6PCV: PDB entry 6PCV

Single Particle Reconstruction of Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1 bound to G protein beta gamma subunits. Determined by electron microscopy at 3.2 Å resolution. Released 23 Oct 2019.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Bos taurus
Chains: 3
Atoms: 9,035
Mol. weight: 231.48 kDa
Released: 23 Oct 2019

Explore 6PCV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PCV contains 37 α-helices and 63 β-strands across 3 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: 30 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	510-521	12
β-strand	532-534	3	1
β-strand	537-539	3	1
β-strand	542-544	3	2
α-helix	545-555	11
α-helix	561-573	13
β-strand	577-579	3	2
β-strand	592-595	4	2
α-helix	596-602	7
β-strand	616-628	13	3
β-strand	637-640	4	4
β-strand	647-651	5	4
α-helix	656-660	5
α-helix	662-663	2
β-strand	667	1	4
β-strand	668-671	4	3
β-strand	675	1	3
α-helix	681-693	13
β-strand	698-703	6	3
β-strand	707-713	7	5
β-strand	721-725	5	5
β-strand	729-735	7	5
α-helix	739-743	5
α-helix	749	1
β-strand	750-754	5	5
β-strand	757-758	2	5
α-helix	765-768	4
β-strand	787-789	3	5
α-helix	792-802	11
β-strand	841-847	7	5
β-strand	852-860	9	3
β-strand	861	1	6
β-strand	866-874	9	3
α-helix	880-894	15
α-helix	934-946	13
β-strand	953	1	7
α-helix	954-956	3
α-helix	965-967	3
α-helix	969	1
β-strand	970	1	7
β-strand	973-982	10	3
β-strand	1015-1026	12	3
α-helix	1027-1028	2
α-helix	1319-1346	28
α-helix	1360-1374	15
β-strand	1376-1382	7	3
α-helix	1390-1406	17
β-strand	1409-1415	7	3
β-strand	1421	1	5
β-strand	1427-1432	6	3
β-strand	1437-1443	7	3
α-helix	1445-1449	5
α-helix	1455-1457	3
β-strand	1462-1466	5	3
β-strand	1469	1	3
α-helix	1481-1517	37
α-helix	1528-1550	23
α-helix	1552-1553	2
α-helix	1564-1574	11
β-strand	1577-1583	7	3
α-helix	1588-1604	17
β-strand	1608	1	6
α-helix	1613-1622	10
α-helix	1628-1633	6
α-helix	1650-1653	4

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	8
β-strand	58-63	6	9
β-strand	69-74	6	9
β-strand	78-83	6	9
β-strand	89-94	6	9
β-strand	100-105	6	10
β-strand	111-116	6	10
β-strand	120-125	6	10
β-strand	134-140	7	10
β-strand	149-151	3	11
β-strand	156-160	5	11
β-strand	166-170	5	11
β-strand	175-180	6	11
α-helix	186	1
β-strand	187-192	6	12
β-strand	199-203	5	12
β-strand	208-210	3	12
β-strand	220-222	3	12
β-strand	229-234	6	13
β-strand	240-245	6	13
β-strand	250-254	5	13
β-strand	260-264	5	13
α-helix	272-273	2
β-strand	275-278	4	14
β-strand	284-288	5	14
β-strand	293-298	6	14
β-strand	304-309	6	14
β-strand	317-320	4	8
β-strand	327-330	4	8
β-strand	336-339	4	8

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	30-43	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1	A	protein	1635	Homo sapiens	Q8TCU6 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	81	Bos taurus	P63212 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PCV_1 Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1 (chains A)
GEFAAARESERQLRLRLCVLNEILGTERDYVGTLRFLQSAFLHRIRQNVADSVEKGLTEE
NVKVLFSNIEDILEVHKDFLAALEYCLHPEPQSQHELGNVFLKFKDKFCVYEEYCSNHEK
ALRLLVELNKIPTVRAFLLSCMLLGGRKTTDIPLEGYLLSPIQRICKYPLLLKELAKRTP
GKHPDHPAVQSALQAMKTVCSNINETKRQMEKLEALEQLQSHIEGWEGSNLTDICTQLLL
QGTLLKISAGNIQERAFFLFDNLLVYCKRKSRVTGSKKSTKRTKSINGSLYIFRGRINTE
VMEVENVEDGTADYHSNGYTVTNGWKIHNTAKNKWFVCMAKTAEEKQKWLDAIIREREQR
ESLKLGMERDAYVMIAEKGEKLYHMMMNKKVNLIKDRRRKLSTVPKCFLGNEFVAWLLEI
GEISKTEEGVNLGQALLENGIIHHVSDKHQFKNEQVMYRFRYDDGTYKARSELEDIMSKG
VRLYCRLHSLYTPVIKDRDYHLKTYKSVLPGSKLVDWLLAQGDCQTREEAVALGVGLCNN
GFMHHVLEKSEFRDESQYFRFHADEEMEGTSSKNKQLRNDFKLVENILAKRLLILPQEED
YGFDIEEKNKAVVVKSVQRGSLAEVAGLQVGRKIYSINEDLVFLRPFSEVESILNQSFCS
RRPLRLLVATKAKEIIKIPDQPDTLCFQIRGAAPPYVYAVGRGSEAMAAGLCAGQCILKV
NGSNVMNDGAPEVLEHFQAFRSRREEALGLYQWIYHTHEDAQEARASQEASTEDPSGEQA
QEEDQADSAFPLLSLGPRLSLCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVRCHVLEKIV
EPRGCFGLTAKILEAFAANDSVFVENCRRLMALSSAIVTMPHFEFRNICDTKLESIGQRI
ACYQEFAAQLKSRVSPPFKQAPLEPHPLCGLDFCPTNCHINLMEVSYPKTTPSVGRSFSI
RFGRKPSLIGLDPEQGHLNPMSYTQHCITTMAAPSWKCLPAAEGDPQGQGLHDGSFGPAS
GTLGQEDRGLSFLLKQEDREIQDAYLQLFTKLDVALKEMKQYVTQINRLLSTITEPTSGG
SCDASLAEEASSLPLVSEESEMDRSDHGGIKKVCFKVAEEDQEDSGHDTMSYRDSYSECN
SNRDSVLSYTSVRSNSSYLGSDEMGSGDELPCDMRIPSDKQDKLHGCLEHLFNQVDSINA
LLKGPVMSRAFEETKHFPMNHSLQEFKQKEECTIRGRSLIQISIQEDPWNLPNSIKTLVD
NIQRYVEDGKNQLLLALLKCTDTELQLRRDAIFCQALVAAVCTFSEQLLAALGYRYNNNG
EYEESSRDASRKWLEQVAATGVLLHCQSLLSPATVKEERTMLEDIWVTLSELDNVTFSFK
QLDENYVANTNVFYHIEGSRQALKVIFYLDSYHFSKLPSRLEGGASLRLHTALFTKVLEN
VEGLPSPGSQAAEDLQQDINAQSLEKVQQYYRKLRAFYLERSNLPTDASTTAVKIDQLIR
PINALDELCRLMKSFVHPKPGAAGSVGAGLIPISSELCYRLGACQMVMCGTGMQRSTLSV
SLEQAAILARSHGLLPKCIMQATDIMRKQGPRVEILAKNLRVKDQMPQGAPRLYRLCQPP
VDGDLHHHHHHHHHH

Sequence of entity 2 (B), FASTA

>6PCV_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>6PCV_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
HHHHHHHHHHMASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPL
LTPVPASENPFREKKFFSAIL

Primary citation

Cryo-electron microscopy structure and analysis of the P-Rex1-G beta gamma signaling scaffold. Cash, J.N., Urata, S., Li, S. et al. Sci Adv (2019) 5:eaax8855-eaax8855. DOI 10.1126/sciadv.aax8855 · PubMed

Other PDB entries of the same protein (UniProt Q8TCU6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5D3X 1.69 Å, Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound
5D3V 1.85 Å, Crystal Structure of the P-Rex1 PH domain with Citrate Bound
5D3W 1.85 Å, Crystal Structure of the P-Rex1 PH domain with Sulfate Bound
5D27 1.92 Å, Crystal Structure of the P-Rex1 PH domain
4YON 1.95 Å, P-Rex1:Rac1 complex
5D3Y 1.95 Å, Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound
3QIK 2.29 Å, Crystal structure of the first PDZ domain of PREX1
6VSK 3.12 Å, Crystal structure of the P-Rex1 DEP1 domain
5FI1 3.2 Å, Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42
7RX9 3.22 Å, Structure of autoinhibited P-Rex1
5FI0 3.28 Å, Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1
8TUA 4.1 Å, Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4)

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