6EM4: Ribosome production factor 1
State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes. Determined by electron microscopy at 4.1 Å resolution. Released 27 Dec 2017.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae
- Chains
- 37
- Atoms
- 45,400
- Mol. weight
- 2258.68 kDa
- Released
- 27 Dec 2017
Explore 6EM4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6EM4 contains 265 α-helices and 274 β-strands across 34 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 3: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-11 | 8 | |
| β-strand | 18-20 | 3 | 15 |
| β-strand | 26-28 | 3 | 15 |
| β-strand | 37 | 1 | 15 |
| β-strand | 50-55 | 6 | 16 |
| β-strand | 60-65 | 6 | 16 |
| α-helix | 67-70 | 4 | |
| β-strand | 77-81 | 5 | 16 |
| α-helix | 86-96 | 11 | |
| α-helix | 102-116 | 15 | |
| α-helix | 121-126 | 6 | |
| β-strand | 135-136 | 2 | 17 |
| α-helix | 141-144 | 4 | |
| α-helix | 149-156 | 8 | |
| α-helix | 158-170 | 13 | |
Chain 4: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-30 | 16 | |
| α-helix | 39-54 | 16 | |
| α-helix | 59-75 | 17 | |
| α-helix | 79-81 | 3 | |
| α-helix | 95-109 | 15 | |
| α-helix | 118-134 | 17 | |
| α-helix | 143-154 | 12 | |
| α-helix | 168-176 | 9 | |
| α-helix | 214-226 | 13 | |
| α-helix | 232-241 | 10 | |
Chain 5: 10 helices, 33 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 18 |
| β-strand | 12-17 | 6 | 18 |
| β-strand | 22 | 1 | 19 |
| β-strand | 23 | 1 | 20 |
| β-strand | 30 | 1 | 19 |
| β-strand | 34-38 | 5 | 18 |
| α-helix | 43-45 | 3 | |
| β-strand | 47-52 | 6 | 21 |
| β-strand | 57-62 | 6 | 21 |
| β-strand | 67-76 | 10 | 21 |
| β-strand | 104-114 | 11 | 21 |
| α-helix | 120-126 | 7 | |
| β-strand | 140-145 | 6 | 22 |
| β-strand | 154-159 | 6 | 22 |
| β-strand | 163-169 | 7 | 22 |
| β-strand | 175-182 | 8 | 22 |
| α-helix | 184 | 1 | |
| α-helix | 186-187 | 2 | |
| β-strand | 189-192 | 4 | 23 |
| β-strand | 204-209 | 6 | 23 |
| β-strand | 212-219 | 8 | 23 |
| α-helix | 220 | 1 | |
| β-strand | 226-231 | 6 | 23 |
| α-helix | 234-237 | 4 | |
| α-helix | 242-245 | 4 | |
| β-strand | 248-253 | 6 | 24 |
| α-helix | 255-257 | 3 | |
| α-helix | 261-262 | 2 | |
| β-strand | 269-274 | 6 | 24 |
| β-strand | 278-283 | 6 | 24 |
| β-strand | 292-295 | 4 | 24 |
| α-helix | 298-300 | 3 | |
| β-strand | 303-309 | 7 | 25 |
| β-strand | 317 | 1 | 26 |
| β-strand | 323 | 1 | 26 |
| β-strand | 332-337 | 6 | 25 |
| β-strand | 342-345 | 4 | 25 |
| β-strand | 351 | 1 | 25 |
| β-strand | 366-370 | 5 | 20 |
| β-strand | 374-378 | 5 | 20 |
| β-strand | 383-388 | 6 | 20 |
| β-strand | 394-399 | 6 | 20 |
| β-strand | 404-411 | 8 | 18 |
Chain A: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 35-37 | 3 | 30 |
| β-strand | 38 | 1 | 31 |
| α-helix | 43-55 | 13 | |
| β-strand | 61 | 1 | 30 |
| β-strand | 65 | 1 | 31 |
| α-helix | 74-81 | 8 | |
| β-strand | 86-90 | 5 | 30 |
| β-strand | 98-102 | 5 | 30 |
| β-strand | 110-112 | 3 | 30 |
| β-strand | 134-137 | 4 | 32 |
| β-strand | 138 | 1 | 33 |
| α-helix | 147-158 | 12 | |
| β-strand | 173-177 | 5 | 32 |
| β-strand | 181-182 | 2 | 34 |
| β-strand | 185-186 | 2 | 34 |
Chain B: 10 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| β-strand | 36 | 1 | 57 |
| β-strand | 43 | 1 | 58 |
| β-strand | 45-59 | 15 | 59 |
| β-strand | 71-80 | 10 | 59 |
| β-strand | 84-95 | 12 | 60 |
| β-strand | 98-106 | 9 | 60 |
| α-helix | 112-117 | 6 | |
| α-helix | 131-137 | 7 | |
| α-helix | 144-153 | 10 | |
| β-strand | 157-163 | 7 | 60 |
| α-helix | 176-177 | 2 | |
| β-strand | 178-182 | 5 | 60 |
| β-strand | 183 | 1 | 58 |
| β-strand | 185 | 1 | 57 |
| α-helix | 188-197 | 10 | |
| α-helix | 201 | 1 | |
| β-strand | 202-203 | 2 | 60 |
| α-helix | 204 | 1 | |
| β-strand | 214-220 | 7 | 59 |
| β-strand | 274-286 | 13 | 59 |
| β-strand | 311 | 1 | 61 |
| β-strand | 314 | 1 | 61 |
| β-strand | 321-324 | 4 | 59 |
| β-strand | 335-339 | 5 | 59 |
| α-helix | 348-351 | 4 | |
| β-strand | 355-359 | 5 | 59 |
| α-helix | 373-380 | 8 | |
Chain C: 21 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-9 | 4 | 62 |
| β-strand | 15-20 | 6 | 62 |
| α-helix | 32-42 | 11 | |
| β-strand | 62-63 | 2 | 63 |
| α-helix | 75 | 1 | |
| β-strand | 76-77 | 2 | 63 |
| β-strand | 88 | 1 | 63 |
| α-helix | 97-99 | 3 | |
| α-helix | 102-104 | 3 | |
| α-helix | 115-127 | 13 | |
| α-helix | 128-130 | 3 | |
| α-helix | 133-138 | 6 | |
| β-strand | 150-152 | 3 | 62 |
| α-helix | 154-156 | 3 | |
| α-helix | 162-172 | 11 | |
| α-helix | 177-183 | 7 | |
| β-strand | 186-187 | 2 | 64 |
| α-helix | 191-195 | 5 | |
| β-strand | 199-200 | 2 | 64 |
| β-strand | 206-209 | 4 | 62 |
| α-helix | 215-218 | 4 | |
| β-strand | 226-229 | 4 | 62 |
| α-helix | 235-238 | 4 | |
| α-helix | 240-242 | 3 | |
| β-strand | 248-251 | 4 | 62 |
| α-helix | 252-262 | 11 | |
| α-helix | 276-279 | 4 | |
| α-helix | 287-290 | 4 | |
| α-helix | 295-297 | 3 | |
| α-helix | 300-302 | 3 | |
| α-helix | 323-326 | 4 | |
| α-helix | 331-336 | 6 | |
Chain D: 7 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 268 | 1 | 27 |
| β-strand | 269 | 1 | 28 |
| α-helix | 276-286 | 11 | |
| β-strand | 292-296 | 5 | 29 |
| α-helix | 301-309 | 9 | |
| β-strand | 316-318 | 3 | 29 |
| α-helix | 325-336 | 12 | |
| β-strand | 342-346 | 5 | 29 |
| β-strand | 360-363 | 4 | 29 |
| β-strand | 389-391 | 3 | 29 |
| β-strand | 393 | 1 | 28 |
| β-strand | 414 | 1 | 27 |
| α-helix | 419-421 | 3 | |
| α-helix | 426-432 | 7 | |
| α-helix | 438-455 | 18 | |
| α-helix | 468-474 | 7 | |
Chain e: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-19 | 2 | |
| α-helix | 50-53 | 4 | |
| α-helix | 55-57 | 3 | |
| α-helix | 58-60 | 3 | |
| α-helix | 61-63 | 3 | |
| β-strand | 66 | 1 | 65 |
| β-strand | 72-76 | 5 | 65 |
| α-helix | 79-82 | 4 | |
| β-strand | 92-96 | 5 | 65 |
| α-helix | 102-115 | 14 | |
| β-strand | 119 | 1 | 65 |
| β-strand | 126-127 | 2 | 17 |
26 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ribosome production factor 1 | x | protein | 295 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38805 (AlphaFold model) |
| 60S ribosomal protein L7-A | F | protein | 244 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P05737 (AlphaFold model) |
| Protein MAK16 | 3 | protein | 306 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P10962 (AlphaFold model) |
| Ribosomal RNA-processing protein 1 | 4 | protein | 278 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P35178 (AlphaFold model) |
| Ribosome biogenesis protein NSA1 | 5 | protein | 463 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53136 |
| Ribosome biogenesis protein BRX1 | A | protein | 291 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q08235 |
| rRNA-processing protein EBP2 | J | protein | 427 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P36049 |
| Ribosome biogenesis protein RLP24 | u | protein | 199 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q07915 |
| Nucleolar protein 16 | v | protein | 231 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40007 |
| Eukaryotic translation initiation factor 6 | y | protein | 245 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12522 |
| 60S ribosomal protein L3 | B | protein | 387 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P14126 |
| 60S ribosomal protein L4-A | C | protein | 362 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P10664 |
25 more molecules are not listed.
Sequence of entity 1 (x), FASTA
>6EM4_1 Ribosome production factor 1 (chains x)
MALGNEINITNKLKRQEIFADIKHEKNKERHTMRRKRAKEERENPELREQRLKENVTQTI
ENTRVYDETINKEVEGDEDDLMRYFNSNSNEPPKIFLTTNVNAKKSAYEFANILIEILPN
VTFVKRKFGYKLKEISDICIKRNFTDIVIINEDKKKVTGLTFIHLPEGPTFYFKLSSFVE
VKKIVGHGRPTSHIPELILNNFQTRLGQTVGRLFQSILPQNPDIEGRQVITLHNQRDYIF
FRRHRYVFKDNERVGLQELGPQFTLKLKRLQRGIKEETEWEHKPEMDKEKKKFYL
Sequence of entity 2 (F), FASTA
>6EM4_2 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Sequence of entity 3 (3), FASTA
>6EM4_3 Protein MAK16 (chains 3)
MSDEIVWQVINQSFCSHRIKAPNGQNFCRNEYNVTGLCTRQSCPLANSKYATVKCDNGKL
YLYMKTPERAHTPAKLWERIKLSKNYTKALQQIDEHLLHWSKFFRHKCKQRFTKLTQVMI
TERRLALREEERHYVGVAPKVKRREQNRERKALVAAKIEKAIEKELMDRLKSGAYGDKPL
NVDEKVWKKIMGQMEEENSQDEEEDWDEEEESDDGEVEYVADDGEGEYVDVDDLEKWLAD
SDREASSASESESDSESESDSDSDEENKNSAKRRKKGTSAKTKRPKVEIEYEEEHEVQNA
EQEVAQ
Sequence of entity 4 (4), FASTA
>6EM4_4 Ribosomal RNA-processing protein 1 (chains 4)
METSNFVKQLSSNNRKTRVNALEALKKYLTAKQFKENKQIEFNKLWKGLYYAMWFSDRPR
PQQRLANELGELHGLYFDPKDNSTADELTTNDKAFIKFSRGFWKVMCFEWFNIDRYRLDK
YLLLIRRVLFSQLKYLQSRNWDKKLVDEYIKKVLRWLPLSGSPKVYTGIPIHIVDILLDE
WERLLKDGDEDDEDEENKEEEMRKIAESAKKTPLADVIAIFQDIVADYNNSKVLREKIKE
DLFSDTRLVSWDILEGETQHNDSSNESEEEEEEEWKGF
Sequence of entity 5 (5), FASTA
>6EM4_5 Ribosome biogenesis protein NSA1 (chains 5)
MRLLVSCVDSGSIKEVLCNIGTDTSVQSALQPFHVAPHLAEGLKAYVDRMWVISEDEAIL
ARNSGVVELVKISKHLKENEALQVDPKGESKNEKSLSDDLPKFDISEFEITSSVSDLFDD
AKLESLSSKSVKRTKLVDGFVTLCPIKKDSSNNTFVAATKSGLLHIIKKGEDKKLIKLAS
LGLKAPVEFLQLYDLEDTDTDKYIFAYGGEENLIKLVEIDSSFQSLKQIWEAKNVKNDRL
DMRVPVWPMALRFLEPSPGKTEKGKLNYQFAAITRWSHLTKYSTQHGRKPFAQIDLLPNR
EPLSQMEVFDAKGENVVSSLGNFQSETFNELNVITTDYKKNVFKFDGNGRMLGKVGRDDI
TGSSTYIHVHDGKYLLQGGLDRYVRIFDIKTNKMLVKVYVGSRINFIVMLDDVEIEMPLS
PSAKAAKGKQKRKVTELEEDADELWNKLEGKVAASKASKKSKI
Sequence of entity 6 (A), FASTA
>6EM4_6 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
Sequence of entity 7 (J), FASTA
>6EM4_7 rRNA-processing protein EBP2 (chains J)
MAKGFKLKELLSHQKEIEKAEKLENDLKKKKSQELKKEEPTIVTASNLKKLEKKEKKADV
KKEVAADTEEYQSQALSKKEKRKLKKELKKMQEQDATEAQKHMSGDEDESGDDREEEEEE
EEEEEGRLDLEKLAKSDSESEDDSESENDSEEDEDVVAKEESEEKEEQEEEQDVPLSDVE
FDSDADVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDT
ERELAFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKK
AREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSLKNKRKHNEIDHSEFNVGVEE
EVEGKRFDRGRPNGKRAAKNAKYGQGGMKRFKRKNDATSSADVSGFSSRKMKGKTNRPGK
SRRARRF
Sequence of entity 8 (u), FASTA
>6EM4_8 Ribosome biogenesis protein RLP24 (chains u)
MRIYQCHFCSSPCYPGHGIMFVRNDAKEFRFCRSKCHKAFKQRRNPRKLKWTKAFRKAAG
KELAVDSTLTFAQRRNVPVRYNRELVATTLKAMARIEEIRQKRERAFYKNRMRGNKEKDF
LRDKKLVESNPELLRIREVEIARKLAKEQERAESVSEQEESEEEEEDMEIDSDEEEEEQL
EKQKILLKNRRRNTKKIAF
Sequence of entity 9 (v), FASTA
>6EM4_9 Nucleolar protein 16 (chains v)
MTSVRKRKMNRSSVGKATRRNKDKQRKINIQSNPIIAANWDYSLTMAQNYKKLGLRAKLQ
TPAGGKEADLSKVVKRIPLTKPVLDEDEDEDEGEDEQNDYNAATVELDENEIPEGGARIQ
RDKNGDVVRVVYGKKKNFDADEDVNEIKARDTTEETEVVKKLEELASRPVIRKERSQSER
EEEWLEKLYKKHGDDYKKMFFDKKLNIYQQSEGDLKRRLLRWKKRNGIASK
Sequence of entity 10 (y), FASTA
>6EM4_10 Eukaryotic translation initiation factor 6 (chains y)
MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIG
RMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPD
IDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQVP
LVAGTVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRLQDAQPESISGNLRDTL
IETYS
Sequence of entity 11 (B), FASTA
>6EM4_11 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 12 (C), FASTA
>6EM4_12 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Primary citation
Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Kater, L., Thoms, M., Barrio-Garcia, C. et al. Cell (2017) 171:1599-1610.e14. DOI 10.1016/j.cell.2017.11.039 · PubMed
Other PDB entries of the same protein (UniProt P38805 (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)
- 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)
- 6EM5 4.3 Å, State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of…
- 7OHS 4.38 Å, Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae
- 6CB1 4.6 Å, Yeast nucleolar pre-60S ribosomal subunit (state 3)
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