4F02: PABP-binding site of eIF4G

Crystal structure of the PABP-binding site of eIF4G in complex with RRM1-2 of PABP and poly(A). Determined by X-ray diffraction at 2.0 Å resolution. Released 8 Aug 2012.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,663
Mol. weight: 60.87 kDa
Released: 8 Aug 2012

Explore 4F02 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F02 contains 22 α-helices and 28 β-strands across 4 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: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	1
α-helix	24-31	8
α-helix	32-34	3
β-strand	37-44	8	1
β-strand	51-59	9	1
α-helix	62-72	11
β-strand	76-77	2	2
β-strand	80-81	2	2
β-strand	83-86	4	1
α-helix	92-96	5
β-strand	100-104	5	3
α-helix	112-119	8
α-helix	120-122	3
β-strand	125-133	9	3
β-strand	136-145	10	3
α-helix	148-158	11
β-strand	162-163	2	4
β-strand	166-167	2	4
α-helix	168	1
β-strand	169-172	4	3
α-helix	176-183	8

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	180-181	2
β-strand	182-184	3	4
α-helix	185-187	3
β-strand	190-191	2	4
α-helix	193-197	5

Chain D: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	5
α-helix	24-31	8
α-helix	32-34	3
β-strand	37-44	8	5
β-strand	51-59	9	5
α-helix	62-72	11
β-strand	76-77	2	6
β-strand	80-81	2	6
β-strand	83-86	4	5
α-helix	92-96	5
β-strand	100-104	5	7
α-helix	112-119	8
α-helix	120-122	3
β-strand	125-133	9	7
β-strand	136-145	10	7
α-helix	148-158	11
β-strand	162-163	2	8
β-strand	166-167	2	8
β-strand	169-172	4	7
α-helix	176-180	5

Chain F: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	182-184	3	8
α-helix	185-187	3
β-strand	190-191	2	8
α-helix	193-196	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyadenylate-binding protein 1	A, D	protein	213	Homo sapiens	P11940 (AlphaFold model)
RNA (5'-r(apapapapapapapapapap*a)-3')	B, E	RNA	11
Eukaryotic translation initiation factor 4 gamma 1	C, F	protein	27	Homo sapiens	Q04637 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4F02_1 Polyadenylate-binding protein 1 (chains A, D)
GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA
YVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKAL
YDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS
RKEREAELGARAKEFYPYDVPDYAGSSGRIVTD

Sequence of entity 2 (B, E), FASTA

>4F02_2 RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') (chains B, E)
AAAAAAAAAAA

Sequence of entity 3 (C, F), FASTA

>4F02_3 Eukaryotic translation initiation factor 4 gamma 1 (chains C, F)
KTIRIRDPNQGGKDITEEIMSGARTAY

Primary citation

Interdomain Allostery Promotes Assembly of the Poly(A) mRNA Complex with PABP and eIF4G. Safaee, N., Kozlov, G., Noronha, A.M. et al. Mol Cell (2012) 48:375-386. DOI 10.1016/j.molcel.2012.09.001 · PubMed

Other PDB entries of the same protein (UniProt P11940 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KUJ 1.4 Å, Crystal structure of C-terminal domain of PABPC1 in complex with binding region of eRF3a
3KUS 1.4 Å, Crystal structure of the MLLE domain of poly(A)-binding protein in complex with the…
2X04 1.49 Å, Crystal structure of the PABC-TNRC6C complex
3KTP 1.5 Å, Structural basis of GW182 recognition by poly(A)-binding protein
3KUT 1.5 Å, Crystal structure of the MLLE domain of poly(A)-binding protein in complex with the…
3KTR 1.7 Å, Structural basis of ataxin-2 recognition by poly(A)-binding protein
3PTH 1.7 Å, The PABC1 MLLE domain bound to the variant PAM2 motif of LARP4B
3PKN 1.8 Å, Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif…
4F25 1.9 Å, Crystal structure of the second RRM domain of human PABPC1 at pH 6.0
5DX1 1.93 Å, Crystal structure of CARM1, sinefungin, and PABP1 peptide (R455)
7BN3 1.93 Å, Crystal structure of C-terminal domain of PABPC1 in complex with Nucleoprotein from…
5DX8 1.94 Å, Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R455)

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