4V4N: Preprotein translocase subunit SecE

Structure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex. Determined by electron microscopy at 9.0 Å resolution. Released 9 Jul 2014.

Method: Electron microscopy
Resolution: 9.0 Å
Organisms: Methanococcus jannaschii, Methanococcus jannaschii
Chains: 69
Atoms: 171,094
Mol. weight: 2556.27 kDa
Released: 9 Jul 2014

Explore 4V4N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V4N contains 310 α-helices and 402 β-strands across 65 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 A5: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	62
β-strand	22-26	5	62
β-strand	33-36	4	62
β-strand	46-48	3	62
β-strand	54-59	6	62
α-helix	71-78	8

Chain A7: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-24	22
α-helix	26-28	3
α-helix	30-63	34

Chain A8: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	27-28	2	5
α-helix	30-47	18

Chain Aa: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	74
β-strand	19	1	75
β-strand	22	1	75
α-helix	25-27	3
α-helix	28-43	16
β-strand	47-50	4	76
α-helix	52-59	8
β-strand	70-74	5	74
β-strand	87-90	4	76
β-strand	91	1	74

Chain AA: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	67
β-strand	27-34	8	67
β-strand	48-50	3	68
α-helix	59-61	3
β-strand	62-64	3	69
α-helix	69-76	8
α-helix	85-92	8
β-strand	106-108	3	69
β-strand	109	1	70
α-helix	111-113	3
α-helix	114-125	12
β-strand	139	1	70
α-helix	142-150	9
β-strand	153-155	3	68
β-strand	162-164	3	67
β-strand	168-169	2	67
α-helix	174-190	17
β-strand	199-206	8	67
β-strand	212-214	3	67

Chain Ab: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	49-52	4
α-helix	63-65	3
α-helix	66-68	3
β-strand	80	1	93
β-strand	83-84	2	94
β-strand	98	1	93
β-strand	101-102	2	94
α-helix	108-121	14

Chain AB: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	15-17	3
α-helix	32-34	3
β-strand	41-51	11	85
β-strand	56-63	8	85
β-strand	68-71	4	85
α-helix	72-73	2
β-strand	74	1	86
β-strand	78	1	12
β-strand	82-85	4	85
β-strand	93	1	87
β-strand	95-98	4	87
α-helix	103	1
β-strand	107-109	3	87
β-strand	129-134	6	87
β-strand	139-142	4	87
β-strand	148-151	4	87
β-strand	156-159	4	87
β-strand	162	1	86
α-helix	175-184	10
β-strand	217	1	88
α-helix	222	1
β-strand	230	1	88

Chain AC: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	42-54	13	97
β-strand	65-74	10	97
α-helix	75-77	3
β-strand	79-88	10	98
β-strand	93-100	8	98
α-helix	127-130	4
α-helix	139-155	17
β-strand	160-168	9	98
β-strand	182-186	5	98
α-helix	192-202	11
α-helix	209-212	4
β-strand	218-224	7	97
α-helix	225-227	3
β-strand	229-231	3	99
α-helix	233-236	4
β-strand	272-274	3	99
β-strand	278-292	15	97
β-strand	319-325	7	97
β-strand	335-340	6	97
β-strand	358	1	97

57 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
Preprotein translocase subunit SecE	A7	protein	67	Methanococcus jannaschii	Q57817 (AlphaFold model)
Preprotein translocase subunit SecG	A8	protein	52	Methanococcus jannaschii	P60460 (AlphaFold model)
50S ribosomal protein L39E	Af	protein	51	Methanococcus jannaschii
50S ribosomal protein L19E	AQ	protein	150	Methanococcus jannaschii
50S ribosomal protein L22P	AS	protein	150	Methanococcus jannaschii
50S ribosomal protein L23P	AT	protein	84	Methanococcus jannaschii
50S ribosomal protein L24P	AU	protein	121	Methanococcus jannaschii
50S ribosomal protein L29P	AW	protein	72	Methanococcus jannaschii
Protein translocase subunit SecY	AX	protein	436	Methanococcus jannaschii	Q60175 (AlphaFold model)
E-tRNA	B1	RNA	77	Methanococcus jannaschii
16S ribosomal RNA	B2	RNA	1495	Methanococcus jannaschii
30S ribosomal protein L7AE	AG, B3	protein	123	Methanococcus jannaschii

55 more molecules are not listed.

Sequence of entity 1 (A7), FASTA

>4V4N_1 Preprotein translocase subunit SecE (chains A7)
MKTDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPAT
YIKGILK

Sequence of entity 2 (A8), FASTA

>4V4N_2 Preprotein translocase subunit SecG (chains A8)
MSKREETGLATSAGLIRYMDETFSKIRVKPEHVIGVTVAFVIIEAILTYGRF

Sequence of entity 3 (Af), FASTA

>4V4N_3 50S ribosomal protein L39E (chains Af)
MARNKPLAKKLRLAKALKQNRRVPVWVIVKTNRRVLTHPKRRYWRRTKLKE

Sequence of entity 4 (AQ), FASTA

>4V4N_4 50S ribosomal protein L19E (chains AQ)
MNTLKMQRRIAAEILKCGENRIWIDPERIDDVASAITREDIKRLIKEGVIKKKPIKGQSR
YRAKIRHEQKKKGRHRGPGSRKGKKTARMGKKELWIKTIRALRKELRKLKAQKKIDRKTY
RMLYIRAKGGQFKNKHQLYLFLEEHGLLKK

Sequence of entity 5 (AS), FASTA

>4V4N_5 50S ribosomal protein L22P (chains AS)
GYSFQNFDPKRMARASARDLRISPKLAVEVCRELRGMMLNDALRYLDDVIALKRPVPLKR
YNDSQGHKPGKGFGPGRYPVKVAKAIKKVLLNVKNNAVQKGLDPDKLKIIHIAAHKGPVL
RGWYPRAFGRATPFNEQTTHIEVVVEEIRR

Sequence of entity 6 (AT), FASTA

>4V4N_6 50S ribosomal protein L23P (chains AT)
PYKVIIRPVVTEKAISLIEKENKLTFIVDRRATKQDIKRAVEEIFNVKVEKVNTLITPRG
EKKAYVKLKPEYSASEVAARLGLF

Sequence of entity 7 (AU), FASTA

>4V4N_7 50S ribosomal protein L24P (chains AU)
MKISSKQPRKQRKFLYNAPLHVRQKLMSAPLSRELREKYKVRNLPVRVGDKVRIMRGDYK
GHEGKVVEVDLKRYRIYVEGATLRKTNGTEVFYPIHPSNVMIIELNLEDEKRKKIIERRA
G

Sequence of entity 8 (AW), FASTA

>4V4N_8 50S ribosomal protein L29P (chains AW)
MKPSEIREMSIEEIDAKIRELRLQLAKERGLLTMGTSLENPMVIRNLRRDIARLLTIKKE
KLREREKGKVKK

Sequence of entity 9 (AX), FASTA

>4V4N_9 Protein translocase subunit SecY (chains AX)
MKKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQ
TITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCF
VEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQ
TIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRI
KGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYL
STPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFR
KSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLR
EKVSELHPAIAKLLNK

Sequence of entity 10 (B1), FASTA

>4V4N_10 E-tRNA (chains B1)
GGGGCGGUAGCUCAGCCUGGGAGAGCACCGGACUGAAGAUCCGGGUGUCGGGGGUUCAAA
UCCCCCCCGCCCCACCA

Sequence of entity 11 (B2), FASTA

>4V4N_11 16S ribosomal RNA (chains B2)
AUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCA
AGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUAC
CCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUG
GAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCCCGCCCGAGGAUGCGGCGGCGGCCGAU
UAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGG
GAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAA
ACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGC
UUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCG
CGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCG
GGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGC
GGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUC
CCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGCGCGGA
AGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGC
UAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGC
CUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGG
GUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGA
UGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAG
CUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGC
CAGUCCCUCCCGCUCGGGAGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAA
GGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAU
GGGCGGGACAAUGGGACCCGACCUCGAAAGGGGAAGGGAAUCCCCUAAACCCGCCCUCAG
UUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGUGUCA
UCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGC
GGAGUCCGGGUGAGGCCUGAUCUCCUUCGGGAGGUCAGGUCGAGCCCGGGCUCCGUGAGG
GGGGAGAAGUCGUAACAAGGUAACCGUAGGGGAACCUACGGCUCGAUCACCUCCU

Sequence of entity 12 (AG, B3), FASTA

>4V4N_12 30S ribosomal protein L7AE (chains AG, B3)
MAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPE
EIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKE
LMK

Primary citation

Structure of the SecY channel during initiation of protein translocation. Park, E., Menetret, J.F., Gumbart, J.C. et al. Nature (2013) 506:102-106. DOI 10.1038/nature12720 · PubMed

Other PDB entries of the same protein (UniProt Q57817 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RH5 3.2 Å, The structure of a protein conducting channel
1RHZ 3.5 Å, The structure of a protein conducting channel
2YXQ 3.5 Å, The plug domain of the SecY protein stablizes the closed state of the translocation…
2YXR 3.6 Å, The plug domain of the SecY protein stablizes the closed state of the translocation…
3DKN 8.7 Å, Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum
3BO0 9.6 Å, Ribosome-SecY complex
3BO1 9.6 Å, Ribosome-SecY complex

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