6DJL: Rab11 GEF SH3BP5

Crystal structure of the Rab11 GEF SH3BP5 bound to nucleotide free Rab11A. Determined by X-ray diffraction at 3.1 Å resolution. Released 26 Sept 2018.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,888
Mol. weight: 222.9 kDa
Released: 26 Sept 2018

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

Secondary structure: helices and β-sheets

6DJL contains 47 α-helices and 28 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
α-helix	20-22	3
α-helix	24-28	5
β-strand	34	1	1
β-strand	47-55	9	1
β-strand	58-66	9	1
α-helix	77-81	5
β-strand	86-91	6	1
α-helix	96-112	17
β-strand	118-123	6	1
α-helix	136-145	10
β-strand	149-152	4	1
α-helix	159-180	22

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	44-91	48
α-helix	96-98	3
α-helix	99-145	47
α-helix	147-151	5
α-helix	153-200	48
α-helix	202-260	59

Chain C: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	45-91	47
α-helix	94-97	4
α-helix	99-133	35
α-helix	138-146	9
α-helix	153-155	3
α-helix	163-200	38
α-helix	202-263	62

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	45-89	45
α-helix	99-137	39
α-helix	139-145	7
α-helix	151-158	8
α-helix	162-200	39
α-helix	202-262	61

Chain E: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	40-42	3
α-helix	44-91	48
α-helix	94-145	52
α-helix	147-151	5
α-helix	153-200	48
α-helix	202-263	62

Chain F: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	2
α-helix	24-27	4
β-strand	33-34	2	2
β-strand	48-55	8	2
β-strand	58-65	8	2
α-helix	74-80	7
β-strand	86-92	7	2
α-helix	96-112	17
β-strand	118-124	7	2
α-helix	136-145	10
β-strand	149-153	5	2
α-helix	159-180	22

Chain G: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	3
α-helix	24-28	5
β-strand	33-34	2	3
β-strand	47-55	9	3
β-strand	58-66	9	3
α-helix	71-73	3
α-helix	77-81	5
β-strand	86-91	6	3
α-helix	96-112	17
β-strand	118-123	6	3
α-helix	136-145	10
β-strand	149-152	4	3
α-helix	160-180	21

Chain H: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	4
β-strand	33-34	2	4
β-strand	46-55	10	4
β-strand	58-67	10	4
α-helix	71-73	3
α-helix	77-81	5
β-strand	86-92	7	4
α-helix	96-112	17
β-strand	118-124	7	4
α-helix	136-145	10
β-strand	149-153	5	4
α-helix	159-180	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-11A	A, F, G, H	protein	219	Homo sapiens	P62491 (AlphaFold model)
SH3 domain-binding protein 5	B, C, D, E	protein	266	Homo sapiens	O60239 (AlphaFold model)

Sequence of entity 1 (A, F, G, H), FASTA

>6DJL_1 Ras-related protein Rab-11A (chains A, F, G, H)
GSHMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDG
KTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI
VIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS
QKQMSDRRENDMSPSNNVVPIHVPPTTENKPKVQCCQNI

Sequence of entity 2 (B, C, D, E), FASTA

>6DJL_2 SH3 domain-binding protein 5 (chains B, C, D, E)
GMDAALKRSRSEEPAEILPPARDEEEEEEEGMEQGLEEEEEVDPRIQGELEKLNQSTDDI
NRRETELEDARQKFRSVLVEATVKLDELVKKIGKAVEDSKPYWEARRVARQAQLEAQKAT
QDFQRATEVLRAAKETISLAEQRLLEDDKRQFDSAWQEMLNHATQRVMEAEQTKTRSELV
HKETAARYNAAMGRMRQLEKKLKRAINKSKPYFELKAKYYVQLEQLKKTVDDLQAKLTLA
KGEYKMALKNLEMISDEIHERRRSSA

Primary citation

Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5. Jenkins, M.L., Margaria, J.P., Stariha, J.T.B. et al. Nat Commun (2018) 9:3772-3772. DOI 10.1038/s41467-018-06196-z · PubMed

Other PDB entries of the same protein (UniProt P62491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OIX 1.7 Å, X-ray structure of the small G protein Rab11a in complex with GDP and Pi
2D7C 1.75 Å, Crystal structure of human Rab11 in complex with FIP3 Rab-binding domain
2HV8 1.86 Å, Crystal structure of GTP-bound Rab11 in complex with FIP3
1OIV 1.98 Å, X-ray structure of the small G protein Rab11a in complex with GDP
1YZK 2.0 Å, GppNHp bound Rab11 GTPase
4C4P 2.0 Å, Crystal Structure of Wild-Type Rab11 Complexed to FIP2
1OIW 2.05 Å, X-ray structure of the small G protein Rab11a in complex with GTPgammaS
5JCZ 2.06 Å, Rab11 bound to MyoVa-GTD
6IY1 2.11 Å, Structure of human Ras-related protein Rab11
4LX0 2.19 Å, Crystal structure of Myo5b globular tail domain in complex with active Rab11a
5EZ5 2.4 Å, Crystal structure of active Rab11A (S20V) in complex with GTP
2GZD 2.44 Å, Crystal Structure of Rab11 in Complex with Rab11-FIP2

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