6B7Z: Human insulin degrading enzyme

Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11 heavy chain and FAB H11 light chain. Determined by electron microscopy at 6.5 Å resolution. Released 10 Jan 2018.

Method: Electron microscopy
Resolution: 6.5 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 21,840
Mol. weight: 316.02 kDa
Released: 10 Jan 2018

Explore 6B7Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B7Z contains 109 α-helices and 164 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, 33 β-strands

Element	Residues	Length	Sheet
β-strand	63-68	6	1
β-strand	73-79	7	1
β-strand	87-92	6	1
α-helix	96-98	3
α-helix	106-113	8
α-helix	126-133	8
β-strand	139-142	4	1
β-strand	147-152	6	1
α-helix	158-166	9
α-helix	176-195	20
α-helix	197-207	11
α-helix	214-216	3
α-helix	224-228	5
α-helix	229-231	3
α-helix	237-243	7
α-helix	244-249	6
β-strand	254-260	7	1
α-helix	264-274	11
α-helix	283-285	3
β-strand	303-304	2	2
β-strand	311-316	6	2
β-strand	319-320	2	3
α-helix	330-338	9
α-helix	346-352	7
β-strand	356-364	9	2
α-helix	365	1
β-strand	370-371	2	3
β-strand	372-379	8	2
α-helix	381-384	4
α-helix	387-404	18
α-helix	408-423	16
α-helix	430-441	12
α-helix	461-470	10
α-helix	473-475	3
β-strand	477-482	6	2
β-strand	491-492	2	4
β-strand	499-500	2	4
α-helix	504-506	3
α-helix	507-515	9
α-helix	524-527	4
α-helix	538-540	3
β-strand	549-553	5	5
β-strand	558-561	4	5
β-strand	571-576	6	5
α-helix	581-584	4
α-helix	587-613	27
β-strand	616-622	7	5
β-strand	627-634	8	5
α-helix	638-650	13
α-helix	656-670	15
α-helix	673-675	3
α-helix	678-689	12
α-helix	697-703	7
α-helix	704-706	3
α-helix	709-719	11
β-strand	722	1	6
β-strand	727-731	5	5
α-helix	735-753	19
β-strand	756	1	6
α-helix	767-771	5
β-strand	782	1	7
β-strand	789-795	7	8
α-helix	802-814	13
α-helix	817-819	3
α-helix	820-827	8
β-strand	832	1	8
β-strand	836-837	2	9
β-strand	840	1	10
β-strand	843	1	10
β-strand	846-847	2	9
β-strand	850-852	3	8
α-helix	856-876	21
α-helix	879-893	15
α-helix	902-912	11
α-helix	920-928	9
α-helix	934-939	6
α-helix	940-944	5
β-strand	953-958	6	8
β-strand	959	1	7
α-helix	986-989	4
α-helix	995-1000	6

Chain B: 41 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	63-68	6	11
β-strand	74-79	6	11
β-strand	87-92	6	11
α-helix	96-98	3
α-helix	106-113	8
α-helix	126-133	8
β-strand	139	1	12
β-strand	147-148	2	11
β-strand	150	1	12
β-strand	151-152	2	11
α-helix	158-170	13
α-helix	176-191	16
α-helix	197-207	11
α-helix	214-216	3
α-helix	224-227	4
α-helix	230-233	4
α-helix	237-244	8
α-helix	245-249	5
β-strand	254-260	7	11
α-helix	264-271	8
β-strand	300	1	13
β-strand	303-304	2	13
β-strand	312-316	5	13
β-strand	319-320	2	14
α-helix	330-337	8
α-helix	346-352	7
β-strand	359	1	13
β-strand	362-364	3	15
β-strand	370-371	2	14
β-strand	372-374	3	15
β-strand	375-378	4	13
α-helix	382-385	4
α-helix	387-404	18
α-helix	408-423	16
α-helix	433-443	11
α-helix	461-470	10
α-helix	473-475	3
β-strand	477-481	5	13
α-helix	483-485	3
β-strand	491-492	2	16
β-strand	499-500	2	16
α-helix	507-515	9
α-helix	537-539	3
β-strand	549-553	5	17
β-strand	558-563	6	17
β-strand	571	1	18
β-strand	572-579	8	17
α-helix	587-614	28
β-strand	618-622	5	17
β-strand	626-631	6	17
β-strand	634	1	18
α-helix	638-650	13
α-helix	657-673	17
α-helix	678-688	11
α-helix	697-703	7
α-helix	709-720	12
β-strand	724-731	8	17
α-helix	736-752	17
α-helix	761-763	3
α-helix	769-771	3
β-strand	777	1	19
β-strand	780	1	20
β-strand	790-791	2	21
β-strand	793-794	2	19
β-strand	799	1	21
α-helix	802-819	18
α-helix	820-827	8
β-strand	833-840	8	21
β-strand	843-851	9	21
α-helix	856-876	21
α-helix	879-893	15
α-helix	900-912	13
α-helix	920-930	11
α-helix	933-941	9
β-strand	954-955	2	19
β-strand	957	1	20
β-strand	958	1	21
α-helix	995-998	4
α-helix	1006-1009	4

Chain C: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	22
β-strand	14	1	23
β-strand	19-28	10	22
α-helix	36	1
β-strand	37-41	5	24
β-strand	49-55	7	24
β-strand	60-63	4	24
β-strand	71-76	6	22
β-strand	81-89	9	22
α-helix	91-93	3
β-strand	95-97	3	25
β-strand	98-101	4	24
β-strand	111	1	24
β-strand	116-118	3	25
β-strand	119	1	23
β-strand	128-131	4	26
β-strand	132	1	27
β-strand	143-146	4	28
β-strand	148-153	6	26
β-strand	161-162	2	29
β-strand	167	1	29
β-strand	172-173	2	30
α-helix	174-176	3
β-strand	184-187	4	26
β-strand	188-189	2	30
β-strand	190-193	4	28
α-helix	196-199	4
β-strand	203-207	5	29
β-strand	214-218	5	29

Chain D: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	31
β-strand	11-13	3	32
β-strand	20-26	7	31
β-strand	36-39	4	32
β-strand	46-50	5	32
β-strand	54-55	2	32
α-helix	56	1
β-strand	63-66	4	31
β-strand	73-76	4	31
β-strand	86-89	4	32
β-strand	90	1	33
β-strand	99	1	33
β-strand	103-106	4	32
α-helix	112-114	3
β-strand	119	1	34
α-helix	120	1
β-strand	121	1	27
α-helix	122	1
α-helix	123-127	5
β-strand	131-140	10	34
β-strand	145-151	7	35
β-strand	155-156	2	35
β-strand	160-164	5	34
β-strand	174-182	9	34
α-helix	184-187	4
β-strand	192-199	8	35
β-strand	206-211	6	35

Chain E: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	36
β-strand	14	1	37
β-strand	19-25	7	38
β-strand	26	1	36
α-helix	36	1
β-strand	37-41	5	39
β-strand	49-53	5	39
β-strand	62-63	2	39
β-strand	72-76	5	38
β-strand	81-89	9	38
α-helix	91-93	3
β-strand	95-97	3	40
β-strand	98-101	4	39
β-strand	111	1	39
β-strand	116-118	3	40
β-strand	119	1	37
β-strand	128-131	4	41
β-strand	132	1	42
β-strand	140	1	43
β-strand	143-146	4	43
β-strand	148-153	6	41
β-strand	161-162	2	44
β-strand	167	1	44
β-strand	171-173	3	43
α-helix	174-176	3
β-strand	184-187	4	41
β-strand	188-193	6	43
α-helix	196-199	4
β-strand	203-208	6	44
β-strand	213-218	6	44

Chain F: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	45
β-strand	11-13	3	46
β-strand	20-26	7	45
β-strand	36-39	4	46
β-strand	45-50	6	46
β-strand	54-55	2	46
α-helix	56	1
β-strand	63-66	4	45
β-strand	72-76	5	45
β-strand	86-89	4	46
β-strand	90	1	47
β-strand	99	1	47
β-strand	103-106	4	46
α-helix	112-114	3
β-strand	119	1	48
α-helix	120	1
β-strand	121	1	42
α-helix	122	1
α-helix	123-127	5
β-strand	131-140	10	48
β-strand	145-151	7	49
β-strand	154-156	3	49
β-strand	160-164	5	48
β-strand	174-182	9	48
α-helix	184-187	4
β-strand	192-199	8	49
β-strand	206-211	6	49

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>6B7Z_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

>6B7Z_2 FAB H11 heavy chain (chains C, E)
EVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASIYSYSGSTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARHYSAVAGLDYWGQGTLVTVFNQ
IKPPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 3 (D, F), FASTA

>6B7Z_3 FAB H11 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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