5GPY: Human TFIIE complex

Name: PDB 5GPY: Crystal structure of the human TFIIE complex
Published: 2016-11-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of the human TFIIE complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Nov 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,368
Mol. weight: 38.14 kDa
Ligands: ZN
Released: 2 Nov 2016

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

Secondary structure: helices and β-sheets

5GPY contains 15 α-helices and 13 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: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	12-25	14
α-helix	28-39	12
β-strand	43-44	2	1
α-helix	45-52	8
α-helix	56-68	13
β-strand	72-80	9	1
β-strand	86-94	9	1
α-helix	96-122	27
β-strand	127-128	2	2
β-strand	135-136	2	2
α-helix	138-142	5
β-strand	145-146	2	3
β-strand	151-152	2	3
β-strand	153	1	4
α-helix	159	1
β-strand	160	1	4
α-helix	161	1
β-strand	162-163	2	2
α-helix	176-193	18

Chain B: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	148-161	14
β-strand	166-167	2	5
α-helix	168-174	7
α-helix	178-184	7
α-helix	186-188	3
β-strand	189-193	5	5
β-strand	199-203	5	5
α-helix	214-221	8
α-helix	230-240	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
General transcription factor IIE subunit 1	A	protein	220	Homo sapiens	P29083 (AlphaFold model)
Transcription initiation factor IIE subunit beta	B	protein	108	Homo sapiens	P29084 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5GPY_1 General transcription factor IIE subunit 1 (chains A)
GSHMADPDVLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNSCVKEEDMLELLKFDRK
QLRSVLNNLKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETD
ERDSTNRASFKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEEDESAMPKKDARTLL
ARFNEQIEPIYALLRETEDVNLAYEILEPEPTEIPALKQS

Sequence of entity 2 (B), FASTA

>5GPY_2 Transcription initiation factor IIE subunit beta (chains B)
GSHMPKYNVRDKKALLRLLDQHDQRGLGGILLEDIEEALPNSQKAVKALGDQILFVNRPD
KKKILFFNDKSCQFSVDEEFQKLWRSVTVDSMDEEKIEEYLKRQGISS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Crystal Structure of Human General Transcription Factor TFIIE at Atomic Resolution. Miwa, K., Kojima, R., Obita, T. et al. J Mol Biol (2016) 428:4258-4266. DOI 10.1016/j.jmb.2016.09.008 · PubMed

Other PDB entries of the same protein (UniProt P29083 (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
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
7NVV 2.9 Å, XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3)
8S52 2.9 Å, RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt
8S51 3.1 Å, RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt
7EGB 3.3 Å, TFIID-based holo PIC on SCP promoter
8S54 3.4 Å, RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state b (composite…
8S55 3.4 Å, RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite…
8S5N 3.4 Å, RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt
7EG9 3.7 Å, TFIID-based intermediate PIC on SCP promoter
29TK 3.9 Å, RNA polymerase II elongation complex with the +1 nucleosome

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