5M54: PDB entry 5M54

Mechanism of microtubule minus-end recognition and protection by CAMSAP proteins. Determined by electron microscopy at 8.0 Å resolution. Released 4 Oct 2017.

Method: Electron microscopy
Resolution: 8.0 Å
Organisms: Homo sapiens, Bos taurus
Chains: 5
Atoms: 14,605
Mol. weight: 210.09 kDa
Ligands: GTP, MG, GDP, TA1
Released: 4 Oct 2017

Explore 5M54 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M54 contains 96 α-helices and 76 β-strands across 5 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: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	11
α-helix	10-26	17
β-strand	53-55	3	12
β-strand	61-63	3	12
β-strand	65-69	5	11
α-helix	72-79	8
β-strand	92-94	3	11
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	132-140	9	11
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	11
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-204	5	11
α-helix	206-215	10
α-helix	224-238	15
β-strand	248	1	13
α-helix	255-258	4
β-strand	269-272	4	13
α-helix	280-282	3
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312	1	14
β-strand	315-321	7	13
α-helix	325-337	13
β-strand	343	1	14
β-strand	353-355	3	13
α-helix	359-361	3
α-helix	368-370	3
β-strand	373-379	7	13
α-helix	384-401	18
α-helix	406-409	4
α-helix	415-437	23

Chains B and E: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	15
α-helix	10-27	18
β-strand	30	1	16
β-strand	36	1	16
α-helix	42-47	4
α-helix	49-52	4
β-strand	53-56	4	17
β-strand	60-63	4	17
β-strand	65-68	4	15
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-93	2	15
α-helix	103-104	2
α-helix	105-109	5
α-helix	112-126	15
β-strand	132-140	9	15
α-helix	148-160	13
β-strand	165-172	8	15
α-helix	173-174	2
α-helix	183-197	15
β-strand	200-202	3	15
β-strand	204-205	2	15
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
α-helix	252-259	8
β-strand	262	1	18
β-strand	265	1	18
β-strand	267-268	2	15
β-strand	269-272	4	19
α-helix	280-282	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	19
β-strand	312-321	10	19
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	19
β-strand	351-356	6	19
α-helix	359-360	2
β-strand	373-381	9	19
α-helix	384-401	18
α-helix	405-411	7
α-helix	415-436	22

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	1487-1493	7
α-helix	1494-1498	5
α-helix	1505-1517	13
β-strand	1524-1527	4	1
β-strand	1534-1538	5	1
β-strand	1549-1552	4	1
β-strand	1563-1570	8	1
β-strand	1575-1579	5	1
β-strand	1590-1593	4	1

Chain D: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	2
α-helix	10-26	17
β-strand	53-55	3	3
β-strand	61-63	3	3
β-strand	65-69	5	2
α-helix	72-79	8
β-strand	92-94	3	2
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	132-140	9	2
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	2
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-204	5	2
α-helix	206-215	10
α-helix	224-238	15
β-strand	248	1	4
α-helix	255-258	4
β-strand	269-272	4	4
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312	1	5
β-strand	315-321	7	4
α-helix	325-337	13
β-strand	343	1	5
β-strand	353-355	3	4
α-helix	359-361	3
α-helix	368-370	3
β-strand	373-379	7	4
α-helix	384-401	18
α-helix	406-409	4
α-helix	415-437	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calmodulin-regulated spectrin-associated protein 1	C	protein	117	Homo sapiens	Q5T5Y3 (AlphaFold model)
Tubulin alpha chain	A, D	protein	438	Bos taurus	P81947 (AlphaFold model)
Tubulin beta-2B chain	B, E	protein	426	Bos taurus	Q6B856 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>5M54_1 Calmodulin-regulated spectrin-associated protein 1 (chains C)
KSNKPIIHNAISHCCLAGKVNEPHKNSILEELEKCDANHYIILFRDAGCQFRALYCYYPD
TEEIYKLTGTGPKNITKKMIDKLYKYSSDRKQFNLIPAKTMSVSVDALTIHNHLWQP

Sequence of entity 2 (A, D), FASTA

>5M54_2 Tubulin alpha chain (chains A, D)
RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKH
VPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDR
IRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAV
VEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITAS
LRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQ
MVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPT
VVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEA
REDMAALEKDYEEVGVDS

Sequence of entity 3 (B, E), FASTA

>5M54_3 Tubulin beta-2B chain (chains B, E)
REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVP
RAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVR
KESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVE
PYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLR
FPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMA
ACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGL
KMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSE
YQQYQD

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
TA1	Taxol	C47 H51 N O14	2

Primary citation

A structural model for microtubule minus-end recognition and protection by CAMSAP proteins. Atherton, J., Jiang, K., Stangier, M.M. et al. Nat Struct Mol Biol (2017) 24:931-943. DOI 10.1038/nsmb.3483 · PubMed

Other PDB entries of the same protein (UniProt Q5T5Y3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QUS 3.7 Å, HsCKK (human CAMSAP1) decorated 13pf taxol-GDP microtubule
6QVJ 3.8 Å, HsCKK (human CAMSAP1) decorated 14pf taxol-GDP microtubule
5M5C 4.8 Å, Mechanism of microtubule minus-end recognition and protection by CAMSAP proteins

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