1W7P: Endosomal complex ESCRT-II

The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36). Determined by X-ray diffraction at 3.6 Å resolution. Released 29 Sept 2004.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 4
Atoms: 6,134
Mol. weight: 138.25 kDa
Released: 29 Sept 2004

Explore 1W7P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1W7P contains 44 α-helices and 28 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: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	26-49	24
α-helix	50-56	7
α-helix	58-71	14
α-helix	75-78	4
α-helix	86-105	20
β-strand	113-115	3	1
α-helix	116-118	3
α-helix	119-124	6
α-helix	125-127	3
α-helix	131-140	10
α-helix	141-144	4
β-strand	148-152	5	1
β-strand	155-159	5	1
α-helix	164-166	3
α-helix	167-175	9
β-strand	181-182	2	2
α-helix	184-190	7
α-helix	196-207	12
β-strand	212-214	3	2
β-strand	222-224	3	2
α-helix	227-230	4

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	11-14	4
α-helix	20-40	21
β-strand	45-47	3	3
β-strand	51-52	2	4
β-strand	73-74	2	4
α-helix	75-77	3
α-helix	79-81	3
α-helix	87-99	13
β-strand	103-106	4	3
α-helix	116-118	3
β-strand	120-123	4	3
α-helix	128-132	5
α-helix	135-141	7
β-strand	148-150	3	5
α-helix	151-155	5
α-helix	170-177	8
α-helix	178-180	3
β-strand	188-190	3	5
β-strand	195-198	4	5

Chain C: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	11-14	4
α-helix	20-40	21
β-strand	45-47	3	6
β-strand	51-52	2	7
β-strand	73-74	2	7
α-helix	87-99	13
β-strand	103-106	4	6
α-helix	116-118	3
β-strand	120-123	4	6
α-helix	128-142	15
β-strand	148-149	2	8
α-helix	151-155	5
α-helix	170-176	7
α-helix	178-180	3
β-strand	188-191	4	8
β-strand	194-198	5	8

Chain D: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	404-421	18
β-strand	434-436	3	9
α-helix	437-444	8
α-helix	445-449	5
α-helix	457-464	8
α-helix	467-470	4
β-strand	476-479	4	9
β-strand	485-488	4	9
α-helix	492-503	12
α-helix	511-518	8
β-strand	527	1	9
α-helix	529-541	13
β-strand	545-550	6	10
β-strand	553-558	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VPS22, YPL002C	A	protein	233	SACCHAROMYCES CEREVISIAE	Q12483 (AlphaFold model)
VPS25, YJR102C	B, C	protein	202	SACCHAROMYCES CEREVISIAE	P47142 (AlphaFold model)
VPS36P, YLR417W	D	protein	566	SACCHAROMYCES CEREVISIAE	Q06696 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1W7P_1 VPS22, YPL002C (chains A)
MKQFGLAAFDELKDGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEF
RSKFMHMCSSIGIDPLSLFDRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELE
KVHFRKLNVGLDDLEKSIDMLKSLECFEIFQIRGKKFLRSVPNELTSDQTKILEICSILG
YSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPSWITRQL

Sequence of entity 2 (B, C), FASTA

>1W7P_2 VPS25, YJR102C (chains B, C)
MSALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDNELDS
GSTDNDDSKKISKNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTR
YFILWKSLDSWASLILQWFEDSGKLNQVITLYELSEGDETVNWEFHRMPESLLYYCLKPL
CDRNRATMLKDENDKVIAIKVV

Sequence of entity 3 (D), FASTA

>1W7P_3 VPS36P, YLR417W (chains D)
MEYWHYVETTSSGQPLLREGEKDIFIDQSVGLYHGKSKILQRQRGRIFLTSQRIIYIDDA
KPTQNSLGLELDDLAYVNYSSGFLTRSPRLILFFKDPSSKDELGKSAETASADVVSTWVC
PICMVSNETQGEFTKDTLPTPICINCGVPADYELTKSSINCSNAIDPNANPQNQFGVNSE
NICPACTFANHPQIGNCEICGHRLPNASKVRSKLNRLNFHDSRVHIELEKNSLARNKSSH
SALSSSSSTGSSTEFVQLSFRKSDGVLFSQATERALENILTEKNKHIFNQNVVSVNGVDM
RKGASSHEYNNEVPFIETKLSRIGISSLEKSRENQLLNNDILFNNALTDLNKLMSLATSI
ERLYKNSNITMKTKTLNLQDESTVNEPKTRRPLLILDREKFLNKELFLDEIAREIYEFTL
SEFKDLNSDTNYMIITLVDLYAMYNKSMRIGTGLISPMEMREACERFEHLGLNELKLVKV
NKRILCVTSEKFDVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCV
DEGDLLIDKQLSGIYYYKNSYWPSHI

Primary citation

Escrt-II, an Endosome-Associated Complex Required for Protein Sorting: Crystal Structure and Interactions with Escrt-III and Membranes. Teo, H., Perisic, O., Gonzalez, B. et al. Dev Cell (2004) 7:559. DOI 10.1016/J.DEVCEL.2004.09.003 · PubMed

Other PDB entries of the same protein (UniProt Q12483 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U5T 3.6 Å, Structure of the ESCRT-II endosomal trafficking complex

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