8DCP: PI 3-kinase alpha with nanobody 3-126

PI 3-kinase alpha with nanobody 3-126. Determined by electron microscopy at 2.41 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,595
Mol. weight: 211.45 kDa
Released: 21 Sept 2022

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

Secondary structure: helices and β-sheets

8DCP contains 63 α-helices and 51 β-strands across 2 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: 54 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	21-25	5	1
β-strand	31-35	5	1
β-strand	41	1	2
α-helix	42-51	10
α-helix	65-67	3
β-strand	69-73	5	1
β-strand	74	1	3
β-strand	79-82	4	1
β-strand	88	1	2
α-helix	90-92	3
β-strand	94	1	3
β-strand	98-102	5	1
α-helix	108-121	14
α-helix	126-129	4
α-helix	134-154	21
α-helix	160-166	7
β-strand	171	1	4
α-helix	176-178	3
α-helix	179-182	4
β-strand	189-196	8	5
β-strand	205-212	8	5
α-helix	217-231	15
β-strand	250-254	5	5
β-strand	260-261	2	5
α-helix	267-269	3
β-strand	270	1	4
α-helix	271-279	9
β-strand	284-289	6	5
α-helix	290-295	6
α-helix	306-308	3
β-strand	325-326	2	6
α-helix	327-329	3
β-strand	333-341	9	7
β-strand	353-362	10	8
β-strand	365-366	2	8
β-strand	371-372	2	8
β-strand	376-377	2	8
β-strand	382-392	11	7
α-helix	393-395	3
β-strand	401-409	9	8
β-strand	419-428	10	8
β-strand	430	1	9
β-strand	435	1	6
β-strand	436	1	9
β-strand	439-444	6	7
β-strand	446-447	2	8
α-helix	448-449	2
α-helix	461-462	2
β-strand	472-477	6	7
β-strand	484-485	2	6
α-helix	486-488	3
α-helix	489-495	7
α-helix	499-502	4
α-helix	525-535	11
α-helix	545-553	9
α-helix	558-560	3
α-helix	562-564	3
α-helix	565-570	6
α-helix	577-588	12
α-helix	590-592	3
α-helix	595-598	4
α-helix	600-602	3
α-helix	609-622	14
α-helix	625-630	6
α-helix	632-637	6
α-helix	638-641	4
α-helix	648-659	12
α-helix	661-673	13
α-helix	681-694	14
α-helix	698-721	24
α-helix	728-738	11
α-helix	742-747	6
β-strand	751-752	2	10
β-strand	760-761	2	10
β-strand	764	1	11
α-helix	766-768	3
β-strand	770-771	2	11
β-strand	779-784	6	11
α-helix	790-793	4
β-strand	796-803	8	11
α-helix	808-827	20
β-strand	838-842	5	11
β-strand	845-849	5	11
α-helix	850-851	2
β-strand	854-856	3	12
α-helix	857-863	7
α-helix	872-874	3
α-helix	876-884	9
α-helix	889-911	23
α-helix	913-916	4
β-strand	921-924	4	12
β-strand	929-931	3	12
α-helix	958-964	7
α-helix	975-992	18
α-helix	995-1003	9
α-helix	1016-1025	10
α-helix	1032-1047	16

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	334	1	13
α-helix	340-346	7
β-strand	354-358	5	13
β-strand	369-374	6	13
β-strand	377-382	6	13
α-helix	383	1
β-strand	384-386	3	14
β-strand	389-391	3	14
α-helix	396	1
β-strand	398	1	14
α-helix	401-410	10
α-helix	413-415	3
β-strand	426-427	2	13
α-helix	442-508	67
α-helix	511-513	3
α-helix	518-587	70
α-helix	591-595	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	protein	1096	Homo sapiens	P42336 (AlphaFold model)
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	protein	723	Homo sapiens	P27986 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8DCP_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (chains A)
MSYYHHHHHHDYDIPTTENLYFQGAMGSMPPRPSSGELWGIHLMPPRILVECLLPNGMIV
TLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDL
RLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVD
LRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKIN
HDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKY
IRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINS
ALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIY
IPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGL
EDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAG
LSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSV
KWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYL
IQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYC
RACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFL
SPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDML
TLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQF
NSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHI
DFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIR
QHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWT
TKMDWIFHTIKQHALN

Sequence of entity 2 (B), FASTA

>8DCP_2 Phosphatidylinositol 3-kinase regulatory subunit alpha (chains B)
MAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIGWLNGYNE
TTGERGDFPGTYVEYIGRKKISPPTPKPRPPRPLPVAPGSSKTEADVEQQALTLPDLAEQ
FAPPDIAPPLLIKLVEAIEKKGLECSTLYRTQSSSNLAELRQLLDCDTPSVDLEMIDVHV
LADAFKRYLLDLPNPVIPAAVYSEMISLAPEVQSSEEYIQLLKKLIRSPSIPHQYWLTLQ
YLLKHFFKLSQTSSKNLLNARVLSEIFSPMLFRFSAASSDNTENLIKVIEILISTEWNER
QPAPALPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDAS
TKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLD
VKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKR
TAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDS
RRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGNE
NTEDQYSLVEDDEDLPHHDEKTWNVGSSNRNKAENLLRGKRDGTFLVRESSKQGCYACSV
VVDGEVKHCVINKTATGYGFAEPYNLYSSLKELVLHYQHTSLVQHNDSLNVTLAYPVYAQ
QRR

Primary citation

Nanobodies and chemical cross-links advance the structural and functional analysis of PI3K alpha. Hart, J.R., Liu, X., Pan, C. et al. Proc Natl Acad Sci U S A (2022) 119:e2210769119-e2210769119. DOI 10.1073/pnas.2210769119 · PubMed

Other PDB entries of the same protein (UniProt P42336 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CMK 1.75 Å, Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue…
9ASF 1.77 Å, Crystal structure of HLA-A*03:01 in complex with a wild-type PIK3CA peptide analogue…
9CX0 1.92 Å, Crystal structure of HLA-A*03:01 E152V mutant in complex with a mutant PIK3CA peptide
7L1C 1.96 Å, Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide
9CWY 1.98 Å, Crystal structure of HLA-A*03:02 in complex with a wild-type PIK3CA peptide
8EXL 1.99 Å, Crystal structure of PI3K-alpha in complex with taselisib
9CX1 2.0 Å, Crystal structure of HLA-A*03:01 L156Q mutant in complex with a mutant PIK3CA peptide
9CML 2.01 Å, Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue…
9ASG 2.03 Å, Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide analogue (Trp-6…
7L1B 2.04 Å, Crystal structure of HLA-A*03:01 in complex with a wild-type PIK3CA peptide
9CWZ 2.05 Å, Crystal structure of HLA-A*03:02 in complex with a mutant PIK3CA peptide
7JIU 2.12 Å, Human PI3KDELTA in complex with compound 2F

Browse structure collections

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