7A6F: Nanodisc reconstituted human ABCB1

Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and zosuquidar. Determined by electron microscopy at 3.5 Å resolution. Released 14 Oct 2020.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 12,655
Mol. weight: 193.33 kDa
Ligands: ZQU, CLR
Released: 14 Oct 2020

Explore 7A6F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A6F contains 57 α-helices and 85 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, 30 β-strands

Element	Residues	Length	Sheet
α-helix	45-61	17
α-helix	64-79	16
α-helix	107-156	50
α-helix	169-172	4
α-helix	173-177	5
α-helix	178-186	9
α-helix	188-210	23
α-helix	215-220	6
α-helix	222-236	15
α-helix	247-259	13
α-helix	261-267	7
α-helix	270-322	53
α-helix	328-344	17
α-helix	350-370	21
β-strand	383	1	1
β-strand	392-395	4	2
β-strand	398-399	2	3
β-strand	410-411	2	3
β-strand	414-417	4	2
β-strand	422-426	5	4
α-helix	433-440	8
β-strand	450-453	4	2
β-strand	457	1	2
β-strand	461	1	1
α-helix	464-469	6
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	533-546	14
β-strand	551-554	4	4
α-helix	563-574	12
β-strand	581-585	5	4
α-helix	589-591	3
β-strand	597-602	6	4
β-strand	605-608	4	4
α-helix	612-618	7
α-helix	621-629	9
α-helix	700-702	3
α-helix	708-740	33
β-strand	742	1	6
α-helix	745-796	52
α-helix	801-804	4
α-helix	811-826	16
α-helix	827-831	5
α-helix	832-839	8
α-helix	840-844	5
α-helix	845-851	7
α-helix	855-861	7
α-helix	865-879	15
α-helix	888-902	15
α-helix	904-908	5
α-helix	914-964	51
α-helix	971-992	22
α-helix	999-1012	14
β-strand	1035-1042	8	7
β-strand	1053-1060	8	7
β-strand	1066-1068	3	8
α-helix	1076-1083	8
β-strand	1093-1096	4	7
β-strand	1099	1	7
α-helix	1108-1112	5
β-strand	1126	1	9
α-helix	1127-1133	7
α-helix	1142-1151	10
α-helix	1156-1160	5
β-strand	1168	1	9
α-helix	1178-1190	13
β-strand	1198	1	8
α-helix	1211-1219	9
β-strand	1228-1230	3	8
β-strand	1242-1243	2	8
β-strand	1246-1247	2	10
β-strand	1250-1251	2	10
β-strand	1255	1	8
α-helix	1258-1261	4
α-helix	1266-1270	5

Chain B: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	11
β-strand	5	1	12
β-strand	10-11	2	13
β-strand	18-24	7	12
β-strand	38-43	6	13
β-strand	50-51	2	13
β-strand	67-72	6	12
β-strand	75-81	7	12
β-strand	90-95	6	13
β-strand	102	1	13
β-strand	104	1	11
β-strand	107-109	3	13
β-strand	116	1	14
β-strand	119	1	15
β-strand	122	1	16
α-helix	124	1
β-strand	125	1	17
α-helix	126	1
α-helix	127-132	6
β-strand	137	1	18
β-strand	139	1	16
β-strand	140	1	19
β-strand	142	1	15
β-strand	144	1	20
β-strand	145	1	14
β-strand	151-155	5	21
β-strand	159-160	2	21
β-strand	164	1	18
β-strand	167-168	2	19
α-helix	170-172	3
β-strand	178	1	20
β-strand	180-181	2	19
β-strand	184	1	18
α-helix	188-192	5
β-strand	198-201	4	21
α-helix	204-206	3
β-strand	207-208	2	21

Chain C: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	12	1	23
β-strand	17-25	9	22
α-helix	29-31	3
β-strand	32	1	6
β-strand	34-40	7	24
β-strand	44-51	8	24
β-strand	58-59	2	24
β-strand	68-73	6	22
β-strand	78-84	7	22
β-strand	92	1	25
β-strand	93-98	6	24
β-strand	100	1	26
β-strand	104	1	26
β-strand	109	1	24
β-strand	115	1	25
β-strand	117	1	23
β-strand	123	1	27
β-strand	126-130	5	17
α-helix	133-135	3
β-strand	142-151	10	17
β-strand	152	1	27
β-strand	157-160	4	28
β-strand	181-189	9	17
β-strand	199-205	7	28
β-strand	210-216	7	28

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

>7A6F_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

>7A6F_2 MRK16 Fab-fragment light chain (chains B)
DVLMTQTPVSLSVSLGDQASISCRSSQSIVHSTGNTYLEWYLQKPGQSPKLLIYKISNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQASHAPRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C), FASTA

>7A6F_3 MRK16 Fab-fragment heavy chain (chains C)
EVILVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVATISSGGGNTYY
PDSVKGRFTISRDNAKNNLYLQMSSLRSEDTALYYCARYYRYEAWFASWGQGTLVTVSAA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP

Ligands and cofactors

ID	Name	Formula	Copies
ZQU	Zosuquidar	C32 H31 F2 N3 O2	2
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
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
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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