1C9B: General transcription factor iib

Crystal structure of a human tbp core domain-human tfiib core domain complex bound to an extended, modified adenoviral major late promoter (ADMLP). Determined by X-ray diffraction at 2.65 Å resolution. Released 10 Jan 2000.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 20
Atoms: 19,199
Mol. weight: 272.22 kDa
Released: 10 Jan 2000

Explore 1C9B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1C9B contains 93 α-helices and 62 β-strands across 10 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.

Chains A, M and Q: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	111-113	3
α-helix	114-127	14
α-helix	132-148	17
α-helix	156-170	15
α-helix	177-182	6
α-helix	188-201	14
α-helix	207-209	3
α-helix	212-221	10
α-helix	226-241	16
α-helix	250-263	14
α-helix	271-278	8
α-helix	282-292	11
α-helix	293-295	3
α-helix	296-299	4

Chains B and N: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	163	1
β-strand	164-173	10	1
α-helix	180-186	7
β-strand	200-202	3	1
β-strand	205	1	2
β-strand	208	1	2
β-strand	210-213	4	1
β-strand	218-224	7	1
α-helix	227-243	17
β-strand	251-263	13	1
β-strand	268	1	3
α-helix	270-277	8
β-strand	291-295	5	1
β-strand	300-304	5	1
β-strand	309-315	7	1
α-helix	318-333	16
β-strand	336	1	3

Chain E: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	114-127	14
α-helix	132-148	17
α-helix	156-170	15
α-helix	177-182	6
α-helix	188-201	14
α-helix	212-221	10
α-helix	226-241	16
α-helix	250-263	14
α-helix	271-278	8
α-helix	282-292	11
α-helix	293-295	3
α-helix	296-299	4

Chain F: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	163	1
β-strand	164-173	10	4
α-helix	180-186	7
β-strand	200-202	3	4
β-strand	205	1	5
β-strand	208	1	5
β-strand	210-213	4	4
β-strand	218-224	7	4
α-helix	227-243	17
β-strand	251-263	13	4
β-strand	268	1	6
α-helix	270-277	8
β-strand	291-294	4	4
β-strand	301-304	4	4
β-strand	309-315	7	4
α-helix	318-333	16
β-strand	336	1	6

Chain I: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	111-113	3
α-helix	114-127	14
α-helix	132-148	17
α-helix	156-170	15
α-helix	177-182	6
α-helix	188-201	14
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	282-292	11
α-helix	293-295	3
α-helix	296-299	4

Chains J and R: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	163	1
β-strand	164-173	10	7
α-helix	180-186	7
β-strand	200-202	3	7
β-strand	205	1	8
β-strand	208	1	8
β-strand	210-213	4	7
β-strand	218-224	7	7
α-helix	227-243	17
β-strand	251-263	13	7
β-strand	268	1	9
α-helix	270-277	8
β-strand	281-282	2	7
β-strand	291-295	5	7
β-strand	300-304	5	7
β-strand	309-315	7	7
α-helix	318-333	16
β-strand	336	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Admlp tata-box DNA containing iib recognition element	C, G, K, O, S	DNA	18
Admlp tata-box DNA containing iib recognition element	D, H, L, P, T	DNA	18
General transcription factor iib	A, E, I, M, Q	protein	207	Homo sapiens	Q00403 (AlphaFold model)
Tata box binding protein	B, F, J, N, R	protein	180	Homo sapiens	P20226 (AlphaFold model)

Sequence of entity 1 (C, G, K, O, S), FASTA

>1C9B_1 ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT (chains C, G, K, O, S)
GGGCGCCTATAAAAGGGG

Sequence of entity 2 (D, H, L, P, T), FASTA

>1C9B_2 ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT (chains D, H, L, P, T)
CCCCCTTTTATAGGCGCC

Sequence of entity 3 (A, E, I, M, Q), FASTA

>1C9B_3 GENERAL TRANSCRIPTION FACTOR IIB (chains A, E, I, M, Q)
SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACR
QEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQ
MAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY
RLIYPRAPDLFPTDFKFDTPVDKLPQL

Sequence of entity 4 (B, F, J, N, R), FASTA

>1C9B_4 TATA BOX BINDING PROTEIN (chains B, F, J, N, R)
GSGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSG
KMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTH
QQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK

Primary citation

Structural basis of preinitiation complex assembly on human pol II promoters. Tsai, F.T., Sigler, P.B. EMBO J (2000) 19:25-36. DOI 10.1093/emboj/19.1.25 · 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
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
7ZX7 3.4 Å, Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter…

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