3ZN8: Signal recognition particle protein

Structural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex. Determined by electron microscopy at 12.0 Å resolution. Released 6 Mar 2013.

Method: Electron microscopy
Resolution: 12.0 Å
Organisms: ESCHERICHIA COLI, SULFOLOBUS SOLFATARICUS, SACCHAROMYCES CEREVISIAE
Chains: 5
Atoms: 7,453
Mol. weight: 109.08 kDa
Ligands: MG
Released: 6 Mar 2013

Explore 3ZN8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ZN8 contains 38 α-helices and 21 β-strands across 4 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: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	22-23	2
α-helix	24-39	16
α-helix	45-61	17
α-helix	70-86	17
β-strand	99-104	6	1
α-helix	111-125	15
β-strand	131-133	3	1
α-helix	139-152	14
β-strand	156-157	2	1
α-helix	158-160	3
α-helix	165-178	14
β-strand	183-187	5	1
α-helix	196-209	14
β-strand	214-219	6	1
α-helix	224-236	13
β-strand	241-245	5	1
β-strand	267-270	4	1
β-strand	280-281	2	1
α-helix	284-290	7

Chain D: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	212-215	4
α-helix	225-235	11
α-helix	242-255	14
α-helix	264-267	4
α-helix	268-280	13
β-strand	283	1	2
β-strand	294-299	6	3
α-helix	306-320	15
β-strand	324-325	2	3
β-strand	326-327	2	4
α-helix	334-344	11
β-strand	351-352	2	4
α-helix	363-369	7
β-strand	378-382	5	3
α-helix	390-401	12
β-strand	414-417	4	3
β-strand	418-420	3	2
α-helix	425-437	13
β-strand	443-446	4	2
α-helix	454-458	5
β-strand	468-469	2	2
β-strand	470	1	5
β-strand	471	1	2
α-helix	481	1
β-strand	482	1	5
α-helix	483	1
α-helix	485-492	8

Chain M: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	329-336	8
α-helix	337-339	3
α-helix	347-349	3
α-helix	362-364	3
α-helix	365-370	6
α-helix	377-380	4
α-helix	392-394	3
α-helix	397-400	4
α-helix	402-405	4
α-helix	411-427	17

Chain S: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	452-454	3
α-helix	456-458	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle protein	A	protein	294	ESCHERICHIA COLI	O07347 (AlphaFold model)
Signal recognition particle receptor ftsy	D	protein	295	ESCHERICHIA COLI	P10121 (AlphaFold model)
4.5 S RNA	G	RNA	88	ESCHERICHIA COLI
Signal recognition particle 54 kda protein	M	protein	125	SULFOLOBUS SOLFATARICUS	Q97ZE7 (AlphaFold model)
Dipeptidyl aminopeptidase B	S	protein	14	SACCHAROMYCES CEREVISIAE	P18962 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3ZN8_1 SIGNAL RECOGNITION PARTICLE PROTEIN (chains A)
FQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALG
KQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY
YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR
DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG
LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG

Sequence of entity 2 (D), FASTA

>3ZN8_2 SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY (chains D)
RSLLKTKENLGSGFISLFRGKKIDDDLFEELEEQLLIADVGVETTRKIITNLTEGASRKQ
LRDAEALYGLLKEEMGEILAKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLARQFEQQ
GKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAAKARNIDVLI
ADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFHEAVGL
TGITLTKLDGTAKGGVIFSVADQFGIPIRYIGVGERIEDLRPFKADDFIEALFAR

Sequence of entity 3 (G), FASTA

>3ZN8_3 4.5 S RNA (chains G)
UGGUGCAGCGCAGCGCGGACGCCCGAACCUGGUCAGAGCCGGAAGGCAGCAGCCAUAAGG
GAUGCUUUGCGGGUGCCGUUGCCUUCCG

Sequence of entity 4 (M), FASTA

>3ZN8_4 SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (chains M)
LEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGIMLPTPSEDQ
LKIGEEKIRRWLAALNSMTYKELENPNIIDKSRMRRIAEGSGLEVEEVRELLEWYNNMNR
LLKMV

Sequence of entity 5 (S), FASTA

>3ZN8_5 DIPEPTIDYL AMINOPEPTIDASE B (chains S)
GIILVLLIWGTVLL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Structural Basis of Signal Sequence Surveillance and Selection by the Srp-Sr Complex. Von Loeffelholz, O., Knoops, K., Ariosa, A. et al. Nat Struct Mol Biol (2013) 20:604. DOI 10.1038/NSMB.2546 · PubMed

Other PDB entries of the same protein (UniProt O07347 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LS1 1.1 Å, T. aquaticus Ffh NG Domain at 1.1A Resolution
2J45 1.14 Å, Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution
2J46 1.14 Å, Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution
2C04 1.15 Å, GMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution
2C03 1.24 Å, GDP complex of srp gtpase ffh ng domain
1JPN 1.9 Å, GMPPNP Complex of SRP GTPase NG Domain
1RJ9 1.9 Å, Structure of the heterodimer of the conserved GTPase domains of the Signal Recognition…
2J7P 1.97 Å, GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY
2NG1 2.02 Å, N and gtpase domains of the signal sequence recognition protein ffh from thermus aquaticus
1NG1 2.03 Å, N and gtpase domains of the signal sequence recognition protein ffh from thermus aquaticus
1FFH 2.05 Å, N and gtpase domains of the signal sequence recognition protein ffh from thermus aquaticus
1OKK 2.05 Å, Homo-heterodimeric complex of the srp gtpases

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