8QFS: SidH from Legionella pneumophila

Cryo-EM structure of SidH from Legionella pneumophila. Determined by electron microscopy at 2.7 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Chains: 3
Atoms: 13,294
Mol. weight: 324.36 kDa
Ligands: GTP, MG
Released: 11 Oct 2023

Explore 8QFS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QFS contains 86 α-helices and 35 β-strands across 2 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: 69 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	11-16	6
α-helix	18-32	15
β-strand	39	1	8
α-helix	41-45	5
α-helix	55-59	5
α-helix	64-87	24
α-helix	105-123	19
α-helix	127-137	11
α-helix	141-152	12
α-helix	156-157	2
α-helix	170-173	4
α-helix	190-204	15
α-helix	230-243	14
α-helix	254-266	13
α-helix	280-289	10
α-helix	290-294	5
α-helix	295-309	15
β-strand	311	1	8
α-helix	312	1
α-helix	318-338	21
α-helix	389-410	22
α-helix	413-426	14
α-helix	430-435	6
α-helix	440-442	3
α-helix	445-465	21
α-helix	467-478	12
α-helix	485-488	4
α-helix	492-498	7
α-helix	502-507	6
α-helix	510-546	37
α-helix	572-606	35
α-helix	622-638	17
α-helix	642-654	13
α-helix	664-667	4
α-helix	668-670	3
α-helix	671-706	36
α-helix	708-709	2
α-helix	713-717	5
α-helix	722-726	5
α-helix	730-736	7
α-helix	737-742	6
α-helix	743-749	7
β-strand	750	1	9
α-helix	752-758	7
α-helix	767-769	3
α-helix	780-805	26
α-helix	822-843	22
α-helix	849-858	10
α-helix	860-862	3
β-strand	863	1	10
β-strand	865	1	10
α-helix	885-896	12
α-helix	910-925	16
α-helix	935-952	18
α-helix	961-977	17
α-helix	984-1012	29
α-helix	1020-1038	19
α-helix	1242-1258	17
α-helix	1277-1287	11
α-helix	1297-1311	15
α-helix	1328-1348	21
β-strand	1351	1	9
α-helix	1352	1
α-helix	1355-1368	14
α-helix	1389-1408	20
α-helix	1412-1420	9
α-helix	1425-1439	15
α-helix	1501-1507	7
α-helix	1508-1510	3
α-helix	1517-1527	11
α-helix	1533-1553	21
α-helix	1561-1564	4
α-helix	1569-1580	12
α-helix	1583-1617	35

Chain C: 17 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	1
α-helix	25-39	15
α-helix	47-50	4
α-helix	54-59	6
β-strand	66-71	6	1
β-strand	76-81	6	1
α-helix	82-83	2
α-helix	86-88	3
α-helix	89-96	8
β-strand	101-107	7	1
α-helix	114-125	12
β-strand	131-136	6	1
α-helix	144-160	17
β-strand	170-172	3	1
α-helix	175-180	6
α-helix	183-199	17
α-helix	201-203	3
β-strand	206	1	2
α-helix	210-211	2
β-strand	212-214	3	2
β-strand	217-221	5	3
β-strand	225-231	7	3
β-strand	234	1	2
β-strand	237-238	2	4
β-strand	242-246	5	2
β-strand	252-255	4	2
β-strand	256-260	5	3
β-strand	265-266	2	3
β-strand	268-269	2	4
α-helix	270	1
β-strand	274-279	6	3
α-helix	284-286	3
β-strand	289	1	5
β-strand	291	1	5
β-strand	292-294	3	2
β-strand	302-311	10	6
α-helix	312-313	2
α-helix	314-316	3
β-strand	323-324	2	7
β-strand	330-333	4	6
β-strand	336-343	8	6
α-helix	344-345	2
β-strand	350-351	2	7
β-strand	356-367	12	6
β-strand	374-379	6	6
β-strand	382-392	11	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Tu	C	protein	394	Escherichia coli 'BL21-Gold(DE3)pLysS AG'	P0CE48 (AlphaFold model)
tRNA	B	RNA	76	Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Protein SidH	A	protein	2248	Escherichia coli 'BL21-Gold(DE3)pLysS AG'	Q5ZRQ1

Sequence of entity 1 (C), FASTA

>8QFS_1 Elongation factor Tu (chains C)
MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Sequence of entity 2 (B), FASTA

>8QFS_2 tRNA (chains B)
GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGXCCUUGGUUCGAUU
CCGAGUCCGGGCACCA

Sequence of entity 3 (A), FASTA

>8QFS_3 Protein SidH (chains A)
MKHHHHHHHHHHSAGLEVLFQGPMKRTIETYIIYLKEDLKIADTCKTIKDGLLKSITDKT
HFSEELATYFERDNPNAPFKVNTTDPTQVAVLKKLLNALENAEKSFRAIENIDISRDRYT
AMIAKDAVMVSYKAVHEIYAALQLINHSNSDIQDIVGPHIQKLLPQMALASKALGNFAPE
HPEESAGAVLAGVVNMLPTEKPTESESLGKLSNLIFELPHYFEELQKLIATGASGIATKS
ITSAEDYQSAMIKKANETKYYFEQLSSKSGLLAIPSYLSIVKRLIAHSTDLVNAGAPLTK
QAYLDAVAKLEDIKHNILPQLISELEMVEESMGLKPGLLTDPALEQMNKYYTQLAEQVDN
IAKAAGVLDTVSDYSDSIGGKIVRFLAGDSKKLDVGPKLTPAPDLGVLMDDVFIQKRRSN
QESRLNEARLSSEDKSVLAAANRFFDKIGSYNSIHKAWSKWSLANISQSEKDALIKEYKQ
FQPHFAALYPDIDKLVVDALTQPTGSNIVSRLYSSDYKQLWSSDHFKQVLSCKDSVLSSI
QQSLAQSEFKAKLIEKTMSHSEETAYSMNNKTTNLTTRVQPFEPLKFTLEDDKPVEYYHK
RVIAASNQILELERAQKGVAEFFNYIQKKYPHENPSFDSLDESDKEFLRKAYKTFQPQLL
ALKHDDINTRLVSSLTSSKPTDPPLRLTDLVSLKSGINDYLNEKISDLNQDKTTLLDKEE
EAREEQYAKNPLVAKGAELEKQTLFGQMSKLKLSKSVDDFFNKKFQTYLKDNLSPEVWKQ
LSSNGETLDFDKIPYLEFHKDSPEVAMYKQLINSMHYMKNGLEKLESLNDYGDPNNIYHR
TRFVMTTFNALVMNICFSKYYVMEAGNNPGLKAIVQEGLDLLKPLEGMPLIGDYLKTTEK
QEPPKQNIITAWKKQQAVVESGLSKGPKPKTDQQLISEQLGKIQEAIDNFDGDLEVSDSA
REKIKTQIGEFAKGISGLSFGPGSVKKILAALTKLETQLSNLDKESPEVTLGKLKDIHSE
LNAQFRAAAEYTEYHSGQKFGSYSNNISTIVSNFCNGLVSNLPLKQEPAPKVKAPEKPVT
PVITGTTNPHEVVFGTKHEEFNSVYQPYLLLKRITDEFRDQNNPYKPSFDELKEEAVSYY
DKIQPLLESVDPKFDKNFIAKHKESSTLLKAIDEVMSMRQRINNPESSFAKLKDLHLEGD
FEKEENKEKFRQLYKEIQPYLHKIDSTYDQTQFLEGLKTAKDFSGALQRIMNEENALQQS
TSLKDTSYLQLIAESLYQIPVKLNKLKAEPDTPEPSKEEIDANVKAFVEGLNGLSFGPGS
VKKILSTAAKLQMQLSDIGKEGRELTMGRLKEIQAEFGTILMAAADNAEFHLGLKPGTYS
RTVSERFEKFYSSLIVNLPLEKDQTGLELLIDTTSTQKRLAREMERLESVKEDTSAIDTK
KSIFGTEHEQFSTLYQPYASLRHIAKDIEDGVHMNLYERTLEELKEEASNEYKKIQPYLA
KINPEFTEDYISKTDGEYSLLHAIDRVFEERHKINKPSSPFDKLRDLYLDGDFEKEENKE
QFLQLYAELQPHLIKINYQYDLAYFLRELQTPEDFKAATERIINDESKLQELITGLDDTK
RLKVKLCEERIGYFIDLLKKQELEVGPEKIQAFKEKIFFNYIHANVNSALDAKIGSHAEQ
FLQFIEKDFLDKKNEILEKITIDQDMEEEIAKAIDRIAPDIINNKIESFKKLLFDSYIQS
DIKNSLHNELGIYTSLFIDKISPEIHLHQSEILGNVAFDSKMGAEIGSKINAITPGILLN
NNPLKEAYVDLNNTLKEINTLLDEENKKTRDNPCRNEKIAKLTSLKDRLSDLDSIPKENT
VEFLKKMQEETRSSLKSLESNDALINIYDVLNSLKETIENGSDLPEIKKDKLQMISDVQN
ILSNFDKNPAERLNLAVQILNDSNPEVLSKTKGNFLIGEAFKGQVFTNYINTKISEQLNN
ELGPYGKVFLKQIMPDFIAKKSEIIKEIAIDNMETGLETQFKIHAPAIFEKNKELKAAYE
QLNVHLKEVQSLIEAEEKKPKGNPCREEKIAALRSHQSQLMNTQRIPDHETLRFLQEQNK
SAKSFMGKLEKYDTMISVYDSLTEIREHVSNHKSLSKEIKDEKIQEISKMEDMLKTTSKE
PSIRLAEVKAHGLSDQCKNVLLKNSDNFLVSFFKTLFSKLFNIKNENETLVSSFKQRLQN
IKGPEPVATPMETPENEAPLVNANITRF

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Primary citation

Structural basis for the toxicity of Legionella pneumophila effector SidH. Sharma, R., Adams, M., Griffith-Jones, S. et al. Nat Commun (2023) 14:7068-7068. DOI 10.1038/s41467-023-42683-8 · PubMed

Other PDB entries of the same protein (UniProt P0CE48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BVN 2.3 Å, E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa
9T38 2.45 Å, Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu
6EZE 2.47 Å, The open conformation of E.coli Elongation Factor Tu in complex with GDPNP.
1DG1 2.5 Å, Whole, unmodified, ef-tu(elongation factor tu).
1EFU 2.5 Å, Elongation factor complex ef-tu/ef-ts from escherichia coli
3MMP 2.5 Å, Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and…
1EFM 2.7 Å, Structure of the GDP domain of ef-tu and location of the amino acids homologous to ras…
5AFI 2.9 Å, 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM
5WDT 3.0 Å, 70S ribosome-EF-Tu H84A complex with GppNHp
5WFS 3.0 Å, 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)
5WE4 3.1 Å, 70S ribosome-EF-Tu wt complex with GppNHp
8G7Q 3.1 Å, Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and…

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