2XKV: Atomic Model of the SRP-FtsY Early Conformation

Atomic Model of the SRP-FtsY Early Conformation. Determined by electron microscopy at 13.5 Å resolution. Released 15 Dec 2010.

Method: Electron microscopy
Resolution: 13.5 Å
Organism: ESCHERICHIA COLI
Chains: 4
Atoms: 6,620
Mol. weight: 110.29 kDa
Released: 15 Dec 2010

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

Secondary structure: helices and β-sheets

2XKV contains 30 α-helices and 16 β-strands across 3 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: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	25-39	15
α-helix	45-59	15
α-helix	71-86	16
α-helix	92-95	4
β-strand	99-105	7	1
α-helix	111-114	4
α-helix	118-121	4
β-strand	129-133	5	1
α-helix	144-152	9
β-strand	156-158	3	1
α-helix	159-160	2
α-helix	165-178	14
β-strand	183-187	5	1
α-helix	196-209	14
β-strand	213-219	7	1
α-helix	226-235	10
β-strand	241-245	5	1
α-helix	257-263	7
α-helix	265-266	2
β-strand	267-271	5	1
β-strand	279-281	3	1
α-helix	287-289	3

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	24-33	10
α-helix	37-41	5
α-helix	43-45	3
α-helix	51-58	8

Chain D: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	28-39	12
α-helix	49-56	8
α-helix	64-67	4
α-helix	69-76	8
β-strand	104-109	6	2
α-helix	115-125	11
β-strand	133-136	4	2
α-helix	148-153	6
β-strand	160-161	2	2
α-helix	174-181	8
β-strand	187-190	4	2
α-helix	207-213	7
β-strand	223-228	6	2
α-helix	236-246	11
β-strand	251-254	4	2
α-helix	269-272	4
α-helix	275-276	2
β-strand	277-281	5	2
β-strand	289-291	3	2
α-helix	296-299	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle protein	A	protein	294	ESCHERICHIA COLI	O07347 (AlphaFold model)
4.5S RNA	B	RNA	114	ESCHERICHIA COLI
Signal recognition particle protein	C	protein	69	ESCHERICHIA COLI	P0AGD7 (AlphaFold model)
Cell division protein ftsy	D	protein	303	ESCHERICHIA COLI	P83749 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2XKV_1 SIGNAL RECOGNITION PARTICLE PROTEIN (chains A)
MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEAL
GKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLAL
YYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEA
RDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT
GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM

Sequence of entity 2 (B), FASTA

>2XKV_2 4.5S RNA (chains B)
GGGGGCUCUGUUGGUUCUCUGUGCUCUGUGCUCUGUUUACCAGGUCAGGUCCGAAAGGAA
GCAGCCAAGGCAGAGACGCAGAGCAGGCAGAUGUAGCUGGCAGGGCCCCCACCC

Sequence of entity 3 (C), FASTA

>2XKV_3 SIGNAL RECOGNITION PARTICLE PROTEIN (chains C)
FDLNDFLEQKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFD
DMQRMMKKM

Sequence of entity 4 (D), FASTA

>2XKV_4 CELL DIVISION PROTEIN FTSY (chains D)
GFFDRLKAGLAKTRERLLKAIPWGGNLEEVLEELEMALLAADVGLSATEEILQEVRASGR
KDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIAK
LGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAMK
ARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAK
KFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEAL
LED

Primary citation

Cryo-Em Structure of the E. Coli Translating Ribosome in Complex with Srp and its Receptor. Estrozi, L.F., Boehringer, D., Shan, S.-O. et al. Nat Struct Mol Biol (2011) 18:88. DOI 10.1038/NSMB.1952 · 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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