6D0Y: PGC-1beta C-terminus

Name: PDB 6D0Y: X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding Complex
Published: 2018-04-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding Complex. Determined by X-ray diffraction at 2.68 Å resolution. Released 25 Apr 2018.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,644
Mol. weight: 115.46 kDa
Ligands: MG, GTA
Released: 25 Apr 2018

Explore 6D0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D0Y contains 57 α-helices and 15 β-strands across 3 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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	29-37	9
β-strand	41-45	5	4
α-helix	53-60	8
α-helix	61-63	3
β-strand	66-73	8	4
β-strand	80-88	9	4
α-helix	91-96	6
α-helix	97-101	5
β-strand	105-106	2	5
β-strand	109-110	2	5
β-strand	112-115	4	4
β-strand	125	1	4
α-helix	134-136	3
β-strand	143	1	6
β-strand	148	1	6

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11

Chain C: 50 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	27-36	10
α-helix	46-59	14
α-helix	61-78	18
α-helix	80-82	3
α-helix	83-96	14
α-helix	98-117	20
α-helix	121-136	16
β-strand	140	1	1
α-helix	142-153	12
α-helix	154-157	4
α-helix	163-187	25
α-helix	190-204	15
α-helix	211-214	4
β-strand	217	1	2
β-strand	227	1	3
α-helix	228-241	14
α-helix	252-256	5
α-helix	257-261	5
α-helix	263-265	3
β-strand	266	1	1
α-helix	267-271	5
α-helix	273-276	4
α-helix	282-285	4
β-strand	287	1	3
α-helix	294-296	3
α-helix	302-305	4
α-helix	309-325	17
α-helix	329-337	9
α-helix	347-359	13
α-helix	370-382	13
α-helix	387-400	14
α-helix	402-404	3
β-strand	405	1	2
α-helix	407-422	16
α-helix	430-436	7
α-helix	444-459	16
α-helix	462-468	7
α-helix	471-476	6
α-helix	478-480	3
α-helix	498-509	12
α-helix	514-520	7
α-helix	541-554	14
α-helix	559-568	10
α-helix	570-576	7
α-helix	580-594	15
α-helix	598-610	13
α-helix	616-623	8
α-helix	626-631	6
α-helix	635-669	35
α-helix	687-731	45
α-helix	738-753	16
α-helix	755-758	4
α-helix	759-761	3
α-helix	762-764	3
α-helix	765-769	5
α-helix	776-792	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear cap-binding protein subunit 1	C	protein	782	Homo sapiens	Q09161 (AlphaFold model)
Nuclear cap-binding protein subunit 2	A	protein	176	Homo sapiens	P52298 (AlphaFold model)
Peroxisome proliferator-activated receptor gamma coactivator 1-beta	B	protein	31	Homo sapiens	Q86YN6 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6D0Y_1 Nuclear cap-binding protein subunit 1 (chains C)
MANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLLPEK
LTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHVIAA
PSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFANTESY
LKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDSILCE
ALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENLHCII
KSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIELCKL
QPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDCLSQDPE
SPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPVNPTCIYKYGDESSNSLPGHSVAL
CLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFNPLKIEVFVQTLLHLAAKSFSHS
FSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAAVANW
IFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELEEAKEKLARQHKRRSDDDDRSSD
RKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTPWYKN
CIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQAAENLYFQGHHHH
HH

Sequence of entity 2 (A), FASTA

>6D0Y_2 Nuclear cap-binding protein subunit 2 (chains A)
GPLHMGGSPEFPGRLEAADPMSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSC
TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY
INGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

Sequence of entity 3 (B), FASTA

>6D0Y_3 Peroxisome proliferator-activated receptor gamma coactivator 1-beta (chains B)
XSEEALPASGKSKYEAMDFDSLLKEAQQSLH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GTA	P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate	C21 H30 N10 O17 P3	1

Primary citation

Transcriptional coactivator PGC-1 alpha contains a novel CBP80-binding motif that orchestrates efficient target gene expression. Cho, H., Rambout, X., Gleghorn, M.L. et al. Genes Dev (2018) 32:555-567. DOI 10.1101/gad.309773.117 · PubMed

Other PDB entries of the same protein (UniProt Q09161 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1H2V 2.0 Å, Structure of the human nuclear cap-binding-complex (CBC)
1H6K 2.0 Å, nuclear Cap Binding Complex
1H2T 2.1 Å, Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue…
1N52 2.11 Å, Cap Binding Complex
3FEY 2.2 Å, Crystal structure of the CBC-importin alpha complex.
1H2U 2.4 Å, Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue…
9HFL 2.62 Å, Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and…
1N54 2.72 Å, Cap Binding Complex m7GpppG free
5OOB 2.79 Å, Complex of human nuclear cap-binding complex with M7GTP and nelf-E C-terminal peptide
5OO6 2.8 Å, Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide
8BY6 3.19 Å, Structure of the human nuclear cap-binding complex bound to NCBP3(560-620) and…
8SRR 3.22 Å, Cryo-EM structure of the CBC-ALYREF complex

Browse structure collections

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