6GX7: Tubulin-CopN-alphaRep complex

Tubulin-CopN-alphaRep complex. Determined by X-ray diffraction at 3.19 Å resolution. Released 24 Apr 2019.

Method: X-ray diffraction
Resolution: 3.19 Å
Organisms: Ovis aries, synthetic construct, Chlamydia pneumoniae
Chains: 8
Atoms: 20,341
Mol. weight: 323.1 kDa
Ligands: MG, GTP
Released: 24 Apr 2019

Explore 6GX7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GX7 contains 171 α-helices and 69 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: 27 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-107	5
α-helix	111-126	16
β-strand	134-140	7	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	3
β-strand	277	1	4
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	3
α-helix	307-309	3
β-strand	312-321	10	3
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	3
α-helix	344	1
β-strand	352-356	5	3
α-helix	359-361	3
β-strand	368	1	4
α-helix	369-370	2
β-strand	373-381	9	3
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-410	6
α-helix	416-435	20

Chain B: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-27	18
β-strand	30	1	6
β-strand	35	1	7
β-strand	36	1	6
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-55	3	8
α-helix	56	1
β-strand	60	1	7
β-strand	61-63	3	8
β-strand	65-69	5	5
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-107	5
α-helix	110-127	18
β-strand	132-140	9	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	5
α-helix	183-197	15
β-strand	200-205	6	5
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	5
β-strand	269-273	5	9
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-321	10	9
α-helix	325-337	13
α-helix	340-342	3
β-strand	343	1	9
β-strand	351-356	6	9
α-helix	359-360	2
β-strand	373-381	9	9
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-410	6
α-helix	416-437	22

Chain C: 27 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	11
β-strand	61-63	3	11
β-strand	65-69	5	10
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	10
α-helix	103-107	5
α-helix	111-126	16
β-strand	134-140	7	10
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	10
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	10
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	12
β-strand	277	1	13
α-helix	285-287	3
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	12
α-helix	307-309	3
β-strand	312-321	10	12
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	12
α-helix	344	1
β-strand	352-356	5	12
α-helix	359-361	3
β-strand	368	1	13
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-435	21

Chain D: 25 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	14
α-helix	10-27	18
β-strand	30	1	15
β-strand	35	1	16
β-strand	36	1	15
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	16
β-strand	60-63	4	16
β-strand	65-69	5	14
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	14
α-helix	103-107	5
α-helix	110-127	18
β-strand	134-140	7	14
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	14
α-helix	183-197	15
β-strand	200-205	6	14
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	14
β-strand	269-273	5	17
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	17
α-helix	307-309	3
β-strand	312-321	10	17
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	17
β-strand	351-356	6	17
α-helix	359-360	2
β-strand	373-381	9	17
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-410	6
α-helix	415-437	23

Chain E: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	13-22	10
α-helix	28-41	14
α-helix	44-46	3
α-helix	47-53	7
α-helix	59-72	14
α-helix	75-77	3
α-helix	78-84	7
α-helix	90-103	14
α-helix	106-108	3
α-helix	109-115	7
α-helix	121-134	14
α-helix	137-139	3
α-helix	140-145	6
α-helix	146-148	3
α-helix	152-165	14
α-helix	168-180	13
α-helix	183-194	12

Chain F: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	13-22	10
α-helix	28-41	14
α-helix	44-46	3
α-helix	47-53	7
α-helix	59-72	14
α-helix	75-77	3
α-helix	78-84	7
α-helix	90-103	14
α-helix	106-108	3
α-helix	109-115	7
α-helix	121-134	14
α-helix	137-139	3
α-helix	140-146	7
α-helix	152-165	14
α-helix	168-180	13
α-helix	184-194	11

Chain G: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	96-101	6
α-helix	109-118	10
α-helix	125-135	11
α-helix	139-152	14
α-helix	158-175	18
α-helix	177-184	8
α-helix	186-196	11
α-helix	200-211	12
α-helix	217-225	9
α-helix	230-246	17
α-helix	257-293	37
α-helix	304-316	13
α-helix	322-333	12
α-helix	337-353	17
α-helix	356-358	3
α-helix	362-378	17

Chain H: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	96-101	6
α-helix	109-118	10
α-helix	125-135	11
α-helix	139-152	14
α-helix	158-175	18
α-helix	177-184	8
α-helix	186-196	11
α-helix	200-210	11
α-helix	217-225	9
α-helix	230-250	21
α-helix	257-293	37
α-helix	297-299	3
α-helix	304-316	13
α-helix	322-333	12
α-helix	337-353	17
α-helix	356-358	3
α-helix	362-380	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A, C	protein	451	Ovis aries	D0VWZ0 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
iiiA5 ALPHAREP	E, F	protein	201	synthetic construct
Low calcium response E	G, H	protein	336	Chlamydia pneumoniae	Q9Z8L4 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6GX7_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>6GX7_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E, F), FASTA

>6GX7_3 iiiA5 ALPHAREP (chains E, F)
MRGSHHHHHHTDPEKVEMYIKNLQDDSGLVRYFAADALGKIGDERAVEPLIKALKDEDPW
VRREAAGALGQIGDERAVEPLIKALKDEDRYVRRIAARALGKIGDERAVEPLIKALKDED
WQVREDAAKALGQIGDERAVEPLIKALKDEDTTVRLEAALALGKIGGERVRAAMEKLAET
GTGFARKVAVNYLETHKSLIS

Sequence of entity 4 (G, H), FASTA

>6GX7_4 Low calcium response E (chains G, H)
MGSSHHHHHHSSGLVPRGSHMSESTEEKPDTDLADKYASGNSEISGQELRGLRDAIGDDA
SPEDILALVQEKIKDPALQSTALDYLVQTTPPSQGKLKEALIQARNTHTEQFGRTAIGAK
NILFASQEYADQLNVSPSGLRSLYLEVTGDTHTCDQLLSMLQDRYTYQDMAIVSSFLMKG
MATELKRQGPYVPSAQLQVLMTETRNLQAVLTSYDYFESRVPILLDSLKAEGIQTPSDLN
FVKVAESYHKIINDKFPTASKVEREVRNLIGDDVDSVTGVLNLFFSALRQTSSRLFSSAD
KRQQLGAMIANALDAVNINNEDYPKASDFPKPYPWS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	4

Water and common crystallization additives (GOL, MES, SO4, PGE) are not listed.

Primary citation

Insight into microtubule nucleation from tubulin-capping proteins. Campanacci, V., Urvoas, A., Cantos-Fernandes, S. et al. Proc Natl Acad Sci U S A (2019) 116:9859-9864. DOI 10.1073/pnas.1813559116 · PubMed

Other PDB entries of the same protein (UniProt D0VWZ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EYP 1.9 Å, Tubulin-darpin complex
3RYC 2.1 Å, Tubulin: RB3 stathmin-like domain complex
9F07 2.21 Å, Tubulin:stathmin:darpin:tau MTBR3 complex
4DRX 2.22 Å, GTP-Tubulin in complex with a DARPIN
6TDE 2.29 Å, Tubulin-inhibitor complex
3RYI 2.4 Å, GDP-Tubulin: rb3 stathmin-like domain complex
5KX5 2.5 Å, Crystal structure of tubulin-stathmin-TTL-Compound 11 complex
3RYF 2.52 Å, GTP-Tubulin: RB3 Stathmin-like domain complex
4F6R 2.64 Å, Tubulin:Stathmin-like domain complex
6GVN 2.69 Å, Tubulin:TM-3 DARPin complex
3UT5 2.73 Å, Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex
6H9B 2.75 Å, 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin…

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