4WJV: Rsa4

Crystal structure of Rsa4 in complex with the Nsa2 binding peptide. Determined by X-ray diffraction at 3.2 Å resolution. Released 19 Nov 2014.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Saccharomyces cerevisiae, Escherichia coli
Chains: 12
Atoms: 23,675
Mol. weight: 348.68 kDa
Released: 19 Nov 2014

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

Secondary structure: helices and β-sheets

4WJV contains 126 α-helices and 237 β-strands across 10 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: 6 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	139	1	1
β-strand	146-151	6	2
β-strand	158-163	6	2
β-strand	168-172	5	2
β-strand	177-182	6	2
β-strand	189-194	6	3
β-strand	201-205	5	3
β-strand	210-213	4	3
β-strand	220	1	3
β-strand	225	1	3
β-strand	232-237	6	4
α-helix	238-239	2
α-helix	240-242	3
β-strand	251-255	5	4
β-strand	259-264	6	4
β-strand	269-275	7	4
β-strand	281-286	6	5
β-strand	291-296	6	5
β-strand	301-305	5	5
α-helix	306-308	3
β-strand	311-316	6	5
β-strand	323-328	6	6
α-helix	333-336	4
α-helix	344-346	3
α-helix	349-364	16
β-strand	365	1	7
β-strand	370	1	7
β-strand	374-378	5	6
β-strand	383-387	5	6
β-strand	391-398	8	6
β-strand	405-410	6	8
β-strand	416-421	6	8
β-strand	426-430	5	8
β-strand	436-440	5	8
β-strand	447-452	6	9
β-strand	458-463	6	9
β-strand	468-472	5	9
β-strand	477-481	5	9
β-strand	489-494	6	10
β-strand	500-505	6	10
β-strand	510	1	1
β-strand	511-514	4	10

Chain B: 6 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	139	1	11
β-strand	146-151	6	12
β-strand	158-163	6	12
β-strand	168-172	5	12
β-strand	177-182	6	12
β-strand	189-194	6	13
β-strand	201-205	5	13
β-strand	210-213	4	13
β-strand	220	1	13
β-strand	225	1	13
β-strand	232-237	6	14
α-helix	238-239	2
α-helix	240-242	3
β-strand	251-255	5	14
β-strand	260-264	5	14
β-strand	269-274	6	14
β-strand	281-286	6	15
β-strand	291-296	6	15
β-strand	301-305	5	15
α-helix	306-308	3
β-strand	311-316	6	15
β-strand	323-328	6	16
α-helix	333-336	4
α-helix	344-346	3
α-helix	349-364	16
β-strand	365	1	17
β-strand	370	1	17
β-strand	374-378	5	16
β-strand	383-387	5	16
β-strand	391-398	8	16
β-strand	405-410	6	18
β-strand	416-421	6	18
β-strand	426-430	5	18
β-strand	436-440	5	18
β-strand	447-452	6	19
β-strand	458-463	6	19
β-strand	468-472	5	19
β-strand	477-481	5	19
β-strand	489-494	6	20
β-strand	500-505	6	20
β-strand	510	1	11
β-strand	511-514	4	20

Chains C and D: 6 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	139	1	21
β-strand	146-151	6	22
β-strand	158-163	6	22
β-strand	168-172	5	22
β-strand	177-182	6	22
β-strand	189-194	6	23
β-strand	201-205	5	23
β-strand	210-213	4	23
β-strand	220	1	23
β-strand	225	1	23
β-strand	232-237	6	24
α-helix	238-239	2
α-helix	240-242	3
β-strand	251-255	5	24
β-strand	259-264	6	24
β-strand	269-275	7	24
β-strand	281-286	6	25
β-strand	291-296	6	25
β-strand	301-305	5	25
α-helix	306-308	3
β-strand	311-316	6	25
β-strand	323-328	6	26
α-helix	333-336	4
α-helix	344-346	3
α-helix	349-364	16
β-strand	365	1	27
β-strand	370	1	27
β-strand	374-378	5	26
β-strand	383-386	4	26
β-strand	396-398	3	26
β-strand	405-410	6	28
β-strand	416-421	6	28
β-strand	426-430	5	28
β-strand	436-440	5	28
β-strand	447-452	6	29
β-strand	458-463	6	29
β-strand	468-472	5	29
β-strand	477-482	6	29
β-strand	489-494	6	30
β-strand	500-505	6	30
β-strand	510	1	21
β-strand	511-514	4	30

Chains E and F: 25 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	41
α-helix	27-41	15
β-strand	45-48	4	41
α-helix	53-60	8
α-helix	62-64	3
β-strand	69-73	5	41
α-helix	74-76	3
α-helix	77-82	6
β-strand	86	1	42
α-helix	87-89	3
α-helix	93-96	4
β-strand	99	1	43
α-helix	101-106	6
β-strand	108-109	2	44
β-strand	112-113	2	44
β-strand	115-121	7	41
β-strand	124-128	5	45
β-strand	138	1	46
α-helix	141-150	10
β-strand	155-157	3	45
α-helix	164-171	8
α-helix	172-174	3
β-strand	177-181	5	47
β-strand	186-192	7	47
α-helix	196-210	15
α-helix	220-228	9
β-strand	232-237	6	45
α-helix	239-241	3
α-helix	242-246	5
β-strand	252-255	4	45
α-helix	256-258	3
β-strand	259	1	46
β-strand	260	1	48
β-strand	263	1	48
α-helix	264-265	2
β-strand	268-269	2	49
β-strand	270-276	7	41
β-strand	277	1	42
α-helix	283-289	7
α-helix	290-294	5
α-helix	297-304	8
β-strand	311-312	2	41
β-strand	314	1	43
α-helix	315-321	7
α-helix	325-336	12
β-strand	338-339	2	49
α-helix	340-341	2
α-helix	346-362	17
α-helix	367-379	13

Chain G: 25 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	59
α-helix	27-41	15
β-strand	45-48	4	59
α-helix	53-60	8
α-helix	62-64	3
β-strand	69-73	5	59
α-helix	74-76	3
α-helix	77-82	6
β-strand	86-87	2	59
α-helix	88-89	2
α-helix	93-96	4
β-strand	99	1	60
α-helix	101-106	6
β-strand	108-109	2	61
β-strand	112-113	2	61
β-strand	115-121	7	59
β-strand	124-128	5	62
β-strand	138	1	63
α-helix	141-150	10
β-strand	157	1	62
α-helix	164-171	8
α-helix	172-174	3
β-strand	177-181	5	64
β-strand	186-192	7	64
α-helix	196-210	15
α-helix	220-228	9
β-strand	234-237	4	62
α-helix	239-241	3
α-helix	242-246	5
β-strand	252-255	4	62
α-helix	256-258	3
β-strand	259-260	2	63
β-strand	263-264	2	63
α-helix	265	1
β-strand	268-269	2	65
β-strand	270-277	8	59
α-helix	283-289	7
α-helix	290-294	5
α-helix	297-304	8
β-strand	311-312	2	59
β-strand	314	1	60
α-helix	315-321	7
α-helix	325-336	12
β-strand	338-339	2	65
α-helix	340-341	2
α-helix	346-362	17
α-helix	367-379	13

Chain H: 25 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	66
α-helix	27-41	15
β-strand	45-48	4	66
α-helix	53-60	8
α-helix	62-64	3
β-strand	69-73	5	66
α-helix	74-76	3
α-helix	77-82	6
β-strand	86	1	67
α-helix	87-89	3
α-helix	93-96	4
β-strand	99	1	68
α-helix	101-106	6
β-strand	108-109	2	69
β-strand	112-113	2	69
β-strand	115-121	7	66
β-strand	124-128	5	70
β-strand	138	1	71
α-helix	141-150	10
β-strand	157	1	70
α-helix	164-171	8
α-helix	172-174	3
β-strand	177-181	5	72
β-strand	186-192	7	72
α-helix	196-210	15
α-helix	220-228	9
β-strand	234-237	4	70
α-helix	239-241	3
α-helix	242-246	5
β-strand	252-255	4	70
α-helix	256-258	3
β-strand	259-260	2	71
β-strand	263-264	2	71
α-helix	265	1
β-strand	268-269	2	73
β-strand	270-276	7	66
β-strand	277	1	67
α-helix	283-289	7
α-helix	290-294	5
α-helix	297-304	8
β-strand	311-312	2	66
β-strand	314	1	68
α-helix	315-321	7
α-helix	325-336	12
β-strand	338-339	2	73
α-helix	340-341	2
α-helix	345-362	18
α-helix	367-379	13

Chains J and L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	89-91	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosome assembly protein 4	A, B, C, D	protein	381	Saccharomyces cerevisiae	P25382 (AlphaFold model)
Maltose-binding periplasmic protein	E, F, G, H	protein	381	Escherichia coli	P0AEX9 (AlphaFold model)
Ribosome biogenesis protein NSA2	I, J, K, L	protein	22	Saccharomyces cerevisiae	P40078 (AlphaFold model)

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

>4WJV_1 Ribosome assembly protein 4 (chains A, B, C, D)
MGSAIAGHGSTILCSAFAPHTSSRMVTGAGDNTARIWDCDTQTPMHTLKGHYNWVLCVSW
SPDGEVIATGSMDNTIRLWDPKSGQCLGDALRGHSKWITSLSWEPIHLVKPGSKPRLASS
SKDGTIKIWDTVSRVCQYTMSGHTNSVSCVKWGGQGLLYSGSHDRTVRVWDINSQGRCIN
ILKSHAHWVNHLSLSTDYALRIGAFDHTGKKPSTPEEAQKKALENYEKICKKNGNSEEMM
VTASDDYTMFLWNPLKSTKPIARMTGHQKLVNHVAFSPDGRYIVSASFDNSIKLWDGRDG
KFISTFRGHVASVYQVAWSSDCRLLVSCSKDTTLKVWDVRTRKLSVDLPGHKDEVYTVDW
SVDGKRVCSGGKDKMVRLWTH

Sequence of entity 2 (E, F, G, H), FASTA

>4WJV_2 Maltose-binding periplasmic protein (chains E, F, G, H)
MKHHHHHHPMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQV
AATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAV
EALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFK
YENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPW
AWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGL
EAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINA
ASGRQTVDAALAAAQTNAAAA

Sequence of entity 3 (I, J, K, L), FASTA

>4WJV_3 Ribosome biogenesis protein NSA2 (chains I, J, K, L)
MDTDGDALPTYLLDREQNNTAK

Primary citation

A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation. Baler, J., Paternoga, H., Holdermann, I. et al. J Cell Biol (2014) 207:481-498. DOI 10.1083/jcb.201408111 · PubMed

Other PDB entries of the same protein (UniProt P25382 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state
7V08 2.36 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1…
7UQB 2.43 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a…
7UQZ 2.44 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1…
4WJU 2.8 Å, Crystal structure of Rsa4 from Saccharomyces cerevisiae
7UG6 2.9 Å, Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922
6YLG 3.0 Å, Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement)
3JCT 3.08 Å, Cryo-em structure of eukaryotic pre-60S ribosomal subunits
6YLH 3.1 Å, Rix1-Rea1 pre-60S particle - full composite structure
7OHQ 3.1 Å, Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae
7BT6 3.12 Å, Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87…
6M62 3.2 Å, Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae…

Browse structure collections

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