6EM1: Ribosome production factor 1

Name: PDB 6EM1: State C (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 C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes. Determined by electron microscopy at 3.6 Å resolution. Released 27 Dec 2017.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae
Chains: 43
Atoms: 99,980
Mol. weight: 2482.07 kDa
Ligands: ZN
Released: 27 Dec 2017

Explore 6EM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EM1 contains 308 α-helices and 330 β-strands across 40 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	20	1	14
β-strand	26	1	14
β-strand	50-55	6	15
β-strand	60-65	6	15
α-helix	68-71	4
β-strand	77	1	15
β-strand	81	1	15
α-helix	86-96	11
α-helix	102-116	15
α-helix	122-125	4
β-strand	135-136	2	16
α-helix	141-144	4
α-helix	147-156	10
α-helix	158-167	10

Chain 4: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	15-31	17
α-helix	39-54	16
α-helix	62-70	9
α-helix	72-75	4
α-helix	92-108	17
α-helix	118-134	17
β-strand	135	1	22
α-helix	143-149	7
α-helix	168-181	14
α-helix	221-225	5
α-helix	232-241	10

Chain 5: 5 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	25
β-strand	13-17	5	25
β-strand	23	1	26
α-helix	30-32	3
β-strand	34-38	5	25
β-strand	47	1	27
β-strand	51-52	2	28
β-strand	57-59	3	28
β-strand	62	1	27
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
β-strand	189-192	4	30
β-strand	204-209	6	30
β-strand	212-219	8	30
β-strand	226-231	6	30
α-helix	234-237	4
α-helix	242-245	4
β-strand	248-251	4	31
β-strand	254	1	31
α-helix	255-258	4
β-strand	269-274	6	31
β-strand	278-283	6	31
β-strand	292-295	4	31
β-strand	303-308	6	32
β-strand	317	1	31
β-strand	323	1	31
β-strand	332-337	6	32
β-strand	342-346	5	32
β-strand	351	1	32
β-strand	366	1	33
β-strand	369-370	2	26
β-strand	374-377	4	26
β-strand	378	1	33
β-strand	383-388	6	26
β-strand	393-399	7	26
β-strand	404-411	8	25

Chain A: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	35-37	3	35
β-strand	38	1	36
α-helix	43-55	13
β-strand	61	1	35
β-strand	65	1	36
α-helix	74-81	8
β-strand	87-90	4	35
β-strand	98-100	3	35
β-strand	112	1	35
α-helix	133-135	3
β-strand	136	1	37
β-strand	137-138	2	38
α-helix	141-143	3
α-helix	147-156	10
α-helix	157-161	5
β-strand	176	1	37
β-strand	177	1	39
β-strand	180-182	3	40
β-strand	185-187	3	40
β-strand	190	1	39

Chain b: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-27	13
α-helix	39-65	27
α-helix	76-83	8
α-helix	88-116	29
α-helix	122-141	20
α-helix	142-144	3
α-helix	146-159	14
β-strand	168-172	5	43
α-helix	180-187	8
β-strand	205-211	7	43
β-strand	214-220	7	43
α-helix	234-245	12
β-strand	248	1	43
β-strand	251-254	4	43
α-helix	264-273	10
α-helix	275-278	4
α-helix	279-281	3
β-strand	284-287	4	43
α-helix	309-311	3
β-strand	319	1	43
α-helix	325-341	17
α-helix	380-384	5
α-helix	386-388	3
α-helix	399-406	8
α-helix	425-428	4
β-strand	435-436	2	44
β-strand	439-440	2	44
α-helix	441-443	3
α-helix	449-464	16

Chain B: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	79
α-helix	40-41	2
β-strand	43	1	80
β-strand	45-59	15	81
β-strand	71-80	10	81
β-strand	84-95	12	82
β-strand	98-106	9	82
α-helix	112-116	5
α-helix	143-153	11
β-strand	157-163	7	82
α-helix	176-177	2
β-strand	178-182	5	82
β-strand	183	1	80
β-strand	185	1	79
α-helix	188-195	8
β-strand	202-203	2	82
β-strand	213-220	8	81
β-strand	274-286	13	81
β-strand	311	1	83
β-strand	314	1	83
β-strand	321-326	6	81
β-strand	335-339	5	81
α-helix	348-351	4
α-helix	352-354	3
β-strand	355-359	5	81
α-helix	373-375	3
α-helix	377-380	4

Chain C: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	87
α-helix	14	1
β-strand	15-21	7	87
α-helix	22	1
α-helix	32-43	12
β-strand	62-64	3	88
β-strand	75-77	3	88
β-strand	88	1	88
α-helix	98-99	2
α-helix	115-128	14
α-helix	133-137	5
β-strand	150-152	3	87
α-helix	154-156	3
α-helix	162-172	11
α-helix	175-183	9
β-strand	186-187	2	89
α-helix	192-194	3
β-strand	199-200	2	89
α-helix	205	1
β-strand	206-209	4	87
α-helix	215-220	6
β-strand	226-229	4	87
α-helix	235-238	4
β-strand	248-251	4	87
α-helix	252-262	11
α-helix	276-279	4
α-helix	287-290	4
α-helix	295-297	3
α-helix	323-326	4
α-helix	331-336	6

Chain D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	268	1	74
β-strand	269	1	75
α-helix	275-286	12
β-strand	292-296	5	76
α-helix	302-311	10
β-strand	317-318	2	76
α-helix	325-336	12
β-strand	343-346	4	76
β-strand	360-363	4	76
α-helix	366-367	2
α-helix	372-377	6
β-strand	389-391	3	76
β-strand	393	1	75
β-strand	414	1	74
α-helix	427-433	7
α-helix	438-455	18
α-helix	468-474	7

32 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	Q08235
Nucleolar GTP-binding protein 1	b	protein	647	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02892
rRNA-processing protein EBP2	J	protein	427	Saccharomyces cerevisiae	P36049
Ribosome biogenesis protein NSA2	r	protein	261	Saccharomyces cerevisiae	P40078
Nuclear GTP-binding protein NUG1	s	protein	520	Saccharomyces cerevisiae	P40010
Ribosome biogenesis protein RLP24	u	protein	199	Saccharomyces cerevisiae	Q07915
Nucleolar protein 16	v	protein	231	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40007

31 more molecules are not listed.

Sequence of entity 1 (x), FASTA

>6EM1_1 Ribosome production factor 1 (chains x)
MALGNEINITNKLKRQEIFADIKHEKNKERHTMRRKRAKEERENPELREQRLKENVTQTI
ENTRVYDETINKEVEGDEDDLMRYFNSNSNEPPKIFLTTNVNAKKSAYEFANILIEILPN
VTFVKRKFGYKLKEISDICIKRNFTDIVIINEDKKKVTGLTFIHLPEGPTFYFKLSSFVE
VKKIVGHGRPTSHIPELILNNFQTRLGQTVGRLFQSILPQNPDIEGRQVITLHNQRDYIF
FRRHRYVFKDNERVGLQELGPQFTLKLKRLQRGIKEETEWEHKPEMDKEKKKFYL

Sequence of entity 2 (F), FASTA

>6EM1_2 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 3 (3), FASTA

>6EM1_3 Protein MAK16 (chains 3)
MSDEIVWQVINQSFCSHRIKAPNGQNFCRNEYNVTGLCTRQSCPLANSKYATVKCDNGKL
YLYMKTPERAHTPAKLWERIKLSKNYTKALQQIDEHLLHWSKFFRHKCKQRFTKLTQVMI
TERRLALREEERHYVGVAPKVKRREQNRERKALVAAKIEKAIEKELMDRLKSGAYGDKPL
NVDEKVWKKIMGQMEEENSQDEEEDWDEEEESDDGEVEYVADDGEGEYVDVDDLEKWLAD
SDREASSASESESDSESESDSDSDEENKNSAKRRKKGTSAKTKRPKVEIEYEEEHEVQNA
EQEVAQ

Sequence of entity 4 (4), FASTA

>6EM1_4 Ribosomal RNA-processing protein 1 (chains 4)
METSNFVKQLSSNNRKTRVNALEALKKYLTAKQFKENKQIEFNKLWKGLYYAMWFSDRPR
PQQRLANELGELHGLYFDPKDNSTADELTTNDKAFIKFSRGFWKVMCFEWFNIDRYRLDK
YLLLIRRVLFSQLKYLQSRNWDKKLVDEYIKKVLRWLPLSGSPKVYTGIPIHIVDILLDE
WERLLKDGDEDDEDEENKEEEMRKIAESAKKTPLADVIAIFQDIVADYNNSKVLREKIKE
DLFSDTRLVSWDILEGETQHNDSSNESEEEEEEEWKGF

Sequence of entity 5 (5), FASTA

>6EM1_5 Ribosome biogenesis protein NSA1 (chains 5)
MRLLVSCVDSGSIKEVLCNIGTDTSVQSALQPFHVAPHLAEGLKAYVDRMWVISEDEAIL
ARNSGVVELVKISKHLKENEALQVDPKGESKNEKSLSDDLPKFDISEFEITSSVSDLFDD
AKLESLSSKSVKRTKLVDGFVTLCPIKKDSSNNTFVAATKSGLLHIIKKGEDKKLIKLAS
LGLKAPVEFLQLYDLEDTDTDKYIFAYGGEENLIKLVEIDSSFQSLKQIWEAKNVKNDRL
DMRVPVWPMALRFLEPSPGKTEKGKLNYQFAAITRWSHLTKYSTQHGRKPFAQIDLLPNR
EPLSQMEVFDAKGENVVSSLGNFQSETFNELNVITTDYKKNVFKFDGNGRMLGKVGRDDI
TGSSTYIHVHDGKYLLQGGLDRYVRIFDIKTNKMLVKVYVGSRINFIVMLDDVEIEMPLS
PSAKAAKGKQKRKVTELEEDADELWNKLEGKVAASKASKKSKI

Sequence of entity 6 (A), FASTA

>6EM1_6 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK

Sequence of entity 7 (b), FASTA

>6EM1_7 Nucleolar GTP-binding protein 1 (chains b)
MQLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKVKYTGEGFVEK
FEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISRAKSLVEQVARDYVRLLKFGQ
SLFQCKQLKRAALGRMATIVKKLRDPLAYLEQVRQHIGRLPSIDPNTRTLLICGYPNVGK
SSFLRCITKSDVDVQPYAFTTKSLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSI
YAIAHLRSCVLYFMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINKTDIIRPEDLDE
ERAQLLESVKEVPGVEIMTSSCQLEENVMEVRNKACEKLLASRIENKLKSQSRINNVLNK
IHVAQPQARDDVKRTPFIPESVKNLKKYDPEDPNRRKLARDIEAENGGAGVFNVNLKDKY
LLEDDEWKNDIMPEILDGKNVYDFLDPEIAAKLQALEEEEEKLENEGFYNSDDEEEIYDG
FEASEVDDIKEKAAWIRNRQKTMIAEARNRKSLKNKAIMPRSKLTKSFGKMEEHMSTLGH
DMSALQDKQNRAARKNRYVERGSDVVFGDQDALTASTENGVKLRQTDRLLDGVADGSMRS
KADRMAKMERRERNRHAKQGESDRHNAVSLSKHLFSGKRGVGKTDFR

Sequence of entity 8 (J), FASTA

>6EM1_8 rRNA-processing protein EBP2 (chains J)
MAKGFKLKELLSHQKEIEKAEKLENDLKKKKSQELKKEEPTIVTASNLKKLEKKEKKADV
KKEVAADTEEYQSQALSKKEKRKLKKELKKMQEQDATEAQKHMSGDEDESGDDREEEEEE
EEEEEGRLDLEKLAKSDSESEDDSESENDSEEDEDVVAKEESEEKEEQEEEQDVPLSDVE
FDSDADVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDT
ERELAFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKK
AREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSLKNKRKHNEIDHSEFNVGVEE
EVEGKRFDRGRPNGKRAAKNAKYGQGGMKRFKRKNDATSSADVSGFSSRKMKGKTNRPGK
SRRARRF

Sequence of entity 9 (r), FASTA

>6EM1_9 Ribosome biogenesis protein NSA2 (chains r)
MPQNDYIERHIKQHGKRLDHEERKRKREARESHKISERAQKLTGWKGKQFAKKRYAEKVS
MRKKIKAHEQSKVKGSSKPLDTDGDALPTYLLDREQNNTAKAISSSIKQKRLEKADKFSV
PLPKVRGISEEEMFKVIKTGKSRSKSWKRMITKHTFVGEGFTRRPVKMERIIRPSALRQK
KANVTHPELGVTVFLPILAVKKNPQSPMYTQLGVLTKGTIIEVNVSELGMVTAGGKVVWG
KYAQVTNEPDRDGCVNAVLLV

Sequence of entity 10 (s), FASTA

>6EM1_10 Nuclear GTP-binding protein NUG1 (chains s)
MRVRKRQSRRTSTKLKEGIKKKASAHRKKEKKMAKKDVTWRSRSKKDPGIPSNFPYKAKI
LEEIEAKKMKDLEERELAKQQRLEARKAAKEQGVDAMDEDMIEDDENGLAALVESAQQAA
AEYEGTPSNDADVRDDELDVIDYNIDFYGEDVEGESELEKSRKAYDKIFKSVIDASDVIL
YVLDARDPESTRSRKVEEAVLQSQGKRLILILNKVDLIPPHVLEQWLNYLKSSFPTIPLR
ASSGAVNGTSFNRKLSQTTTASALLESLKTYSNNSNLKRSIVVGVIGYPNVGKSSVINAL
LARRGGQSKACPVGNEAGVTTSLREIKIDNKLKILDSPGICFPSENKKRSKVEHEAELAL
LNALPAKHIVDPYPAVLMLVKRLAKSDEMTESFKKLYEIPPIPANDADTFTKHFLIHVAR
KRGRLGKGGIPNLASAGLSVLNDWRDGKILGWVLPNTSAAASQQDKQNLSTINTGTKQAP
IAANESTIVSEWSKEFDLDGLFSSLDKAIDASKDQDTMME

Sequence of entity 11 (u), FASTA

>6EM1_11 Ribosome biogenesis protein RLP24 (chains u)
MRIYQCHFCSSPCYPGHGIMFVRNDAKEFRFCRSKCHKAFKQRRNPRKLKWTKAFRKAAG
KELAVDSTLTFAQRRNVPVRYNRELVATTLKAMARIEEIRQKRERAFYKNRMRGNKEKDF
LRDKKLVESNPELLRIREVEIARKLAKEQERAESVSEQEESEEEEEDMEIDSDEEEEEQL
EKQKILLKNRRRNTKKIAF

Sequence of entity 12 (v), FASTA

>6EM1_12 Nucleolar protein 16 (chains v)
MTSVRKRKMNRSSVGKATRRNKDKQRKINIQSNPIIAANWDYSLTMAQNYKKLGLRAKLQ
TPAGGKEADLSKVVKRIPLTKPVLDEDEDEDEGEDEQNDYNAATVELDENEIPEGGARIQ
RDKNGDVVRVVYGKKKNFDADEDVNEIKARDTTEETEVVKKLEELASRPVIRKERSQSER
EEEWLEKLYKKHGDDYKKMFFDKKLNIYQQSEGDLKRRLLRWKKRNGIASK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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…
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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