7A65: Nanodisc reconstituted, drug-free human ABCB1

Nanodisc reconstituted, drug-free human ABCB1 in complex with MRK16 Fab. Determined by electron microscopy at 3.9 Å resolution. Released 14 Oct 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 12,521
Mol. weight: 191.5 kDa
Ligands: CLR
Released: 14 Oct 2020

Explore 7A65 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A65 contains 66 α-helices and 75 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: 55 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	36-39	4
α-helix	45-81	37
α-helix	107-157	51
α-helix	162-165	4
α-helix	168-186	19
α-helix	188-210	23
α-helix	212-220	9
α-helix	222-236	15
α-helix	241-259	19
α-helix	261-266	6
α-helix	270-322	53
α-helix	328-347	20
α-helix	349-370	22
β-strand	392-394	3	1
β-strand	398	1	2
β-strand	415-417	3	1
β-strand	422-426	5	3
α-helix	433-438	6
β-strand	448	1	2
β-strand	452	1	1
β-strand	457	1	1
α-helix	458-460	3
α-helix	463-468	6
β-strand	470-473	4	3
β-strand	483	1	4
α-helix	484-487	4
α-helix	488-491	4
α-helix	497-507	11
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	563-575	13
β-strand	581-585	5	3
α-helix	589-591	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	700-705	6
α-helix	708-722	15
α-helix	724-740	17
β-strand	742	1	5
α-helix	745-798	54
α-helix	801-805	5
α-helix	807-809	3
α-helix	812-826	15
α-helix	827-831	5
α-helix	832-853	22
α-helix	855-862	8
α-helix	865-880	16
α-helix	891-902	12
α-helix	903-905	3
α-helix	913-965	53
α-helix	971-994	24
α-helix	996-997	2
α-helix	998-1013	16
β-strand	1026	1	6
β-strand	1035-1041	7	7
β-strand	1056-1060	5	7
β-strand	1066-1069	4	8
α-helix	1077-1083	7
β-strand	1091-1096	6	7
β-strand	1099-1100	2	7
β-strand	1104	1	6
α-helix	1106-1112	7
β-strand	1114-1115	2	8
α-helix	1127-1132	6
α-helix	1142-1151	10
α-helix	1155-1159	5
α-helix	1164-1166	3
α-helix	1171-1173	3
α-helix	1178-1190	13
β-strand	1196-1200	5	8
α-helix	1208-1221	14
β-strand	1226-1230	5	8
α-helix	1235-1238	4
β-strand	1242-1247	6	8
β-strand	1250-1253	4	8
β-strand	1256	1	8
α-helix	1257-1262	6
α-helix	1266-1271	6

Chain B: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	9
β-strand	10-14	5	10
β-strand	19-25	7	9
β-strand	38-43	6	10
β-strand	50-53	4	10
β-strand	67-72	6	9
β-strand	75-80	6	9
β-strand	90-95	6	10
β-strand	102-103	2	10
β-strand	108-112	5	10
β-strand	116	1	11
β-strand	119-123	5	12
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	12
β-strand	145	1	11
β-strand	151-155	5	13
β-strand	159-161	3	13
β-strand	164-168	5	12
α-helix	169-172	4
β-strand	178-187	10	12
α-helix	188-192	5
β-strand	196-201	6	13
β-strand	211-216	6	13

Chain C: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	17-25	9	14
α-helix	29-31	3
β-strand	32	1	5
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	58-59	2	16
β-strand	69-73	5	14
β-strand	78-84	7	14
α-helix	88-90	3
β-strand	92-98	7	16
β-strand	100	1	17
β-strand	104	1	17
β-strand	109	1	16
β-strand	113-115	3	16
β-strand	116-117	2	15
β-strand	123	1	18
β-strand	128-130	3	19
α-helix	133-135	3
β-strand	138	1	19
β-strand	141-151	11	19
β-strand	152	1	18
β-strand	157-160	4	20
α-helix	161-163	3
β-strand	165	1	20
β-strand	169-171	3	19
α-helix	172-174	3
β-strand	175-177	3	19
β-strand	180-190	11	19
β-strand	200-205	6	20
α-helix	206-208	3
β-strand	210-215	6	20
α-helix	216	1

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

>7A65_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

>7A65_2 MRK16 Fab-fragment light chain (chains B)
DVLMTQTPVSLSVSLGDQASISCRSSQSIVHSTGNTYLEWYLQKPGQSPKLLIYKISNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQASHAPRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C), FASTA

>7A65_3 MRK16 Fab-fragment heavy chain (chains C)
EVILVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVATISSGGGNTYY
PDSVKGRFTISRDNAKNNLYLQMSSLRSEDTALYYCARYYRYEAWFASWGQGTLVTVSAA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	6

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
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

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