α-helix	68-74	7
β-strand	77-83	7	1
α-helix	87-104	18
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
β-strand	145	1	2
β-strand	150	1	2
α-helix	152-164	13

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	40-46	7	1
β-strand	57-63	7	1
α-helix	68-79	12
β-strand	91-97	7	1
β-strand	100-103	4	1
α-helix	104-105	2
α-helix	110-114	5
β-strand	125-130	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTPase HRas	A	protein	170	Homo sapiens	P01112 (AlphaFold model)
Afadin	B	protein	99	Mus musculus	Q9QZQ1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6AMB_1 GTPase HRas (chains A)
HMMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDT
AGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKC
DLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKL

Sequence of entity 2 (B), FASTA

>6AMB_2 Afadin (chains B)
EFHGVMRFYFQDKAAGNFATKCIRVSSTATTQDVIETLAEKFRPDMRMLSSPKYSLYEVH
VSGERRLDIDEKPLVVQLNWNKDDREGRFVLKNENDAIP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

Primary citation

Evolution of AF6-RAS association and its implications in mixed-lineage leukemia. Smith, M.J., Ottoni, E., Ishiyama, N. et al. Nat Commun (2017) 8:1099-1099. DOI 10.1038/s41467-017-01326-5 · PubMed

Other PDB entries of the same protein (UniProt P01112 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2CE2 1.0 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GDP
2EVW 1.05 Å, Crystal structure analysis of a fluorescent form of H-Ras p21 in complex with R-caged GTP
24SQ 1.08 Å, Human HRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AP6296
8TBG 1.2 Å, Tricomplex of RMC-7977, HRAS WT, and CypA
2CLD 1.22 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GDP (2)
2CL6 1.24 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with S-caged GTP
2CL7 1.25 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GTP
5WDQ 1.25 Å, H-Ras mutant L120A bound to GMP-PNP at 100K
1CTQ 1.26 Å, Structure of P21RAS in complex with gppnhp at 100 K
2CLC 1.3 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GTP (2)
3K8Y 1.3 Å, Allosteric modulation of H-Ras GTPase
3OIW 1.3 Å, H-RasG12V with allosteric switch in the "on" state

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