7PDV: RBM5 RRM1-zinc finger

Crystal structure of RBM5 RRM1-zinc finger in complex with RNA. Determined by X-ray diffraction at 3.49 Å resolution. Released 24 Aug 2022.

Method: X-ray diffraction
Resolution: 3.49 Å
Organism: Homo sapiens
Chains: 5
Atoms: 3,426
Mol. weight: 59.09 kDa
Ligands: ZN
Released: 24 Aug 2022

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

Secondary structure: helices and β-sheets

7PDV contains 8 α-helices and 32 β-strands across 4 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: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	1
α-helix	20-24	5
β-strand	38-40	3	1
β-strand	50-54	5	1
α-helix	59-68	10
β-strand	74-75	2	2
β-strand	78-79	2	2
β-strand	82-84	3	1

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	3
α-helix	20-24	5
β-strand	37-40	4	3
β-strand	50-55	6	3
α-helix	62-64	3
β-strand	74-75	2	4
β-strand	78-79	2	4
β-strand	83-84	2	3
β-strand	95	1	5
β-strand	102	1	5

Chain E: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	6
α-helix	20-23	4
β-strand	38-39	2	6
β-strand	43	1	7
β-strand	46	1	7
β-strand	50-54	5	6
α-helix	59-66	8
β-strand	74-75	2	8
β-strand	78-79	2	8
β-strand	83	1	6
β-strand	94-95	2	9
β-strand	102-103	2	9

Chain G: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	10
α-helix	20-23	4
β-strand	37-39	3	10
β-strand	52-55	4	10
α-helix	59-69	11
β-strand	74-75	2	11
β-strand	78-79	2	11
β-strand	83-84	2	10
β-strand	94-96	3	12
β-strand	101-103	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA binding motif protein 5 isoform 1	A, C, E, G	protein	119	Homo sapiens	P52756 (AlphaFold model)
RNA (5'-r(pupgpgpcpupcpupupcpu)-3')	F	RNA	10	Homo sapiens

Sequence of entity 1 (A, C, E, G), FASTA

>7PDV_1 RNA binding motif protein 5 isoform 1 (chains A, C, E, G)
MGERESKTIMLRGLPTTITESDIREMMESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQ
DATSWMEANQKKLVIQGKHIAMHYSNPRPKFEDWLCNKCGLNNFRKRLKCFRCGADKFD

Sequence of entity 2 (F), FASTA

>7PDV_2 RNA (5'-R(P*UP*GP*GP*CP*UP*CP*UP*UP*CP*U)-3') (chains F)
UGGCUCUUCU

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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:

7PCV 2.42 Å, Crystal structure of RBM5 RRM1-zinc finger
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…
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

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