3H2U: Human raver1 RRM1, RRM2, and RRM3 domains

Human raver1 RRM1, RRM2, and RRM3 domains in complex with human vinculin tail domain Vt. Determined by X-ray diffraction at 2.75 Å resolution. Released 28 Jul 2009.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,167
Mol. weight: 105.2 kDa
Released: 28 Jul 2009

Explore 3H2U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3H2U contains 38 α-helices and 44 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: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	896-910	15
β-strand	912	1	1
α-helix	918-936	19
α-helix	943-971	29
β-strand	972	1	2
α-helix	975-986	12
α-helix	988-1005	18
α-helix	1013-1044	32
β-strand	1048	1	2
β-strand	1060	1	1

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	41-56	16
β-strand	60-64	5	3
α-helix	72-78	7
β-strand	84-90	7	3
β-strand	95-100	6	3
α-helix	103-113	11
β-strand	117-118	2	4
β-strand	121-122	2	4
α-helix	123	1
β-strand	124-127	4	3
α-helix	128-129	2
β-strand	133-137	5	5
α-helix	145-152	8
β-strand	158-165	8	5
β-strand	172-180	9	5
α-helix	183-193	11
β-strand	197-198	2	6
β-strand	201-202	2	6
β-strand	204-208	5	5
β-strand	222-226	5	7
α-helix	228-229	2
α-helix	235-241	7
β-strand	250-255	6	7
β-strand	261-268	8	7
α-helix	272-282	11
β-strand	286-287	2	8
β-strand	290-291	2	8
α-helix	292	1
β-strand	293-296	4	7
α-helix	297-298	2
α-helix	303-315	13

Chain C: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	896-909	14
β-strand	912	1	9
α-helix	918-936	19
α-helix	943-970	28
β-strand	972	1	10
α-helix	975-986	12
α-helix	988-1005	18
α-helix	1013-1043	31
β-strand	1048	1	10
β-strand	1060	1	9

Chain D: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	41-56	16
β-strand	60-64	5	11
α-helix	72-78	7
β-strand	86-90	5	11
β-strand	95-99	5	11
α-helix	103-113	11
β-strand	117-118	2	12
β-strand	121-122	2	12
β-strand	124-127	4	11
α-helix	128-129	2
β-strand	133-137	5	13
α-helix	145-152	8
α-helix	153-155	3
β-strand	158-165	8	13
β-strand	172-180	9	13
α-helix	183-193	11
β-strand	197-198	2	14
β-strand	201-202	2	14
β-strand	204-207	4	13
α-helix	215-218	4
β-strand	222-226	5	15
α-helix	228-229	2
α-helix	236-241	6
β-strand	250-254	5	15
β-strand	262-268	7	15
α-helix	272-282	11
β-strand	286-287	2	16
β-strand	290-291	2	16
β-strand	293-296	4	15
α-helix	297-298	2
α-helix	303-315	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	A, C	protein	188	Homo sapiens	P18206 (AlphaFold model)
Raver-1	B, D	protein	283	Homo sapiens	Q8IY67 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3H2U_1 Vinculin (chains A, C)
EEKDEEFPEQKAGEVINQPMMMAARQLHDEARKWSSKGNDIIAAAKRMALLMAEMSRLVR
GGSGTKRALIQCAKDIAKASDEVTRLAKEVAKQCTDKRIRTNLLQVCERIPTISTQLKIL
STVKATMLGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRW
VRKTPWYQ

Sequence of entity 2 (B, D), FASTA

>3H2U_2 Raver-1 (chains B, D)
LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFV
TLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSL
ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALL
HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA
QQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATALNRG

Primary citation

Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions. Lee, J.H., Rangarajan, E.S., Yogesha, S.D. et al. Structure (2009) 17:833-842. DOI 10.1016/j.str.2009.04.010 · PubMed

Other PDB entries of the same protein (UniProt P18206 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LN2 1.0 Å, The second SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin
4LNP 1.41 Å, The first SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin
3RF3 1.61 Å, Shigella IpaA-VBS3 in complex with human vinculin
1YDI 1.8 Å, Human Vinculin Head Domain (VH1, 1-258) in Complex with Human Alpha-Actinin's…
3S90 1.97 Å, Human vinculin head domain Vh1 (residues 1-252) in complex with murine talin (VBS33;…
3TJ5 1.99 Å, human vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding…
3MYI 2.2 Å, Human metavinculin tail domain
4DJ9 2.25 Å, Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin…
1RKE 2.35 Å, Human vinculin head (1-258) in complex with human vinculin tail (879-1066)
1SYQ 2.42 Å, Human vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin…
5L0I 2.45 Å, Human metavinculin MVt R975W cardiomyopathy-associated mutant (residues 959-1134)
3VF0 2.54 Å, Raver1 in complex with metavinculin L954 deletion mutant

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