4B9K: Transcription elongation factor B polypeptide 2

Name: PDB 4B9K: pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide bound
Published: 2012-10-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide bound. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 Oct 2012.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: HOMO SAPIENS
Chains: 12
Atoms: 11,711
Mol. weight: 173.73 kDa
Ligands: TG0
Released: 24 Oct 2012

Explore 4B9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4B9K contains 71 α-helices and 106 β-strands across 12 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: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
β-strand	10	1	2
β-strand	12-19	8	1
β-strand	23	1	3
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	1
β-strand	49-50	2	1
α-helix	51-52	2
β-strand	56	1	3
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-79	7	1
β-strand	80	1	5
β-strand	85	1	5
α-helix	86-88	3
β-strand	90	1	2
α-helix	91-100	10
α-helix	101-103	3

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	1
β-strand	28-32	5	1
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	1
α-helix	67-83	17
α-helix	90-94	5
α-helix	100-110	11

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	6
α-helix	83	1
β-strand	84-89	6	7
β-strand	95-97	3	7
β-strand	101	1	7
β-strand	106-112	7	6
β-strand	116-121	6	7
β-strand	127	1	7
β-strand	129-130	2	6
β-strand	133	1	6
β-strand	136	1	7
α-helix	146	1
β-strand	147-152	6	6
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-198	5

Chain D: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	10	1	9
β-strand	12-19	8	8
β-strand	23	1	10
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	8
β-strand	49-50	2	8
α-helix	51-52	2
β-strand	56	1	10
β-strand	68	1	11
β-strand	71	1	11
α-helix	72	1
β-strand	73-79	7	8
α-helix	85-88	4
β-strand	90	1	9
α-helix	91-99	9

Chain E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	8
β-strand	28-32	5	8
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	8
α-helix	67-83	17
α-helix	89-94	6
α-helix	100-110	11

Chain F: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	12
α-helix	83	1
β-strand	84-89	6	13
β-strand	95-97	3	13
β-strand	101	1	13
β-strand	106-112	7	12
β-strand	116-121	6	13
β-strand	127	1	13
β-strand	129-130	2	12
β-strand	133	1	12
β-strand	136	1	13
α-helix	142-144	3
α-helix	145-146	2
β-strand	147-152	6	12
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-202	9

Chains G and J: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	14
β-strand	10	1	15
β-strand	12-19	8	14
β-strand	23	1	16
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	14
β-strand	49-50	2	14
α-helix	51-52	2
β-strand	56	1	16
β-strand	68	1	17
β-strand	71	1	17
α-helix	72	1
β-strand	73-79	7	14
β-strand	80-81	2	18
β-strand	84-85	2	18
α-helix	86-88	3
β-strand	90	1	15
α-helix	91-100	10

Chain H: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	14
β-strand	28-32	5	14
α-helix	33-36	4
α-helix	40-47	8
β-strand	59-61	3	14
α-helix	67-83	17
α-helix	90-94	5
α-helix	97-110	14

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription elongation factor B polypeptide 2	A, D, G, J	protein	104	HOMO SAPIENS	Q15370 (AlphaFold model)
Transcription elongation factor B polypeptide 1	B, H, K	protein	97	HOMO SAPIENS	Q15369 (AlphaFold model)
Von hippel-lindau disease tumor suppressor	C, F, I, L	protein	171	HOMO SAPIENS	P40337 (AlphaFold model)
Transcription elongation factor B polypeptide 1	E	protein	97	HOMO SAPIENS	Q15369 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>4B9K_1 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 (chains A, D, G, J)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 2 (B, H, K), FASTA

>4B9K_2 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 (chains B, H, K)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (C, F, I, L), FASTA

>4B9K_3 VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR (chains C, F, I, L)
SMSENLYFQGSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLP
PGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERC
LQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 4 (E), FASTA

>4B9K_4 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 (chains E)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Ligands and cofactors

ID	Name	Formula	Copies
TG0	(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl…	C24 H26 N4 O3 S	4

Water and common crystallization additives (ACT) are not listed.

Primary citation

Small-Molecule Inhibitors of the Interaction between the E3 Ligase Vhl and Hif1 Alpha. Buckley, D.L., Gustafson, J.L., Van Molle, I. et al. Angew Chem Int Ed Engl (2012) 51:11463. DOI 10.1002/ANIE.201206231 · PubMed

Other PDB entries of the same protein (UniProt Q15370 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
9GIO 1.49 Å, Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of…
7JTO 1.7 Å, Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and…
8BDS 1.72 Å, Ternary complex between VCB, BRD4-BD1 and PROTAC 48
4AJY 1.73 Å, von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
6GMR 1.75 Å, pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol
6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
6I7Q 1.8 Å, Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha…
8BB3 1.8 Å, Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker…
6GFX 1.83 Å, pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing…
1LM8 1.85 Å, Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex

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