6EM3: Ribosome production factor 1

Name: PDB 6EM3: State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Published: 2017-12-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes. Determined by electron microscopy at 3.2 Å resolution. Released 27 Dec 2017.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 33
Atoms: 38,436
Mol. weight: 2149.83 kDa
Released: 27 Dec 2017

Explore 6EM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EM3 contains 237 α-helices and 215 β-strands across 30 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
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	25
β-strand	12-17	6	25
β-strand	22	1	26
β-strand	23	1	27
β-strand	30	1	26
β-strand	34-38	5	25
α-helix	43-45	3
β-strand	47-52	6	28
β-strand	57-62	6	28
β-strand	67-76	10	28
β-strand	104-114	11	28
α-helix	120-126	7
β-strand	140-145	6	29
β-strand	154-159	6	29
β-strand	163-169	7	29
β-strand	175-182	8	29
α-helix	184	1
α-helix	186-187	2
β-strand	189-192	4	30
β-strand	204-209	6	30
β-strand	212-219	8	30
α-helix	220	1
β-strand	226-231	6	30
α-helix	234-237	4
α-helix	242-245	4
β-strand	248-253	6	31
α-helix	255-257	3
α-helix	261-262	2
β-strand	269-274	6	31
β-strand	278-283	6	31
β-strand	292-295	4	31
α-helix	298-300	3
β-strand	303-309	7	32
β-strand	317	1	33
β-strand	323	1	33
β-strand	332-337	6	32
β-strand	342-345	4	32
β-strand	351	1	32
β-strand	366-370	5	27
β-strand	374-378	5	27
β-strand	383-388	6	27
β-strand	394-399	6	27
β-strand	404-411	8	25

Chain A: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	35-37	3	37
β-strand	38	1	38
α-helix	43-55	13
β-strand	61	1	37
β-strand	65	1	38
α-helix	74-81	8
β-strand	86-90	5	37
β-strand	98-102	5	37
β-strand	110-112	3	37
β-strand	134-137	4	39
α-helix	147-158	12
β-strand	173-177	5	39
β-strand	181-182	2	40
β-strand	185-186	2	40

Chain B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	259-262	4
α-helix	263-265	3
α-helix	268-269	2
α-helix	270-285	16
α-helix	291-300	10
α-helix	329-331	3
α-helix	342-344	3
α-helix	346-347	2
α-helix	348-356	9
α-helix	384-395	12

Chain C: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	41
β-strand	15-20	6	41
α-helix	32-42	11
β-strand	62-63	2	42
α-helix	75	1
β-strand	76-77	2	42
β-strand	88	1	42
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	41
α-helix	154-156	3
α-helix	162-172	11
α-helix	177-183	7
β-strand	186-187	2	43
α-helix	191-195	5
β-strand	199-200	2	43
β-strand	206-209	4	41
α-helix	215-218	4
β-strand	226-229	4	41
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	41
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	5
β-strand	269	1	6
α-helix	276-286	11
β-strand	292-296	5	7
α-helix	301-309	9
β-strand	316-318	3	7
α-helix	325-336	12
β-strand	342-346	5	7
β-strand	360-363	4	7
β-strand	389-391	3	7
β-strand	393	1	6
β-strand	414	1	5
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	44
β-strand	72-76	5	44
α-helix	79-82	4
β-strand	92-96	5	44
α-helix	102-115	14
β-strand	119	1	44
β-strand	126-127	2	17

22 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
Nucleolar protein 16	v	protein	231	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40007
60S ribosomal protein L4-A	C	protein	362	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P10664
60S ribosomal protein L32	e	protein	130	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38061
60S ribosomal protein L6-A	E	protein	176	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02326
60S ribosomal protein L33-A	f	protein	107	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05744

21 more molecules are not listed.

Sequence of entity 1 (x), FASTA

>6EM3_1 Ribosome production factor 1 (chains x)
MALGNEINITNKLKRQEIFADIKHEKNKERHTMRRKRAKEERENPELREQRLKENVTQTI
ENTRVYDETINKEVEGDEDDLMRYFNSNSNEPPKIFLTTNVNAKKSAYEFANILIEILPN
VTFVKRKFGYKLKEISDICIKRNFTDIVIINEDKKKVTGLTFIHLPEGPTFYFKLSSFVE
VKKIVGHGRPTSHIPELILNNFQTRLGQTVGRLFQSILPQNPDIEGRQVITLHNQRDYIF
FRRHRYVFKDNERVGLQELGPQFTLKLKRLQRGIKEETEWEHKPEMDKEKKKFYL

Sequence of entity 2 (F), FASTA

>6EM3_2 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 3 (3), FASTA

>6EM3_3 Protein MAK16 (chains 3)
MSDEIVWQVINQSFCSHRIKAPNGQNFCRNEYNVTGLCTRQSCPLANSKYATVKCDNGKL
YLYMKTPERAHTPAKLWERIKLSKNYTKALQQIDEHLLHWSKFFRHKCKQRFTKLTQVMI
TERRLALREEERHYVGVAPKVKRREQNRERKALVAAKIEKAIEKELMDRLKSGAYGDKPL
NVDEKVWKKIMGQMEEENSQDEEEDWDEEEESDDGEVEYVADDGEGEYVDVDDLEKWLAD
SDREASSASESESDSESESDSDSDEENKNSAKRRKKGTSAKTKRPKVEIEYEEEHEVQNA
EQEVAQ

Sequence of entity 4 (4), FASTA

>6EM3_4 Ribosomal RNA-processing protein 1 (chains 4)
METSNFVKQLSSNNRKTRVNALEALKKYLTAKQFKENKQIEFNKLWKGLYYAMWFSDRPR
PQQRLANELGELHGLYFDPKDNSTADELTTNDKAFIKFSRGFWKVMCFEWFNIDRYRLDK
YLLLIRRVLFSQLKYLQSRNWDKKLVDEYIKKVLRWLPLSGSPKVYTGIPIHIVDILLDE
WERLLKDGDEDDEDEENKEEEMRKIAESAKKTPLADVIAIFQDIVADYNNSKVLREKIKE
DLFSDTRLVSWDILEGETQHNDSSNESEEEEEEEWKGF

Sequence of entity 5 (5), FASTA

>6EM3_5 Ribosome biogenesis protein NSA1 (chains 5)
MRLLVSCVDSGSIKEVLCNIGTDTSVQSALQPFHVAPHLAEGLKAYVDRMWVISEDEAIL
ARNSGVVELVKISKHLKENEALQVDPKGESKNEKSLSDDLPKFDISEFEITSSVSDLFDD
AKLESLSSKSVKRTKLVDGFVTLCPIKKDSSNNTFVAATKSGLLHIIKKGEDKKLIKLAS
LGLKAPVEFLQLYDLEDTDTDKYIFAYGGEENLIKLVEIDSSFQSLKQIWEAKNVKNDRL
DMRVPVWPMALRFLEPSPGKTEKGKLNYQFAAITRWSHLTKYSTQHGRKPFAQIDLLPNR
EPLSQMEVFDAKGENVVSSLGNFQSETFNELNVITTDYKKNVFKFDGNGRMLGKVGRDDI
TGSSTYIHVHDGKYLLQGGLDRYVRIFDIKTNKMLVKVYVGSRINFIVMLDDVEIEMPLS
PSAKAAKGKQKRKVTELEEDADELWNKLEGKVAASKASKKSKI

Sequence of entity 6 (A), FASTA

>6EM3_6 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK

Sequence of entity 7 (J), FASTA

>6EM3_7 rRNA-processing protein EBP2 (chains J)
MAKGFKLKELLSHQKEIEKAEKLENDLKKKKSQELKKEEPTIVTASNLKKLEKKEKKADV
KKEVAADTEEYQSQALSKKEKRKLKKELKKMQEQDATEAQKHMSGDEDESGDDREEEEEE
EEEEEGRLDLEKLAKSDSESEDDSESENDSEEDEDVVAKEESEEKEEQEEEQDVPLSDVE
FDSDADVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDT
ERELAFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKK
AREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSLKNKRKHNEIDHSEFNVGVEE
EVEGKRFDRGRPNGKRAAKNAKYGQGGMKRFKRKNDATSSADVSGFSSRKMKGKTNRPGK
SRRARRF

Sequence of entity 8 (v), FASTA

>6EM3_8 Nucleolar protein 16 (chains v)
MTSVRKRKMNRSSVGKATRRNKDKQRKINIQSNPIIAANWDYSLTMAQNYKKLGLRAKLQ
TPAGGKEADLSKVVKRIPLTKPVLDEDEDEDEGEDEQNDYNAATVELDENEIPEGGARIQ
RDKNGDVVRVVYGKKKNFDADEDVNEIKARDTTEETEVVKKLEELASRPVIRKERSQSER
EEEWLEKLYKKHGDDYKKMFFDKKLNIYQQSEGDLKRRLLRWKKRNGIASK

Sequence of entity 9 (C), FASTA

>6EM3_9 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD

Sequence of entity 10 (e), FASTA

>6EM3_10 60S ribosomal protein L32 (chains e)
MASLPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNISQPKIGYGSN
KKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNISAKNRVVILARAKALGIKVT
NPKGRLALEA

Sequence of entity 11 (E), FASTA

>6EM3_11 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 12 (f), FASTA

>6EM3_12 60S ribosomal protein L33-A (chains f)
MAESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVR
GSKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI

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)
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…
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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