5K1H: PDB entry 5K1H

eIF3b relocated to the intersubunit face to interact with eIF1 and below the eIF2 ternary-complex. from the structure of a partial yeast 48S preinitiation complex in closed conformation. Determined by electron microscopy at 4.9 Å resolution. Released 13 Jul 2016.

Method: Electron microscopy
Resolution: 4.9 Å
Organisms: Homo sapiens, Oryctolagus cuniculus
Chains: 2
Atoms: 4,760
Mol. weight: 71.59 kDa
Released: 13 Jul 2016

Explore 5K1H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K1H contains 13 α-helices and 43 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-50	49

Chain B: 12 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	89-93	5	1
α-helix	95-98	4
α-helix	102-113	12
α-helix	114-116	3
β-strand	120-124	5	1
α-helix	128-130	3
α-helix	131-133	3
β-strand	135-140	6	1
α-helix	144-152	9
β-strand	156-157	2	2
β-strand	163-164	2	2
β-strand	167	1	1
α-helix	190-201	12
β-strand	207-213	7	3
β-strand	218-224	7	3
β-strand	231-236	6	3
β-strand	243-245	3	4
β-strand	252-256	5	4
β-strand	259-264	6	4
β-strand	269-274	6	4
β-strand	281-284	4	5
β-strand	290-294	5	5
β-strand	307-311	5	5
β-strand	317-321	5	5
β-strand	333-334	2	6
β-strand	340-345	6	6
β-strand	348-353	6	6
β-strand	358-359	2	6
α-helix	360-362	3
β-strand	365	1	6
β-strand	372-375	4	7
β-strand	381-386	6	7
α-helix	393-394	2
β-strand	395-400	6	7
β-strand	405-411	7	7
β-strand	415-422	8	8
β-strand	428-435	8	8
β-strand	444-451	8	8
β-strand	459-465	7	8
β-strand	468-473	6	9
α-helix	474	1
β-strand	480-484	5	9
β-strand	490-497	8	9
β-strand	503-512	10	9
β-strand	516-519	4	10
β-strand	525-529	5	10
β-strand	537-542	6	10
β-strand	547-553	7	10
β-strand	559-562	4	11
β-strand	568-572	5	11
β-strand	583-588	6	11
β-strand	592-598	7	11
β-strand	604-607	4	3
α-helix	608-609	2
α-helix	635-646	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 3 subunit B	B	protein	576	Homo sapiens	P55884 (AlphaFold model)
eIF3a C-terminal tail	A	protein	54	Oryctolagus cuniculus

Sequence of entity 1 (B), FASTA

>5K1H_1 Eukaryotic translation initiation factor 3 subunit B (chains B)
GDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT
KGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYMTISDEWDIPEKQPFKD
LGNLRYWLEEAECRDQYSVIFESGDRTSIFWNDVKDPVSIEERARWTETYVRWSPKGTYL
ATFHQRGIALWGGEKFKQIQRFSHQGVQLIDFSPCERYLVTFSPLMDTQDDPQAIIIWDI
LTGHKKRGFHCESSAHWPIFKWSHDGKFFARMTLDTLSIYETPSMGLLDKKSLKISGIKD
FSWSPGGNIIAFWVPEDKDIPARVTLMQLPSRQEIRVRNLFNVVDCKLHWQKNGDYLCVK
VDRTPKGTQGVVTNFEIFRMREKQVPVDVVEMKETIIAFAWEPNGSKFAVLHGEAPRISV
SFYHVKSNGKIELSKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIA
EHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPP
TLLSQEQIKQIKKDLKKYSKIFEQKDRLSQSKASKE

Sequence of entity 2 (A), FASTA

>5K1H_2 eIF3a C-terminal tail (chains A)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Primary citation

eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition. Simonetti, A., Brito Querido, J., Myasnikov, A.G. et al. Mol Cell (2016) 63:206-217. DOI 10.1016/j.molcel.2016.05.033 · PubMed

Other PDB entries of the same protein (UniProt P55884 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
8PJ6 2.9 Å, Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and…
6ZON 3.0 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
8PJ4 3.2 Å, Structure of human 48S translation initiation complex after eIF5 release (48S-4)
8PJ1 3.4 Å, Structure of human 48S translation initiation complex in open codon scanning state (48S-1)
8PJ2 3.4 Å, Structure of human 48S translation initiation complex in AUG recognition state after…
7A09 3.5 Å, Structure of a human ABCE1-bound 43S pre-initiation complex - State III
8OZ0 3.5 Å, Structure of a human 48S translation initiation complex with eIF4F and eIF4A
8XXN 3.6 Å, Cryo-EM structure of the human 43S ribosome with PDCD4
6ZMW 3.7 Å, Structure of a human 48S translational initiation complex
7QP7 3.7 Å, Structure of the human 48S initiation complex in closed state (h48S AUG closed)

Browse structure collections

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