7PCV: RBM5 RRM1-zinc finger

Crystal structure of RBM5 RRM1-zinc finger. Determined by X-ray diffraction at 2.42 Å resolution. Released 17 Aug 2022.

Method: X-ray diffraction
Resolution: 2.42 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,889
Mol. weight: 28.09 kDa
Ligands: ZN
Released: 17 Aug 2022

Explore 7PCV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PCV contains 6 α-helices and 20 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: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
α-helix	20-27	8
α-helix	34-35	2
β-strand	37-42	6	1
β-strand	48-55	8	1
α-helix	59-69	11
β-strand	74-75	2	2
β-strand	78-79	2	2
β-strand	81-85	5	1
β-strand	94-95	2	3
β-strand	102-103	2	3
β-strand	109	1	4
β-strand	116	1	4

Chain B: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	5
α-helix	20-27	8
α-helix	33-35	3
β-strand	37-42	6	5
β-strand	48-55	8	5
α-helix	59-68	10
β-strand	74-75	2	6
β-strand	78-79	2	6
β-strand	81-85	5	5
β-strand	94-95	2	7
β-strand	102-103	2	7
β-strand	109	1	8
β-strand	116	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-binding protein 5	A, B	protein	119	Homo sapiens	P52756 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7PCV_1 RNA-binding protein 5 (chains A, B)
MGERESKTIMLRGLPTTITESDIREMMESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQ
DATSWMEANQKKLVIQGKHIAMHYSNPRPKFEDWLCNKCCLNNFRKRLKCFRCGADKFD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural basis for specific RNA recognition by the alternative splicing factor RBM5. Soni, K., Jagtap, P.K.A., Martinez-Lumbreras, S. et al. Nat Commun (2023) 14:4233-4233. DOI 10.1038/s41467-023-39961-w · PubMed

Other PDB entries of the same protein (UniProt P52756 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9ZE2 3.26 Å, Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (core)
9ZE0 3.43 Å, Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Proximal DHX15…
7PDV 3.49 Å, Crystal structure of RBM5 RRM1-zinc finger in complex with RNA
9ZEC 3.61 Å, Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 1)
9ZE3 3.93 Å, Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Distal DHX15…
9ZED 3.94 Å, Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 2)
2LK0 Solution structure and binding studies of the RanBP2-type zinc finger of RBM5
2LK1 Solution structure and binding studies of the RanBP2-type zinc finger of RBM5
2LKZ Solution structure of the second RRM domain of RBM5
5MF9 Solution structure of the RBM5 OCRE domain in complex with polyproline SmN peptide.
5MFY RBM5 OCRE domain

Browse structure collections

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