6BF9: 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. Determined by electron microscopy at 7.2 Å resolution. Released 7 Feb 2018.

Method: Electron microscopy
Resolution: 7.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 21,836
Mol. weight: 316.02 kDa
Released: 7 Feb 2018

Explore 6BF9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BF9 contains 109 α-helices and 167 β-strands across 6 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: 48 helices, 37 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	229-231	3
α-helix	237-244	8
α-helix	245-249	5
β-strand	254-260	7	1
α-helix	265-274	10
α-helix	283-285	3
β-strand	300	1	2
β-strand	303-304	2	2
β-strand	312-320	9	2
α-helix	323-325	3
α-helix	330-338	9
α-helix	346-353	8
β-strand	359-364	6	2
β-strand	370-378	9	2
α-helix	381-385	5
α-helix	387-404	18
α-helix	409-423	15
α-helix	433-440	8
α-helix	441-443	3
α-helix	461-470	10
β-strand	477-481	5	2
β-strand	491-492	2	3
β-strand	499-500	2	3
α-helix	504-506	3
α-helix	507-515	9
α-helix	524-528	5
α-helix	536-540	5
β-strand	552-553	2	4
β-strand	557-562	6	4
β-strand	571-574	4	4
β-strand	577	1	5
β-strand	578-579	2	4
α-helix	581-583	3
α-helix	587-614	28
β-strand	616-617	2	4
β-strand	620-622	3	5
β-strand	627-629	3	5
β-strand	631-634	4	4
α-helix	638-650	13
α-helix	656-670	15
α-helix	671-674	4
α-helix	678-689	12
α-helix	697-702	6
α-helix	703-705	3
α-helix	709-719	11
β-strand	722	1	6
β-strand	724-731	8	4
α-helix	735-753	19
β-strand	756	1	6
α-helix	757-759	3
β-strand	769	1	7
β-strand	776-777	2	8
β-strand	782	1	9
β-strand	789-795	7	8
β-strand	799	1	8
α-helix	802-814	13
α-helix	817-819	3
α-helix	820-826	7
β-strand	836-840	5	8
β-strand	843-847	5	8
β-strand	850-852	3	8
α-helix	856-875	20
α-helix	879-893	15
α-helix	900-911	12
α-helix	920-928	9
α-helix	934-944	11
β-strand	953-958	6	8
β-strand	959	1	9
α-helix	986-991	6
α-helix	995-1000	6
β-strand	1004	1	7
α-helix	1008-1010	3

Chain B: 47 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	63-69	7	10
β-strand	73-79	7	10
β-strand	87-92	6	10
α-helix	96-98	3
α-helix	106-113	8
α-helix	126-133	8
β-strand	139	1	10
β-strand	142	1	10
β-strand	147-152	6	10
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	237-243	7
α-helix	244-249	6
β-strand	254-260	7	10
α-helix	268-274	7
α-helix	283-285	3
β-strand	300	1	11
β-strand	303-304	2	11
β-strand	312-319	8	11
α-helix	330-338	9
α-helix	346-352	7
β-strand	361-365	5	11
β-strand	371-378	8	11
α-helix	382-384	3
α-helix	387-404	18
α-helix	409-423	15
α-helix	433-439	7
α-helix	461-470	10
β-strand	477-481	5	11
β-strand	491-492	2	12
β-strand	499-500	2	12
α-helix	504-506	3
α-helix	507-515	9
α-helix	524-527	4
β-strand	549-553	5	13
β-strand	558-562	5	13
β-strand	571-579	9	13
α-helix	581-583	3
α-helix	587-612	26
β-strand	618-622	5	13
β-strand	626-634	9	13
α-helix	638-650	13
α-helix	656-672	17
α-helix	673-675	3
α-helix	678-689	12
α-helix	697-702	6
α-helix	703-706	4
α-helix	709-721	13
β-strand	722	1	14
β-strand	724-731	8	13
α-helix	735-753	19
β-strand	756	1	14
α-helix	757-759	3
β-strand	769	1	7
α-helix	770-771	2
β-strand	776-777	2	15
β-strand	780-781	2	15
β-strand	789-795	7	15
β-strand	799	1	16
α-helix	802-814	13
α-helix	817-821	5
α-helix	822-827	6
β-strand	832-837	6	15
β-strand	840	1	16
β-strand	843	1	16
β-strand	846-852	7	15
α-helix	856-875	20
α-helix	879-893	15
α-helix	900-911	12
α-helix	920-928	9
α-helix	933-944	12
β-strand	953-958	6	15
α-helix	995-1000	6
β-strand	1004	1	7
α-helix	1008-1010	3

Chain C: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	17
β-strand	15	1	18
β-strand	21-28	8	17
β-strand	37-42	6	19
β-strand	48-50	3	19
β-strand	52-55	4	20
β-strand	60-63	4	20
β-strand	71-76	6	17
β-strand	81-86	6	17
α-helix	91-93	3
β-strand	96-101	6	19
β-strand	102	1	21
β-strand	109	1	21
β-strand	117	1	19
β-strand	120	1	18
β-strand	128-131	4	22
β-strand	143-151	9	22
α-helix	156-159	4
β-strand	162	1	23
β-strand	171-173	3	22
α-helix	174-176	3
β-strand	186-193	8	22
β-strand	203-205	3	23
β-strand	208	1	24
β-strand	213	1	24
β-strand	216-218	3	23

Chain D: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	25
β-strand	12-13	2	26
β-strand	20-26	7	25
β-strand	34	1	27
β-strand	36-39	4	28
β-strand	45-50	6	28
β-strand	54-55	2	28
α-helix	56	1
β-strand	64-68	5	25
β-strand	71-76	6	25
β-strand	86	1	28
β-strand	87	1	29
β-strand	91	1	27
α-helix	96-97	2
β-strand	103	1	29
β-strand	105-106	2	26
β-strand	112	1	30
α-helix	113-114	2
β-strand	117-119	3	31
α-helix	123-126	4
β-strand	131-136	6	31
β-strand	140	1	32
β-strand	141	1	30
β-strand	145-151	7	33
β-strand	162-164	3	31
β-strand	174	1	32
β-strand	176-182	7	31
α-helix	184-187	4
β-strand	193-199	7	33
β-strand	206	1	33

Chain E: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	34
β-strand	14-15	2	35
β-strand	24-28	5	34
β-strand	37-42	6	36
β-strand	50	1	36
β-strand	52-55	4	37
β-strand	60-63	4	37
β-strand	71-76	6	34
β-strand	81-86	6	34
α-helix	91-93	3
β-strand	95-102	8	36
β-strand	109-112	4	36
β-strand	116-118	3	36
β-strand	119-120	2	35
β-strand	128-131	4	38
β-strand	143	1	39
β-strand	146-151	6	38
α-helix	157-158	2
β-strand	159-162	4	40
β-strand	172-178	7	38
β-strand	184-190	7	38
β-strand	193	1	39
β-strand	203-208	6	40
β-strand	213-218	6	40

Chain F: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	41
β-strand	11-13	3	42
β-strand	20-26	7	41
β-strand	34-38	5	43
β-strand	39	1	42
β-strand	46-50	5	43
β-strand	54-55	2	43
α-helix	56	1
β-strand	57	1	44
β-strand	59	1	44
β-strand	63-68	6	41
β-strand	71-76	6	41
β-strand	86-87	2	42
β-strand	89-91	3	43
α-helix	96-97	2
β-strand	103-106	4	42
β-strand	112	1	45
β-strand	115-117	3	46
α-helix	123-126	4
β-strand	131-140	10	46
β-strand	141	1	45
β-strand	145-151	7	47
β-strand	155-156	2	47
β-strand	162-164	3	46
β-strand	174-182	9	46
α-helix	184-187	4
β-strand	192	1	48
β-strand	193-199	7	47
β-strand	206-208	3	47
β-strand	211	1	48

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	P0DOX7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6BF9_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

>6BF9_2 Fab H11-E heavy chain (chains C, E)
EVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASIYSYSGSTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARHYSAVAGLDYWGQGTLVTVFNQ
IKPPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 3 (D, F), FASTA

>6BF9_3 Fab H11-E light chain (chains D, F)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDYTLTISSLQPEDFATYYCQQSYFNPITFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNR

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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