5O7X: S. Cerevisiae core factor

Name: PDB 5O7X: Crystal structure of S. Cerevisiae core factor at 3.2A resolution
Published: 2017-08-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of S. Cerevisiae core factor at 3.2A resolution. Determined by X-ray diffraction at 3.2 Å resolution. Released 2 Aug 2017.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 18
Atoms: 63,438
Mol. weight: 1334.62 kDa
Ligands: MG
Released: 2 Aug 2017

Explore 5O7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O7X contains 303 α-helices and 204 β-strands across 18 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: 15 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	62-66	5	1
β-strand	173-174	2	2
β-strand	182-187	6	3
α-helix	191-194	4
β-strand	200-207	8	3
β-strand	213-221	9	3
β-strand	225-227	3	3
β-strand	234-237	4	3
β-strand	242-246	5	4
β-strand	260-265	6	4
β-strand	269-274	6	4
β-strand	278	1	5
β-strand	283	1	5
β-strand	286-289	4	4
α-helix	290-291	2
β-strand	300-304	5	6
β-strand	315-320	6	6
β-strand	323-328	6	6
β-strand	344-350	7	6
β-strand	361-365	5	7
β-strand	372-376	5	7
β-strand	379-384	6	7
β-strand	389-392	4	7
β-strand	404-406	3	8
β-strand	414-417	4	8
β-strand	422-425	4	8
β-strand	440	1	8
β-strand	450-457	8	9
β-strand	462-469	8	9
β-strand	476-484	9	9
β-strand	488-491	4	9
β-strand	495-497	3	9
β-strand	505-510	6	1
β-strand	535-541	7	1
β-strand	547-552	6	1
α-helix	572-578	7
α-helix	583-585	3
α-helix	587-612	26
α-helix	617-643	27
α-helix	645-647	3
α-helix	664-667	4
α-helix	672-685	14
α-helix	697-704	8
α-helix	711-723	13
α-helix	729-744	16
α-helix	755-765	11
α-helix	768-773	6

Chains B, E, H, K, N and Q: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	101-123	23
α-helix	128-144	17
α-helix	158-171	14
α-helix	178-186	9
α-helix	209-216	8
α-helix	225-236	12
α-helix	249-259	11
α-helix	265-277	13
α-helix	302-319	18
α-helix	330-339	10
α-helix	345-355	11
α-helix	362-367	6
α-helix	371-384	14
α-helix	406-414	9
α-helix	438-448	11
α-helix	472-490	19
α-helix	495-511	17

Chain C: 17 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-35	25
α-helix	75-83	9
α-helix	159-172	14
α-helix	176-178	3
α-helix	182-193	12
β-strand	196-197	2	2
α-helix	202-204	3
α-helix	208-225	18
α-helix	229-241	13
α-helix	250-260	11
α-helix	267-277	11
α-helix	307-321	15
α-helix	346-349	4
α-helix	351-354	4
α-helix	362-375	14
α-helix	402-416	15
α-helix	429-439	11

Chain D: 15 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	62-66	5	10
β-strand	173-174	2	11
β-strand	182-187	6	12
α-helix	191-194	4
β-strand	200-207	8	12
β-strand	213-221	9	12
β-strand	225-227	3	12
β-strand	234-237	4	12
β-strand	242-246	5	13
β-strand	260-265	6	13
β-strand	269-274	6	13
β-strand	278	1	14
β-strand	283	1	14
β-strand	286-289	4	13
α-helix	290-291	2
β-strand	300-304	5	15
β-strand	315-320	6	15
β-strand	323-328	6	15
β-strand	344-350	7	15
β-strand	361-366	6	16
β-strand	371-376	6	16
β-strand	379-384	6	16
β-strand	389-392	4	16
β-strand	404-406	3	17
β-strand	414-417	4	17
β-strand	422-425	4	17
β-strand	440	1	17
β-strand	450-457	8	18
β-strand	462-469	8	18
β-strand	476-484	9	18
β-strand	488-491	4	18
β-strand	495-497	3	18
β-strand	505-510	6	10
β-strand	535-541	7	10
β-strand	547-552	6	10
α-helix	572-578	7
α-helix	583-585	3
α-helix	587-612	26
α-helix	617-643	27
α-helix	645-647	3
α-helix	664-667	4
α-helix	672-685	14
α-helix	697-704	8
α-helix	711-723	13
α-helix	729-744	16
α-helix	755-765	11
α-helix	768-773	6

Chains F, L and R: 18 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-35	25
α-helix	75-83	9
α-helix	159-167	9
α-helix	169-172	4
α-helix	176-178	3
α-helix	182-193	12
β-strand	196-197	2	11
α-helix	202-204	3
α-helix	208-225	18
α-helix	229-241	13
α-helix	250-260	11
α-helix	267-277	11
α-helix	307-321	15
α-helix	346-349	4
α-helix	351-354	4
α-helix	362-375	14
α-helix	402-416	15
α-helix	429-439	11

Chains G and P: 16 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	62-66	5	19
β-strand	173-174	2	20
β-strand	182-187	6	21
α-helix	191-194	4
β-strand	200-207	8	21
β-strand	213-221	9	21
β-strand	225-227	3	21
β-strand	234-237	4	21
β-strand	242-246	5	22
β-strand	260-265	6	22
β-strand	269-274	6	22
β-strand	278	1	23
β-strand	283	1	23
β-strand	286-289	4	22
α-helix	290-291	2
β-strand	300-304	5	24
β-strand	315-320	6	24
β-strand	323-328	6	24
α-helix	329-331	3
β-strand	344-350	7	24
β-strand	361-365	5	25
β-strand	372-376	5	25
β-strand	379-384	6	25
β-strand	389-392	4	25
β-strand	404-406	3	26
β-strand	414-417	4	26
β-strand	422-425	4	26
β-strand	440	1	26
β-strand	450-457	8	27
β-strand	462-469	8	27
β-strand	476-484	9	27
β-strand	488-491	4	27
β-strand	495-497	3	27
β-strand	505-510	6	19
β-strand	535-541	7	19
β-strand	547-552	6	19
α-helix	572-578	7
α-helix	583-585	3
α-helix	587-612	26
α-helix	617-643	27
α-helix	645-647	3
α-helix	664-667	4
α-helix	672-685	14
α-helix	697-704	8
α-helix	711-723	13
α-helix	729-744	16
α-helix	755-765	11
α-helix	768-773	6

Chains I and O: 18 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-35	25
α-helix	75-83	9
α-helix	159-167	9
α-helix	169-174	6
α-helix	176-178	3
α-helix	182-193	12
β-strand	196-197	2	20
α-helix	202-204	3
α-helix	208-225	18
α-helix	229-241	13
α-helix	250-260	11
α-helix	267-277	11
α-helix	307-321	15
α-helix	346-349	4
α-helix	351-354	4
α-helix	362-375	14
α-helix	402-416	15
α-helix	429-439	11

Chains J and M: 16 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	62-66	5	28
β-strand	173-174	2	29
β-strand	182-187	6	30
α-helix	191-194	4
β-strand	200-207	8	30
β-strand	213-221	9	30
β-strand	225-227	3	30
β-strand	234-237	4	30
β-strand	242-246	5	31
β-strand	260-265	6	31
β-strand	269-274	6	31
β-strand	278	1	32
β-strand	283	1	32
β-strand	286-289	4	31
α-helix	290-291	2
β-strand	300-304	5	33
β-strand	315-320	6	33
β-strand	323-328	6	33
α-helix	329-331	3
β-strand	344-350	7	33
β-strand	361-366	6	34
β-strand	371-376	6	34
β-strand	379-384	6	34
β-strand	389-392	4	34
β-strand	404-406	3	35
β-strand	414-417	4	35
β-strand	422-425	4	35
β-strand	440	1	35
β-strand	450-457	8	36
β-strand	462-469	8	36
β-strand	476-484	9	36
β-strand	488-491	4	36
β-strand	495-497	3	36
β-strand	505-510	6	28
β-strand	535-541	7	28
β-strand	547-552	6	28
α-helix	572-578	7
α-helix	583-585	3
α-helix	587-612	26
α-helix	617-643	27
α-helix	645-647	3
α-helix	664-667	4
α-helix	672-685	14
α-helix	697-704	8
α-helix	711-723	13
α-helix	729-744	16
α-helix	755-765	11
α-helix	768-773	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA polymerase I-specific transcription initiation factor RRN6	A, D, G, J, M, P	protein	894	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32786 (AlphaFold model)
RNA polymerase I-specific transcription initiation factor RRN7	B, E, H, K, N, Q	protein	514	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40992 (AlphaFold model)
RNA polymerase I-specific transcription initiation factor RRN11	C, F, I, L, O, R	protein	507	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q04712 (AlphaFold model)

Sequence of entity 1 (A, D, G, J, M, P), FASTA

>5O7X_1 RNA polymerase I-specific transcription initiation factor RRN6 (chains A, D, G, J, M, P)
MSEGQIPSSDVLGSQLGVGVQGASLYCPQENYTTKKQEKPQWLRPVDDTLAEDALDLHIV
VKSLLCDTAIRYISDDKVLQESDADDDLITSDIDEDTDNQGDTSIVVNPVIPVVPKDVHF
FKKVDVGNDSMFGVNCDTPVSFQDYIPSDLLRNLDDTLQESTNSSRPMQDAFFWDPTVAN
RLDSQYIQTASDLRNYRDGTEIIAYASGKTGSVLNIAVLTRQNTLHLNRHNNVTSIELHS
PIKSIKIPGASESIGRRSNLVGIITENSFQIFRIESVHSRSCDVMVSSSEPLYFVEIDDL
QVVDFAFNPWDLQQFAIIDIKGNWSIGRIPKNFNNNNKRKLQLIDNLHGTIFDPEELSSW
KRIEWFSHFQKILVFDRSKMIEIDFMNNWQTEVVQAKAWSNIRDYKRIDDKNGILLTSRE
IIIVGASESNDPVRRISWKHDLDPDDTTLRITVQKVKKPDHILLVAFVYSMRHKRIYMHV
FSHRKANLFQSLGCSTVLEIPGGTPTGIETILTLDHIDDESRREEDADENFELVVDFLVK
LRNSSEVYYYALSNTQNSEPNKQETPIIVDHPEWASLFNNADEREKESIGALVSQIKLKE
RERISRVQNLIEHENSHDEDKYLQDLGYRLSIATNELLESWQKTKDESILSGSLSHSKLK
NLLENSDSFASIPEFSSLLDQFFQYYQDQDVTFIGFEKLLHLFLHEDVPGLDIFYNKLLQ
CWVLVSPQAELLTKEIVKDIIWSLARLEKPSLFEPIQNEISRSLSGPYQDIISSWDMDDI
NEEDESNEFNFDSQFSAPFNGRPPFNLNSQSQIPTIKSSQSSGLARRKRILKTQSQKATP
LSQSTQNLSVLPDSMTPAFTLMQPPSSQISFVNDSQPRNSQKAKKKKKRIRGFG

Sequence of entity 2 (B, E, H, K, N, Q), FASTA

>5O7X_2 RNA polymerase I-specific transcription initiation factor RRN7 (chains B, E, H, K, N, Q)
MSTFIRGPICGTDNCPSRLWRIIDGRRTCQYGHVMEGDVEFNDDEDDLNGLGAGVITRRL
NLTTNATGSFQSSQLTNSQLLQQQQRQSHKKFKKLIGHEAKLLFLKSFQFILKRQIRWLI
TEMRFPKEFEHVAKIIWLKILKTINDQPQEELKLQLHMTSTISILYLASTHLSLPVYTCD
YIKWICTAKMPYFQASEILPKSWRIQLPNYYVSILEGSISPFNGQLYNKIALTCGMIHFK
EFFNSEISCQGLLLKLVMQCALPPEFYFYTKQVIEFEETDIRNLTLWERTDERHTGRVSN
HAELRVLSYFMLTINWMLSFDRDRQYPLKWILSLTESLTQRTTTSESIGRNIVKVVYPDK
PTSSDYFQWSEEETLEFLKWMEKQFLPTQTKSLHNENGSMEMTIDQKIARRKLYKIFPLD
REANHDGEFNDSTHQLTFIEDLQERYAKQTPFFESNKIRDSLNYQEANPPARKEAIGRLL
THIASQLLVDFAISKEQLKDCISRIKNACLHRMN

Sequence of entity 3 (C, F, I, L, O, R), FASTA

>5O7X_3 RNA polymerase I-specific transcription initiation factor RRN11 (chains C, F, I, L, O, R)
MFEVPITLTNRKFAQRRKLKYQYINYISRRFDRISKKSTTTDSLPTPENSAAENNDEEEG
QNSEAGTYRRSVLQQKKRRRERHWRSVVGEIYSTTESETDSQEEETEEGGEHDTGIDKED
SDEERKFWKKYEKPEKSFEIWRTVSSQNKQPINKQKMTYHNFKKIEKIPLRKMEIPLLHC
TKENKLYFQSISRGLEPLKTSTSEVRNYRTRHIVTLTDLLHLNVSRHNWSLAYKIFATLI
RIPGVQIKSLWGIGVEILDNLSNSSSGLDFLQWMCQIYSSKSRFVQNINYRSIVPPFQTG
SRTHTAKFAITYLWSSLINCQKSMEPSSNIIDKPFDTENDLLQELIDKISEWVLTPPFME
DAEVWFIYASCHLLKADTLSRQFVNDNKNNDLIGLDRDIKINQVIKHIHYVRTFLKICLD
KGGFAVPSRLIENQLKSFESRLYGEAQDIQERDVANVYDSIDNSSVENSFGDVYETNAEF
LDTQLMDLSPEDNGLDEMHYSDEDSSE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural Basis of RNA Polymerase I Transcription Initiation. Engel, C., Gubbey, T., Neyer, S. et al. Cell (2017) 169:120-131.e22. DOI 10.1016/j.cell.2017.03.003 · PubMed

Other PDB entries of the same protein (UniProt P32786 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RUI 2.7 Å, RNA Polymerase I Pre-initiation complex DNA opening intermediate 2
6RQL 2.9 Å, RNA Polymerase I Closed Conformation 2 (CC2)
6RWE 3.0 Å, RNA Polymerase I Open Complex conformation 2
6RRD 3.1 Å, RNA Polymerase I Pre-initiation complex DNA opening intermediate 1
5N61 3.4 Å, RNA polymerase I initially transcribing complex
6RUO 3.5 Å, RNA Polymerase I Open Complex conformation 1
6TPS 3.54 Å, early intermediate RNA Polymerase I Pre-initiation complex - eiPIC
6RQH 3.7 Å, RNA Polymerase I Closed Conformation 1 (CC1)
5W5Y 3.8 Å, RNA polymerase I Initial Transcribing Complex
5W66 3.9 Å, RNA polymerase I Initial Transcribing Complex State 3
5W64 4.2 Å, RNA Polymerase I Initial Transcribing Complex State 1
5W65 4.3 Å, RNA polymerase I Initial Transcribing Complex State 2

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