5SUM: Ribosome assembly factor NSA1

Ribosome assembly factor NSA1. Determined by X-ray diffraction at 2.8 Å resolution. Released 26 Apr 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 6,165
Mol. weight: 104.77 kDa
Released: 26 Apr 2017

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

Secondary structure: helices and β-sheets

5SUM contains 24 α-helices and 68 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: 12 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	1
α-helix	13-15	3
β-strand	17-23	7	1
β-strand	27-28	2	2
β-strand	35	1	2
α-helix	36-37	2
β-strand	39-43	5	1
α-helix	48-50	3
β-strand	52-59	8	3
β-strand	62-67	6	3
β-strand	71-81	11	3
α-helix	82-83	2
β-strand	107-108	2	4
β-strand	109-119	11	3
α-helix	125-129	5
β-strand	145-150	6	5
β-strand	159-164	6	5
β-strand	168-174	7	5
β-strand	180-187	8	5
α-helix	189	1
α-helix	191	1
β-strand	194-197	4	6
α-helix	198	1
β-strand	208-214	7	6
β-strand	217-224	8	6
β-strand	231-236	6	6
α-helix	239-242	4
β-strand	253-259	7	7
α-helix	260-263	4
β-strand	274-279	6	7
β-strand	283-288	6	7
β-strand	297-300	4	7
α-helix	303-305	3
β-strand	308-314	7	8
β-strand	322	1	7
β-strand	328	1	7
α-helix	333-335	3
β-strand	337-342	6	8
β-strand	347-351	5	8
β-strand	356-359	4	8
β-strand	371-375	5	2
β-strand	379-383	5	2
β-strand	388-393	6	2
β-strand	399-404	6	2
β-strand	409-414	6	1
β-strand	420-421	2	4

Chain B: 12 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	9
α-helix	13-15	3
β-strand	17-23	7	9
β-strand	27-28	2	10
β-strand	35	1	10
α-helix	36-37	2
β-strand	39-43	5	9
α-helix	48-50	3
β-strand	52-59	8	11
β-strand	62-67	6	11
β-strand	71-81	11	11
α-helix	82-83	2
β-strand	107-108	2	12
β-strand	109-119	11	11
α-helix	125-129	5
β-strand	145-150	6	13
β-strand	159-164	6	13
β-strand	168-174	7	13
β-strand	180-187	8	13
α-helix	189	1
α-helix	191	1
β-strand	194-197	4	14
α-helix	198	1
β-strand	209-214	6	14
β-strand	217-224	8	14
β-strand	231-236	6	14
α-helix	239-242	4
β-strand	253-259	7	15
α-helix	260-263	4
β-strand	274-279	6	15
β-strand	283-288	6	15
β-strand	297-300	4	15
α-helix	303-305	3
β-strand	308-313	6	16
β-strand	322	1	15
β-strand	328	1	15
α-helix	333-335	3
β-strand	337-342	6	16
β-strand	347-351	5	16
β-strand	356-359	4	16
β-strand	371-375	5	10
β-strand	379-383	5	10
β-strand	388-393	6	10
β-strand	399-404	6	10
β-strand	409-414	6	9
β-strand	420-421	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosome biogenesis protein NSA1	A, B	protein	468	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53136 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5SUM_1 Ribosome biogenesis protein NSA1 (chains A, B)
GAMGSMRLLVSCVDSGSIKEVLCNIGTDTSVQSALQPFHVAPHLAEGLKAYVDRMWVISE
DEAILARNSGVVELVKISKHLKENEALQVDPKGESKNEKSLSDDLPKFDISEFEITSSVS
DLFDDAKLESLSSKSVKRTKLVDGFVTLCPIKKDSSNNTFVAATKSGLLHIIKKGEDKKL
IKLASLGLKAPVEFLQLYDLEDTDTDKYIFAYGGEENLIKLVEIDSSFQSLKQIWEAKNV
KNDRLDMRVPVWPMALRFLEPSPGKTEKGKLNYQFAAITRWSHLTKYSTQHGRKPFAQID
LLPNREPLSQMEVFDAKGENVVSSLGNFQSETFNELNVITTDYKKNVFKFDGNGRMLGKV
GRDDITGSSTYIHVHDGKYLLQGGLDRYVRIFDIKTNKMLVKVYVGSRINFIVMLDDVEI
EMPLSPSAKAAKGKQKRKVTELEEDADELWNKLEGKVAASKASKKSKI

Primary citation

Ribosome assembly factor. Lo, Y.H., Stanley, R.E. To be published.

Other PDB entries of the same protein (UniProt P53136 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SUI 1.3 Å, Ribosome assembly factor NSA1: C-terminal truncation
6EN7 2.4 Å, Crystal structure of the ribosome assembly factor Nsa1
8V83 2.53 Å, 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
8V84 2.7 Å, 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
6EM3 3.2 Å, State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of…
7OHX 3.3 Å, Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34…
7OHW 3.5 Å, Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25…
6EM1 3.6 Å, State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S…
5Z3G 3.65 Å, Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP)
6C0F 3.7 Å, Yeast nucleolar pre-60S ribosomal subunit (state 2)
6EM4 4.1 Å, State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of…
6EM5 4.3 Å, State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of…

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