7A69: Nanodisc reconstituted human ABCB1

Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and vincristine. Determined by electron microscopy at 3.2 Å resolution. Released 21 Oct 2020.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 12,637
Mol. weight: 193.1 kDa
Ligands: R1Q, CLR
Released: 21 Oct 2020

Explore 7A69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A69 contains 59 α-helices and 77 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: 49 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	45-80	36
α-helix	107-156	50
α-helix	162-165	4
α-helix	168-186	19
α-helix	188-210	23
α-helix	212-236	25
α-helix	241-257	17
α-helix	261-267	7
α-helix	270-323	54
α-helix	328-346	19
α-helix	349-370	22
β-strand	383	1	1
α-helix	384-385	2
β-strand	392-398	7	2
β-strand	415-417	3	2
β-strand	422-426	5	3
α-helix	433-440	8
β-strand	448-453	6	2
β-strand	457	1	2
α-helix	458-460	3
β-strand	461	1	1
α-helix	463-468	6
β-strand	470-473	4	3
β-strand	483	1	4
α-helix	484-489	6
α-helix	497-506	10
α-helix	511-515	5
β-strand	523	1	4
α-helix	526-528	3
α-helix	533-545	13
β-strand	551-555	5	3
α-helix	563-573	11
β-strand	581-585	5	3
β-strand	597-602	6	3
β-strand	605-608	4	3
α-helix	612-618	7
α-helix	621-629	9
α-helix	700-703	4
α-helix	708-736	29
β-strand	742	1	5
α-helix	745-797	53
α-helix	801-804	4
α-helix	812-853	42
α-helix	855-861	7
α-helix	865-880	16
α-helix	887-902	16
α-helix	904-910	7
α-helix	914-965	52
α-helix	971-981	11
α-helix	986-994	9
α-helix	996-997	2
α-helix	999-1013	15
β-strand	1026	1	6
β-strand	1035-1041	7	7
β-strand	1043	1	8
β-strand	1051	1	8
β-strand	1056-1060	5	7
β-strand	1066-1069	4	9
α-helix	1078-1083	6
β-strand	1091-1096	6	7
β-strand	1099-1100	2	7
β-strand	1104	1	6
α-helix	1106-1112	7
β-strand	1114-1116	3	9
α-helix	1128-1131	4
α-helix	1139-1141	3
α-helix	1142-1151	10
α-helix	1155-1159	5
α-helix	1171-1173	3
α-helix	1178-1190	13
β-strand	1196-1200	5	9
α-helix	1208-1222	15
β-strand	1226-1230	5	9
α-helix	1235-1238	4
β-strand	1242-1247	6	9
β-strand	1250-1256	7	9
α-helix	1257-1262	6
α-helix	1266-1271	6

Chain B: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	10
β-strand	10-13	4	11
β-strand	18-22	5	12
β-strand	23-24	2	10
β-strand	38-43	6	11
β-strand	50-52	3	11
β-strand	67-72	6	12
β-strand	75-81	7	12
β-strand	90-95	6	11
β-strand	102	1	11
β-strand	108-111	4	11
β-strand	116	1	13
β-strand	119-123	5	14
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-142	9	14
β-strand	144	1	15
β-strand	145	1	13
β-strand	151	1	16
β-strand	153-155	3	16
β-strand	159-161	3	16
β-strand	164-168	5	14
α-helix	169-172	4
β-strand	178	1	15
β-strand	180-187	8	14
α-helix	188-192	5
β-strand	196-201	6	16
β-strand	211-216	6	16

Chain C: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	17
β-strand	10-11	2	18
β-strand	17-24	8	17
α-helix	28-30	3
β-strand	31	1	5
β-strand	33-38	6	19
β-strand	44-50	7	19
β-strand	57-58	2	19
β-strand	64	1	17
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	87-89	3
β-strand	91-99	9	19
β-strand	103-108	6	19
β-strand	112-114	3	19
β-strand	115-116	2	18
α-helix	119-121	3
β-strand	122	1	20
β-strand	127-129	3	21
α-helix	132-134	3
β-strand	140-150	11	21
β-strand	151	1	20
β-strand	156-159	4	22
α-helix	160-162	3
β-strand	164	1	22
β-strand	169-176	8	21
β-strand	179-189	11	21
β-strand	198-204	7	22
α-helix	205-207	3
β-strand	209-215	7	22

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>7A69_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

>7A69_2 MRK16 Fab-fragment light chain (chains B)
DVLMTQTPVSLSVSLGDQASISCRSSQSIVHSTGNTYLEWYLQKPGQSPKLLIYKISNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQASHAPRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C), FASTA

>7A69_3 MRK16 Fab-fragment heavy chain (chains C)
EVILVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVATISSGGGNTYY
PDSVKGRFTISRDNAKNNLYLQMSSLRSEDTALYYCARYYRYEAWFASWGQGTLVTVSAA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP

Ligands and cofactors

ID	Name	Formula	Copies
R1Q	vincristine	C46 H56 N4 O10	1
CLR	Cholesterol	C27 H46 O	8

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
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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