6IXV: SH3BP5-Rab11a

Crystal structure of SH3BP5-Rab11a. Determined by X-ray diffraction at 3.8 Å resolution. Released 20 Mar 2019.

Method: X-ray diffraction
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,750
Mol. weight: 203.99 kDa
Ligands: PO4
Released: 20 Mar 2019

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

Secondary structure: helices and β-sheets

6IXV contains 43 α-helices and 32 β-strands across 8 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, 0 β-strands

Element	Residues	Length
α-helix	45-88	44
α-helix	95-132	38
α-helix	135-145	11
α-helix	147-151	5
α-helix	153-160	8
α-helix	162-200	39
α-helix	202-230	29
α-helix	232-260	29

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	44-88	45
α-helix	92-145	54
α-helix	147-151	5
α-helix	154-200	47
α-helix	202-207	6
α-helix	209-262	54

Chain C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	42-90	49
α-helix	95-132	38
α-helix	138-141	4
α-helix	153-156	4
α-helix	162-200	39
α-helix	202-258	57

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	43-88	46
α-helix	95-142	48
α-helix	152-157	6
α-helix	165-200	36
α-helix	202-259	58

Chain E: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	13-17	5	1
α-helix	24-27	4
β-strand	33-34	2	1
β-strand	48-55	8	1
β-strand	58-65	8	1
α-helix	77-81	5
β-strand	86-92	7	1
α-helix	96-109	14
β-strand	118-125	8	1
α-helix	136-145	10
β-strand	149-154	6	1
α-helix	159-172	14

Chain F: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	2
β-strand	13-18	6	2
β-strand	33-34	2	2
β-strand	48-55	8	2
β-strand	58-65	8	2
β-strand	86-92	7	2
α-helix	96-109	14
β-strand	118-124	7	2
α-helix	130-132	3
α-helix	136-145	10
β-strand	149-152	4	2
α-helix	159-172	14

Chain G: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	3
β-strand	13-18	6	3
β-strand	33-34	2	3
β-strand	48-55	8	3
β-strand	58-65	8	3
α-helix	76-80	5
β-strand	86-92	7	3
α-helix	97-109	13
β-strand	118-124	7	3
α-helix	136-145	10
β-strand	149-152	4	3
α-helix	159-168	10

Chain H: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	4
β-strand	13-17	5	4
α-helix	24-27	4
β-strand	33-34	2	4
β-strand	48-55	8	4
β-strand	58-65	8	4
α-helix	76-80	5
β-strand	86-92	7	4
α-helix	96-109	14
β-strand	118-124	7	4
α-helix	136-143	8
β-strand	149-152	4	4
α-helix	161-168	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SH3 domain-binding protein 5	A, B, C, D	protein	269	Homo sapiens	O60239 (AlphaFold model)
Ras-related protein Rab-11A	E, F, G, H	protein	175	Homo sapiens	P62491 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6IXV_1 SH3 domain-binding protein 5 (chains A, B, C, D)
SHSEEPAEILPPARDEEEEEEEGMEQGLEEEEEVDPRIQGELEKLNQSTDDINRRETELE
DARQKFRSVLVEATVKLDELVKKIGKAVEDSKPYWEARRVARQAQLEAQKATQDFQRATE
VLRAAKETISLAEQRLLEDDKRQFDSAWQEMLNHATQRVMEAEQTKTRSELVHKETAARY
NAAMGRMRQLEKKLKRAINKSKPYFELKAKYYVQLEQLKKTVDDLQAKLTLAKGEYKMAL
KNLEMISDEIHERRRSSAMGPRGCGVGAE

Sequence of entity 2 (E, F, G, H), FASTA

>6IXV_2 Ras-related protein Rab-11A (chains E, F, G, H)
SHMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGK
TIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIV
IMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIY

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3

Primary citation

Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Goto-Ito, S., Morooka, N., Yamagata, A. et al. Life Sci Alliance (2019) 2. DOI 10.26508/lsa.201900297 · PubMed

Other PDB entries of the same protein (UniProt O60239 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4H3B 2.08 Å, Crystal Structure of JNK3 in Complex with SAB Peptide
6DJL 3.1 Å, Crystal structure of the Rab11 GEF SH3BP5 bound to nucleotide free Rab11A
6IXE 3.35 Å, Crystal structure of SeMet apo SH3BP5 (I41)
6IXF 3.6 Å, Crystal structure of SeMet apo SH3BP5 (P41)
6IXG 3.8 Å, Crystal structure of native apo SH3BP5 (P41)

Browse structure collections

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