7Z0O: Transcription factor UAF

Name: PDB 7Z0O: Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA
Published: 2022-04-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA. Determined by electron microscopy at 2.8 Å resolution. Released 27 Apr 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae
Chains: 10
Atoms: 11,864
Mol. weight: 289.98 kDa
Released: 27 Apr 2022

Explore 7Z0O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z0O contains 77 α-helices and 40 β-strands across 8 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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	42-44	3	1
α-helix	45-48	4
α-helix	49-59	11
α-helix	65-78	14
β-strand	84-85	2	2
α-helix	87-114	28
β-strand	119-120	2	3
α-helix	122-132	11

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	32-41	10
β-strand	46-47	2	3
α-helix	52-76	25
β-strand	81-82	2	2
α-helix	84-92	9

Chain C: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	40-41	2	4
α-helix	49-54	6
β-strand	63	1	5
α-helix	65-78	14
β-strand	83-85	3	6
α-helix	87-114	28
β-strand	120	1	7
α-helix	122-131	10

Chain D: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-21	17
β-strand	35-37	3	8
β-strand	56-58	3	1
β-strand	60-62	3	8
α-helix	64-76	13
α-helix	79-81	3
α-helix	82-85	4
α-helix	86-88	3
α-helix	94-109	16
α-helix	112-113	2
α-helix	124	1
β-strand	125-126	2	3
α-helix	127-128	2
α-helix	129-146	18
α-helix	147-149	3
α-helix	151-152	2
β-strand	153	1	9
α-helix	154	1
β-strand	163	1	5
α-helix	165-174	10
α-helix	176-178	3
α-helix	182-184	3
β-strand	187-188	2	4
α-helix	191-193	3
β-strand	194	1	7
β-strand	195	1	9
α-helix	196-217	22
α-helix	220-223	4
β-strand	225	1	6
β-strand	226-228	3	10
β-strand	242-244	3	6
α-helix	246-255	10
α-helix	258-260	3
α-helix	265-275	11
α-helix	290-301	12
α-helix	341-362	22

Chain E: 22 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	37-53	17
α-helix	56-72	17
α-helix	78-88	11
α-helix	91-93	3
β-strand	96	1	11
β-strand	111	1	12
α-helix	130-159	30
α-helix	162	1
β-strand	163	1	13
α-helix	164	1
α-helix	170-171	2
α-helix	172-207	36
β-strand	228	1	11
α-helix	230-239	10
α-helix	245-252	8
α-helix	253-257	5
α-helix	259-261	3
α-helix	264-267	4
α-helix	268-270	3
α-helix	271-276	6
α-helix	278-280	3
α-helix	287-293	7
β-strand	298-300	3	10
α-helix	301-305	5
α-helix	312-339	28
α-helix	347-350	4
α-helix	353-355	3

Chain F: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	23-30	8
α-helix	42-47	6
α-helix	50-54	5
α-helix	68-82	15
α-helix	84-86	3
β-strand	90	1	11
α-helix	92-108	17
β-strand	112-115	4	14
β-strand	120-123	4	14
α-helix	126-131	6
β-strand	133	1	13

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-15	12
α-helix	25-36	12
α-helix	44-57	14
α-helix	68-85	18

Chain H: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	65	1
β-strand	66-75	10	12
α-helix	79-80	2
α-helix	82-88	7
β-strand	93	1	12
β-strand	102-106	5	12
β-strand	111-115	5	12
β-strand	120-124	5	12
α-helix	129-146	18
β-strand	153-165	13	12
α-helix	174-178	5
β-strand	183-184	2	12
β-strand	193-197	5	12
β-strand	202-206	5	12
β-strand	211-217	7	12
α-helix	220-235	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, C	protein	136	Saccharomyces cerevisiae	P61830 (AlphaFold model)
Histone H4	B	protein	103	Saccharomyces cerevisiae	P02309 (AlphaFold model)
RNA polymerase I-specific transcription initiation factor RRN5	D	protein	364	Saccharomyces cerevisiae	Q02983 (AlphaFold model)
RNA polymerase I-specific transcription initiation factor RRN9	E	protein	366	Saccharomyces cerevisiae	P53437 (AlphaFold model)
RNA polymerase I-specific transcription initiation factor RRN10	F	protein	145	Saccharomyces cerevisiae	P38204
Upstream activation factor subunit UAF30	G	protein	228	Saccharomyces cerevisiae	Q08747
TATA-box-binding protein	H	protein	242	Saccharomyces cerevisiae	P13393
Non-template DNA	N	DNA	151	Saccharomyces cerevisiae
Template DNA	T	DNA	151	Saccharomyces cerevisiae

Sequence of entity 1 (A, C), FASTA

>7Z0O_1 Histone H3 (chains A, C)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS

Sequence of entity 2 (B), FASTA

>7Z0O_2 Histone H4 (chains B)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG

Sequence of entity 3 (D), FASTA

>7Z0O_3 RNA polymerase I-specific transcription initiation factor RRN5 (chains D)
SMEHQQLRKYVELYNKEVEEFYNGAASGRPAEFHPSKVHVKSIHEKAGTANAGVEISSVG
VDWDSEEKNTFFWCLSRYSIHRVDEWRSLLPRKSAMEILGYYRLLRRASASARSRKAGDD
GAPIAYEMSAEWVALETKLSETVMAITEGAAEVADEEGHCEGLIDYESWKRRWVAIYSHS
RIAEIRPLPRHALPLSRSATQTLERCVSRYTRTLLWCTALAGMASRSVSARAAESRGHKS
LPTVVTRRQVERALCTEARSRDLHVLPRRIVLTLRKWELDYPREGKLFRTKEMAHLFLQS
QLSRRDAPPVHQDENQENQENQENQEQDNTASEGESEAERDEIDEADLFRSALHENQLLK
WLSK

Sequence of entity 4 (E), FASTA

>7Z0O_4 RNA polymerase I-specific transcription initiation factor RRN9 (chains E)
SMSDLDEESQIETQIDAPIEDIIRGSELTTTTADKETLKSANELLDSLEHSHRVDLSLHL
YSAYLLKRLLYKANEKKHFYEVNQFVKTQIKDNWTSWPNPNTIIDPSVDKLYEDIPEGIA
NVSVQPGEISNRALMHASDMMRVELDAQWQKFLSKSALDHDVTLDVDELNIPNEISRNIL
VKLDSLFEGLHDKIAKENEFDVRQDKHSNNIRANQIDDEPMQANRRIKYTYHDLVSRGCE
MNEDMTDIYMKSLELYNDIPEKYKKRKFRLPKQILKKYHQPKKTSSYLKELLSKTREDFI
PVEKLLKDKRLTSKDKSKLQRLNREETEDALNKRTFFQVKGYLEDENEISDYELDDCLIE
LPNGNI

Sequence of entity 5 (F), FASTA

>7Z0O_5 RNA polymerase I-specific transcription initiation factor RRN10 (chains F)
MDRNVYEACSNIIKEFGTHVVSADEVLAEKIDNAVPIPFKTREEIDADVEKDRNEGVFEG
NIIPDIDLRVVHYYATQLCLNKYPHLINAFDETSLITLGLLIEKWVKDYLTSIQTEQGRQ
SKVIGKGPCEFISKHIDYRHAPGNI

Sequence of entity 6 (G), FASTA

>7Z0O_6 Upstream activation factor subunit UAF30 (chains G)
MAELNDYSTMIDILLSDMDLETVTTKKVRMALKEVYAIDVESQGKAINKLIRKHLDLVKE
RPRFERSLEDLLKENATLAIELTKEITVSKRSSGEEKNDSETKGTHVEKKKGTVSKSPIS
TRKVTLSKSLASLLGEHELTRTEVVRRLWAYIKAHNLQNPNNKKEILCDEKLELILGKST
NMFEMHKILASHMTEPKKISDCPPLIQEVRRKEKPIVSDSEQSDTKGI

Sequence of entity 7 (H), FASTA

>7Z0O_7 TATA-box-binding protein (chains H)
GHMADEERLKEFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTS
ATSGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFAS
GKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFS
HGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFR
KM

Sequence of entity 8 (N), FASTA

>7Z0O_8 Non-template DNA (chains N)
GAAAAAAAAAATATACGCTAAGATTTTTGGAGAATAGCTTAAATTGAAGTTTTTCTCGGC
GAGAAATACGTAGTTAAGGCAGAGCGACAGAGAGGGCAAAAGAAAATAAAAGTAAGATTT
TAGTTTGTAATGGGAGGGGGGGTTTAGTCAT

Sequence of entity 9 (T), FASTA

>7Z0O_9 Template DNA (chains T)
ATGACTAAACCCCCCCTCCCATTACAAACTAAAATCTTACTTTTATTTTCTTTTGCCCTC
TCTGTCGCTCTGCCTTAACTACGTATTTCTCGCCGAGAAAAACTTCAATTTAAGCTATTC
TCCAAAAATCTTAGCGTATATTTTTTTTTTC

Primary citation

Mechanism of RNA polymerase I selection by transcription factor UAF. Baudin, F., Murciano, B., Fung, H.K.H. et al. Sci Adv (2022) 8:eabn5725-eabn5725. DOI 10.1126/sciadv.abn5725 · PubMed

Other PDB entries of the same protein (UniProt P61830 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KMJ 1.4 Å, Crystal structure of Sth1 bromodomain in complex with H3K14Ac
7F3S 1.4 Å, Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
8I3F 1.62 Å, Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
2H2G 1.63 Å, The Structural Basis of Sirtuin substrate affinity
7F4E 1.78 Å, Crystal structure of Hst2 in complex with H3K9bz peptide
5D7E 1.9 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9ac
7F4A 2.0 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide
1M1D 2.2 Å, Tetrahymena GCN5 with bound bisubstrate analog inhibitor
1QSN 2.2 Å, Crystal structure of tetrahymena GCN5 with bound coenzyme a and histone H3 peptide
2IDC 2.2 Å, Structure of the Histone H3-Asf1 Chaperone Interaction
5IOK 2.22 Å, Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr

Browse structure collections

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