8EMW: Phospholipase C beta 3

Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes. Determined by electron microscopy at 3.5 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 5
Atoms: 11,714
Mol. weight: 229.14 kDa
Ligands: CA
Released: 24 May 2023

Explore 8EMW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EMW contains 39 α-helices and 121 β-strands across 5 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: 29 helices, 54 β-strands

Element	Residues	Length	Sheet
α-helix	20-23	4
β-strand	26-28	3	1
β-strand	41-43	3	1
β-strand	44-45	2	2
β-strand	51	1	3
β-strand	52-53	2	2
β-strand	54-55	2	4
β-strand	61-62	2	4
β-strand	65	1	3
α-helix	66-68	3
β-strand	69-74	6	5
α-helix	75-77	3
α-helix	84-90	7
β-strand	103-108	6	5
β-strand	119-121	3	5
β-strand	122	1	1
α-helix	128-139	12
α-helix	142-144	3
α-helix	151-154	4
α-helix	158-162	5
β-strand	170-171	2	6
α-helix	172-178	7
α-helix	183-193	11
β-strand	202-203	2	6
α-helix	210-220	11
α-helix	224-232	9
β-strand	240-241	2	7
α-helix	244-253	10
α-helix	272-279	8
β-strand	291-292	2	7
α-helix	293-299	7
β-strand	326-328	3	8
β-strand	330-331	2	9
β-strand	336	1	10
β-strand	344	1	11
β-strand	345	1	10
α-helix	348-356	9
β-strand	360	1	12
β-strand	363	1	13
β-strand	365-366	2	14
β-strand	376-377	2	14
β-strand	385	1	11
β-strand	387-388	2	14
α-helix	390-397	8
β-strand	408-411	4	12
β-strand	412	1	13
α-helix	419-432	14
α-helix	434-436	3
β-strand	437	1	12
α-helix	453-455	3
β-strand	463-466	4	12
α-helix	584-586	3
α-helix	590-592	3
β-strand	599	1	15
α-helix	605-611	7
β-strand	617	1	15
β-strand	620-621	2	16
α-helix	633-639	7
β-strand	644	1	15
β-strand	647-648	2	16
α-helix	662-665	4
β-strand	672	1	16
β-strand	673-674	2	9
β-strand	698-700	3	8
α-helix	701-702	2
α-helix	703-705	3
β-strand	726-730	5	17
β-strand	731-734	4	18
β-strand	745-752	8	19
β-strand	759	1	19
β-strand	763	1	19
β-strand	775	1	18
α-helix	779-780	2
β-strand	781-786	6	17
β-strand	793-800	8	19
β-strand	805-809	5	19
β-strand	812	1	19
β-strand	819-821	3	18
β-strand	824-826	3	19
β-strand	832-837	6	19
β-strand	839-842	4	18
β-strand	845-846	2	17
α-helix	868-880	13

Chain B: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	5-25	21
α-helix	30-33	4
α-helix	34-36	3
β-strand	47-51	5	20
β-strand	58-61	4	21
β-strand	69-74	6	21
β-strand	78-83	6	21
β-strand	91-94	4	21
β-strand	100-103	4	22
β-strand	111-116	6	22
β-strand	121-125	5	22
β-strand	135-139	5	22
β-strand	148-151	4	23
β-strand	157-160	4	23
β-strand	165	1	24
β-strand	168	1	25
β-strand	178	1	25
β-strand	181	1	24
β-strand	187-192	6	26
β-strand	198-203	6	26
β-strand	207-212	6	26
β-strand	218-223	6	26
β-strand	229-234	6	27
β-strand	240-245	6	27
β-strand	250-254	5	27
β-strand	262-264	3	27
β-strand	273-278	6	28
β-strand	284-289	6	28
β-strand	294-298	5	28
β-strand	307-308	2	28
β-strand	315-317	3	20
β-strand	320	1	20
β-strand	327-331	5	20
β-strand	336-339	4	20

Chain C: 3 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	13-25	13
β-strand	47-51	5	29
β-strand	58	1	30
β-strand	62-63	2	31
β-strand	69-72	4	31
β-strand	74	1	30
β-strand	78-79	2	32
β-strand	80-83	4	31
β-strand	88-89	2	31
β-strand	93-94	2	32
β-strand	105	1	33
β-strand	111-112	2	33
β-strand	120-121	2	34
β-strand	124-125	2	33
β-strand	135	1	33
β-strand	139-140	2	34
β-strand	146-151	6	35
β-strand	156-161	6	35
β-strand	165-170	6	35
β-strand	176-181	6	35
β-strand	187-192	6	36
β-strand	198-203	6	36
β-strand	208-212	5	36
β-strand	217-222	6	36
β-strand	232-234	3	37
β-strand	240-243	4	37
β-strand	250	1	38
β-strand	253-254	2	37
β-strand	260	1	37
β-strand	264	1	38
α-helix	272-273	2
β-strand	276-278	3	39
β-strand	284-287	4	39
β-strand	295-298	4	39
β-strand	303-307	5	39
β-strand	315-320	6	29
β-strand	327-331	5	29
β-strand	336-339	4	29

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	30-43	14

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	30-42	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3	A	protein	1232	Homo sapiens	Q01970 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B, C	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D, G	protein	70	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8EMW_1 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 (chains A)
GPSRATMALQLEPPTVVETLRRGSKFIKWDEETSSRNLVTLRVDPNGFFLYWTGPNMEVD
TLDISSIRDTRTGRYARLPKDPKIREVLGFGGPDARLEEKLMTVVSGPDPVNTVFLNFMA
VQDDTAKVWSEELFKLAMNILAQNASRNTFLRKAYTKLKLQVNQDGRIPVKNILKMFSAD
KKRVETALESCGLKFNRSESIRPDEFSLEIFERFLNKLCLRPDIDKILLEIGAKGKPYLT
LEQLMDFINQKQRDPRLNEVLYPPLRPSQARLLIEKYEPNQQFLERDQMSMEGFSRYLGG
EENGILPLEALDLSTDMTQPLSAYFINSSHNTYLTAGQLAGTSSVEMYRQALLWGCRCVE
LDVWKGRPPEEEPFITHGFTMTTEVPLRDVLEAIAETAFKTSPYPVILSFENHVDSAKQQ
AKMAEYCRSIFGDALLIEPLDKYPLAPGVPLPSPQDLMGRILVKNKKRHRPSAGGPDSAG
RKRPLEQSNSALSESSAATEPSSPQLGSPSSDSCPGLSNGEEVGLEKPSLEPQKSLGDEG
LNRGPYVLGPADREDEEEDEEEEEQTDPKKPTTDEGTASSEVNATEEMSTLVNYIEPVKF
KSFEAARKRNKCFEMSSFVETKAMEQLTKSPMEFVEYNKQQLSRIYPKGTRVDSSNYMPQ
LFWNVGCQLVALNFQTLDVAMQLNAGVFEYNGRSGYLLKPEFMRRPDKSFDPFTEVIVDG
IVANALRVKVISGQFLSDRKVGIYVEVDMFGLPVDTRRKYRTRTSQGNSFNPVWDEEPFD
FPKVVLPTLASLRIAAFEEGGKFVGHRILPVSAIRSGYHYVCLRNEANQPLCLPALLIYT
EASDYIPDDHQDYAEALINPIKHVSLMDQRARQLAALIGESEAQAGQETCQDTQSQQLGS
QPSSNPTPSPLDASPRRPPGPTTSPASTSLSSPGQRDDLIASILSEVAPTPLDELRGHKA
LVKLRSRQERDLRELRKKHQRKAVTLTRRLLDGLAQAQAEGRCRLRPGALGGAADVEDTK
EGEDEAKRYQEFQNRQVQSLLELREAQVDAEAQRRLEHLRQALQRLREVVLDANTTQFKR
LKEMNEREKKELQKILDRKRHNSISEAKMRDKHKKEAELTEINRRHITESVNSIRRLEEA
QKQRHDRLVAGQQQVLQQLAEEEPKLLAQLAQECQEQRARLPQEIRRSLLGEMPEGLGDG
PLVACASNGHAPGSSGHLSGADSESQEENTQL

Sequence of entity 2 (B, C), FASTA

>8EMW_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B, C)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D, G), FASTA

>8EMW_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D, G)
GPMASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASE
NPFREKKFFC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

G beta gamma activates PIP2 hydrolysis by recruiting and orienting PLC beta on the membrane surface. Falzone, M.E., MacKinnon, R. Proc Natl Acad Sci U S A (2023) 120:e2301121120-e2301121120. DOI 10.1073/pnas.2301121120 · PubMed

Other PDB entries of the same protein (UniProt Q01970 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SQ2 2.6 Å, Reprocessed and refined structure of Phospholipase C-beta and Gq signaling complex
4QJ3 3.0 Å, Structure of a fragment of human phospholipase C-beta3 delta472-559, in complex with…
4QJ4 3.3 Å, Structure of a fragment of human phospholipase C-beta3 delta472-569, bound to IP3 and in…
8EMX 3.3 Å, Phospholipase C beta 3 (PLCb3) in complex with Gbg on lipid nanodiscs
8UQO 3.37 Å, PLCb3-Gbg-Gaq complex on membranes
8UQN 3.4 Å, PLCb3-Gaq complex on membranes
4QJ5 3.41 Å, Structure of a fragment of human phospholipase C-beta3 delta472-581, bound to IP3 and in…
8EMV 3.6 Å, Phospholipase C beta 3 (PLCb3) in solution
4GNK 4.0 Å, Crystal structure of Galphaq in complex with full-length human PLCbeta3
9Y7H 4.4 Å, Gb1g2 crosslinked to PLCb3
9YAP 4.5 Å, Gbg crosslinked to PLCb3 - second conformation
9YAO 7.0 Å, Gbg crosslinked to PLCb3 - second conformation

Browse structure collections

About this viewer

MolViewer shows 8EMW directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.