4ROD: Human TFIIB-related factor 2 (Brf2) and TBP

Human TFIIB-related factor 2 (Brf2) and TBP bound to TRNAU1 promoter. Determined by X-ray diffraction at 2.7 Å resolution. Released 30 Dec 2015.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 5,047
Mol. weight: 78.01 kDa
Released: 30 Dec 2015

Explore 4ROD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ROD contains 26 α-helices and 14 β-strands across 2 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: 21 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	67-82	16
α-helix	87-101	15
α-helix	104-107	4
α-helix	111-128	18
α-helix	135-142	8
α-helix	146-159	14
α-helix	164-167	4
α-helix	169-178	10
β-strand	186	1	1
β-strand	189	1	1
α-helix	191-193	3
α-helix	197-213	17
α-helix	222-237	16
α-helix	239-242	4
α-helix	247-253	7
α-helix	262-277	16
α-helix	281-284	4
α-helix	294-296	3
α-helix	297-302	6
α-helix	304-313	10
α-helix	374-376	3
α-helix	386-390	5
β-strand	393	1	2
α-helix	396-406	11

Chain B: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	163	1
β-strand	164-173	10	3
α-helix	180-186	7
β-strand	187	1	2
β-strand	190-193	4	3
β-strand	197-204	8	3
β-strand	209-213	5	3
β-strand	218-224	7	3
α-helix	227-243	17
β-strand	251-263	13	3
α-helix	270-276	7
β-strand	281-282	2	3
β-strand	291-295	5	3
β-strand	300-304	5	3
β-strand	309-315	7	3
α-helix	318-333	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor IIIB 50 kDa subunit	A	protein	360	Homo sapiens	Q9HAW0 (AlphaFold model)
TATA-box-binding protein	B	protein	183	Homo sapiens	P20226 (AlphaFold model)
Template strand	N	DNA	28	synthetic construct
Non-template strand	T	DNA	28	synthetic construct

Sequence of entity 1 (A), FASTA

>4ROD_1 Transcription factor IIIB 50 kDa subunit (chains A)
GPNEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYRHSGIRAARLQKKEVLVG
CCVLITCRQHNWPLTMGAICTLLYADLDVFSSTYMQIVKLLGLDVPSLCLAELVKTYCSS
FKLFQASPSVPAKYVEDKEKMLSRTMQLVELANETWLVTGRHPLPVITAATFLAWQSLQP
ADRLSCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAWLRVLRLDKRSVVKHIGD
LLQHRQSLVRSAFRDGTAEVETREKEPPGWGQGQGEGEVGNNSLGLPQGKRPASPALLLP
PCMLKSPKRICPVPPVSTVTGDENISDSEIEQYLRTPQEVRDFQRAQAARQAATSVPNPP

Sequence of entity 2 (B), FASTA

>4ROD_2 TATA-box-binding protein (chains B)
GPSGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSS
GKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLT
HQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFR
KTT

Sequence of entity 3 (N), FASTA

>4ROD_3 Template strand (chains N)
TTTTGCGATCCTTATATAGCTGCGCGGG

Sequence of entity 4 (T), FASTA

>4ROD_4 Non-template strand (chains T)
CCCGCGCAGCTATATAAGGATCGCAAAA

Primary citation

Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2. Gouge, J., Satia, K., Guthertz, N. et al. Cell (2015) 163:1375-1387. DOI 10.1016/j.cell.2015.11.005 · PubMed

Other PDB entries of the same protein (UniProt Q9HAW0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ROC 1.9 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter
4ROE 2.2 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to RPPH1 promoter
5N9G 2.7 Å, TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-
9K39 2.8 Å, Human RNA Polymerase III de novo transcribing complex 8 (TC8)
9K36 2.9 Å, Human RNA Polymerase III de novo transcribing complex 12 (TC12)
9K2G 3.0 Å, Human RNA Polymerase III de novo transcribing complex 13 (TC13)
9K3U 3.0 Å, Human RNA Polymerase III de novo transcribing complex 5 (TC5)
9K38 3.1 Å, Human RNA Polymerase III de novo transcribing complex 6 (TC6)
9FSO 3.28 Å, Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1)
9LXN 3.3 Å, Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP)
9FSP 3.39 Å, RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2)
8IUH 3.4 Å, RNA polymerase III pre-initiation complex open complex 1

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