2WWA: Idle yeast Ssh1 complex

Name: PDB 2WWA: Cryo-EM structure of idle yeast Ssh1 complex bound to the yeast 80S ribosome
Published: 2009-12-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of idle yeast Ssh1 complex bound to the yeast 80S ribosome. Determined by electron microscopy at 8.9 Å resolution. Released 8 Dec 2009.

Method: Electron microscopy
Resolution: 8.9 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 15
Atoms: 14,301
Mol. weight: 261.78 kDa
Released: 8 Dec 2009

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

Secondary structure: helices and β-sheets

2WWA contains 55 α-helices and 41 β-strands across 11 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: 24 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	30-42	13
α-helix	64	1
α-helix	69-72	4
α-helix	85-100	16
α-helix	110-134	25
α-helix	149-158	10
α-helix	162-170	9
α-helix	171-175	5
α-helix	180-185	6
α-helix	188-197	10
α-helix	216-225	10
α-helix	247-260	14
β-strand	268-269	2	1
β-strand	285-286	2	1
α-helix	293-301	9
α-helix	302-304	3
α-helix	315-319	5
β-strand	331	1	2
β-strand	346	1	2
β-strand	358	1	3
α-helix	365-380	16
α-helix	382-387	6
α-helix	393-405	13
α-helix	424-427	4
α-helix	429-431	3
α-helix	434-444	11
β-strand	445	1	3
α-helix	461-469	9
α-helix	470-474	5

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	23-30	8
α-helix	44-53	10
α-helix	61-78	18

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	63-77	15

Chain H: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	4
β-strand	19	1	4
α-helix	32-46	15
β-strand	78	1	5
β-strand	86	1	5
β-strand	88	1	6
β-strand	94	1	6
α-helix	115-126	12
α-helix	135-138	4
β-strand	150-152	3	7
α-helix	154-156	3
α-helix	163-172	10
α-helix	191-193	3
β-strand	206-209	4	8
β-strand	226-229	4	8
α-helix	235-238	4
β-strand	248	1	8
β-strand	249-251	3	7
α-helix	254-259	6

Chain I: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	14-18	5	9
β-strand	22	1	10
α-helix	29-34	6
α-helix	41-53	13
α-helix	86-98	13
β-strand	116-120	5	9
β-strand	127-132	6	11
β-strand	135-139	5	11
β-strand	144	1	10
β-strand	145-151	7	9

Chain J: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	22-24	3	12
α-helix	29-33	5
α-helix	40-47	8
β-strand	50-52	3	12

Chain K: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	63-65	3	13
α-helix	70-79	10
β-strand	81-86	6	13
α-helix	92-103	12
β-strand	107-113	7	13
β-strand	120-126	7	13

Chain L: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
α-helix	12-19	8
β-strand	32-34	3	14
α-helix	38-43	6
β-strand	47-49	3	14
β-strand	55-58	4	15
β-strand	69	1	15
β-strand	70-74	5	16
β-strand	79-82	4	16
β-strand	98-99	2	16
α-helix	101-103	3
β-strand	104-108	5	15
α-helix	115-120	6

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sec sixty-one protein homolog	A	protein	490	SACCHAROMYCES CEREVISIAE	P38353 (AlphaFold model)
Protein transport protein SSS1	B	protein	80	SACCHAROMYCES CEREVISIAE	P35179 (AlphaFold model)
Protein transport protein SEB2	C	protein	87	SACCHAROMYCES CEREVISIAE	P52871 (AlphaFold model)
25S rRNA	D	RNA	63	SACCHAROMYCES CEREVISIAE
25S rRNA	E	RNA	34	SACCHAROMYCES CEREVISIAE
25S rRNA	F	RNA	25	SACCHAROMYCES CEREVISIAE
25S rRNA	G	RNA	18	SACCHAROMYCES CEREVISIAE
60S ribosomal protein L4-B	H	protein	362	SACCHAROMYCES CEREVISIAE	P49626 (AlphaFold model)
60S ribosomal protein L17-a	I	protein	184	SACCHAROMYCES CEREVISIAE	P05740
60S ribosomal protein L19	J	protein	189	SACCHAROMYCES CEREVISIAE	P0CX82
60S ribosomal protein L25	K	protein	142	SACCHAROMYCES CEREVISIAE	P04456
60S ribosomal protein L26-a	L	protein	127	SACCHAROMYCES CEREVISIAE	P05743

3 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>2WWA_1 SEC SIXTY-ONE PROTEIN HOMOLOG (chains A)
MSGFRLIDIVKPILPILPEVELPFEKLPFDDKIVYTIFAGLIYLFAQFPLVGLPKATTPN
VNDPIYFLRGVFGCEPRTLLEFGLFPNISSGLILQLLAGLKVIKVNFKIQSDRELFQSLT
KVFAIVQYVILTNIFIFAGYFGDDLSVVQIGLINFQLVGAGIFTTLLAEVIDKGFGFSSG
AMIINTVVIATNLVADTFGVSQIKVGEDDQTEAQGALINLIQGLRSKHKTFIGGIISAFN
RDYLPNLTTTIIVLAIAIIVCYLQSVRVELPIRSTRARGTNNVYPIKLLYTGCLSVLFSY
TILFYIHIFAFVLIQLVAKNEPTHIICKIMGHYENANNLLAVPTFPLSLLAPPTSFFKGV
TQQPLTFITYSAFILVTGIWFADKWQAISGSSARDVALEFKDQGITLMGRREQNVAKELN
KVIPIAAVTGASVLSLITVIGESLGLKGKAAGIVVGIAGGFSLLEVITIEYQQSGGQSAL
NQVLGVPGAM

Sequence of entity 2 (B), FASTA

>2WWA_2 PROTEIN TRANSPORT PROTEIN SSS1 (chains B)
MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIA
VGIIGYAIKLIHIPIRYVIV

Sequence of entity 3 (C), FASTA

>2WWA_3 PROTEIN TRANSPORT PROTEIN SEB2 (chains C)
MAASVPPGGQRILQKRRQAQSIKEKQAKQTPTSTRQAGYGGSSSSILKLYTDEANGFRVD
SLVVLFLSVGFIFSVIALHLLTKFTHI

Sequence of entity 4 (D), FASTA

>2WWA_4 25S RRNA (chains D)
AGAACGCAGCGAAAUGCGAUACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCU
UUG

Sequence of entity 5 (E), FASTA

>2WWA_5 25S RRNA (chains E)
UGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUAC

Sequence of entity 6 (F), FASTA

>2WWA_6 25S RRNA (chains F)
CCACGUCAACAGCAGUUGGACGUGG

Sequence of entity 7 (G), FASTA

>2WWA_7 25S RRNA (chains G)
GCCAGCACCUUUGCUGGC

Sequence of entity 8 (H), FASTA

>2WWA_8 60S RIBOSOMAL PROTEIN L4-B (chains H)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFAETLK
HD

Sequence of entity 9 (I), FASTA

>2WWA_9 60S RIBOSOMAL PROTEIN L17-A (chains I)
MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF
RRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN
QAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQK
RIAA

Sequence of entity 10 (J), FASTA

>2WWA_10 60S RIBOSOMAL PROTEIN L19 (chains J)
MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSK
SRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLY
HVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEK
RDALLKEDA

Sequence of entity 11 (K), FASTA

>2WWA_11 60S RIBOSOMAL PROTEIN L25 (chains K)
MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSY
KVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI

Sequence of entity 12 (L), FASTA

>2WWA_12 60S RIBOSOMAL PROTEIN L26-A (chains L)
MAKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVR
GSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQ
RKGGKLE

Primary citation

Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome. Becker, T., Bhushan, S., Jarasch, A. et al. Science (2009) 326:1369. DOI 10.1126/SCIENCE.1178535 · PubMed

Other PDB entries of the same protein (UniProt P38353 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WW9 8.6 Å, Cryo-EM structure of the active yeast Ssh1 complex bound to the yeast 80S ribosome

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