2PM9: Protein transport protein SEC31

Name: PDB 2PM9: Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat
Published: 2007-07-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: protein transport

Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat. Determined by X-ray diffraction at 3.3 Å resolution. Released 3 Jul 2007.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 5,196
Mol. weight: 78.84 kDa
Released: 3 Jul 2007

Explore 2PM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PM9 contains 7 α-helices and 68 β-strands across 2 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: 2 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
β-strand	12	1	2
β-strand	15	1	3
β-strand	22-25	4	3
β-strand	26	1	2
β-strand	28	1	4
β-strand	43-46	4	3
α-helix	50-52	3
β-strand	65-70	6	4
β-strand	77-81	5	4
β-strand	86-89	4	4
β-strand	100-103	4	4
β-strand	113-116	4	5
β-strand	123	1	6
β-strand	124-127	4	5
β-strand	133-134	2	5
β-strand	135	1	7
β-strand	137	1	6
β-strand	151	1	7
β-strand	165-168	4	8
β-strand	175-179	5	8
β-strand	185-189	5	8
β-strand	194-199	6	8
α-helix	209-211	3
β-strand	212-217	6	9
β-strand	224-229	6	9
β-strand	239-241	3	9
β-strand	250	1	9
β-strand	260-265	6	10
β-strand	273-277	5	10
β-strand	281-285	5	10
β-strand	292-297	6	10
β-strand	306-308	3	1
β-strand	315-318	4	1
β-strand	324-329	6	1
β-strand	385-387	3	11
β-strand	391-393	3	11
β-strand	395	1	12
β-strand	402	1	12
β-strand	405	1	11

Chain B: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
α-helix	11	1
β-strand	12-15	4	13
β-strand	25-28	4	13
β-strand	32-39	8	13
β-strand	42-50	9	13
β-strand	56-61	6	14
α-helix	62-63	2
α-helix	64-66	3
β-strand	69-74	6	14
β-strand	79-83	5	14
α-helix	85-87	3
β-strand	90-95	6	14
β-strand	102-107	6	15
α-helix	108-109	2
β-strand	115-120	6	15
β-strand	124-129	6	15
β-strand	139-142	4	15
β-strand	148-150	3	16
β-strand	153	1	16
β-strand	172-177	6	16
β-strand	182-186	5	16
β-strand	195-196	2	16
β-strand	209-212	4	17
β-strand	220-226	7	17
β-strand	230-231	2	17
β-strand	232	1	18
β-strand	234-236	3	17
β-strand	244	1	17
β-strand	247	1	18
β-strand	259-262	4	19
β-strand	269-272	4	19
β-strand	278-281	4	19
β-strand	282	1	20
β-strand	290	1	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC31	A	protein	416	Saccharomyces cerevisiae	P38968 (AlphaFold model)
Protein transport protein SEC13	B	protein	297	Saccharomyces cerevisiae	Q04491 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2PM9_1 Protein transport protein SEC31 (chains A)
GAMGSMVKLAEFSRTATFAWSHDKIPLLVSGTVSGTVDANFSTDSSLELWSLLAADSEKP
IASLQVDSKFNDLDWSHNNKIIAGALDNGSLELYSTNEANNAINSMARFSNHSSSVKTVK
FNAKQDNVLASGGNNGEIFIWDMNKCTESPSNYTPLTPGQSMSSVDEVISLAWNQSLAHV
FASAGSSNFASIWDLKAKKEVIHLSYTSPNSGIKQQLSVVEWHPKNSTRVATATGSDNDP
SILIWDLRNANTPLQTLNQGHQKGILSLDWCHQDEHLLLSSGRDNTVLLWNPESAEQLSQ
FPARGNWCFKTKFAPEAPDLFACASFDNKIEVQTLQNLTNTLDEQETETKQQESETDFWN
NVSREESKEKPSVFHLQAPTWYGEPSPAAHWAFGGKLVQITPDGKGVSITNPKISG

Sequence of entity 2 (B), FASTA

>2PM9_2 Protein transport protein SEC13 (chains B)
MVVIANAHNEMIHDAVMDYYGKRMATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVD
WAHPKFGTILASCSYDGKVMIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPMLLVAS
SDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADN
LVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYMASVSQDRTCIIWTQDNEQ
GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Primary citation

Structure and Organization of Coat Proteins in the COPII Cage. Fath, S., Mancias, J.D., Bi, X. et al. Cell (2007) 129:1325-1336. DOI 10.1016/j.cell.2007.05.036 · PubMed

Other PDB entries of the same protein (UniProt P38968 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PM7 2.35 Å, Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat,…
2PM6 2.45 Å, Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native…
2QTV 2.5 Å, Structure of Sec23-Sar1 complexed with the active fragment of Sec31
3MZL 2.8 Å, Sec13/Sec31 edge element, loop deletion mutant
6ZG6 12.0 Å, COPII on membranes, outer coat vertex
4BZJ 40.0 Å, The structure of the COPII coat assembled on membranes
4BZK 40.0 Å, The structure of the COPII coat assembled on membranes
6ZG5 40.0 Å, COPII on membranes, outer coat right-handed rod, class1
6ZL0 40.0 Å, COPII on membranes, outer coat left-handed rod

Browse structure collections

About this viewer

MolViewer shows 2PM9 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.