4RND: Subunit DF-assembly of the eukaryotic V-ATPase

Crystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase. Determined by X-ray diffraction at 3.18 Å resolution. Released 10 Dec 2014.

Method: X-ray diffraction
Resolution: 3.18 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 4
Atoms: 4,749
Mol. weight: 85.7 kDa
Released: 10 Dec 2014

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

Secondary structure: helices and β-sheets

4RND contains 27 α-helices and 18 β-strands across 4 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: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-75	47
α-helix	79-85	7
β-strand	92-101	10	1
β-strand	104-113	10	1
α-helix	118-120	3
α-helix	128-171	44
α-helix	172-177	6
α-helix	178-202	25

Chain B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	7-12	6	2
α-helix	14-23	10
β-strand	28	1	3
β-strand	35	1	3
β-strand	37-39	3	2
α-helix	47-55	9
α-helix	56-60	5
β-strand	64-70	7	2
α-helix	71-76	6
α-helix	78-83	6
β-strand	90-94	5	2
α-helix	102-103	2
α-helix	108-115	8

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-75	38
α-helix	79-85	7
β-strand	92-101	10	4
β-strand	104-113	10	4
α-helix	118-120	3
α-helix	128-175	48
α-helix	177-199	23

Chain D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	5
α-helix	14-23	10
β-strand	28	1	6
β-strand	35	1	6
β-strand	37-40	4	5
α-helix	47-55	9
α-helix	56-60	5
β-strand	64-70	7	5
α-helix	71-76	6
α-helix	78-83	6
β-strand	90-94	5	5
β-strand	96	1	7
β-strand	99	1	7
α-helix	100-102	3
α-helix	103-105	3
α-helix	107-113	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V-type proton ATPase subunit D	A, C	protein	256	Saccharomyces cerevisiae S288c	P32610 (AlphaFold model)
V-type proton ATPase subunit F	B, D	protein	118	Saccharomyces cerevisiae S288c	P39111 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4RND_1 V-type proton ATPase subunit D (chains A, C)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 2 (B, D), FASTA

>4RND_2 V-type proton ATPase subunit F (chains B, D)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Primary citation

Crystal Structure of Subunits D and F in Complex Gives Insight into Energy Transmission of the Eukaryotic V-ATPase from Saccharomyces cerevisiae. Balakrishna, A.M., Basak, S., Manimekalai, M.S. et al. J Biol Chem (2015) 290:3183-3196. DOI 10.1074/jbc.M114.622688 · PubMed

Other PDB entries of the same protein (UniProt P32610 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9COP 2.7 Å, Yeast RAVE bound to V-ATPase V1 complex
7TMO 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1
7TMP 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2
7TMQ 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 3
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
9NN1 3.7 Å, Yeast V1-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

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