5Z1G: Brx1 and Ebp2 complex

Structure of the Brx1 and Ebp2 complex. Determined by X-ray diffraction at 2.29 Å resolution. Released 11 Apr 2018.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 5,459
Mol. weight: 80.8 kDa
Released: 11 Apr 2018

Explore 5Z1G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z1G contains 23 α-helices and 32 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.

Chains A and C: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	198-208	11
α-helix	212-214	3
α-helix	217-219	3
β-strand	222-224	3	1
α-helix	239-263	25
α-helix	270-271	2
β-strand	278	1	2
α-helix	282-288	7

Chain B: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	33-37	5	3
α-helix	43-55	13
β-strand	59-61	3	3
α-helix	73-80	8
β-strand	85-92	8	3
β-strand	96-102	7	3
β-strand	109-118	10	3
β-strand	130	1	4
β-strand	133	1	5
α-helix	134-135	2
β-strand	136-139	4	3
α-helix	141-144	4
α-helix	147-160	14
β-strand	170	1	5
β-strand	175-182	8	3
β-strand	185-194	10	3
β-strand	211-214	4	3
β-strand	218-227	10	3
β-strand	235-238	4	3
α-helix	245-253	9

Chain D: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	33-37	5	1
α-helix	43-55	13
β-strand	59-61	3	1
α-helix	73-80	8
β-strand	85-92	8	1
β-strand	96-102	7	1
β-strand	109-118	10	1
β-strand	130	1	2
β-strand	133	1	6
β-strand	136-139	4	1
α-helix	141-144	4
α-helix	147-160	14
β-strand	170	1	6
β-strand	175-182	8	1
β-strand	185-194	10	1
β-strand	211-214	4	1
β-strand	218-227	10	1
β-strand	235-238	4	1
α-helix	245-253	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
rRNA-processing protein EBP2	A, C	protein	110	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P36049 (AlphaFold model)
Ribosome biogenesis protein BRX1	B, D	protein	234	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q08235 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5Z1G_1 rRNA-processing protein EBP2 (chains A, C)
DVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDTERELA
FYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEE

Sequence of entity 2 (B, D), FASTA

>5Z1G_2 Ribosome biogenesis protein BRX1 (chains B, D)
QFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSRKEPKLDTKKDLQQLNEIAELYNCNN
VLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTMDELNFTGNCLKGSRPVLSFDQRFES
SPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFSIVDDKIWVRTYEISHSTKNKEEYED
GEEDISLVEIGPRFVMTVILILEGSFGGPKIYENKQYVSPNVVRAQIKQQAAEE

Primary citation

Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate. Zhou, D., Zhu, X., Zheng, S. et al. Protein Cell (2019) 10:120-130. DOI 10.1007/s13238-018-0526-7 · PubMed

Other PDB entries of the same protein (UniProt P36049 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8V83 2.53 Å, 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
8V87 2.66 Å, 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
8V84 2.7 Å, 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
10ZY 2.74 Å, Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
11AA 2.78 Å, Yeast co-transcriptional pre-60S assembly intermediate Nop12 RNP
10ZZ 2.8 Å, Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP*
7NAC 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
7R7A 3.04 Å, State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
7R6K 3.17 Å, State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region
6EM3 3.2 Å, State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of…
6ELZ 3.3 Å, State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S…
7OHW 3.5 Å, Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25…

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