5C4G: Ras-related protein Rab-11A

Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with the inhibitor BQR695 in complex with GDP loaded Rab11. Determined by X-ray diffraction at 3.2 Å resolution. Released 20 Jan 2016.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,800
Mol. weight: 86.39 kDa
Ligands: BQR, GDP, MG
Released: 20 Jan 2016

Explore 5C4G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C4G contains 34 α-helices and 20 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 B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	14-17	4	1
α-helix	24-31	8
β-strand	47-54	8	1
β-strand	59-66	8	1
α-helix	78-81	4
β-strand	86-92	7	1
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	1
α-helix	129-131	3
α-helix	136-145	10
β-strand	149-152	4	1
β-strand	154	1	2
β-strand	159	1	2
α-helix	161-170	10

Chain E: 27 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	129-135	7
α-helix	141-150	10
α-helix	154-163	10
α-helix	164-166	3
α-helix	169-173	5
α-helix	176-184	9
α-helix	188-202	15
α-helix	206-218	13
α-helix	234-240	7
α-helix	308-323	16
α-helix	330-341	12
α-helix	344-347	4
β-strand	361-365	5	3
α-helix	368-370	3
β-strand	372-373	2	3
β-strand	382-390	9	3
α-helix	398-401	4
α-helix	522-531	10
β-strand	541-549	9	3
α-helix	555-573	19
α-helix	582-584	3
β-strand	585-586	2	3
β-strand	593-595	3	3
α-helix	597-598	2
β-strand	601-603	3	4
α-helix	604-610	7
α-helix	615-622	8
α-helix	629-652	24
β-strand	654	1	5
β-strand	662-665	4	4
β-strand	670-672	3	4
β-strand	678	1	5
α-helix	697-702	6
α-helix	709-726	18
α-helix	729-739	11
α-helix	746-748	3
α-helix	753-759	7
α-helix	767-779	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-11A	B	protein	219	Homo sapiens	P62491 (AlphaFold model)
Phosphatidylinositol 4-kinase beta	E	protein	529	Homo sapiens	Q9UBF8 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5C4G_1 Ras-related protein Rab-11A (chains B)
GSHMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDG
KTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI
VIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS
QKQMSDRRENDMSPSNNVVPIHVPPTTENKPKVQCCQNI

Sequence of entity 2 (E), FASTA

>5C4G_2 Phosphatidylinositol 4-kinase beta (chains E)
GSHMQNNSAKQSWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYL
PQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSDMHISTQRHSRGTKL
RKLILSDELKPANLKRTAANPKVENEDEPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQ
RLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFD
TTSVPARIPENRRDPEDPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLR
QELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSL
LDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDF
GFILSSSPRNLGFETSAFKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQI
VEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSMRS

Ligands and cofactors

ID	Name	Formula	Copies
BQR	N~2~-[7-(3,4-dimethoxyphenyl)quinoxalin-2-yl]-N-methylglycinamide	C19 H20 N4 O3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIII beta with Rab11. Fowler, M.L., McPhail, J.A., Jenkins, M.L. et al. Protein Sci (2016) 25:826-839. DOI 10.1002/pro.2879 · 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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