5LQX: F-ATPase from Pichia angusta, state3

Structure of F-ATPase from Pichia angusta, state3. Determined by electron microscopy at 7.9 Å resolution. Released 16 Nov 2016.

Method: Electron microscopy
Resolution: 7.9 Å
Organisms: Ogataea angusta, Bos taurus
Chains: 30
Atoms: 24,174
Mol. weight: 557.79 kDa
Ligands: ADP, MG, ATP
Released: 16 Nov 2016

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

Secondary structure: helices and β-sheets

5LQX contains 209 α-helices and 187 β-strands across 30 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 1: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1002-1029	28

Chain 2: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1002-1024	23

Chain 3: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1002-1015	14

Chain 4: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1002-1025	24

Chain A: 18 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
β-strand	35-37	3	1
β-strand	40-43	4	1
β-strand	50	1	2
β-strand	53-56	4	1
β-strand	62-68	7	1
β-strand	73-77	5	1
β-strand	91-96	6	1
β-strand	98-101	4	3
α-helix	103-105	3
β-strand	109-110	2	4
β-strand	116	1	4
β-strand	127-130	4	3
β-strand	141	1	5
β-strand	147	1	6
β-strand	162	1	6
β-strand	166	1	4
β-strand	168-169	2	7
β-strand	171	1	8
α-helix	178-186	9
α-helix	189-192	4
β-strand	202-208	7	4
α-helix	212-224	13
β-strand	231-236	6	4
α-helix	242-246	5
α-helix	248-260	13
β-strand	265-271	7	4
α-helix	273-285	13
α-helix	300-308	9
β-strand	314	1	5
β-strand	322-325	4	4
β-strand	330	1	8
α-helix	340-347	8
β-strand	350-352	3	7
β-strand	373-374	2	7
α-helix	383-401	19
α-helix	403-406	4
α-helix	409-411	3
α-helix	414-429	16
α-helix	440-452	13
α-helix	463-474	12
α-helix	479-487	9
α-helix	493-506	14

Chain B: 20 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	1
β-strand	40-45	6	1
α-helix	49-50	2
β-strand	53-56	4	1
β-strand	62-68	7	1
β-strand	73-77	5	1
α-helix	81-83	3
α-helix	88	1
β-strand	89-96	8	1
β-strand	98-101	4	9
β-strand	104	1	10
β-strand	109-110	2	11
β-strand	116	1	11
β-strand	124	1	10
β-strand	127-130	4	9
α-helix	134-136	3
β-strand	141	1	12
β-strand	147-148	2	13
α-helix	153-156	4
β-strand	161-162	2	13
β-strand	166	1	11
β-strand	168	1	14
β-strand	169-171	3	15
α-helix	177-186	10
α-helix	189-192	4
β-strand	201-208	8	11
α-helix	212-224	13
β-strand	231-236	6	11
α-helix	242-246	5
α-helix	248-260	13
β-strand	265-271	7	11
α-helix	273-285	13
α-helix	300-308	9
β-strand	313	1	11
β-strand	314	1	12
β-strand	322-327	6	11
β-strand	328-330	3	15
α-helix	339-345	7
β-strand	350-351	2	14
β-strand	354	1	15
β-strand	367	1	15
β-strand	373-374	2	14
α-helix	383-388	6
α-helix	392-404	13
α-helix	414-429	16
α-helix	440-451	12
α-helix	463-473	11
α-helix	479-487	9
α-helix	493-507	15

Chain C: 20 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
β-strand	31-37	7	1
β-strand	40-45	6	1
β-strand	50	1	16
β-strand	53-57	5	1
β-strand	62-68	7	1
β-strand	73-77	5	1
β-strand	89-96	8	1
β-strand	98-101	4	17
β-strand	104	1	18
β-strand	109-110	2	19
β-strand	116	1	19
β-strand	124	1	18
β-strand	127-130	4	17
α-helix	134-136	3
β-strand	141	1	20
α-helix	153-156	4
β-strand	166	1	19
β-strand	168	1	21
β-strand	169-171	3	22
α-helix	177-186	10
α-helix	189-192	4
β-strand	201-208	8	19
α-helix	212-223	12
β-strand	231-236	6	19
α-helix	242-246	5
α-helix	248-260	13
β-strand	265-271	7	19
α-helix	273-285	13
α-helix	300-309	10
β-strand	314	1	20
β-strand	322-325	4	19
β-strand	328-330	3	22
α-helix	339-345	7
β-strand	350-351	2	21
β-strand	354	1	22
α-helix	357-361	5
β-strand	367	1	22
β-strand	373-374	2	21
α-helix	383-388	6
α-helix	392-403	12
α-helix	404-407	4
α-helix	417-429	13
α-helix	440-451	12
α-helix	463-476	14
α-helix	479-487	9
α-helix	493-505	13

Chain D: 17 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
β-strand	20-24	5	1
β-strand	36-38	3	1
β-strand	40	1	23
β-strand	46	1	23
β-strand	49-54	6	1
β-strand	59-64	6	1
β-strand	72	1	16
β-strand	76-79	4	1
β-strand	85-87	3	24
α-helix	90-92	3
β-strand	93	1	25
β-strand	96-97	2	25
β-strand	103	1	25
β-strand	115-117	3	24
β-strand	128	1	26
β-strand	134-135	2	27
α-helix	147	1
β-strand	148-149	2	27
β-strand	153-155	3	25
β-strand	158	1	28
α-helix	165-172	8
β-strand	183-186	4	25
α-helix	192-203	12
β-strand	216-219	4	25
α-helix	227-231	5
α-helix	233-246	14
β-strand	252-256	5	25
β-strand	257	1	29
α-helix	261-268	8
α-helix	286-294	9
β-strand	300	1	26
β-strand	305-309	5	25
β-strand	310	1	29
β-strand	312	1	28
α-helix	327-329	3
β-strand	332-333	2	25
β-strand	336	1	30
α-helix	338-341	4
β-strand	349	1	30
β-strand	355	1	25
α-helix	366-389	24
α-helix	394-396	3
α-helix	399-414	16
α-helix	423-426	4
α-helix	429-430	2
α-helix	435-445	11
α-helix	464-474	11

21 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
ATP synthase subunit f	1	protein	31	Ogataea angusta
ATP synthase AAP1 subunit	2	protein	25	Ogataea angusta
ATP synthase subunit a	3	protein	17	Ogataea angusta
ATP synthase subunit b	4	protein	27	Ogataea angusta
ATP synthase alpha subunit	A, B, C	protein	510	Ogataea angusta	C0HK51 (AlphaFold model)
ATP synthase beta subunit	D, E, F	protein	476	Ogataea angusta	W1QA59 (AlphaFold model)
ATP synthase gamma subunit	G	protein	269	Ogataea angusta	C0HK53 (AlphaFold model)
ATP synthase delta subunit	H	protein	138	Ogataea angusta	W1QBD1 (AlphaFold model)
ATP synthase epsilon subunit	I	protein	63	Ogataea angusta	A0A1L1QK34
ATP synthase inhibitor protein IF1	J	protein	66	Bos taurus	P01096
ATP synthase subunit c	K, L, M, N, O, P, Q, R, S, T	protein	76	Ogataea angusta	C0HK59
ATP synthase OSCP subunit	U	protein	194	Ogataea angusta	C0HK56

5 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>5LQX_1 ATP synthase subunit f (chains 1)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 2 (2), FASTA

>5LQX_2 ATP synthase AAP1 subunit (chains 2)
XXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (3), FASTA

>5LQX_3 ATP synthase subunit a (chains 3)
XXXXXXXXXXXXXXXXX

Sequence of entity 4 (4), FASTA

>5LQX_4 ATP synthase subunit b (chains 4)
XXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 5 (A, B, C), FASTA

>5LQX_5 ATP synthase alpha subunit (chains A, B, C)
ATAKAAPTEVSSILESKIRGVSDEANLDETGRVLSVGDGIARVFGLNNCQAEELVEFASG
VKGMALNLEPGQVGIVLFGSDREVKEGEIVKRTGKIVDVPIGPGMLGRVVDALGNPIDGK
GPIEATGYAIAQLKAPGILPRRSVFEPMQTGLKAVDALVPIGRGQRELIIGDRQTGKTAV
ALDTILNQKRWNDGNDESKKLYCVYVAVGQKRSTVAQLVQTLEQNDAMKYSIVVAATASE
AAPLQYLAPFTACAIAEWFRDNGKHALIVYDDLSKQAVAYRQLSLLLRRPPGREAYPGDV
FYLHSRLLERAAKMSDANGGGSLTALPVIETQGGDVSAYIPTNVISITDGQIFLEAELFY
KGIRPAINVGLSVSRVGSAAQVKAMKQVAGSLKLFLAQYREVAAFAQFGSDLDASTKQTL
SRGERLTQLLKQKQYSPQASEEQVPVIYAGVNGFLDNIPIERIPEFEEQFIAYLKANEGD
ILEAIRTKGELSSELLDKLKSATETFVATF

Sequence of entity 6 (D, E, F), FASTA

>5LQX_6 ATP synthase beta subunit (chains D, E, F)
ATAGPASGKIRAVIGAVVDVQFEQGELPAILNALTIDQGNNQKLVLEVAQHLGENAVRAI
AMDGTEGLVRGQTVVDTGAPISVPVGRGTLGRIINVVGEPIDERGPIECKQRNPIHADPP
SFVEQSTEAEVLETGIKVVDLLAPYARGGKIGLFGGAGVGKTVFIQELINNIAKAHGGFS
VFTGVGERTREGNDLYREMKETGVINLEGESKVALVFGQMNEPPGARARVALTGLTIAEY
FRDEEGQDVLLFVDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGLLQERITTTRKG
SVTSVQAVYVPADDLTDPAPATTFAHLDATTVLSRGISELGIYPAVDPLDSKSRLLDVSV
VGQEHYDVATGVQQTLQAYKSLQDIIAILGMDELSEQDKLTVERARKIQRFLSQPFAVAE
VFTGIEGKLVRLKDTIASFKAVLEGKYDHLPENAFYMVGGIEDVVAKAEKIAAEAN

Sequence of entity 7 (G), FASTA

>5LQX_7 ATP synthase gamma subunit (chains G)
ATLREIETRLKSIKNIEKITNTMKVVASTRMGRAQRAMASSRAFREGDSDFFATAETSTP
ETAEKTLIIAVSSDKGLCGSIHSQIAKATRAKLQETPNADVVTIGDKIKAQMLRTHSSNV
VLSFNGVGKEAPTFWEASLIADEIRKLGDYDKIEVMYNKFVSGVAFEPSVFPSFSPISIE
ESPKLSEFELEEDQAIPTSLSQISLTNAILNAMAEGYASEISARRNAMDNASKNAGEMIN
KYSILYNRTRQAVITNELVDIITGASSLD

Sequence of entity 8 (H), FASTA

>5LQX_8 ATP synthase delta subunit (chains H)
AEAVNPDVLKVSLVAPHQAIFTNKEVSQVNLPASSGEMGVLANHVPTVEELAPGVVEVIE
SSGTASKYFVSGGFASILPGSKLSISTVEAHPLDAFSSENIKSLLAEAQKNASSADETVA
AEAAIEIEVLEALQAAVH

Sequence of entity 9 (I), FASTA

>5LQX_9 ATP synthase epsilon subunit (chains I)
SSWQKAGISFNKYLAIAARTVQRSLKNDLKVAAEKRYISDAKVQKLEKGNVVSTTDLASN
KSA

Sequence of entity 10 (J), FASTA

>5LQX_10 ATP synthase inhibitor protein IF1 (chains J)
GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEI
HHHHHH

Sequence of entity 11 (K, L, M, N, O, P, Q, R, S, T), FASTA

>5LQX_11 ATP synthase subunit c (chains K, L, M, N, O, P, Q, R, S, T)
MQLVLAAKYIGAAIATIGLTGAGIGIAIVFAALINGTSRNPSLRNTLFPFAILGFALSEA
TGLFCLMISFLLLYGV

Sequence of entity 12 (U), FASTA

>5LQX_12 ATP synthase OSCP subunit (chains U)
ASAAPIKPPVQLFGLDGTYATALFSASAKDSSIEKTFQSVQKLSSTISKDAKVAQVLSNP
ALSLNSRKEVVSVLSKELKLEPVVSNLLTVLAENNRLSLFDSIAKQFSVLNDAYNGVVEA
TVVSAKPLDSKILNRLTKSITNSKYVGPGKTLKIKNEVDPEILGGLIVEVADKSVDLSLA
SKVNKLNKVLSETI

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5
MG	Magnesium ion	Mg	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Structure of the mitochondrial ATP synthase fromPichia angustadetermined by electron cryo-microscopy. Vinothkumar, K.R., Montgomery, M.G., Liu, S. et al. Proc Natl Acad Sci U S A (2016) 113:12709-12714. DOI 10.1073/pnas.1615902113 · PubMed

Other PDB entries of the same protein (UniProt C0HK51 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5LQY 7.8 Å, Structure of F-ATPase from Pichia angusta, in state2

Browse structure collections

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