5N1A: Utp4 from Chaetomium thermophilum

Crystal structure of Utp4 from Chaetomium thermophilum. Determined by X-ray diffraction at 2.15 Å resolution. Released 14 Jun 2017.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Chains: 2
Atoms: 11,717
Mol. weight: 202.94 kDa
Released: 14 Jun 2017

Explore 5N1A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N1A contains 39 α-helices and 122 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: 20 helices, 61 β-strands

Element	Residues	Length	Sheet
β-strand	-9--4	6	1
β-strand	-1-6	8	1
α-helix	11-13	3
β-strand	16-21	6	2
β-strand	25	1	3
α-helix	31-36	6
β-strand	44-48	5	2
β-strand	53-57	5	2
α-helix	59-61	3
β-strand	64-69	6	2
β-strand	79-84	6	4
α-helix	85-87	3
β-strand	88-89	2	5
β-strand	95-96	2	5
α-helix	97-99	3
β-strand	100-105	6	4
β-strand	110-115	6	4
β-strand	120-126	7	4
β-strand	132-137	6	6
α-helix	138-140	3
β-strand	153-158	6	6
β-strand	162-167	6	6
α-helix	169-171	3
β-strand	174-181	8	6
β-strand	189-194	6	7
β-strand	199-204	6	7
β-strand	208-213	6	7
β-strand	219-224	6	7
β-strand	240-243	4	8
β-strand	249-252	4	8
β-strand	257-261	5	8
β-strand	268-273	6	8
β-strand	279-284	6	9
β-strand	291-295	5	9
β-strand	300-305	6	9
α-helix	306	1
β-strand	313-319	7	9
β-strand	326-334	9	3
β-strand	337-344	8	3
β-strand	350-353	4	3
α-helix	354-356	3
β-strand	363-364	2	3
α-helix	365-366	2
β-strand	374-377	4	10
β-strand	382-387	6	10
β-strand	390-396	7	10
β-strand	417-424	8	10
β-strand	433-436	4	11
β-strand	442-446	5	11
β-strand	451-461	11	11
β-strand	467-472	6	11
β-strand	483-486	4	12
β-strand	492-497	6	12
β-strand	501-506	6	12
β-strand	507-512	6	13
β-strand	515-520	6	13
α-helix	521-523	3
β-strand	524-526	3	12
α-helix	527-530	4
α-helix	535-538	4
α-helix	545-547	3
β-strand	549-554	6	14
β-strand	560-565	6	14
β-strand	570-576	7	14
α-helix	577	1
β-strand	613-616	4	14
α-helix	620-622	3
α-helix	624-626	3
β-strand	630-635	6	15
α-helix	639-640	2
β-strand	647-651	5	15
β-strand	656-660	5	15
β-strand	665-666	2	15
α-helix	668-672	5
α-helix	675-677	3
β-strand	689-695	7	16
β-strand	698-703	6	16
β-strand	707-711	5	16
β-strand	827-829	3	16
β-strand	835-841	7	1
β-strand	858-864	7	1

Chain B: 19 helices, 61 β-strands

Element	Residues	Length	Sheet
β-strand	-9--4	6	17
β-strand	-1-6	8	17
α-helix	11-13	3
β-strand	16-21	6	18
β-strand	25	1	19
β-strand	44-48	5	18
β-strand	53-57	5	18
α-helix	59-61	3
β-strand	64-69	6	18
β-strand	79-84	6	20
α-helix	85-87	3
β-strand	88-89	2	21
β-strand	95-96	2	21
α-helix	97-99	3
β-strand	100-105	6	20
β-strand	110-115	6	20
β-strand	120-126	7	20
β-strand	132-137	6	22
α-helix	138-141	4
α-helix	146-149	4
β-strand	153-158	6	22
β-strand	163-167	5	22
α-helix	169-171	3
β-strand	174-178	5	22
β-strand	189-194	6	23
β-strand	199-204	6	23
β-strand	208-213	6	23
β-strand	219-224	6	23
β-strand	240-243	4	24
β-strand	249-252	4	24
β-strand	257-261	5	24
β-strand	268-273	6	24
β-strand	279-284	6	25
β-strand	291-295	5	25
β-strand	299-305	7	25
α-helix	306	1
β-strand	313-320	8	25
β-strand	326-334	9	19
β-strand	337-344	8	19
β-strand	350-353	4	19
α-helix	354-356	3
β-strand	363-364	2	19
α-helix	365-366	2
β-strand	374-377	4	26
β-strand	382-387	6	26
β-strand	390-396	7	26
β-strand	417-424	8	26
β-strand	433-436	4	27
β-strand	442-446	5	27
β-strand	451-461	11	27
β-strand	467-472	6	27
β-strand	483-486	4	28
β-strand	492-497	6	28
β-strand	501-506	6	28
β-strand	507-512	6	29
β-strand	515-520	6	29
α-helix	521-523	3
β-strand	524-526	3	28
α-helix	527-530	4
α-helix	535-538	4
α-helix	545-547	3
β-strand	549-554	6	30
β-strand	560-565	6	30
β-strand	570-576	7	30
β-strand	613-616	4	30
α-helix	620-622	3
α-helix	624-626	3
β-strand	630-635	6	31
α-helix	639-640	2
β-strand	647-651	5	31
β-strand	656-660	5	31
β-strand	665-666	2	31
α-helix	668-672	5
α-helix	675-677	3
β-strand	689-695	7	32
β-strand	698-703	6	32
β-strand	707-711	5	32
β-strand	827-829	3	32
β-strand	835-841	7	17
β-strand	858-864	7	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
utp4	A, B	protein	908	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SCT7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5N1A_1 utp4 (chains A, B)
MGHHHHHHDYDIPTTENLYFQGAHMDIHRCRFVRYPASAINAVAFTHSALPVVSSSKKYL
QKNIQVRLAIGRANGDIEIWNPLNGGWYQEVIIPGGKDRSVDGLVWVTDPDEEMADGKII
HGKSRLFSIGYTTTITEWDLEKARAKKHASGQHGEIWCFGVQPLPHKANAAAAQNRKLVA
GTVDGNLVLYSIEDGDLKFQKTLTRTPSKKTKFVSIAFQSHNIVIVGCSNSTICAYDVRT
GTMLRQMTLGTDLTGGSKNIIVWAVKCLPNGDIVSGDSTGQVCIWDGKTYTQAQRIQSHT
QDVLCLSVSADGSKIISGGMDRRTAVYEPMAGQSGRWSKVFHRRYHQHDVKAMASFEGKG
MSVVVSGGSDASPIVLPLRALGKEFHRTLPHLPQHPTVLSAPKARYILSWWENEIRIWHL
LNSAQQFLDDPQAPLNLRKNRKFLAQVLIKGASHITSASISEDGTLLAASTPTDVKVFHL
DPAAAQRNGQLYIKKVNMTGTGLGATRVQISPDKRWICWAEEGSKVMISRVHATESADGI
SYTVSVPHKLHRLRRQIPKHILLGGLGSYDRNVSQIAFSADSRMLSVADLAGYIDTWVLR
GPGEGVNGTGGEDSDGESAASSSDSSDEKSEDIAGERWARNPKAAMIPKLSAAPVVLSFS
PTPRDDGDYDLLVVTTLKQLLIFNPLRGMLSEWSRRNTYPKLPEPFRDTRDQVKGIVWQG
QRAWFYGVASLFMFDLSQDFSPEKDLVETNGHKQGTKRKRGAHESGAGSKIEKHSLVPQR
IRAASAPDGTKWEDIEMVDADDQKSVGVSSGVDDDDDETDGSELQRLREENREANSSANA
EKEGPSRAKWWHTYQFRPIMGIVPIEGMMEKKLGAVEGIPPLEVALIERPLSEDDLPERY
FAEGEWER

Primary citation

Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis. Calvino, F.R., Kornprobst, M., Schermann, G. et al. PLoS One (2017) 12:e0178752-e0178752. DOI 10.1371/journal.pone.0178752 · PubMed

Other PDB entries of the same protein (UniProt G0SCT7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9XAG 2.8 Å, Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum,…
9XA8 2.9 Å, Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 WT) from Chaetomium thermophilum,…
9XAF 3.0 Å, Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum,…
9XAH 3.1 Å, Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum,…
5OQL 3.2 Å, Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum
9XA7 3.2 Å, Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 WT) from Chaetomium thermophilum,…
6RXU 3.5 Å, Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum,…
6RXV 4.0 Å, Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum,…
6RXZ 4.4 Å, Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum,…
6RXY 4.7 Å, Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum,…
6RXT 7.0 Å, Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum,…
6RXX 7.1 Å, Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum,…

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