5FLZ: Gamma-TuSC oligomers in a closed conformation

Cryo-EM structure of gamma-TuSC oligomers in a closed conformation. Determined by electron microscopy at 6.9 Å resolution. Released 13 Jan 2016.

Method: Electron microscopy
Resolution: 6.9 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 6
Atoms: 16,942
Mol. weight: 308.27 kDa
Released: 13 Jan 2016

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

Secondary structure: helices and β-sheets

5FLZ contains 100 α-helices and 45 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.

Chain A: 27 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	56-68	13
β-strand	76-77	2	1
β-strand	92-93	2	1
α-helix	100-126	27
α-helix	133-164	32
α-helix	171-204	34
α-helix	244-258	15
α-helix	262-289	28
β-strand	301-303	3	2
β-strand	324-326	3	2
α-helix	333-335	3
α-helix	338-359	22
α-helix	360-362	3
α-helix	373-382	10
α-helix	387-410	24
α-helix	415-425	11
α-helix	432-440	9
α-helix	443-447	5
α-helix	452-468	17
α-helix	477-481	5
β-strand	482-486	5	3
α-helix	556-559	4
β-strand	560-564	5	3
α-helix	570-572	3
α-helix	576-607	32
α-helix	609-611	3
α-helix	624-646	23
α-helix	647-653	7
α-helix	654-664	11
α-helix	669-689	21
α-helix	693-711	19
α-helix	755-783	29
α-helix	788-798	11

Chain B: 25 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	181-192	12
α-helix	215-241	27
α-helix	248-273	26
α-helix	280-286	7
α-helix	288-304	17
α-helix	311-321	11
α-helix	325-352	28
β-strand	364-366	3	4
β-strand	383-385	3	4
α-helix	396-415	20
α-helix	422-436	15
α-helix	442-462	21
α-helix	463-467	5
α-helix	470-481	12
α-helix	486-501	16
α-helix	506-522	17
α-helix	536-540	5
β-strand	541-545	5	5
α-helix	554-557	4
β-strand	558-562	5	5
α-helix	566-568	3
α-helix	578-608	31
α-helix	629-651	23
α-helix	652-658	7
α-helix	659-670	12
α-helix	722-741	20
α-helix	758-778	21
α-helix	799-832	34
α-helix	836-845	10

Chain C: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
α-helix	11-28	18
β-strand	31	1	7
β-strand	36	1	8
β-strand	37	1	7
α-helix	38	1
α-helix	39-41	3
α-helix	50-53	4
β-strand	54-56	3	9
β-strand	61	1	8
β-strand	62-64	3	9
β-strand	66-70	5	6
α-helix	72-80	9
β-strand	92-94	3	6
α-helix	105-114	10
α-helix	116-128	13
β-strand	133-141	9	6
α-helix	146-161	16
β-strand	166-173	8	6
α-helix	174	1
α-helix	183-197	15
β-strand	200-205	6	6
α-helix	206-212	7
α-helix	213-218	6
α-helix	224-238	15
α-helix	252-259	8
β-strand	267-268	2	6
β-strand	269-273	5	10
α-helix	289-295	7
α-helix	315	1
β-strand	316-324	9	10
α-helix	329-342	14
β-strand	355-360	6	10
β-strand	373-380	8	10
α-helix	381-383	3
α-helix	384-400	17
α-helix	405-409	5
α-helix	411-415	5
α-helix	418-438	21
α-helix	440-442	3

Chain D: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	11
α-helix	11-28	18
β-strand	31	1	12
β-strand	36	1	13
β-strand	37	1	12
α-helix	38	1
β-strand	54-56	3	14
β-strand	61	1	13
β-strand	62-64	3	14
β-strand	66-70	5	11
α-helix	72-80	9
α-helix	89-91	3
β-strand	92-94	3	11
α-helix	105-114	10
α-helix	116-129	14
β-strand	133-141	9	11
α-helix	146-161	16
β-strand	166-173	8	11
α-helix	183-197	15
β-strand	200-205	6	11
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-273	7	11
α-helix	289-297	9
β-strand	316-324	9	11
α-helix	329-342	14
β-strand	355-360	6	11
α-helix	361-363	3
α-helix	367-368	2
β-strand	373-380	8	11
α-helix	381-383	3
α-helix	384-400	17
α-helix	405-409	5
α-helix	411-413	3
β-strand	414	1	15
β-strand	416	1	15
α-helix	418-438	21
α-helix	440-442	3

Chains E and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-43	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spindle pole body component SPC97	A	protein	823	SACCHAROMYCES CEREVISIAE	P38863 (AlphaFold model)
Spindle pole body component SPC98	B	protein	846	SACCHAROMYCES CEREVISIAE	P53540 (AlphaFold model)
Tubulin gamma chain	C, D	protein	473	SACCHAROMYCES CEREVISIAE	P53378 (AlphaFold model)
Spindle pole body component 110	E, F	protein	44	SACCHAROMYCES CEREVISIAE

Sequence of entity 1 (A), FASTA

>5FLZ_1 SPINDLE POLE BODY COMPONENT SPC97 (chains A)
MEIKEVDDRAELLRYTNNIPLLGKLVNHQPLWSTNPKLKSFSLEKISAPDQRRVQEALVV
KDLLNVLIGLEGTYIRYFNDYEPSDPETPIEFKIAKKMDPSFKTFSRRIVRYGKQYMILT
RAYEKWSDTSFGMVLQRFAYEIRRFLEDVYLKTLVERLERDFNKVPNFSIRELEQIINET
EVNKQMELLYNIYEEIFREIEERRTNQSSQEDFNNFMDSMKNESSLHLRLMVAFDTTVYP
VPKGGAILKIFQQKILENLGDRSSVMFLKKLLNNISQDYCTMLYEWLTQGILNDPYQEFM
TYDDLEGKTDNIFDTRDRAWDTQYFIRKDVLLRDCDSEEDKNLLFKMLRTGILLKVVRAS
LQIPTIPSNSSDITIQEINDFADLMEGSNLELYVDKCYSRANEIFLKLFFQGYDLINVLK
HLQQIFLGYQSGHNVLKFLTKNMGELTKHYRNDNNANYDKLLQNFELERQSENPNNLMRQ
LLMIQFDTETLPQVLSHYLQIYPEVPENNSANDDSDPLMHANNFKNMNAILFDELSKERT
GAYHGSNLELYTPKSAIYHLKFDINIPYPLNIIISRTCMIKYQIILRYQLVLQYHSRLLD
ETWMDLNKTPSWKYRGYSHTVKRRIVRATRVLHAKMNHFIKTIMEYFNQNVIDKEVYSLE
KCYRNPTLAVAIQNELEGGLTNIMTNRCLSDLIPLQLQIFDIVYKFCKFIKSMRAKLCQL
DPVLYEKHKSGMMKTLNEGYRTNNGGQEDVGYQEDAALELIQKLIEYISNASSIFRKCLI
NFTQELSTEKFDFYDSSSVDAAGIERVLYSIVPPRSASASSQR

Sequence of entity 2 (B), FASTA

>5FLZ_2 SPINDLE POLE BODY COMPONENT SPC98 (chains B)
MELEPTLFGIIEALAPQLLSQSHLQTFVSDVVNLLRSSTKSATQLGPLIDFYKLQSLDSP
ETTIMWHKIEKFLDALFGIQNTDDMVKYLSVFQSLLPSNYRAKIVQKSSGLNMENLANHE
HLLSPVRAPSIYTEASFENMDRFSERRSMVSSPNRYVPSSTYSSVTLRQLSNPYYVNTIP
EEDILKYVSYTLLATTSALFPFDHEQIQIPSKIPNFESGLLHLIFEAGLLYQSLGYKVEK
FRMLNISPMKKALIIEISEELQNYTAFVNNLVSSGTVVSLKSLYREIYENIIRLRIYCRF
TEHLEELSGDTFLIELNIFKSHGDLTIRKIATNLFNSMISLYYEYLMNWLTKGLLRATYG
EFFIAENTDTNGTDDDFIYHIPIEFNQERVPAFIPKELAYKIFMIGKSYIFLEKYCKEVQ
WTNEFSKKYHVLYQSNSYRGISTNFFEIINDQYSEIVNHTNQILNQKFHYRDVVFALKNI
LLMGKSDFMDALIEKANDILATPSDSLPNYKLTRVLQEAVQLSSLRHLMNSPRNSSVING
LDARVLDLGHGSVGWDVFTLDYILYPPLSLVLNVNRPFGRKEYLRIFNFLWRFKKNNYFY
QKEMLKSNDIIRSFKKIRGYNPLIRDIINKLSRISILRTQFQQFNSKMESYYLNCIIEEN
FKEMTRKLQRTENKSQNQFDLIRLNNGTIELNGILTPKAEVLTKSSSSKPQKHAIEKTLN
IDELESVHNTFLTNILSHKLFATNTSEISVGDYSGQPYPTSLVLLLNSVYEFVKVYCNLN
DIGYEIFIKMNLNDHEASNGLLGKFNTNLKEIVSQYKNFKDRLYIFRADLKNDGDEELFL
LSKSLR

Sequence of entity 3 (C, D), FASTA

>5FLZ_3 TUBULIN GAMMA CHAIN (chains C, D)
MGGEIITLQAGQCGNHVGKFLWSQLAKEHAIGTDGLSQLPDSSTERDDDTKPFFRENCRN
KFTPRAIMMDSEPSVIADVENTFRGFFDPRNTWVASDGASAGNSWANGYDIGTRNQDDIL
NKIDKEIDSTDNFEGFQLLHSVAGGTGSGLGSNLLEALCDRYPKKILTTYSVFPARSSEV
VVQSYNTILALRRLIEDSDATVVFDNASLLNISGKVFRNPNIDLQHTNQLISTIISSVTN
SIRFPSYMYSSMSSIYSTLIPSPELHFLSPSFTPFTSDYIHDDIAHKCHSSYDVMLDLLD
PSNSLVSTAMNNPTYFNVYNTIIGNVEPRQISRAMTKLQQRIKFPSWSSSAMHVNIGRRS
PYLPLQPNENEVSGMMLSNMSTVVNVFENACNTFDKVFAKGAFLNNYNVGDLFQSMQNVQ
DEFAESREVVQSLMEDYVAAEQDSYLDDVLVDDENMVGELEEDLDADGDHKLV

Sequence of entity 4 (E, F), FASTA

>5FLZ_4 SPINDLE POLE BODY COMPONENT 110 (chains E, F)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Primary citation

Structure of Gamma-Tubulin Small Complex Based on a Cryo-Em Map, Chemical Cross-Links, and a Remotely Related Structure. Greenberg, C.H., Kollman, J., Zelter, A. et al. J Struct Biol (2016) 194:303. DOI 10.1016/J.JSB.2016.03.006 · PubMed

Other PDB entries of the same protein (UniProt P38863 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M2W 3.0 Å, Engineered disulfide cross-linked closed conformation of the Yeast gamma-TuRC(SS)
7M2X 3.6 Å, Open conformation of the Yeast wild-type gamma-TuRC
7M2Z 3.7 Å, Monomeric single-particle reconstruction of the Yeast gamma-TuSC
7M2Y 4.03 Å, Closed conformation of the Yeast wild-type gamma-TuRC
5FM1 8.0 Å, Structure of gamma-tubulin small complex based on a cryo-EM map, chemical cross-links,…
8QV3 8.2 Å, Structure of the y-Tubulin Small Complex (yTuSC) as part of the native y-Tubulin Ring…
8QV2 9.2 Å, Structure of the native y-Tubulin Ring Complex (yTuRC) capping microtubule minus ends at…
9A15 Integrative structure of the yeast gammaTuSC-Spc110 monomer complex
9A16 Integrative structure of the yeast gammaTuSC-Spc110 dimer complex
9A17 Integrative structure of the yeast gammaTuSC-Spc110 tetramer complex

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