7ZXE: SNAPc containing Pol II pre-initiation complex

Name: PDB 7ZXE: Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC)
Published: 2022-11-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC). Determined by electron microscopy at 3.5 Å resolution. Released 30 Nov 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 10
Atoms: 14,150
Mol. weight: 446.86 kDa
Ligands: ZN
Released: 30 Nov 2022

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

Secondary structure: helices and β-sheets

7ZXE contains 63 α-helices and 46 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: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
α-helix	26-36	11
α-helix	38-41	4
α-helix	48-66	19
β-strand	70	1	4
α-helix	72-87	16
β-strand	97-99	3	5
α-helix	101-116	16
α-helix	120-131	12
β-strand	135-137	3	5
β-strand	138	1	6
β-strand	164	1	4
α-helix	167-171	5
α-helix	174-194	21
α-helix	211-231	21

Chain b: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	7
β-strand	39	1	7
β-strand	42-43	2	8
α-helix	44-54	11
α-helix	77-90	14
α-helix	94-103	10
α-helix	128-143	16
α-helix	151-160	10
α-helix	174-176	3
β-strand	181-187	7	6
α-helix	188-189	2
α-helix	193-195	3
β-strand	201-206	6	6
α-helix	210	1
β-strand	211	1	9
α-helix	222-225	4
α-helix	238-242	5
α-helix	243-246	4
β-strand	250-253	4	6
β-strand	258-260	3	6
α-helix	270-279	10
β-strand	290-291	2	6
β-strand	297	1	9
β-strand	302-303	2	8
β-strand	309-313	5	6
β-strand	317-327	11	6
β-strand	343-345	3	6
β-strand	353	1	10
β-strand	361	1	10
β-strand	364-367	4	11
β-strand	377-379	3	11
α-helix	381-388	8
β-strand	389	1	12
β-strand	395	1	12
β-strand	400-403	4	11

Chain c: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	83-122	40
α-helix	159-162	4
α-helix	163-170	8
α-helix	173-175	3
α-helix	186-220	35
α-helix	226-246	21
α-helix	250-254	5
α-helix	263-265	3
α-helix	266-270	5
α-helix	277-283	7
α-helix	284-288	5
α-helix	296-298	3
α-helix	299-312	14
α-helix	317-323	7
α-helix	330-339	10
α-helix	351-364	14
α-helix	372-375	4
α-helix	384-393	10

Chain d: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-44	43

Chain M: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	118-128	11
α-helix	132-148	17
α-helix	156-170	15
α-helix	177-181	5
α-helix	188-202	15
α-helix	207-209	3
α-helix	212-221	10
α-helix	226-241	16
α-helix	250-264	15
α-helix	271-278	8
α-helix	282-291	10
α-helix	296-299	4

Chain O: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	164-173	10	1
α-helix	180-186	7
β-strand	190-191	2	1
β-strand	199-203	5	1
β-strand	210-214	5	1
β-strand	218-222	5	1
α-helix	227-243	17
β-strand	251-263	13	1
β-strand	268	1	2
α-helix	270-276	7
β-strand	281-282	2	1
β-strand	291-294	4	1
β-strand	301-304	4	1
β-strand	309-315	7	1
α-helix	318-334	17
β-strand	336	1	2

Chain U: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-32	23
α-helix	36-50	15
β-strand	334-344	11	3
β-strand	348-360	13	3
β-strand	363-367	5	3
β-strand	370-375	6	3

Chain V: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	30-48	19
β-strand	56	1	3
β-strand	58-68	11	3
β-strand	71-83	13	3
β-strand	86-98	13	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription initiation factor IIB	M	protein	316	Homo sapiens	Q00403 (AlphaFold model)
Non-template strand	N	DNA	96	Homo sapiens
TATA-box-binding protein	O	protein	339	Homo sapiens	P20226 (AlphaFold model)
Template strand	T	DNA	96	Homo sapiens
Transcription initiation factor IIA subunit 1	U	protein	376	Homo sapiens	P52655 (AlphaFold model)
Transcription initiation factor IIA subunit 2	V	protein	109	Homo sapiens	P52657 (AlphaFold model)
snRNA-activating protein complex subunit 1	a	protein	368	Homo sapiens	Q16533
snRNA-activating protein complex subunit 3	b	protein	411	Homo sapiens	Q92966
snRNA-activating protein complex subunit 4	c	protein	1469	Homo sapiens	Q5SXM2
snRNA-activating protein complex subunit 5	d	protein	98	Homo sapiens	O75971

Sequence of entity 1 (M), FASTA

>7ZXE_1 Transcription initiation factor IIB (chains M)
MASTSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKA
TKDPSRVGDSQNPLLSDGDLSTMIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKE
ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEI
CAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAV
ELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLF
PTDFKFDTPVDKLPQL

Sequence of entity 2 (N), FASTA

>7ZXE_2 Non-template strand (chains N)
GCAAGTGACCGTGTGTGTAAAGAGTGAGGCGTATGAGGCTGTGTCGGGGCAGAGGCACAA
CGTTTCATACTTACCTGGCAGGGGAGATACCATGAT

Sequence of entity 3 (O), FASTA

>7ZXE_3 TATA-box-binding protein (chains O)
MDQNNSLPPYAQGLASPQGAMTPGIPIFSPMMPYGTGLTPQPIQNTNSLSILEEQQRQQQ
QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQAVAAAAVQQSTSQQATQGTSGQAPQ
LFHSQTLTTAPLPGTTPLYPSPMTPMTPITPATPASESSGIVPQLQNIVSTVNLGCKLDL
KTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARV
VQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRI
VLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRKTT

Sequence of entity 4 (T), FASTA

>7ZXE_4 Template strand (chains T)
ATCATGGTATCTCCCCTGCCAGGTAAGTATGAAACGTTGTGCCTCTGCCCCGACACAGCC
TCATACGCCTCACTCTTTACACACACGGTCACTTGC

Sequence of entity 5 (U), FASTA

>7ZXE_5 Transcription initiation factor IIA subunit 1 (chains U)
MANSANTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAVDGFH
SEEQQLLLQVQQQHQPQQQQHHHHHHHQQAQPQQTVPQQAQTQQVLIPASQQATAPQVIV
PDSKLIQHMNASNMSAAATAATLALPAGVTPVQQILTNSGQLLQVVRAANGAQYIFQPQQ
SVVLQQQVIPQMQPGGVQAPVIQQVLAPLPGGISPQTGVIIQPQQILFTGNKTQVIPTTV
AAPTPAQAQITATGQQQPQAQPAQTQAPLVLQVDGTGDTSSEEDEDEEEDYDDDEEEDKE
KDGAEDGQVEEEPLNSEDDVSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNL
NGRDYIFSKAIGDAEW

Sequence of entity 6 (V), FASTA

>7ZXE_6 Transcription initiation factor IIA subunit 2 (chains V)
MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFRG
SLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNTGSNTTE

Sequence of entity 7 (a), FASTA

>7ZXE_7 snRNA-activating protein complex subunit 1 (chains a)
MGTPPGLQTDCEALLSRFQETDSVRFEDFTELWRNMKFGTIFCGRMRNLEKNMFTKEALA
LAWRYFLPPYTFQIRVGALYLLYGLYNTQLCQPKQKIRVALKDWDEVLKFQQDLVNAQHF
DAAYIFRKLRLDRAFHFTAMPKLLSYRMKKKIHRAEVTEEFKDPSDRVMKLITSDVLEEM
LNVHDHYQNMKHVISVDKSKPDKALSLIKDDFFDNIKNIVLEHQQWHKDRKNPSLKSKTN
DGEEKMEGNSQETERCERAESLAKIKSKAFSVVIQASKSRRHRQVKLDSSDSDSASGQGQ
VKATRKKEKKERLKPAGRKMSLRNKGNVQNIHKEDKPLSLSMPVITEEEENESLSGTEFT
ASKKRRKH

Sequence of entity 8 (b), FASTA

>7ZXE_8 snRNA-activating protein complex subunit 3 (chains b)
MAEGSRGGPTCSGVGGRQDPVSGSGGCNFPEYELPELNTRAFHVGAFGELWRGRLRGAGD
LSLREPPASALPGSQAADSDREDAAVARDLDCSLEAAAELRAVCGLDKLKCLEDGEDPEV
IPENTDLVTLGVRKRFLEHREETITIDRACRQETFVYEMESHAIGKKPENSADMIEEGEL
ILSVNILYPVIFHKHKEHKPYQTMLVLGSQKLTQLRDSIRCVSDLQIGGEFSNTPDQAPE
HISKDLYKSAFFYFEGTFYNDKRYPECRDLSRTIIEWSESHDRGYGKFQTARMEDFTFND
LCIKLGFPYLYCHQGDCEHVIVITDIRLVHHDDCLDRTLYPLLIKKHWLWTRKCFVCKMY
TARWVTNNDSFAPEDPCFFCDVCFRMLHYDSEGNKLGEFLAYPYVDPGTFN

Sequence of entity 9 (c), FASTA

>7ZXE_9 snRNA-activating protein complex subunit 4 (chains c)
MDVDAEREKITQEIKELERILDPGSSGSHVEISESSLESDSEADSLPSEDLDPADPPISE
EERWGEASNDEDDPKDKTLPEDPETCLQLNMVYQEVIQEKLAEANLLLAQNREQQEELMR
DLAGSKGTKVKDGKSLPPSTYMGHFMKPYFKDKVTGVGPPANEDTREKAAQGIKAFEELL
VTKWKNWEKALLRKSVVSDRLQRLLQPKLLKLEYLHQKQSKVSSELERQALEKQGREAEK
EIQDINQLPEEALLGNRLDSHDWEKISNINFEGSRSAEEIRKFWQNSEHPSINKQEWSRE
EEERLQAIAAAHGHLEWQKIAEELGTSRSAFQCLQKFQQHNKALKRKEWTEEEDRMLTQL
VQEMRVGSHIPYRRIVYYMEGRDSMQLIYRWTKSLDPGLKKGYWAPEEDAKLLQAVAKYG
EQDWFKIREEVPGRSDAQCRDRYLRRLHFSLKKGRWNLKEEEQLIELIEKYGVGHWAKIA
SELPHRSGSQCLSKWKIMMGKKQGLRRRRRRARHSVRWSSTSSSGSSSGSSGGSSSSSSS
SSEEDEPEQAQAGEGDRALLSPQYMVPDMDLWVPARQSTSQPWRGGAGAWLGGPAASLSP
PKGSSASQGGSKEASTTAAAPGEETSPVQVPARAHGPVPRSAQASHSADTRPAGAEKQAL
EGGRRLLTVPVETVLRVLRANTAARSCTQKEQLRQPPLPTSSPGVSSGDSVARSHVQWLR
HRATQSGQRRWRHALHRRLLNRRLLLAVTPWVGDVVVPCTQASQRPAVVQTQADGLREQL
QQARLASTPVFTLFTQLFHIDTAGCLEVVRERKALPPRLPQAGARDPPVHLLQASSSAQS
TPGHLFPNVPAQEASKSASHKGSRRLASSRVERTLPQASLLASTGPRPKPKTVSELLQEK
RLQEARAREATRGPVVLPSQLLVSSSVILQPPLPHTPHGRPAPGPTVLNVPLSGPGAPAA
AKPGTSGSWQEAGTSAKDKRLSTMQALPLAPVFSEAEGTAPAASQAPALGPGQISVSCPE
SGLGQSQAPAASRKQGLPEAPPFLPAAPSPTPLPVQPLSLTHIGGPHVATSVPLPVTWVL
TAQGLLPVPVPAVVSLPRPAGTPGPAGLLATLLPPLTETRAAQGPRAPALSSSWQPPANM
NREPEPSCRTDTPAPPTHALSQSPAEADGSVAFVPGEAQVAREIPEPRTSSHADPPEAEP
PWSGRLPAFGGVIPATEPRGTPGSPSGTQEPRGPLGLEKLPLRQPGPEKGALDLEKPPLP
QPGPEKGALDLGLLSQEGEAATQQWLGGQRGVRVPLLGSRLPYQPPALCSLRALSGLLLH
KKALEHKATSLVVGGEAERPAGALQASLGLVRGQLQDNPAYLLLRARFLAAFTLPALLAT
LAPQGVRTTLSVPSRVGSESEDEDLLSELELADRDGQPGCTTATCPIQGAPDSGKCSASS
CLDTSNDPDDLDVLRTRHARHTRKRRRLV

Sequence of entity 10 (d), FASTA

>7ZXE_10 snRNA-activating protein complex subunit 5 (chains d)
MLSRLQELRKEEETLLRLKAALHDQLNRLKVEELALQSMISSRRGDEMLSSHTVPEQSHD
MLVHVDNEASINQTTLELSTKSHVTEEEEEEEEEESDS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II. Rengachari, S., Schilbach, S., Kaliyappan, T. et al. Nat Struct Mol Biol (2022) 29:1159-1169. DOI 10.1038/s41594-022-00857-w · PubMed

Other PDB entries of the same protein (UniProt Q00403 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NVU 2.5 Å, RNA polymerase II core pre-initiation complex with open promoter DNA
1C9B 2.65 Å, Crystal structure of a human tbp core domain-human tfiib core domain complex bound to an…
1VOL 2.7 Å, Tfiib (human core domain)/tbp (a.thaliana)/tata element ternary complex
7NVS 2.8 Å, RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal…
7NVT 2.9 Å, RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position
8S52 2.9 Å, RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt
7ZWD 3.0 Å, Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter…
7ZX8 3.0 Å, Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter…
8S51 3.1 Å, RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt
7ZWC 3.2 Å, Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter
7EGB 3.3 Å, TFIID-based holo PIC on SCP promoter
5WH1 3.39 Å, Apo form of the C-terminal region of human Transcription Factor IIB

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