8Y6I: P-glycoprotein

P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in nanodisc. Determined by electron microscopy at 2.54 Å resolution. Released 17 Apr 2024.

Method: Electron microscopy
Resolution: 2.54 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 8,406
Mol. weight: 226.32 kDa
Ligands: R0Z, 3PE, CLR
Released: 17 Apr 2024

Explore 8Y6I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y6I contains 43 α-helices and 43 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: 33 helices, 0 β-strands

Element	Residues	Length
α-helix	36-38	3
α-helix	45-62	18
α-helix	65-88	24
α-helix	107-156	50
α-helix	170-186	17
α-helix	188-210	23
α-helix	212-219	8
α-helix	222-237	16
α-helix	239-258	20
α-helix	262-267	6
α-helix	270-322	53
α-helix	328-347	20
α-helix	350-370	21
α-helix	701-707	7
α-helix	708-722	15
α-helix	724-737	14
α-helix	745-798	54
α-helix	801-805	5
α-helix	811-816	6
α-helix	817-821	5
α-helix	822-824	3
α-helix	825-828	4
α-helix	830-839	10
α-helix	840-844	5
α-helix	845-853	9
α-helix	855-862	8
α-helix	865-880	16
α-helix	892-902	11
α-helix	904-910	7
α-helix	913-923	11
α-helix	925-965	41
α-helix	971-992	22
α-helix	998-1013	16

Chain B: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30	1	3
β-strand	36	1	3
β-strand	38-43	6	2
α-helix	48-49	2
β-strand	50-54	5	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	90-95	6	2
β-strand	103-104	2	2
β-strand	108-112	5	2
α-helix	113	1
β-strand	120-124	5	4
β-strand	138-143	6	4
β-strand	145	1	5
β-strand	165-167	3	4
α-helix	170-173	4
β-strand	179	1	5
β-strand	183-185	3	4
β-strand	198-202	5	6
β-strand	211-215	5	6

Chain C: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7	1
β-strand	10-12	3	2
β-strand	19-25	7	7
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	46-52	7	2
β-strand	58-60	3	2
β-strand	65	1	7
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	111-112	2	2
β-strand	116-120	5	2
β-strand	126	1	8
α-helix	127-128	2
β-strand	129-131	3	9
β-strand	145-147	3	9
β-strand	150-154	5	9
β-strand	155	1	8
β-strand	162-163	2	10
α-helix	164-166	3
β-strand	172-179	8	9
β-strand	184-192	9	9
β-strand	203-208	6	10
β-strand	213-218	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATP-dependent translocase ABCB1,mNeonGreen	A	protein	1534	Homo sapiens	P08183 (AlphaFold model)
UIC2 Fab light chain	B	protein	220	Mus musculus
UIC2 Fab heavy chain	C	protein	225	Mus musculus

Sequence of entity 1 (A), FASTA

>8Y6I_1 ATP-dependent translocase ABCB1,mNeonGreen (chains A)
MDLEGDRNGGAKKKNFFKLNNKSEKDKKEKKPTVSVFSMFRYSNWLDKLYMVVGTLAAII
HGAGLPLMMLVFGEMTDIFANAGNLEDLMSNITNRSDINDTGFFMNLEEDMTRYAYYYSG
IGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEIGWFDVHDVGELNTRLTDDVS
KINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGLSAAVWAKILSSFT
DKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRIGIKKAITANISIG
AAFLLIYASYALAFWYGTTLVLSGEYSIGQVLTVFFSVLIGAFSVGQASPSIEAFANARG
AAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFSYPSRKEVKILKGLNLKVQSG
QTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLREIIGVVSQEPVLF
ATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGAQLSGGQKQRIA
IARALVRNPKILLLDEATSALDTESEAVVQVALDKARKGRTTIVIAHRLSTVRNADVIAG
FDDGVIVEKGNHDELMKEKGIYFKLVTMQTAGNEVELENAADESKSEIDALEMSSNDSRS
SLIRKRSTRRSVRGSQAQDRKLSTKEALDESIPPVSFWRIMKLNLTEWPYFVVGVFCAII
NGGLQPAFAIIFSKIIGVFTRIDDPETKRQNSNLFSLLFLALGIISFITFFLQGFTFGKA
GEILTKRLRYMVFRSMLRQDVSWFDDPKNTTGALTTRLANDAAQVKGAIGSRLAVITQNI
ANLGTGIIISFIYGWQLTLLLLAIVPIIAIAGVVEMKMLSGQALKDKKELEGSGKIATEA
IENFRTVVSLTQEQKFEHMYAQSLQVPYRNSLRKAHIFGITFSFTQAMMYFSYAGCFRFG
AYLVAHKLMSFEDVLLVFSAVVFGAMAVGQVSSFAPDYAKAKISAAHIIMIIEKTPLIDS
YSTEGLMPNTLEGNVTFGEVVFNYPTRPDIPVLQGLSLEVKKGQTLALVGSSGCGKSTVV
QLLERFYDPLAGKVLLDGKEIKRLNVQWLRAHLGIVSQEPILFDCSIAENIAYGDNSRVV
SQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHILLLD
EATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVFQNGRVKEHGTHQQL
LAQKGIYFSMVSVQAGTKRQLEVLFQGPRPRGSKGEEDNMASLPATHELHIFGSINGVDF
DMVGQGTGNPNDGYEELNLKSTKGDLQFSPWILVPHIGYGFHQYLPYPDGMSPFQAAMVD
GSGYQVHRTMQFEDGASLTVNYRYTYEGSHIKGEAQVKGTGFPADGPVMTNSLTAADWCR
SKKTYPNDKTIISTFKWSYTTGNGKRYRSTARTTYTFAKPMAANYLKNQPMYVFRKTELK
HSKTELNFKEWQKAFTDVMGMDELYKHHHHHHHH

Sequence of entity 2 (B), FASTA

>8Y6I_2 UIC2 Fab light chain (chains B)
QVVMTQSPLSLPVSLGDQASISCRSSQSLLHSNGNTYLHWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHIPPWTFGGGTKLDIKRADAAPT
VSIFPPSSEQLTSGGLSVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C), FASTA

>8Y6I_3 UIC2 Fab heavy chain (chains C)
EVQLQESGPELVKTGASVKISCKASGYSFSNYYIHWVKQSHGKSLEWIGFISCYNGATFY
NQKFKGKATFTVDNSSSTAYMKFNSLTFEDSAVYYCARLPIQFGNFYPMDYWGQGTTVTV
SSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT

Ligands and cofactors

ID	Name	Formula	Copies
R0Z	elacridar	C34 H33 N3 O5	3
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	1
CLR	Cholesterol	C27 H46 O	12

Primary citation

Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules. Hamaguchi-Suzuki, N., Adachi, N., Moriya, T. et al. Biochem Biophys Res Commun (2024) 709:149855-149855. DOI 10.1016/j.bbrc.2024.149855 · PubMed

Other PDB entries of the same protein (UniProt P08183 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Y6H 2.49 Å, P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in LMNG detergent
7A69 3.2 Å, Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and vincristine
6C0V 3.4 Å, Molecular structure of human P-glycoprotein in the ATP-bound, outward-facing conformation
9CTG 3.4 Å, SapNP Reconstituted Human ABCB1 bound to ATP gammaS
7A6F 3.5 Å, Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and zosuquidar
7O9W 3.5 Å, Encequidar-bound human P-glycoprotein in complex with UIC2-Fab
6FN1 3.58 Å, Zosuquidar and UIC2 Fab complex of human-mouse chimeric ABCB1 (ABCB1HM)
6QEX 3.6 Å, Nanodisc reconstituted human ABCB1 in complex with UIC2 fab and taxol
7A6C 3.6 Å, Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and elacridar
7A6E 3.6 Å, Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and tariquidar
9CTC 3.6 Å, SapNP reconstituted Human ABCB1 in complex with Zosuquidar and ATP/Mg
9CR8 3.8 Å, SapNP reconstituted human ABCB1

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