5AFF: Symportin 1

Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site. Determined by X-ray diffraction at 3.4 Å resolution. Released 15 Apr 2015.

Method
X-ray diffraction
Resolution
3.4 Å
Organism
CHAETOMIUM THERMOPHILUM
Chains
3
Atoms
5,606
Mol. weight
98.34 kDa
Released
15 Apr 2015

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

Secondary structure: helices and β-sheets

5AFF contains 43 α-helices and 5 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: 38 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix27-4418
α-helix50-6213
α-helix65-739
α-helix76-827
α-helix84-863
α-helix90-10617
α-helix109-1179
α-helix120-13617
α-helix142-1443
α-helix147-17024
α-helix172-1787
α-helix182-19413
α-helix199-21214
α-helix217-2248
α-helix231-24010
α-helix246-25914
α-helix269-2713
α-helix274-2774
α-helix278-2869
α-helix302-32625
α-helix389-3979
α-helix412-4165
α-helix417-4215
α-helix422-4309
α-helix437-45721
α-helix467-48014
α-helix481-4855
α-helix486-4916
α-helix497-51317
α-helix523-53311
α-helix551-5533
α-helix555-56511
α-helix573-58816
α-helix595-60814
α-helix615-6162
α-helix617-6226
α-helix626-64217
α-helix650-67223
Chain B: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix9-146
Chain C: 4 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand17-2371
α-helix29-4214
α-helix45-462
β-strand47-4821
β-strand67-7371
α-helix75-8713
β-strand103-10751
β-strand126-13051
α-helix156-16510

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Symportin 1Aprotein654CHAETOMIUM THERMOPHILUMG0S5S6 (AlphaFold model)
Ribosomal protein L5Bprotein48CHAETOMIUM THERMOPHILUMG0SEG2 (AlphaFold model)
Ribosomal protein L11Cprotein173CHAETOMIUM THERMOPHILUMG0SHQ2 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>5AFF_1 SYMPORTIN 1 (chains A)
MTDPELAKLREDKILPVLKDLKSPDAKSRTTAAGAIANIVQDAKCRKLLLREQVVHIVLT
ETLTDNNIDSRAAGWEILKVLAQEEEADFCVHLYRLDVLTAIEHAAKAVLETLTTSEPPF
SKLLKAQQRLVWDITGSLLVLIGLLALARDEIHEAVATKQTILRLLFRLISADIAPQDIY
EEAISCLTTLSEDNLKVGQAITDDQETHVYDVLLKLATGTDPRAVMACGVLHNVFTSLQW
MDHSPGKDGACDAILIPTLTRALEHVVPGGAKFNGDARYANITLLALVTLASIGTDFQET
LVKGNQGSRESPISAADEEWNGFDDADGDAMDVDQKSSSGEDQEEDYEEIDVKEDDEDDD
DDSITSEMQADMERVVGADGTDDGDLEDLPTLRELIQTAVPQLIRLSNLPIDSDESLTIQ
SHALSALNNISWTISCLEFANGENANIHNAWYPTAKKIWRKTILPILEADSADLKLATQV
TSLAWAVARVLHGETPTDGNPHRKFISLYHSSKQQAGGNSNSIEEPEDPFQGLGVKCIGV
VGSLAHDPAPIEVNREVGVFLVTLLRQSNNVPPAEIVEALNQLFDIYGDEELACDKEVFW
KDGFLKHLEEFLPKMRTLTKGIDKRTQPELRTRADEALLNLGRFVQYKKKHAPK
Sequence of entity 2 (B), FASTA
>5AFF_2 RIBOSOMAL PROTEIN L5 (chains B)
MHHHHHHMAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAK
Sequence of entity 3 (C), FASTA
>5AFF_3 RIBOSOMAL PROTEIN L11 (chains C)
MSSEKAQNPMRELRIQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVYSKARYTVRQFGI
RRNEKIAVHVTVRGPKAEEILERGLKVKEYELRRRNFSETGNFGFGISEHIDLGIKYDPS
IGIYGMDFYCCMTRPGERVAKRRRCKSRIGASHRITREETIRWFKQRFDGIVR

Primary citation

Symportin 1 Chaperones 5S Rnp Assembly During Ribosome Biogenesis by Occupying an Essential Rrna-Binding Site. Calvino, F.R., Kharde, S., Ori, A. et al. Nat Commun (2015) 6:6510. DOI 10.1038/NCOMMS7510 · PubMed

Other PDB entries of the same protein (UniProt G0S5S6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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