3JBQ: IgG1-kappa 2E8 light chain

Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6. Determined by electron microscopy at 11.0 Å resolution. Released 30 Sept 2015.

Method: Electron microscopy
Resolution: 11.0 Å
Organisms: Mus musculus, Bos taurus
Chains: 12
Atoms: 17,450
Mol. weight: 260.03 kDa
Released: 30 Sept 2015

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

Secondary structure: helices and β-sheets

3JBQ contains 89 α-helices and 126 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 1: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	57-67	11
α-helix	76-90	15
β-strand	93-100	8	32
β-strand	103-104	2	33
β-strand	107-108	2	33
β-strand	110-111	2	34
β-strand	112-117	6	32
α-helix	123-126	4
β-strand	135-136	2	34
α-helix	141-149	9
β-strand	153-155	3	35
α-helix	168-172	5
β-strand	179-181	3	35
β-strand	184-186	3	32
β-strand	189-199	11	32
α-helix	207-223	17

Chain 2: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	57-68	12
α-helix	76-90	15
β-strand	93-100	8	36
β-strand	103-104	2	37
β-strand	107-108	2	37
β-strand	110-111	2	38
β-strand	112-117	6	36
β-strand	135-136	2	38
α-helix	141-149	9
β-strand	153-155	3	39
α-helix	167-172	6
β-strand	179-181	3	39
β-strand	184-186	3	36
β-strand	189-199	11	36
α-helix	207-223	17

Chain B: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	533-544	12
α-helix	568-580	13
α-helix	584-588	5
α-helix	592-605	14
α-helix	615-630	16
α-helix	634-636	3
α-helix	640-651	12
α-helix	662-668	7
α-helix	671-675	5
β-strand	677	1	14
β-strand	679	1	14
α-helix	680-692	13
α-helix	701-703	3
α-helix	706-723	18
α-helix	725-739	15
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-786	15
α-helix	789-793	5
α-helix	799-802	4
α-helix	807-809	3
α-helix	813-820	8
α-helix	821-825	5
α-helix	826-834	9
α-helix	840-847	8
α-helix	849-857	9

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	392-403	12
α-helix	410-424	15
β-strand	429-432	4	15
β-strand	436	1	16
β-strand	439-442	4	16
β-strand	457-460	4	16
α-helix	465-472	8
β-strand	476-478	3	15
β-strand	502-506	5	15
β-strand	517-521	5	15
α-helix	529-530	2
α-helix	532-567	36

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	75-81	7

Chain F: 22 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	533-544	12
α-helix	568-580	13
α-helix	585-588	4
α-helix	592-605	14
α-helix	615-629	15
α-helix	634-636	3
α-helix	640-651	12
α-helix	662-668	7
α-helix	671-675	5
β-strand	677	1	17
β-strand	679	1	17
α-helix	680-692	13
α-helix	706-723	18
α-helix	725-739	15
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-792	21
α-helix	799-802	4
α-helix	807-811	5
α-helix	813-821	9
α-helix	822-826	5
α-helix	827-834	8
α-helix	840-847	8
α-helix	849-857	9

Chain G: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	391-403	13
α-helix	410-424	15
β-strand	429-433	5	18
β-strand	436	1	19
β-strand	439-442	4	19
β-strand	457-460	4	19
α-helix	465-472	8
β-strand	476-478	3	18
β-strand	502-506	5	18
β-strand	517-521	5	18
α-helix	529-530	2
α-helix	532-568	37

Chain h: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	27
α-helix	12-13	2
β-strand	19-20	2	27
β-strand	23-25	3	27
β-strand	32-39	8	28
β-strand	46-51	6	28
β-strand	57-59	3	28
β-strand	68-72	5	27
β-strand	77-81	5	27
β-strand	89-96	8	28
β-strand	102	1	22
β-strand	107-108	2	28
β-strand	117	1	29
β-strand	122-124	3	30
α-helix	126-129	4
β-strand	137-145	9	30
β-strand	146	1	29
β-strand	151-154	4	31
β-strand	164	1	30
α-helix	166-168	3
β-strand	175-182	8	30
α-helix	185-187	3
β-strand	194-199	6	31
β-strand	204-209	6	31

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
IgG1-kappa 2E8 light chain	L, l	protein	214	Mus musculus
IgG1-kappa 2E8 heavy chain	H, h	protein	220	Mus musculus
phosphodiesterase 5/6 chimera catalytic domain	B, F	protein	330	Bos taurus	P16586 (AlphaFold model), Q28156 (AlphaFold model)
phosphodiesterase 6 gamma subunit inhibitory peptide	D, X	protein	18	Bos taurus	P04972 (AlphaFold model)
GafB domain of phosphodiesterase 2A	C, G	protein	185	Bos taurus	P14099 (AlphaFold model)
GafA domain of cone phosphodiesterase 6C	1, 2	protein	186	Bos taurus	P52731

Sequence of entity 1 (L, l), FASTA

>3JBQ_1 IgG1-kappa 2E8 light chain (chains L, l)
DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQQKPGQSPKLMIYSASNRYTGVPD
RFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGAGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSATDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H, h), FASTA

>3JBQ_2 IgG1-kappa 2E8 heavy chain (chains H, h)
EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDEIGDTEYV
PKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSAA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 3 (B, F), FASTA

>3JBQ_3 phosphodiesterase 5/6 chimera catalytic domain (chains B, F)
GSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQM
KHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAA
LSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYK
TTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITK
PWPIQQRIAELVATEFWEQGDLERTVLQQQPIPMMDRNKRDELPKLQVGFIDFVCTQLYE
ALTHVSEDCFPLLDGCRKNRQKWQALAEQQ

Sequence of entity 4 (D, X), FASTA

>3JBQ_4 phosphodiesterase 6 gamma subunit inhibitory peptide (chains D, X)
WEAFNHLELHELAQYGII

Sequence of entity 5 (C, G), FASTA

>3JBQ_5 GafB domain of phosphodiesterase 2A (chains C, G)
QKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFD
GGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFP
IKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHL
ANEMM

Sequence of entity 6 (1, 2), FASTA

>3JBQ_6 GafA domain of cone phosphodiesterase 6C (chains 1, 2)
MRLEECNILFELLTEIQDEAGSMEKIVHKTLQRLSQLLAADRCSMFICRSRNGIPEVATR
LLNVTPTSKFEDNLVNPDKETVFPLDIGIAGWVAHTKKFFNIPDVKKNNHFSDYLDKKTG
YTTVNMMAIPITQGKEVLAVVMALNKLNASEFSKEDEEVFKKYLNFISLVLRLEHHHHHH
HHHHHH

Primary citation

Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6. Zhang, Z., He, F., Constantine, R. et al. J Biol Chem (2015) 290:12833-12843. DOI 10.1074/jbc.M115.647636 · PubMed

Other PDB entries of the same protein (UniProt P16586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

10OZ 3.06 Å, Structure of PDE5 PDE6 chimera
3JAB 11.0 Å, Domain organization and conformational plasticity of the G protein effector, PDE6

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