7A6C: Nanodisc reconstituted human ABCB1

Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and elacridar. Determined by electron microscopy at 3.6 Å resolution. Released 14 Oct 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 12,717
Mol. weight: 194.18 kDa
Ligands: R0Z, CLR
Released: 14 Oct 2020

Explore 7A6C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A6C contains 68 α-helices and 76 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: 61 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	45-62	18
α-helix	66-82	17
α-helix	108-156	49
α-helix	162-165	4
α-helix	169-173	5
α-helix	174-178	5
α-helix	179-184	6
α-helix	185-189	5
α-helix	190-210	21
α-helix	212-237	26
α-helix	240-259	20
α-helix	261-266	6
α-helix	271-323	53
α-helix	328-368	41
α-helix	371-373	3
β-strand	383	1	1
β-strand	392-393	2	2
β-strand	398-399	2	3
α-helix	402-404	3
β-strand	410-411	2	3
β-strand	416-417	2	2
β-strand	423-426	4	4
α-helix	433-440	8
β-strand	448	1	3
β-strand	452-453	2	2
β-strand	456-457	2	2
α-helix	458-460	3
β-strand	461	1	1
α-helix	463-469	7
β-strand	470-473	4	4
β-strand	483	1	5
α-helix	484-489	6
α-helix	497-506	10
α-helix	511-515	5
β-strand	523	1	5
α-helix	526-528	3
α-helix	534-546	13
β-strand	551-555	5	4
α-helix	564-574	11
β-strand	581-585	5	4
α-helix	589-591	3
β-strand	597-602	6	4
β-strand	605-608	4	4
β-strand	611	1	4
α-helix	612-618	7
α-helix	621-629	9
α-helix	701-704	4
α-helix	709-723	15
α-helix	726-735	10
α-helix	737-740	4
β-strand	742	1	6
α-helix	745-797	53
α-helix	802-805	4
α-helix	811-816	6
α-helix	817-821	5
α-helix	822-826	5
α-helix	827-831	5
α-helix	832-839	8
α-helix	840-844	5
α-helix	845-853	9
α-helix	857-861	5
α-helix	865-879	15
α-helix	896-902	7
α-helix	914-964	51
α-helix	971-977	7
α-helix	978-983	6
α-helix	984-992	9
α-helix	996-997	2
α-helix	999-1011	13
β-strand	1036-1042	7	7
β-strand	1053-1059	7	7
β-strand	1066-1069	4	8
α-helix	1080-1083	4
β-strand	1091-1095	5	7
β-strand	1096	1	9
β-strand	1099	1	9
α-helix	1106-1112	7
β-strand	1116	1	8
β-strand	1126	1	10
α-helix	1127-1129	3
α-helix	1132-1134	3
α-helix	1142-1151	10
α-helix	1155-1160	6
β-strand	1168	1	10
α-helix	1171-1173	3
α-helix	1178-1192	15
β-strand	1196-1200	5	8
α-helix	1208-1219	12
β-strand	1226-1230	5	8
β-strand	1242-1247	6	8
β-strand	1250-1256	7	8
α-helix	1257-1260	4
α-helix	1266-1270	5

Chain B: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	11
β-strand	10-14	5	12
β-strand	18-25	8	11
β-strand	38	1	13
β-strand	41-43	3	12
β-strand	50	1	12
β-strand	54	1	14
β-strand	58	1	14
β-strand	67-72	6	11
β-strand	75-81	7	11
β-strand	89-92	4	12
β-strand	95	1	13
β-strand	107-112	6	12
β-strand	116	1	15
β-strand	119-123	5	16
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	16
β-strand	145	1	15
β-strand	151-155	5	17
β-strand	159	1	17
β-strand	164-168	5	16
α-helix	169-172	4
β-strand	178-187	10	16
α-helix	188-192	5
β-strand	197-201	5	17
β-strand	211-215	5	17

Chain C: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	18
β-strand	10-11	2	19
β-strand	17-20	4	18
β-strand	23-25	3	18
β-strand	32	1	6
β-strand	34-39	6	19
β-strand	45-51	7	19
β-strand	58-59	2	19
β-strand	68-73	6	18
β-strand	78-84	7	18
β-strand	92-97	6	19
β-strand	100	1	20
β-strand	104	1	20
β-strand	113-116	4	19
α-helix	121-122	2
β-strand	126-130	5	21
α-helix	133-135	3
β-strand	141-151	11	21
β-strand	159-160	2	22
α-helix	161-163	3
β-strand	169-177	9	21
β-strand	180-190	11	21
β-strand	200-202	3	22
β-strand	214-215	2	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Multidrug resistance protein 1	A	protein	1280	Homo sapiens	P08183 (AlphaFold model)
If kappa light chain	B	protein	219	Mus musculus	A2NHM3 (AlphaFold model)
MRK16 Fab-fragment heavy chain	C	protein	218	Mus musculus

Sequence of entity 1 (A), FASTA

>7A6C_1 Multidrug resistance protein 1 (chains A)
MDLEGDRNGGAKKKNFFKLNNKSEKDKKEKKPTVSVFSMFRYSNWLDKLYMVVGTLAAII
HGAGLPLMMLVFGEMTDIFANAGNLEDLMSNITNRSDINDTGFFMNLEEDMTRYAYYYSG
IGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEIGWFDVHDVGELNTRLTDDVS
KINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGLSAAVWAKILSSFT
DKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRIGIKKAITANISIG
AAFLLIYASYALAFWYGTTLVLSGEYSIGQVLTVFFSVLIGAFSVGQASPSIEAFANARG
AAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFSYPSRKEVKILKGLNLKVQSG
QTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLREIIGVVSQEPVLF
ATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGAQLSGGQKQRIA
IARALVRNPKILLLDEATSALDTESEAVVQVALDKARKGRTTIVIAHRLSTVRNADVIAG
FDDGVIVEKGNHDELMKEKGIYFKLVTMQTAGNEVELENAADESKSEIDALEMSSNDSRS
SLIRKRSTRRSVRGSQAQDRKLSTKEALDESIPPVSFWRIMKLNLTEWPYFVVGVFCAII
NGGLQPAFAIIFSKIIGVFTRIDDPETKRQNSNLFSLLFLALGIISFITFFLQGFTFGKA
GEILTKRLRYMVFRSMLRQDVSWFDDPKNTTGALTTRLANDAAQVKGAIGSRLAVITQNI
ANLGTGIIISFIYGWQLTLLLLAIVPIIAIAGVVEMKMLSGQALKDKKELEGAGKIATEA
IENFRTVVSLTQEQKFEHMYAQSLQVPYRNSLRKAHIFGITFSFTQAMMYFSYAGCFRFG
AYLVAHKLMSFEDVLLVFSAVVFGAMAVGQVSSFAPDYAKAKISAAHIIMIIEKTPLIDS
YSTEGLMPNTLEGNVTFGEVVFNYPTRPDIPVLQGLSLEVKKGQTLALVGSSGCGKSTVV
QLLERFYDPLAGKVLLDGKEIKRLNVQWLRAHLGIVSQEPILFDCSIAENIAYGDNSRVV
SQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHILLLD
EATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVFQNGRVKEHGTHQQL
LAQKGIYFSMVSVQAGTKRQ

Sequence of entity 2 (B), FASTA

>7A6C_2 If kappa light chain (chains B)
DVLMTQTPVSLSVSLGDQASISCRSSQSIVHSTGNTYLEWYLQKPGQSPKLLIYKISNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQASHAPRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C), FASTA

>7A6C_3 MRK16 Fab-fragment heavy chain (chains C)
EVILVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVATISSGGGNTYY
PDSVKGRFTISRDNAKNNLYLQMSSLRSEDTALYYCARYYRYEAWFASWGQGTLVTVSAA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP

Ligands and cofactors

ID	Name	Formula	Copies
R0Z	elacridar	C34 H33 N3 O5	2
CLR	Cholesterol	C27 H46 O	10

Primary citation

Cryo-EM structures reveal distinct mechanisms of inhibition of the human multidrug transporter ABCB1. Nosol, K., Romane, K., Irobalieva, R.N. et al. Proc Natl Acad Sci U S A (2020) 117:26245-26253. DOI 10.1073/pnas.2010264117 · 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
8Y6I 2.54 Å, P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in nanodisc
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
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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