4U1D: PDB entry 4U1D

Name: PDB 4U1D: Structure of the PCI domain of translation initiation factor eIF3a
Published: 2014-09-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Structure of the PCI domain of translation initiation factor eIF3a. Determined by X-ray diffraction at 3.3 Å resolution. Released 10 Sept 2014.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 11,013
Mol. weight: 171.04 kDa
Released: 10 Sept 2014

Explore 4U1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U1D contains 91 α-helices and 9 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: 31 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	24-35	12
α-helix	38-41	4
α-helix	45-47	3
α-helix	49-61	13
α-helix	65-79	15
α-helix	83-119	37
α-helix	152-169	18
α-helix	173-175	3
α-helix	176-192	17
α-helix	196-216	21
α-helix	217-219	3
α-helix	230-249	20
α-helix	253-269	17
α-helix	273-275	3
α-helix	276-293	18
α-helix	296-310	15
α-helix	318-333	16
α-helix	336-337	2
α-helix	350-354	5
α-helix	360-362	3
α-helix	363-371	9
α-helix	374-377	4
α-helix	382-388	7
α-helix	389-393	5
α-helix	397-411	15
α-helix	416-420	5
α-helix	421-439	19
β-strand	442-444	3	3
α-helix	445-451	7
α-helix	454-455	2
α-helix	462-474	13
β-strand	480-483	4	3
β-strand	488-491	4	3

Chain B: 30 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	24-35	12
α-helix	38-41	4
α-helix	45-47	3
α-helix	49-61	13
α-helix	65-79	15
α-helix	83-110	28
α-helix	152-169	18
α-helix	173-175	3
α-helix	176-192	17
α-helix	196-217	22
α-helix	230-249	20
α-helix	253-269	17
α-helix	273-275	3
α-helix	276-293	18
α-helix	296-310	15
α-helix	318-333	16
α-helix	336-337	2
α-helix	350-354	5
α-helix	360-362	3
α-helix	363-372	10
α-helix	374-377	4
α-helix	382-388	7
α-helix	389-393	5
α-helix	397-411	15
α-helix	416-420	5
α-helix	421-439	19
β-strand	442-444	3	2
α-helix	445-451	7
α-helix	454-455	2
α-helix	462-474	13
β-strand	481-483	3	2
β-strand	488-490	3	2

Chain C: 30 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	24-35	12
α-helix	38-41	4
α-helix	45-47	3
α-helix	49-61	13
α-helix	65-79	15
α-helix	83-106	24
α-helix	152-169	18
α-helix	176-192	17
α-helix	196-216	21
α-helix	217-219	3
α-helix	230-249	20
α-helix	253-269	17
α-helix	273-275	3
α-helix	276-293	18
α-helix	296-310	15
α-helix	318-333	16
α-helix	336-337	2
α-helix	351-354	4
α-helix	360-362	3
α-helix	363-371	9
α-helix	374-377	4
α-helix	382-388	7
α-helix	389-393	5
α-helix	397-411	15
α-helix	416-420	5
α-helix	421-439	19
β-strand	442-444	3	1
α-helix	445-451	7
α-helix	454-455	2
α-helix	462-474	13
β-strand	481-483	3	1
β-strand	488-490	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 3 subunit A	A, B, C	protein	497	Saccharomyces cerevisiae	P38249 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>4U1D_1 Eukaryotic translation initiation factor 3 subunit A (chains A, B, C)
SNAMAPPPFRPENAIKRADELISVGEKQAALQSLHDFITARRIRWATPSTVEPVVFKFLE
IGVELKKGKLLKDGLHQYKKLIQGSTEGLVSVGAVARKFIDLVESKIASEQTRADELQKQ
EIDDDLEGGVTPENLLISVYESDQSVAGFNDEAITSWLRFTWESYRAVLDLLRNNALLEI
TYSGVVKKTMHFCLKYQRKNEFKRLAEMLRQHLDAANYQQSKSGNNLVDLSDADTLQRYL
DQRFQQVDVSVKLELWHEAYRSIEDVFHLMKISKRAPKPSTLANYYENLVKVFFVSGDPL
LHTTAWKKFYKLYSTNPRATEEEFKTYSSTIFLSAISTQLDEIPSIGYDPHLRMYRLLNL
DAKPTRKEMLQSIIEDESIYGKVDEELKELYDIIEVNFDVDTVKQQLENLLVKLSSKTYF
SQYIAPLRDVIMRRVFVAASQKFTTVSQSELYKLATLPAPLDLSAWDIEKSLLQAAVEDY
VSITIDHESAKVTFAKD

Primary citation

Molecular Architecture of the 40SeIF1eIF3 Translation Initiation Complex. Erzberger, J.P., Stengel, F., Pellarin, R. et al. Cell (2014) 158:1123-1135. DOI 10.1016/j.cell.2014.07.044 · PubMed

Other PDB entries of the same protein (UniProt P38249 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4K51 2.65 Å, Crystal Structure of the PCI domain of eIF3a
8CAH 3.0 Å, Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex
6FYY 3.02 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
8CAS 3.3 Å, Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)
4U1C 3.5 Å, Crystal structure of the eIF3a/eIF3c PCI-domain heterodimer
6FYX 3.5 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
8S8E 3.85 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
3JAP 4.9 Å, Structure of a partial yeast 48S preinitiation complex in closed conformation
6GSM 5.15 Å, Structure of a partial yeast 48S preinitiation complex in open conformation.
6ZCE 5.3 Å, Structure of a yeast ABCE1-bound 43S pre-initiation complex
6GSN 5.75 Å, Structure of a partial yeast 48S preinitiation complex in closed conformation
6ZU9 6.2 Å, Structure of a yeast ABCE1-bound 48S initiation complex

Browse structure collections

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