2WWB: Mammalian SEC61 complex

Name: PDB 2WWB: cryo-EM structure of the mammalian SEC61 complex bound to the actively translating wheat germ 80S ribosome
Published: 2009-12-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

cryo-EM structure of the mammalian SEC61 complex bound to the actively translating wheat germ 80S ribosome. Determined by electron microscopy at 6.48 Å resolution. Released 8 Dec 2009.

Method: Electron microscopy
Resolution: 6.48 Å
Organisms: CANIS LUPUS FAMILIARIS, TRITICUM AESTIVUM
Chains: 15
Atoms: 14,313
Mol. weight: 258.76 kDa
Released: 8 Dec 2009

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

Secondary structure: helices and β-sheets

2WWB contains 57 α-helices and 36 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: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	28-47	20
α-helix	63-69	7
α-helix	83-97	15
α-helix	112-134	23
α-helix	145-170	26
α-helix	179-195	17
β-strand	208	1	1
β-strand	210	1	1
α-helix	216-222	7
α-helix	239-260	22
β-strand	263	1	2
β-strand	269	1	3
α-helix	270	1
β-strand	275	1	3
β-strand	281	1	2
α-helix	288-311	24
α-helix	318-321	4
α-helix	341-344	4
α-helix	359-379	21
α-helix	387-397	11
α-helix	411-438	28
α-helix	444-465	22

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	11-24	14
α-helix	31-39	9
α-helix	42-58	17
α-helix	59-61	3

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	73-87	15

Chain H: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	20-23	4
α-helix	24-26	3
α-helix	32-46	15
α-helix	115-127	13
α-helix	128-130	3
α-helix	134-138	5
β-strand	150	1	4
α-helix	154-157	4
α-helix	162-172	11
α-helix	176-181	6
α-helix	191-193	3
β-strand	206-209	4	4
β-strand	226-229	4	4
α-helix	235-238	4
β-strand	248-249	2	4
α-helix	254-259	6

Chain I: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	14-22	9	5
α-helix	26-35	10
α-helix	41-53	13
α-helix	86-101	16
β-strand	114-120	7	5
β-strand	125-132	8	6
β-strand	135-141	7	6
β-strand	144-151	8	5

Chain J: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	10
β-strand	23-24	2	7
α-helix	29-33	5
α-helix	38-47	10
β-strand	50-51	2	7

Chain K: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	63-66	4	8
α-helix	70-79	10
β-strand	81-86	6	8
α-helix	92-103	12
β-strand	107-113	7	8
β-strand	120-126	7	8

Chain L: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	12-20	9
β-strand	32-34	3	9
α-helix	38-43	6
β-strand	47-49	3	9
α-helix	50-51	2
β-strand	55-58	4	10
β-strand	67-69	3	10
β-strand	70-74	5	11
β-strand	79-82	4	11
β-strand	89	1	12
β-strand	93	1	12
β-strand	99	1	11
α-helix	101-103	3
β-strand	104-108	5	10
α-helix	113-119	7

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
Protein transport protein SEC61 subunit alpha isoform 1	A	protein	476	CANIS LUPUS FAMILIARIS	P38377 (AlphaFold model)
Protein transport protein SEC61 subunit gamma	B	protein	68	CANIS LUPUS FAMILIARIS	P60058 (AlphaFold model)
Protein transport protein SEC61 subunit beta	C	protein	96	CANIS LUPUS FAMILIARIS	P60467 (AlphaFold model)
5.8S rRNA	D	RNA	63	TRITICUM AESTIVUM
25S rRNA	E	RNA	34	TRITICUM AESTIVUM
25S rRNA	F	RNA	25	TRITICUM AESTIVUM
25S rRNA	G	RNA	14	TRITICUM AESTIVUM
60S ribosomal protein L4-B	H	protein	362	TRITICUM AESTIVUM	P49626 (AlphaFold model)
60S ribosomal protein L17-a	I	protein	184	TRITICUM AESTIVUM	P05740
60S ribosomal protein L19	J	protein	189	TRITICUM AESTIVUM
60S ribosomal protein L25	K	protein	142	TRITICUM AESTIVUM	P04456
60S ribosomal protein L26-a	L	protein	127	TRITICUM AESTIVUM	P05743

3 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>2WWB_1 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1 (chains A)
MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFG
MIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLP
NLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSN
LYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVH
AVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTA
AAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF

Sequence of entity 2 (B), FASTA

>2WWB_2 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA (chains B)
MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIP
INNIIVGG

Sequence of entity 3 (C), FASTA

>2WWB_3 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA (chains C)
MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYT
EDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS

Sequence of entity 4 (D), FASTA

>2WWB_4 5.8S RRNA (chains D)
AGAACGCAGCGAAAUGCGAUACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCU
UUG

Sequence of entity 5 (E), FASTA

>2WWB_5 25S RRNA (chains E)
UGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUAC

Sequence of entity 6 (F), FASTA

>2WWB_6 25S RRNA (chains F)
CCACGUCAACAGCAGUUGGACGUGG

Sequence of entity 7 (G), FASTA

>2WWB_7 25S RRNA (chains G)
ACACGUCGCGCGGU

Sequence of entity 8 (H), FASTA

>2WWB_8 60S RIBOSOMAL PROTEIN L4-B (chains H)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFAETLK
HD

Sequence of entity 9 (I), FASTA

>2WWB_9 60S RIBOSOMAL PROTEIN L17-A (chains I)
MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF
RRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN
QAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQK
RIAA

Sequence of entity 10 (J), FASTA

>2WWB_10 60S RIBOSOMAL PROTEIN L19 (chains J)
MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSK
SRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLY
HVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEK
RDALLKEDA

Sequence of entity 11 (K), FASTA

>2WWB_11 60S RIBOSOMAL PROTEIN L25 (chains K)
MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSY
KVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI

Sequence of entity 12 (L), FASTA

>2WWB_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 P38377 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Z3T 2.69 Å, Structure of canine Sec61 inhibited by mycolactone
8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8RJC 2.9 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
7TM3 3.25 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in…
8OJ8 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)
8BTK 3.5 Å, Structure of the TRAP complex with the Sec translocon and a translating ribosome
3JC2 3.6 Å, The structure of the mammalian Sec61 channel opened by a signal sequence
7TUT 3.88 Å, Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in…
6R7Q 3.9 Å, Structure of XBP1u-paused ribosome nascent chain complex with Sec61.
6FTI 4.2 Å, Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the…
6FTJ 4.7 Å, Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the…

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