4DL0: V-type proton ATPase subunit C

Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase. Determined by X-ray diffraction at 2.9 Å resolution. Released 10 Oct 2012.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 7,135
Mol. weight: 109.9 kDa
Ligands: PBM
Released: 10 Oct 2012

Explore 4DL0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DL0 contains 36 α-helices and 24 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.

Chains C and I: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	162-164	3	4
α-helix	181-183	3
β-strand	191-199	9	5
α-helix	200-202	3
α-helix	203-207	5
α-helix	210-212	3
β-strand	217	1	5
β-strand	222	1	6
β-strand	223-227	5	5
β-strand	231-239	9	5
α-helix	240-242	3
α-helix	243-252	10
β-strand	256-258	3	5
α-helix	270-272	3

Chain E: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	6
α-helix	10-111	102
α-helix	114-132	19
β-strand	136-140	5	1
α-helix	146-150	5
α-helix	153-163	11
β-strand	171-174	4	1
α-helix	178-180	3
β-strand	187-191	5	1
β-strand	197-202	6	1
α-helix	203-222	20

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	3-58	56
α-helix	59-61	3
α-helix	67-73	7
α-helix	74-76	3
α-helix	79-89	11
α-helix	91-103	13

Chain J: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	3
α-helix	10-111	102
α-helix	114-132	19
β-strand	136-141	6	4
α-helix	146-150	5
α-helix	153-163	11
β-strand	171-174	4	4
α-helix	178-180	3
β-strand	187-192	6	4
β-strand	197-202	6	4
α-helix	203-222	20

Chain K: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	3-57	55
α-helix	70-73	4
α-helix	74-76	3
α-helix	79-103	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V-type proton ATPase subunit C	C, I	protein	130	Saccharomyces cerevisiae	P31412 (AlphaFold model)
V-type proton ATPase subunit G	G, K	protein	119	Saccharomyces cerevisiae	P48836 (AlphaFold model)
V-type proton ATPase subunit E	E, J	protein	233	Saccharomyces cerevisiae	P22203 (AlphaFold model)

Sequence of entity 1 (C, I), FASTA

>4DL0_1 V-type proton ATPase subunit C (chains C, I)
GPKVPESGSMNLAAAERKKTGDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFE
KSYETLSKNVVPASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYSEELI
DQLKKEHDSA

Sequence of entity 2 (G, K), FASTA

>4DL0_2 V-type proton ATPase subunit G (chains G, K)
GPKVPMSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELK
EFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 3 (E, J), FASTA

>4DL0_3 V-type proton ATPase subunit E (chains E, J)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Ligands and cofactors

ID	Name	Formula	Copies
PBM	Trimethyl lead ion	C3 H9 Pb	2

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

Primary citation

Crystal Structure of the Yeast Vacuolar ATPase Heterotrimeric EGC(head) Peripheral Stalk Complex. Oot, R.A., Huang, L.S., Berry, E.A. et al. Structure (2012) 20:1881-1892. DOI 10.1016/j.str.2012.08.020 · PubMed

Other PDB entries of the same protein (UniProt P31412 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U7L 1.75 Å, Crystal Structure of subunit C (vma5p) of the yeast V-ATPase
4EFA 2.82 Å, Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast…
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae
7TMR 3.5 Å, V-ATPase from Saccharomyces cerevisiae, State 1
9MOY 3.6 Å, Reconstituted yeast V-ATPase bound to Rtc5p
7FDE 3.8 Å, CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
9ODU 3.9 Å, Yeast V-ATPase bound to Rtc5p, rotary state 2
7FDA 4.2 Å, CryoEM Structure of Reconstituted V-ATPase, state1
7FDB 4.8 Å, CryoEM Structures of Reconstituted V-ATPase,State2
6O7V 6.6 Å, Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1
7FDC 6.6 Å, CryoEM Structures of Reconstituted V-ATPase, state3
5VOX 6.8 Å, Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1)

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