6YBV: PDB entry 6YBV

Name: PDB 6YBV: Structure of a human 48S translational initiation complex - eIF2-TC
Published: 2020-09-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Structure of a human 48S translational initiation complex - eIF2-TC. Determined by electron microscopy at 3.8 Å resolution. Released 16 Sept 2020.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,731
Mol. weight: 150.97 kDa
Released: 16 Sept 2020

Explore 6YBV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YBV contains 31 α-helices and 46 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 r: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	4
α-helix	14-15	2
β-strand	19-24	6	5
β-strand	31-36	6	5
β-strand	39	1	4
β-strand	42-47	6	5
α-helix	59-62	4
β-strand	68-75	8	5
β-strand	84-86	3	5
α-helix	92-118	27
α-helix	124-130	7
α-helix	131-136	6
α-helix	137-141	5
α-helix	147-156	10
α-helix	162-165	4
α-helix	170-180	11
β-strand	191-195	5	6
β-strand	196-197	2	7
α-helix	204-217	14
β-strand	226-229	4	6
β-strand	235-239	5	6
α-helix	244-261	18
β-strand	269-270	2	7
β-strand	276	1	6

Chain s: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	177-185	9
α-helix	189	1
β-strand	218-219	2	1
α-helix	222-228	7
α-helix	235-242	8
α-helix	243-245	3
β-strand	248-249	2	1
β-strand	256-258	3	1
α-helix	264-274	11
α-helix	275-279	5
β-strand	281	1	2
β-strand	284	1	2
β-strand	291-293	3	3
β-strand	298-300	3	3

Chain t: 13 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	44-47	4	8
α-helix	54-62	9
α-helix	70-75	6
α-helix	81-82	2
β-strand	84-86	3	8
β-strand	130-134	5	8
α-helix	142-151	10
β-strand	154-159	6	8
α-helix	169-180	12
β-strand	186-189	4	8
α-helix	197-211	15
α-helix	215-218	4
β-strand	221-223	3	8
β-strand	225	1	9
β-strand	230	1	9
α-helix	232-242	11
α-helix	244-246	3
α-helix	253-254	2
β-strand	255-257	3	10
β-strand	279-281	3	11
β-strand	283-285	3	10
β-strand	293-296	4	10
α-helix	312-313	2
β-strand	314-317	4	10
β-strand	321-323	3	11
β-strand	326	1	11
β-strand	337-339	3	11
α-helix	340	1
α-helix	345-348	4
β-strand	357-360	4	10
β-strand	367-368	2	12
β-strand	372-377	6	13
β-strand	403-408	6	13
β-strand	411-413	3	13
β-strand	415-420	6	13
β-strand	424-429	6	13
β-strand	433-434	2	12
β-strand	440-447	8	13
β-strand	450-459	10	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 2 subunit 2	s	protein	333	Homo sapiens	P20042 (AlphaFold model)
Eukaryotic translation initiation factor 2 subunit 1	r	protein	315	Homo sapiens	P05198 (AlphaFold model)
Initiator methionine tRNA	w	RNA	75	Homo sapiens
mRNA	k	RNA	3	Homo sapiens
Eukaryotic translation initiation factor 2 subunit 3	t	protein	472	Homo sapiens	P41091 (AlphaFold model)

Sequence of entity 1 (s), FASTA

>6YBV_1 Eukaryotic translation initiation factor 2 subunit 2 (chains s)
MSGDEMIFDPTMSKKKKKKKKPFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEED
TRKKDASDDLDDLNFFNQKKKKKKTKKIFDIDEAEEGVKDLKIESDVQEPTEPEDDLDIM
LGNKKKKKKNVKFPDEDEILEKDEALEDEDNKKDDGISFSNQTGPAWAGSERDYTYEELL
NRVFNIMREKNPDMVAGEKRKFVMKPPQVVRVGTKKTSFVNFTDICKLLHRQPKHLLAFL
LAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLYFL
QCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN

Sequence of entity 2 (r), FASTA

>6YBV_2 Eukaryotic translation initiation factor 2 subunit 1 (chains r)
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN
KLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLE
YTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNI
NRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTT
TLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEV
DGDDDAEEMEAKAED

Sequence of entity 3 (w), FASTA

>6YBV_3 Initiator methionine tRNA (chains w)
AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAAC
CAUCCUCUGCUACCA

Sequence of entity 4 (k), FASTA

>6YBV_4 mRNA (chains k)
AAA

Sequence of entity 5 (t), FASTA

>6YBV_5 Eukaryotic translation initiation factor 2 subunit 3 (chains t)
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKA
ISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGT
KGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIM
KLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIV
KKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGI
VSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGA
VGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAV
KADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD

Primary citation

Structure of a human 48Stranslational initiation complex. Brito Querido, J., Sokabe, M., Kraatz, S. et al. Science (2020) 369:1220-1227. DOI 10.1126/science.aba4904 · PubMed

Other PDB entries of the same protein (UniProt P20042 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PPL 2.65 Å, MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
9HVE 2.7 Å, Native human eIF2-eIF2B complex
28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
28ZV 2.9 Å, human 48S PIC with mRNA (non-Kozak)
6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
28ZU 3.2 Å, human 48S PIC with Kozak mRNA and eIF1A W70A mutant
8PJ1 3.4 Å, Structure of human 48S translation initiation complex in open codon scanning state (48S-1)
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
6ZMW 3.7 Å, Structure of a human 48S translational initiation complex
9HVF 3.8 Å, Native human PPP1R15B-P-eIF2-eIF2B complex

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