2C7N: Human Rabex-5 residues 1-74

Human Rabex-5 residues 1-74 in complex with Ubiquitin. Determined by X-ray diffraction at 2.1 Å resolution. Released 15 Feb 2006.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: HOMO SAPIENS, BOS TAURUS
Chains: 12
Atoms: 6,437
Mol. weight: 104.56 kDa
Ligands: ZN
Released: 15 Feb 2006

Explore 2C7N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2C7N contains 40 α-helices and 60 β-strands across 12 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	26-27	2
α-helix	29-31	3
α-helix	36-70	35

Chains B, D and F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	3
β-strand	26	1	3
α-helix	27	1
α-helix	29-31	3
α-helix	36-69	34

Chain E: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	6
β-strand	26	1	6
β-strand	28	1	7
α-helix	29-31	3
β-strand	34	1	7
α-helix	36-63	28

Chain G: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	10
β-strand	26	1	10
α-helix	27	1
β-strand	28	1	11
α-helix	29-31	3
β-strand	34	1	11
α-helix	36-69	34

Chain H: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	12
β-strand	12-16	5	12
β-strand	22	1	13
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-45	5	12
β-strand	48-49	2	12
α-helix	50-51	2
β-strand	55	1	13
α-helix	57-59	3
β-strand	66-71	6	12

Chain I: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	14
β-strand	26	1	14
α-helix	27	1
β-strand	28	1	15
α-helix	29-31	3
β-strand	34	1	15
α-helix	36-73	38

Chain J: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	16
β-strand	12-16	5	16
β-strand	22	1	17
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	16
β-strand	48-49	2	16
α-helix	50-51	2
β-strand	55	1	17
α-helix	56-59	4
β-strand	66-70	5	16

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rab guanine nucleotide exchange factor 1	A, C, E, G, I, K	protein	74	HOMO SAPIENS	Q9UJ41 (AlphaFold model)
Ubiquitin	B, D, F, H, J, L	protein	76	BOS TAURUS	P0CH28 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>2C7N_1 RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 (chains A, C, E, G, I, K)
MSLKSERRGIHVDQSDLLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAER
LQREEEEAFASSQS

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>2C7N_2 UBIQUITIN (chains B, D, F, H, J, L)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Crystal Structure of the Ubiquitin Binding Domains of Rabex-5 Reveals Two Modes of Interaction with Ubiquitin. Penengo, L., Mapelli, M., Murachelli, A.G. et al. Cell (2006) 124:1183. DOI 10.1016/J.CELL.2006.02.020 · PubMed

Other PDB entries of the same protein (UniProt Q9UJ41 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4N3X 2.0 Å, Crystal structure of Rabex-5 CC domain
2OT3 2.1 Å, Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21
4N3Y 2.2 Å, Crystal structure of Rabex-5CC and Rabaptin-5C21 complex
1TXU 2.35 Å, Crystal Structure of the Vps9 Domain of Rabex-5
2C7M 2.4 Å, Human Rabex-5 residues 1-74 in complex with Ubiquitin
4N3Z 3.1 Å, Crystal structure of Rabex-5delta and Rabaptin-5C21 complex
4Q9U 4.62 Å, Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex

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