2OT3: Rabex-5 VPS9 domain

Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21. Determined by X-ray diffraction at 2.1 Å resolution. Released 24 Apr 2007.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,642
Mol. weight: 51.42 kDa
Released: 24 Apr 2007

Explore 2OT3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OT3 contains 22 α-helices and 10 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: 13 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	140-147	8
α-helix	150-168	19
α-helix	175-194	20
α-helix	201-223	23
α-helix	231-244	14
α-helix	262-277	16
α-helix	278-280	3
α-helix	284-306	23
β-strand	310	1	1
α-helix	312-326	15
α-helix	331-341	11
α-helix	351-368	18
α-helix	372-374	3
α-helix	378-385	8

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18-25	8	2
α-helix	28-30	3
α-helix	32-39	8
β-strand	53	1	1
β-strand	56-63	8	2
β-strand	66-74	9	2
α-helix	79-84	6
α-helix	85-89	5
β-strand	94-100	7	2
α-helix	104-117	14
α-helix	124-125	2
β-strand	126-132	7	2
α-helix	134-139	6
α-helix	144-153	10
β-strand	157-160	4	2
β-strand	162	1	3
β-strand	167	1	3
α-helix	169-181	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rab5 GDP/GTP exchange factor	A	protein	274	Homo sapiens	Q9UJ41 (AlphaFold model)
Ras-related protein Rab-21	B	protein	170	Homo sapiens	Q9UL25 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2OT3_1 Rab5 GDP/GTP exchange factor (chains A)
GSHHHHHHSIETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQ
DFYHNVAERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIR
ALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIK
ITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAV
AFIEKLDAQSLNLSQEDFDRYMSGQTSPRKQEAE

Sequence of entity 2 (B), FASTA

>2OT3_2 Ras-related protein Rab-21 (chains B)
GSRAYSFKVVLLGEGCVGKTSLVLRYCENKFNDKHITTLQASFLTKKLNIGGKRVNLAIW
DTAGQERFHALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNK
IDLEKERHVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMIET

Primary citation

Structural basis for Rab GTPase activation by VPS9 domain exchange factors. Delprato, A., Lambright, D.G. Nat Struct Mol Biol (2007) 14:406-412. DOI 10.1038/nsmb1232 · 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
2C7N 2.1 Å, Human Rabex-5 residues 1-74 in complex with Ubiquitin
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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