4HLQ: Human rab1b

Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens. Determined by X-ray diffraction at 3.3 Å resolution. Released 16 Jan 2013.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 10
Atoms: 17,765
Mol. weight: 276.73 kDa
Ligands: MG, GDP, BEF
Released: 16 Jan 2013

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

Secondary structure: helices and β-sheets

4HLQ contains 133 α-helices and 33 β-strands across 10 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: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	26-41	16
α-helix	47-55	9
α-helix	63-74	12
α-helix	81-84	4
α-helix	89-92	4
α-helix	96-104	9
α-helix	107-109	3
α-helix	116-136	21
α-helix	146-156	11
α-helix	159-170	12
α-helix	183-190	8
α-helix	192-199	8
α-helix	201-210	10
α-helix	218-223	6
α-helix	232-244	13
α-helix	249-260	12
α-helix	262-266	5
α-helix	272-280	9
α-helix	288-301	14

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	1
α-helix	21-29	9
β-strand	43-52	10	1
β-strand	55-64	10	1
α-helix	68-70	3
α-helix	71-74	4
α-helix	75-77	3
β-strand	83-89	7	1
α-helix	93-109	17
β-strand	115-121	7	1
α-helix	133-143	11
β-strand	147-150	4	1
β-strand	151	1	2
β-strand	157	1	2
α-helix	158-173	16

Chain C: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	26-40	15
α-helix	48-55	8
α-helix	63-73	11
α-helix	81-84	4
α-helix	89-92	4
α-helix	96-104	9
α-helix	116-135	20
α-helix	146-171	26
α-helix	175-178	4
α-helix	183-199	17
α-helix	201-209	9
α-helix	215-217	3
α-helix	218-223	6
α-helix	232-243	12
α-helix	249-260	12
α-helix	262-266	5
α-helix	272-278	7
α-helix	288-301	14

Chain D: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	3
α-helix	21-29	9
α-helix	37-40	4
β-strand	44-52	9	3
β-strand	55-63	9	3
α-helix	68-70	3
α-helix	71-74	4
α-helix	75-77	3
β-strand	83-89	7	3
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	3
α-helix	133-143	11
β-strand	147-150	4	3
α-helix	158-171	14

Chain E: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	28-40	13
α-helix	47-55	9
α-helix	63-73	11
α-helix	81-84	4
α-helix	96-105	10
α-helix	116-136	21
α-helix	146-157	12
α-helix	159-171	13
α-helix	175-178	4
α-helix	183-190	8
α-helix	192-199	8
α-helix	201-210	10
α-helix	215-217	3
α-helix	218-223	6
α-helix	232-244	13
α-helix	249-260	12
α-helix	262-266	5
α-helix	274-280	7
α-helix	288-301	14

Chain F: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	4
α-helix	21-30	10
α-helix	37-40	4
β-strand	44-52	9	4
β-strand	55-63	9	4
α-helix	68-70	3
α-helix	71-74	4
α-helix	75-78	4
β-strand	83-89	7	4
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	4
α-helix	133-142	10
β-strand	147-150	4	4
α-helix	158-173	16

Chain G: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	27-39	13
α-helix	47-56	10
α-helix	63-73	11
α-helix	81-84	4
α-helix	89-92	4
α-helix	96-104	9
α-helix	116-136	21
α-helix	146-157	12
α-helix	159-172	14
α-helix	183-189	7
α-helix	192-199	8
α-helix	201-210	10
α-helix	215-217	3
α-helix	218-221	4
α-helix	232-244	13
α-helix	249-260	12
α-helix	262-265	4
α-helix	272-280	9
α-helix	288-301	14

Chain H: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	5
β-strand	10-15	6	5
α-helix	23-26	4
β-strand	46-52	7	5
β-strand	55-62	8	5
α-helix	68-70	3
β-strand	83-89	7	5
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	5
α-helix	133-141	9
β-strand	147-149	3	5
α-helix	158-170	13

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TBC1 domain family member 20	A, C, E, G, I	protein	305	Homo sapiens	Q96BZ9 (AlphaFold model)
Ras-related protein Rab-1B	B, D, F, H, J	protein	175	Homo sapiens	Q9H0U4 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I), FASTA

>4HLQ_1 TBC1 domain family member 20 (chains A, C, E, G, I)
MALRSAQGDGPTSGHWDGGAEKADFNAKRKKKVAEIHQALNSDPTDVAALRRMAISEGGL
LTDEIRRKVWPKLLNVNANDPPPISGKNLRQMSKDYQQVLLDVRRSLRRFPPGMPEEQRE
GLQEELIDIILLILERNPQLHYYQGYHDIVVTFLLVVGERLATSLVEKLSTHHLRDFMDP
TMDNTKHILNYLMPIIDQVNPELHDFMQSAEVGTIFALSWLITWFGHVLSDFRHVVRLYD
FFLACHPLMPIYFAAVIVLYREQEVLDCDCDMASVHHLLSQIPQDLPYETLISRAGDLFV
QFPPS

Sequence of entity 2 (B, D, F, H, J), FASTA

>4HLQ_2 Ras-related protein Rab-1B (chains B, D, F, H, J)
GHMPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKL
QIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLV
GNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMG

Ligands and cofactors

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

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

Primary citation

Catalytic mechanism of a mammalian Rab-RabGAP complex in atomic detail. Gavriljuk, K., Gazdag, E.M., Itzen, A. et al. Proc Natl Acad Sci U S A (2012) 109:21348-21353. DOI 10.1073/pnas.1214431110 · PubMed

Other PDB entries of the same protein (UniProt Q96BZ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HL4 2.2 Å, Crystal structure of the human TBC1D20 RabGAP domain

Browse structure collections

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