2J37: Model of mammalian srp

Model of mammalian srp bound to 80S rncs. Determined by electron microscopy at 8.7 Å resolution. Released 8 Nov 2006.

Method: Electron microscopy
Resolution: 8.7 Å
Organisms: TRITICUM SP., TRITICUM SP, CANIS SP.
Chains: 8
Atoms: 15,110
Mol. weight: 248 kDa
Released: 8 Nov 2006

Explore 2J37 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2J37 contains 41 α-helices and 23 β-strands across 6 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 4: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	76	1	1
α-helix	80-88	9
β-strand	91-94	4	1
α-helix	103-113	11
β-strand	117-123	7	1
β-strand	131-136	6	1
α-helix	143-147	5

Chain 5: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-13	6
α-helix	16-38	23
α-helix	46-65	20

Chain 6: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	2
α-helix	25-30	6
α-helix	33-35	3
α-helix	36-50	15
β-strand	58-59	2	2
α-helix	61-67	7
β-strand	79-86	8	2
β-strand	91-95	5	2

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	16-18	3	3
α-helix	20-23	4
β-strand	24	1	4
β-strand	41	1	4
α-helix	46-53	8
α-helix	54-56	3
β-strand	59-63	5	3
β-strand	81-85	5	3
β-strand	87	1	5
β-strand	93	1	5
α-helix	102-111	10
α-helix	112-114	3
α-helix	116-119	4

Chain S: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	51-64	14

Chain W: 24 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	25-39	15
α-helix	50-60	11
α-helix	71-87	17
β-strand	102-107	6	6
α-helix	114-127	14
β-strand	132-137	6	6
α-helix	143-155	13
β-strand	159-161	3	6
α-helix	168-181	14
β-strand	186-191	6	6
α-helix	192-193	2
α-helix	199-212	14
β-strand	216-222	7	6
α-helix	229-240	12
β-strand	245-248	4	6
α-helix	258-266	9
β-strand	270-274	5	6
β-strand	282-283	2	6
α-helix	287-292	6
α-helix	304-307	4
α-helix	326-329	4
α-helix	333-338	6
α-helix	358-360	3
α-helix	368-379	12
α-helix	384-388	5
α-helix	392-398	7
α-helix	401-409	9
α-helix	414-428	15
α-helix	439-442	4
α-helix	450-458	9
α-helix	466-475	10
α-helix	482-487	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
60S ribosomal protein L23	4	protein	152	TRITICUM SP.	O81229 (AlphaFold model)
Ribosomal protein L35	5	protein	124	TRITICUM SP.	Q8L805 (AlphaFold model)
Ribosomal protein L31	6	protein	123	TRITICUM SP	Q5XLD9 (AlphaFold model)
Srp RNA	A	RNA	128	CANIS SP.
Signal recognition particle 19 kda protein (SRP19)	B	protein	108	HOMO SAPIENS	P09132 (AlphaFold model)
Signal sequence	S	protein	17	CANIS SP.	Q1WHN3
Signal recognition particle 54 kda protein (SRP54)	W	protein	504	CANIS SP.	P61010
Ribosomal RNA	Z	RNA	280	HALOARCULA MARISMORTUI

Sequence of entity 1 (4), FASTA

>2J37_1 60S RIBOSOMAL PROTEIN L23 (chains 4)
MAPKVAVAKKGDAKAQAAKVAKAVKSGSIKKTAKKIRTSVTFHRPKTLSKARDPKYPRIS
TPGRNKLDQYQILKYPLTTESAMKKIEDNNTLVFIVDLKADKKKIKAAVKKMYDIQAKKV
NTLIRPDGKKKAYVKLTPDYDALDVANKIGII

Sequence of entity 2 (5), FASTA

>2J37_2 RIBOSOMAL PROTEIN L35 (chains 5)
MSSGKVKAGELWNKSKDDLTKQLAELKTELGQLRIQKVASSGSKLNRIHDIRKSIARVLT
VINAKQRAQLRLFYKNKKYAPLDLRAKQTRAIRRRLSPDEKSRVLEKTKKRTVHFPQRKF
AIKA

Sequence of entity 3 (6), FASTA

>2J37_3 RIBOSOMAL PROTEIN L31 (chains 6)
MSEKKRAPGPRKDEVVTREYTVNLHKRLHGCTFKKKAPNAIKEIRKFAQKAMGTNDVRID
VKLNKHIWSSGIRSVPRRVRVRIARKRNDEEDAKEELYSLVTVAEVPQEGLKGLGTKVVE
DED

Sequence of entity 4 (A), FASTA

>2J37_4 SRP RNA (chains A)
GACACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCU
AAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCA
GUAGUGUC

Sequence of entity 5 (B), FASTA

>2J37_5 SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN (SRP19) (chains B)
MRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREW
NRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ

Sequence of entity 6 (S), FASTA

>2J37_6 SIGNAL SEQUENCE (chains S)
LGFPINFLTLYVTVQHK

Sequence of entity 7 (W), FASTA

>2J37_7 SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54) (chains W)
MVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAI
DLEEMASGLNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGKTTTCSK
LAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFK
NENFEIIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEAQAKAFKDKV
DVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISKLLGMGDI
EGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFM
SKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQEL
LTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGL
QSMMRQFQQGAAGNMKGMMGFNNM

Sequence of entity 8 (Z), FASTA

>2J37_8 RIBOSOMAL RNA (chains Z)
CUGCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCACAGCGAUAGUCGGGUGAGAACCC
CGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUGAGGGUUAGCCGGUCC
UAAGUCAUACCGCAACUCGACUAUGACGAAAUGGGAAACGGGUUAAUAUUCCCGUGCCAC
GGGGUCGAUCACGCUGGGCAUCGCCCAGUCGAACCGUCCAACUCCGUGGAAGCCGUAAUG
GCAGGAAGCGGACGAACGGCGGCAUAGGGAAACGUGAUUC

Primary citation

Following the signal sequence from ribosomal tunnel exit to signal recognition particle. Halic, M., Blau, M., Becker, T. et al. Nature (2006) 444:507-511. DOI 10.1038/nature05326 · PubMed

Other PDB entries of the same protein (UniProt O81229 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2GO5 7.4 Å, Structure of signal recognition particle receptor (SR) in complex with signal…

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