8EMX: Phospholipase C beta 3

Phospholipase C beta 3 (PLCb3) in complex with Gbg on lipid nanodiscs. Determined by electron microscopy at 3.3 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 5
Atoms: 11,714
Mol. weight: 229.37 kDa
Ligands: CA
Released: 24 May 2023

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

Secondary structure: helices and β-sheets

8EMX contains 48 α-helices and 100 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: 35 helices, 41 β-strands

Element	Residues	Length	Sheet
α-helix	20-24	5
β-strand	26-31	6	1
β-strand	38-43	6	1
β-strand	44-45	2	2
β-strand	51	1	3
β-strand	52-53	2	2
β-strand	54-55	2	4
α-helix	60	1
β-strand	61-62	2	4
β-strand	65	1	3
β-strand	69-74	6	1
α-helix	75-77	3
α-helix	79-81	3
α-helix	84-90	7
α-helix	98-102	5
β-strand	103-108	6	1
β-strand	116-122	7	1
α-helix	129-139	11
α-helix	149-162	14
β-strand	170-171	2	5
α-helix	172-178	7
α-helix	184-191	8
β-strand	202-203	2	5
α-helix	210-220	11
α-helix	224-233	10
β-strand	241	1	6
α-helix	244-253	10
α-helix	269-279	11
β-strand	291	1	6
α-helix	294-297	4
α-helix	323-325	3
β-strand	326-328	3	7
β-strand	331	1	8
α-helix	348-354	7
β-strand	362-364	3	9
β-strand	365-366	2	10
β-strand	376-377	2	10
β-strand	387-388	2	10
α-helix	389-398	10
β-strand	408-413	6	9
α-helix	419-431	13
α-helix	434-436	3
β-strand	437	1	9
α-helix	451-455	5
β-strand	463-466	4	9
α-helix	578-580	3
α-helix	590-592	3
β-strand	598-599	2	11
α-helix	605-611	7
β-strand	616-617	2	11
β-strand	619-621	3	12
α-helix	622-625	4
α-helix	633-639	7
β-strand	646-648	3	12
α-helix	662-665	4
β-strand	671-672	2	12
β-strand	674	1	8
α-helix	681-689	9
β-strand	698-700	3	7
α-helix	701-702	2
α-helix	703-705	3
β-strand	726-736	11	13
β-strand	745-752	8	14
β-strand	775	1	13
α-helix	779-780	2
β-strand	781-786	6	13
α-helix	789-791	3
β-strand	793-800	8	14
β-strand	805-812	8	14
α-helix	813-815	3
β-strand	819-823	5	13
β-strand	826	1	14
β-strand	832	1	14
β-strand	837-846	10	13
α-helix	868-871	4
α-helix	877-880	4

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	5-25	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-52	6	15
β-strand	58-63	6	16
β-strand	69-74	6	16
β-strand	78-83	6	16
β-strand	91-93	3	16
β-strand	100-103	4	17
β-strand	113	1	18
β-strand	114-116	3	17
β-strand	121-123	3	18
β-strand	137-139	3	18
β-strand	146-151	6	19
β-strand	156-161	6	19
β-strand	165-170	6	19
β-strand	175-181	7	19
β-strand	189-191	3	20
β-strand	198-202	5	20
β-strand	208-212	5	20
β-strand	218-222	5	20
β-strand	229-231	3	21
β-strand	244-245	2	21
β-strand	250-253	4	22
β-strand	260-264	5	22
β-strand	273-278	6	23
β-strand	284-289	6	23
β-strand	295-298	4	23
β-strand	304-307	4	23
β-strand	315-320	6	15
β-strand	327-331	5	15
β-strand	335-339	5	15

Chain C: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-34	5
β-strand	47-50	4	24
β-strand	58-63	6	25
β-strand	69-74	6	25
β-strand	78-83	6	25
β-strand	89-94	6	25
β-strand	103	1	26
β-strand	114	1	26
β-strand	121	1	27
β-strand	124	1	28
β-strand	135	1	28
β-strand	139	1	27
β-strand	146-151	6	29
β-strand	156-161	6	29
β-strand	165-170	6	29
β-strand	176-181	6	29
β-strand	187-192	6	30
β-strand	198-203	6	30
β-strand	207-212	6	30
β-strand	218-221	4	30
β-strand	229-234	6	31
β-strand	240-245	6	31
β-strand	251-254	4	31
β-strand	259-263	5	31
α-helix	271-272	2
β-strand	273-277	5	32
β-strand	284-289	6	32
β-strand	294-298	5	32
β-strand	303-308	6	32
β-strand	315-320	6	24
β-strand	327-331	5	24
β-strand	336-339	4	24

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-23	14
α-helix	30-42	13

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3	A	protein	1234	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

>8EMX_1 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 (chains A)
GPSRASTMHALQLEPPTVVETLRRGSKFIKWDEETSSRNLVTLRVDPNGFFLYWTGPNME
VDTLDISSIRDTRTGRYARLPKDPKIREVLGFGGPDARLEEKLMTVVSGPDPVNTVFLNF
MAVQDDTAKVWSEELFKLAMNILAQNASRNTFLRKAYTKLKLQVNQDGRIPVKNILKMFS
ADKKRVETALESCGLKFNRSESIRPDEFSLEIFERFLNKLCLRPDIDKILLEIGAKGKPY
LTLEQLMDFINQKQRDPRLNEVLYPPLRPSQARLLIEKYEPNQQFLERDQMSMEGFSRYL
GGEENGILPLEALDLSTDMTQPLSAYFINSSHNTYLTAGQLAGTSSVEMYRQALLWGCRC
VELDVWKGRPPEEEPFITHGFTMTTEVPLRDVLEAIAETAFKTSPYPVILSFENHVDSAK
QQAKMAEYCRSIFGDALLIEPLDKYPLAPGVPLPSPQDLMGRILVKNKKRHRPSAGGPDS
AGRKRPLEQSNSALSESSAATEPSSPQLGSPSSDSCPGLSNGEEVGLEKPSLEPQKSLGD
EGLNRGPYVLGPADREDEEEDEEEEEQTDPKKPTTDEGTASSEVNATEEMSTLVNYIEPV
KFKSFEAARKRNKCFEMSSFVETKAMEQLTKSPMEFVEYNKQQLSRIYPKGTRVDSSNYM
PQLFWNVGCQLVALNFQTLDVAMQLNAGVFEYNGRSGYLLKPEFMRRPDKSFDPFTEVIV
DGIVANALRVKVISGQFLSDRKVGIYVEVDMFGLPVDTRRKYRTRTSQGNSFNPVWDEEP
FDFPKVVLPTLASLRIAAFEEGGKFVGHRILPVSAIRSGYHYVCLRNEANQPLCLPALLI
YTEASDYIPDDHQDYAEALINPIKHVSLMDQRARQLAALIGESEAQAGQETCQDTQSQQL
GSQPSSNPTPSPLDASPRRPPGPTTSPASTSLSSPGQRDDLIASILSEVAPTPLDELRGH
KALVKLRSRQERDLRELRKKHQRKAVTLTRRLLDGLAQAQAEGRCRLRPGALGGAADVED
TKEGEDEAKRYQEFQNRQVQSLLELREAQVDAEAQRRLEHLRQALQRLREVVLDANTTQF
KRLKEMNEREKKELQKILDRKRHNSISEAKMRDKHKKEAELTEINRRHITESVNSIRRLE
EAQKQRHDRLVAGQQQVLQQLAEEEPKLLAQLAQECQEQRARLPQEIRRSLLGEMPEGLG
DGPLVACASNGHAPGSSGHLSGADSESQEENTQL

Sequence of entity 2 (B, C), FASTA

>8EMX_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

>8EMX_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…
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…
8EMW 3.5 Å, Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes
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

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