4N3Z: Rabex-5delta and Rabaptin-5C21 complex

Crystal structure of Rabex-5delta and Rabaptin-5C21 complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 23 Jul 2014.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,074
Mol. weight: 58.25 kDa
Ligands: PO4
Released: 23 Jul 2014

Explore 4N3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4N3Z contains 18 α-helices and 0 β-strands across 3 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	142-147	6
α-helix	151-159	9
α-helix	164-170	7
α-helix	176-188	13
α-helix	207-218	12
α-helix	236-244	9
α-helix	245-247	3
α-helix	262-277	16
α-helix	284-306	23
α-helix	309-311	3
α-helix	312-324	13
α-helix	331-340	10
α-helix	352-366	15
α-helix	392-427	36

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	554-585	32
α-helix	597-633	37

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	554-589	36
α-helix	597-633	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rab5 GDP/GTP exchange factor	A	protein	310	Homo sapiens	Q9UJ41 (AlphaFold model)
Rab GTPase-binding effector protein 1	B, C	protein	92	Homo sapiens	Q15276 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4N3Z_1 Rab5 GDP/GTP exchange factor (chains A)
MGHHHHHHSIETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQ
DFYHNVAERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIR
ALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIK
ITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAV
AFIEKLDAQSLNLSQEDFDRYMSQMYKNLDLLSQLNERQERIMNEAKKLEKDLIDWTDGI
AREVQDIVEK

Sequence of entity 2 (B, C), FASTA

>4N3Z_2 Rab GTPase-binding effector protein 1 (chains B, C)
METRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILL
EELQQGLSQAKRDVQEQMAVLMQSREQVSEEL

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3

Primary citation

Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5. Zhang, Z., Zhang, T., Wang, S. et al. Elife (2014) 3:e02687-e02687. DOI 10.7554/eLife.02687 · 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
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
4Q9U 4.62 Å, Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex

Browse structure collections

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