5JCZ: Rab11

Rab11 bound to MyoVa-GTD. Determined by X-ray diffraction at 2.06 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 6
Atoms: 13,842
Mol. weight: 199.09 kDa
Ligands: MG, GDP, BEF
Released: 28 Sept 2016

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

Secondary structure: helices and β-sheets

5JCZ contains 96 α-helices and 26 β-strands across 6 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.

Chains A and D: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
α-helix	24-33	10
α-helix	40-44	5
β-strand	46-55	10	1
β-strand	58-67	10	1
α-helix	74-81	8
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
α-helix	161-176	16

Chain B: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	1475-1476	2	2
α-helix	1479-1481	3
α-helix	1482-1486	5
α-helix	1487-1491	5
α-helix	1506-1520	15
α-helix	1524-1544	21
α-helix	1549-1568	20
α-helix	1573-1575	3
α-helix	1581-1584	4
α-helix	1594-1624	31
α-helix	1625-1629	5
α-helix	1659-1675	17
α-helix	1680-1702	23
α-helix	1706-1708	3
α-helix	1711-1730	20
α-helix	1740-1742	3
α-helix	1743-1753	11
α-helix	1759-1768	10
α-helix	1774-1783	10
α-helix	1792-1795	4
α-helix	1796-1805	10
α-helix	1823-1828	6
α-helix	1836-1838	3
α-helix	1843-1845	3
β-strand	1851-1852	2	2

Chain C: 25 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1475-1476	2	3
α-helix	1479-1481	3
α-helix	1482-1486	5
α-helix	1487-1491	5
α-helix	1499-1501	3
α-helix	1506-1520	15
α-helix	1524-1544	21
α-helix	1549-1568	20
α-helix	1573-1575	3
α-helix	1581-1584	4
β-strand	1591	1	4
α-helix	1594-1623	30
α-helix	1624-1629	6
α-helix	1659-1675	17
α-helix	1680-1702	23
α-helix	1706-1708	3
α-helix	1711-1730	20
α-helix	1738-1741	4
α-helix	1743-1753	11
α-helix	1759-1768	10
α-helix	1774-1783	10
α-helix	1791-1795	5
α-helix	1796-1805	10
α-helix	1806-1808	3
α-helix	1823-1825	3
α-helix	1836-1838	3
α-helix	1843-1845	3
β-strand	1851-1852	2	3

Chain E: 25 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1475-1476	2	6
α-helix	1479-1481	3
α-helix	1482-1486	5
α-helix	1487-1491	5
α-helix	1498-1502	5
α-helix	1506-1520	15
α-helix	1524-1544	21
α-helix	1549-1568	20
α-helix	1573-1575	3
α-helix	1581-1584	4
α-helix	1594-1624	31
α-helix	1625-1629	5
α-helix	1659-1675	17
α-helix	1680-1704	25
α-helix	1711-1730	20
α-helix	1740-1742	3
α-helix	1743-1753	11
α-helix	1759-1768	10
α-helix	1774-1783	10
α-helix	1793-1795	3
α-helix	1796-1805	10
α-helix	1806-1808	3
β-strand	1811	1	4
α-helix	1823-1825	3
α-helix	1836-1838	3
α-helix	1843-1845	3
α-helix	1850	1
β-strand	1851-1852	2	6

Chain I: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	7
α-helix	24-33	10
α-helix	42-44	3
β-strand	46-49	4	7
β-strand	62-67	6	7
α-helix	76-81	6
β-strand	87-92	6	7
α-helix	96-100	5
α-helix	102-112	11
β-strand	119-124	6	7
α-helix	139-145	7
β-strand	149-152	4	7
α-helix	161-173	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-11A	A, D, I	protein	179	Homo sapiens	P62491 (AlphaFold model)
Unconventional myosin-Va	B, C, E	protein	397	Homo sapiens	Q9Y4I1 (AlphaFold model)

Sequence of entity 1 (A, D, I), FASTA

>5JCZ_1 Ras-related protein Rab-11A (chains A, D, I)
GAMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGK
TIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIV
IMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS

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

>5JCZ_2 Unconventional myosin-Va (chains B, C, E)
GAMGSVNIPRKEKDFQGMLEYKKEDEQKLVKNLILELKPRGVAVNLIPGLPAYILFMCVR
HADYLNDDQKVRSLLTSTINSIKKVLKKRGDDFETVSFWLSNTCRFLHCLKQYSGEEGFM
KHNTSRQNEHCLTNFDLAEYRQVLSDLAIQIYQQLVRVLENILQPMIVSGMLEHETIQGV
SGVKPTGLRKRTSSIADEGTYTLDSILRQLNSFHSVMCQHGMDPELIKQVVKQMFYIIGA
ITLNNLLLRKDMCSWSKGMQIRYNVSQLEEWLRDKNLMNSGAKETLEPLIQAAQLLQVKK
KTDDDAEAICSMCNALTTAQIVKVLNLYTPVNEFEERVSVSFIRTIQMRLRDRKDSPQLL
MDAKHIFPVTFPFNPSSLALETIQIPASLGLGFISRV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	3
BEF	Beryllium trifluoride ion	Be F3	3

Water and common crystallization additives (EDO, ACT, GOL) are not listed.

Primary citation

Coordinated recruitment of Spir actin nucleators and myosin V motors to Rab11 vesicle membranes. Pylypenko, O., Welz, T., Tittel, J. et al. Elife (2016) 5. DOI 10.7554/eLife.17523 · 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
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
2GZH 2.47 Å, Crystal Structure of Rab11 in Complex with Rab11-Family Interacting Protein 2

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