6B70: Human insulin degrading enzyme

Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy chain, FAB H11-E light chain and insulin. Determined by electron microscopy at 3.7 Å resolution. Released 27 Dec 2017.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 22,192
Mol. weight: 340 kDa
Released: 27 Dec 2017

Explore 6B70 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B70 contains 103 α-helices and 163 β-strands across 8 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.

Chains a and c: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	13	1	1

Chain A: 42 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	63-69	7	1
β-strand	73-79	7	1
β-strand	86-92	7	1
α-helix	106-113	8
α-helix	126-133	8
β-strand	139-142	4	1
β-strand	147-153	7	1
α-helix	158-166	9
α-helix	176-191	16
α-helix	197-207	11
α-helix	214-216	3
α-helix	223	1
α-helix	224-228	5
α-helix	229-232	4
α-helix	237-247	11
β-strand	254-260	7	1
α-helix	266-274	9
β-strand	300	1	2
β-strand	303-304	2	2
β-strand	311-320	10	2
α-helix	330-338	9
α-helix	346-352	7
β-strand	359-364	6	2
β-strand	370-378	9	2
α-helix	384-386	3
α-helix	387-404	18
α-helix	409-423	15
α-helix	433-440	8
α-helix	461-470	10
α-helix	473-475	3
β-strand	477-482	6	2
β-strand	491-492	2	3
β-strand	499-500	2	3
α-helix	507-515	9
α-helix	536-540	5
β-strand	549-553	5	4
β-strand	557-563	7	4
β-strand	571-579	9	4
α-helix	587-614	28
β-strand	616-622	7	4
β-strand	626-634	9	4
α-helix	638-650	13
α-helix	656-670	15
α-helix	671-675	5
α-helix	678-689	12
α-helix	697-702	6
α-helix	703-705	3
α-helix	709-719	11
β-strand	722	1	5
β-strand	725-731	7	4
α-helix	735-753	19
β-strand	756	1	5
α-helix	757-759	3
β-strand	769	1	6
β-strand	776-780	5	7
β-strand	789-795	7	7
β-strand	799	1	7
α-helix	802-814	13
α-helix	816-819	4
α-helix	820-826	7
β-strand	833-840	8	7
β-strand	843-852	10	7
α-helix	856-875	20
α-helix	879-893	15
α-helix	900-912	13
α-helix	920-928	9
α-helix	933-943	11
β-strand	953-958	6	7
α-helix	986-988	3
β-strand	990	1	7
α-helix	995-1000	6
β-strand	1004	1	6
α-helix	1008-1010	3

Chain B: 46 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	63-69	7	8
β-strand	73-79	7	8
β-strand	87-92	6	8
α-helix	106-115	10
α-helix	126-132	7
β-strand	137-142	6	8
β-strand	147-152	6	8
α-helix	158-163	6
α-helix	167-170	4
α-helix	176-192	17
α-helix	197-207	11
α-helix	214-216	3
α-helix	223	1
α-helix	224-228	5
α-helix	229-232	4
α-helix	237-248	12
α-helix	249-251	3
β-strand	254-260	7	8
α-helix	266-274	9
α-helix	283-285	3
β-strand	300	1	9
β-strand	303-304	2	9
β-strand	311-316	6	9
β-strand	319	1	10
α-helix	330-338	9
α-helix	346-352	7
β-strand	359-362	4	9
β-strand	371	1	10
β-strand	374-378	5	9
α-helix	382-385	4
α-helix	387-404	18
α-helix	408-423	16
α-helix	434-440	7
α-helix	461-468	8
α-helix	473-475	3
β-strand	477-482	6	9
β-strand	491-492	2	11
β-strand	499-500	2	11
α-helix	504-506	3
α-helix	507-514	8
α-helix	536-540	5
β-strand	549-553	5	12
β-strand	558-563	6	12
β-strand	571-579	9	12
α-helix	581-584	4
α-helix	587-613	27
β-strand	616-622	7	12
β-strand	626-634	9	12
α-helix	638-650	13
α-helix	656-672	17
α-helix	673-675	3
α-helix	678-689	12
α-helix	699-702	4
α-helix	703-706	4
α-helix	709-720	12
β-strand	722	1	13
β-strand	724-731	8	12
α-helix	735-753	19
β-strand	756	1	13
α-helix	757-759	3
α-helix	760-762	3
β-strand	769	1	6
β-strand	776-782	7	14
β-strand	789-799	11	14
α-helix	802-819	18
α-helix	820-827	8
β-strand	832-840	9	14
β-strand	843-852	10	14
α-helix	856-873	18
α-helix	879-893	15
α-helix	900-911	12
α-helix	920-928	9
α-helix	933-941	9
β-strand	953-959	7	14
β-strand	990-991	2	14
α-helix	995-1001	7
β-strand	1004	1	6
α-helix	1008-1010	3

Chain C: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	15
β-strand	14-15	2	16
β-strand	19-28	10	15
β-strand	37-42	6	17
β-strand	48-55	8	17
β-strand	60-63	4	17
β-strand	71-76	6	15
β-strand	81-89	9	15
α-helix	91-93	3
β-strand	95-102	8	17
β-strand	109-112	4	17
β-strand	116-118	3	17
β-strand	119-120	2	16
β-strand	128-131	4	18
α-helix	136-138	3
β-strand	143-153	11	18
β-strand	161-162	2	19
β-strand	171-173	3	18
α-helix	174-176	3
β-strand	177-178	2	18
β-strand	184-193	10	18
α-helix	194-196	3
β-strand	203-205	3	19
β-strand	208	1	20
β-strand	213	1	20
β-strand	216-218	3	19

Chain D: 2 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	21
β-strand	11-13	3	22
β-strand	20-26	7	21
β-strand	36-39	4	23
β-strand	46-49	4	23
β-strand	50	1	24
β-strand	54	1	24
β-strand	63-64	2	21
β-strand	67-68	2	21
β-strand	71-76	6	21
β-strand	86-89	4	23
β-strand	90	1	25
β-strand	99	1	25
β-strand	103	1	23
β-strand	104-106	3	22
β-strand	112	1	26
β-strand	117-119	3	27
α-helix	123-126	4
β-strand	131-133	3	28
β-strand	134-140	7	27
β-strand	141	1	26
β-strand	145-151	7	29
β-strand	154-155	2	29
β-strand	163-164	2	27
β-strand	174-177	4	27
β-strand	180-182	3	28
α-helix	184-189	6
β-strand	192-199	8	29
β-strand	207-211	5	29

Chain E: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	30
β-strand	14	1	31
β-strand	20-28	9	30
β-strand	37-42	6	32
β-strand	49-54	6	32
β-strand	62-63	2	32
β-strand	71-76	6	30
β-strand	81-87	7	30
α-helix	91-93	3
β-strand	95-99	5	32
β-strand	101-102	2	33
β-strand	109-111	3	33
β-strand	116-118	3	32
β-strand	119	1	31
β-strand	125	1	34
β-strand	128-132	5	35
α-helix	136-138	3
β-strand	143-153	11	35
β-strand	154	1	34
β-strand	161-162	2	36
β-strand	167	1	36
β-strand	171-173	3	35
α-helix	174-176	3
β-strand	177-179	3	35
β-strand	183-193	11	35
β-strand	202-205	4	36
β-strand	208	1	37
β-strand	213	1	37
β-strand	216-219	4	36

Chain F: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	38
β-strand	11-13	3	39
β-strand	20-26	7	38
β-strand	34-39	6	40
β-strand	45-50	6	40
β-strand	54-55	2	40
α-helix	56	1
β-strand	63-64	2	38
β-strand	67-68	2	38
β-strand	71-76	6	38
β-strand	86-91	6	40
α-helix	96-97	2
β-strand	98-99	2	40
β-strand	103	1	40
β-strand	104-106	3	39
β-strand	112	1	41
β-strand	115-119	5	42
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-140	10	42
β-strand	141	1	41
β-strand	147-151	5	43
β-strand	155	1	43
β-strand	163-164	2	42
β-strand	174-182	9	42
α-helix	184-187	4
β-strand	193-197	5	43
α-helix	205	1
β-strand	206-207	2	43

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Insulin-degrading enzyme	A, B	protein	966	Homo sapiens	P14735 (AlphaFold model)
FAB H11-E heavy chain	C, E	protein	218	Mus musculus, Homo sapiens	P0DOX5 (AlphaFold model)
FAB H11-E light chain	D, F	protein	211	Mus musculus, Homo sapiens	Q6GMX0 (AlphaFold model)
Insulin	a, c	protein	110	Homo sapiens	P01308 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6B70_1 Insulin-degrading enzyme (chains A, B)
AIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDVHIGSLSDPPNIAG
LSHFLEHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDRF
AQFFLSPLFDESAKDREVNAVDSEHEKNVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYT
LETRPNQEGIDVRQELLKFHSAYYSSNLMAVVVLGRESLDDLTNLVVKLFSEVENKNVPL
PEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSNPGHYLGHLIGHEGPGS
LLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIILHMFQYIQKLRAEG
PQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILHYYPLEEVLTAEYLLEEFRPDLIE
MVLDKLRPENVRVAIVSKSFEGKTDRTEEWYGTQYKQEAIPDEVIKKWQNADLNGKFKLP
TKNEFIPTNFEILPLEKEATPYPALIKDTAMSKLWFKQDDKFFLPKANLNFEFFSPFAYV
DPLHSNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILLKKI
IEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTEVAWTKDELKEALD
DVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIMQMVEDTLIEHAHTKPLLPSQLVR
YREVQLPDRGWFVYQQRNEVHNNSGIEIYYQTDMQSTSENMFLELFAQIISEPAFNTLRT
KEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLITMEKSIEDMTEEAFQKH
IQALAIRRLDKPKKLSAESAKYWGEIISQQYNFDRDNTEVAYLKTLTKEDIIKFYKEMLA
VDAPRRHKVSVHVLAREMDSCPVVGEFPCQNDINLSQAPALPQPEVIQNMTEFKRGLPLF
PLVKPH

Sequence of entity 2 (C, E), FASTA

>6B70_2 FAB H11-E heavy chain (chains C, E)
EVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASIYSYSGSTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARHYSAVAGLDYWGQGTLVTVFNQ
IKPPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 3 (D, F), FASTA

>6B70_3 FAB H11-E light chain (chains D, F)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDYTLTISSLQPEDFATYYCQQSYFNPITFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 4 (a, c), FASTA

>6B70_4 Insulin (chains a, c)
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

Primary citation

Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. Zhang, Z., Liang, W.G., Bailey, L.J. et al. Elife (2018) 7. DOI 10.7554/eLife.33572 · PubMed

Other PDB entries of the same protein (UniProt P14735 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3CWW 1.96 Å, Crystal Structure of IDE-bradykinin complex
2G47 2.1 Å, Crystal structure of human insulin-degrading enzyme in complex with amyloid-beta (1-40)
2G56 2.2 Å, crystal structure of human insulin-degrading enzyme in complex with insulin B chain
4PES 2.21 Å, Crystal structure of insulin degrading enzyme complexed with inhibitor tert-butyl…
4PFC 2.21 Å, Crystal structure of insulin degrading enzyme complexed with inhibitor
2G54 2.25 Å, Crystal structure of Zn-bound human insulin-degrading enzyme in complex with insulin B…
3E4Z 2.28 Å, Crystal structure of human insulin degrading enzyme in complex with insulin-like growth…
3E50 2.3 Å, Crystal structure of human insulin degrading enzyme in complex with transforming growth…
4PF7 2.33 Å, Crystal structure of insulin degrading enzyme complexed with inhibitor
3OFI 2.35 Å, Crystal structure of human insulin-degrading enzyme in complex with ubiquitin
2G49 2.5 Å, Crystal structure of human insulin-degrading enzyme in complex with glucagon
4PF9 2.5 Å, Crystal structure of insulin degrading enzyme complexed with inhibitor

Browse structure collections

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