9B9L: RPRD1B C-terminal interacting domain

Name: PDB 9B9L: RPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide
Published: 2024-08-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

RPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide. Determined by X-ray diffraction at 2.5 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,172
Mol. weight: 32.09 kDa
Released: 7 Aug 2024

Explore 9B9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B9L contains 20 α-helices and 2 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: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-13	10
β-strand	17	1	1
α-helix	18-30	13
α-helix	32-34	3
α-helix	35-48	14
α-helix	51-67	17
α-helix	68-70	3
α-helix	74-91	18
α-helix	100-112	13
α-helix	117-123	7

Chain B: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	4-12	9
α-helix	18-30	13
α-helix	32-34	3
α-helix	35-46	12
α-helix	51-53	3
α-helix	54-68	15
α-helix	74-91	18
α-helix	102-111	10
α-helix	117-125	9

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	142-143	2
β-strand	144	1	1
α-helix	145	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulation of nuclear pre-mRNA domain-containing protein 1B	A, B	protein	131	Homo sapiens	Q9NQG5 (AlphaFold model)
Ser-pro-thr-ser-pro-ser-tyr-ser-pro-tpo-ser-pro-ser-tyr-ser	C	protein	15	Homo sapiens	P24928 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9B9L_1 Regulation of nuclear pre-mRNA domain-containing protein 1B (chains A, B)
SFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYL
ANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI
QQLKLSMEDSK

Sequence of entity 2 (C), FASTA

>9B9L_2 SER-PRO-THR-SER-PRO-SER-TYR-SER-PRO-TPO-SER-PRO-SER-TYR-SER (chains C)
SPTSPSYSPTSPSYS

Primary citation

Thr 4 phosphorylation on RNA Pol II occurs at early transcription regulating 3'-end processing. Moreno, R.Y., Panina, S.B., Irani, S. et al. Sci Adv (2024) 10:eadq0350-eadq0350. DOI 10.1126/sciadv.adq0350 · PubMed

Other PDB entries of the same protein (UniProt Q9NQG5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4Q94 1.85 Å, human RPRD1B CID in complex with a RPB1-CTD derived Ser2 phosphorylated peptide
4Q96 1.85 Å, CID of human RPRD1B in complex with an unmodified CTD peptide
4FU3 1.9 Å, CID of human RPRD1B
4HFG 2.0 Å, CID of human RPRD1B
4FLA 2.2 Å, Crystal structure of human RPRD1B, carboxy-terminal domain
4NAD 2.8 Å, Crystal Structure of the C-terminal Domain of CREPT

Browse structure collections

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