6H7W: PDB entry 6H7W

Model of retromer-Vps5 complex assembled on membrane. Determined by electron microscopy at 11.4 Å resolution. Released 26 Sept 2018.

Method: Electron microscopy
Resolution: 11.4 Å
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Chains: 20
Atoms: 50,200
Mol. weight: 750.87 kDa
Released: 26 Sept 2018

Explore 6H7W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H7W contains 240 α-helices and 124 β-strands across 20 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 A, E and F: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	187-196	10	18
β-strand	198	1	19
β-strand	205-213	9	18
β-strand	222-228	7	18
α-helix	229-241	13
α-helix	253-254	2
α-helix	262-280	19
α-helix	285-287	3
α-helix	289-295	7
α-helix	301-308	8
α-helix	333-366	34
α-helix	372-386	15
α-helix	392-415	24
α-helix	416-420	5
α-helix	421-469	49
α-helix	476-548	73

Chains B, G and H: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	187-196	10	16
β-strand	198	1	17
β-strand	205-213	9	16
β-strand	222-228	7	16
α-helix	229-241	13
α-helix	253-254	2
α-helix	262-280	19
α-helix	285-287	3
α-helix	289-295	7
α-helix	301-308	8
α-helix	333-366	34
α-helix	372-386	15
α-helix	392-415	24
α-helix	416-420	5
α-helix	421-471	51
α-helix	476-548	73

Chains C and J: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	9
β-strand	23-27	5	10
α-helix	29-31	3
β-strand	33-37	5	10
β-strand	38-39	2	11
β-strand	45-53	9	9
β-strand	59-61	3	12
β-strand	64-74	11	5
β-strand	77-92	16	5
β-strand	95-97	3	12
β-strand	101-107	7	9
β-strand	117-118	2	5
β-strand	122-132	11	5
β-strand	139-145	7	5
β-strand	146-147	2	11
α-helix	152-154	3
β-strand	160-166	7	13
β-strand	170-176	7	13
β-strand	180-182	3	14
β-strand	186-196	11	13
β-strand	200-213	14	15
β-strand	220-233	14	15
β-strand	241-247	7	13
α-helix	248-250	3
α-helix	253-256	4
β-strand	257-260	4	15
β-strand	264-276	13	15
β-strand	281-288	8	15
β-strand	289-291	3	14
α-helix	292-295	4

Chains D, K, L and V: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	187-196	10	20
β-strand	199	1	19
β-strand	205-213	9	20
β-strand	222-228	7	20
α-helix	229-241	13
α-helix	253-254	2
α-helix	262-280	19
α-helix	285-287	3
α-helix	289-295	7
α-helix	301-308	8

Chains M and O: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	333-383	51
α-helix	392-415	24
α-helix	416-420	5
α-helix	421-469	49
α-helix	476-548	73

Chains N and P: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	187-196	10	27
β-strand	199	1	22
β-strand	205-213	9	27
β-strand	222-228	7	27
α-helix	229-241	13
α-helix	253-254	2
α-helix	262-280	19
α-helix	285-287	3
α-helix	289-295	7
α-helix	301-308	8
α-helix	333-366	34
α-helix	372-385	14
α-helix	392-415	24
α-helix	416-420	5
α-helix	421-471	51
α-helix	476-548	73

Chains Q and R: 47 helices, 0 β-strands

Element	Residues	Length
α-helix	13-32	20
α-helix	38-52	15
α-helix	59-83	25
α-helix	84-86	3
α-helix	92-95	4
α-helix	96-98	3
α-helix	102-119	18
α-helix	124-135	12
α-helix	141-154	14
α-helix	171-193	23
α-helix	201-223	23
α-helix	228-231	4
α-helix	232-236	5
α-helix	237-246	10
α-helix	249-262	14
α-helix	265-269	5
α-helix	272-279	8
α-helix	288-303	16
α-helix	389-403	15
α-helix	408-425	18
α-helix	430-436	7
α-helix	437-442	6
α-helix	443-447	5
α-helix	457-472	16
α-helix	477-481	5
α-helix	484-487	4
α-helix	488-491	4
α-helix	494-497	4
α-helix	498-502	5
α-helix	503-510	8
α-helix	518-532	15
α-helix	561-571	11
α-helix	577-590	14
α-helix	598-600	3
α-helix	603-617	15
α-helix	626-646	21
α-helix	653-671	19
α-helix	674-676	3
α-helix	677-690	14
α-helix	695-709	15
α-helix	717-731	15
α-helix	737-746	10
α-helix	747-750	4
α-helix	772-786	15
α-helix	791-809	19
α-helix	819-834	16
α-helix	840-856	17

Chains S and T: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	34
β-strand	13	1	35
α-helix	22-27	6
β-strand	35-38	4	34
β-strand	43	1	35
α-helix	45-54	10
β-strand	58-60	3	34
β-strand	76-80	5	36
β-strand	83-87	5	36
α-helix	98-108	11
β-strand	112-114	3	36
β-strand	124-127	4	36
β-strand	130-133	4	36
β-strand	156-163	8	34
β-strand	166-177	12	34
β-strand	181-192	12	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 26-like protein	C, J	protein	292	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0S0E6 (AlphaFold model)
Putative vacuolar protein sorting-associated protein	A, B, E, F, G, H, N, P	protein	368	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SH11 (AlphaFold model)
Putative vacuolar protein sorting-associated protein	D, K, L, V	protein	129	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SH11 (AlphaFold model)
Putative vacuolar protein sorting-associated protein	M, O	protein	220	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SH11 (AlphaFold model)
Vacuolar protein sorting-associated protein 29	S, T	protein	193	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0RZB5 (AlphaFold model)
Vacuolar protein sorting-associated protein 35	Q, R	protein	846	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0S709 (AlphaFold model)

Sequence of entity 1 (C, J), FASTA

>6H7W_1 Vacuolar protein sorting-associated protein 26-like protein (chains C, J)
FSTPVDIDIVLADADKRAMVDVKLDKNRREKVPLYMDGESVKGCVTVRPKDGKRLEHTGI
KVQFIGTIEMFFDRGNHYEFLSLVQELAAPGELQHPQTFDFNFKNVEKQYESYNGINVKL
RYFVRVTVSRRMADVIREKDIWVYSYRIPPELNSSIKMDVGIEDCLHIEFEYSKSKYHLK
DVIVGRIYFLLVRLKIKHMELSIIRRETTGVAPNQYNESETLVRFEIMDGSPSRGETIPI
RLFLGGFDLTPTFRDVNKKFSTRYYLSLVLIDEDARRYFKQSEIILYRQPPE

Sequence of entity 2 (A, B, E, F, G, H, N, P), FASTA

>6H7W_2 Putative vacuolar protein sorting-associated protein (chains A, B, E, F, G, H, N, P)
ARPTFHITVGDPHKVGDLATSHIVYSVRTKTTSKAYKQPEFEVKRRYRDFLWLYNTLHSN
NPGVVVPPPPEKQAVGRFESNFVESRRAALEKMLNKIAAHPTLQLDADLKLFLESESFNI
DVKHKERKEPPLGESKGVFGSLGFGGGGNKFVEQDDWFHDRRVYLDALENQLKALLKAMD
NMVAQRKAMAEAAADFSASLHALSTVELSPTLSGPLDALSELQLAIRDVYERQAQQDVLT
FGIIIEEYIRLIGSVKQAFSQRQKAFHSWHSAESELMKKKAAQDKLLRQGKTQQDRLNQV
NAEVIDAERKVHQARLLFEDMGRLLRSELDRFEREKVEDFKSGVETFLESAVEAQKELIE
KWETFLMQ

Sequence of entity 3 (D, K, L, V), FASTA

>6H7W_3 Putative vacuolar protein sorting-associated protein (chains D, K, L, V)
ARPTFHITVGDPHKVGDLATSHIVYSVRTKTTSKAYKQPEFEVKRRYRDFLWLYNTLHSN
NPGVVVPPPPEKQAVGRFESNFVESRRAALEKMLNKIAAHPTLQLDADLKLFLESESFNI
DVKHKERKE

Sequence of entity 4 (M, O), FASTA

>6H7W_4 Putative vacuolar protein sorting-associated protein (chains M, O)
NKFVEQDDWFHDRRVYLDALENQLKALLKAMDNMVAQRKAMAEAAADFSASLHALSTVEL
SPTLSGPLDALSELQLAIRDVYERQAQQDVLTFGIIIEEYIRLIGSVKQAFSQRQKAFHS
WHSAESELMKKKAAQDKLLRQGKTQQDRLNQVNAEVIDAERKVHQARLLFEDMGRLLRSE
LDRFEREKVEDFKSGVETFLESAVEAQKELIEKWETFLMQ

Sequence of entity 5 (S, T), FASTA

>6H7W_5 Vacuolar protein sorting-associated protein 29 (chains S, T)
AFLILVIGNLHIPDRALDIPPKFKKLLSPGKISQTLCLGNLTDRATYDYLRSISPDLKIV
RGRMDVEATSLPLMQVVTHGSLRIGFLEGFTLVSEEPDVLLAEANKLDVDVLCWAGGSHR
FECFEYMDKFFVNPGSATGAFTTDWLAEGEEVVPSFCLMDVQGISLTLYVYQLRKDENGT
ENVAVEKVTYTKP

Sequence of entity 6 (Q, R), FASTA

>6H7W_6 Vacuolar protein sorting-associated protein 35 (chains Q, R)
RLLEDALIAVRQQTAMMRKFLDTPGKLMDALKCCSTLVSELRTSSLSPKQYYELYMAVFD
ALRYLSAHLRENHPVNHLADLYELVQYAGNIIPRLYLMITVGTAYMSIDGAPVKELMKDM
MDMSRGVQHPVRGLFLRYYLSGQARDYLPTGDSDGPEGNLQDSINFILTNFVEMNKLWVR
LQHQGHSRERDLRTQERRELQLLVGSNIVRLSQLVDLPTYRDSILGPLLEQIVQCRDILA
QEYLLEVITQVFPDEYHLHTLDQFLGAVSRLNPHVNVKAIVIGMMNRLSDYAERESQNEP
EEDRAKLEEEALAKLLEKTKLGQNSELEPQNGDHPDTEVSSTTDSAQAPSTADSDTTAVN
GEEEPVRKRRGIPVNVPLYDIFFDQVQHLVQAQHLPIQDTIALCCSLANLSLNIYPERLD
YVDGILAYALAKVKEHANSADLHSQPAQQSLLSLLQSPLRRYVSIFTALSLPTYVSLFQA
QTYPTRRAIAGEIVRTLLKNQTLISTPAHLENVLEILKVLIKEGSQPPAGYPGVVQPRAR
PLETDETMEEQGWLARLVHLIHSDDNDTQFRLLQMTRKAYAEGNERIRTTTPPLITAGLK
LARRFKAREHYDDNWSSQSSSLFKFLHSAISTLYTRVNGPGVADLCLRLFCSCGQVADMT
EFEEVAYEFFAQAFTVYEESISDSKAQFQAVCVIASALHRTRNFGRENYDTLITKCAQHA
SKLLRKPDQCRAVYLASHLWWATPIAARGETEDTELYRDGKRVLECLQRALRVADSCMET
ATSIELFVEILDRYVYYFDQRNESVTTKYLNGLIELIHSNLAGNQQDSASVEASRKHFIQ
TLEMIQ

Primary citation

Structure of the membrane-assembled retromer coat determined by cryo-electron tomography. Kovtun, O., Leneva, N., Bykov, Y.S. et al. Nature (2018) 561:561-564. DOI 10.1038/s41586-018-0526-z · PubMed

Other PDB entries of the same protein (UniProt G0S0E6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BLQ 9.2 Å, Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 complex.

Browse structure collections

About this viewer

MolViewer shows 6H7W directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.