7USL: Integrin alphaM/beta2 ectodomain

Name: PDB 7USL: Integrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5 Fab
Published: 2022-08-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Integrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5 Fab. Determined by electron microscopy at 2.7 Å resolution. Released 17 Aug 2022.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Homo sapiens, Bordetella pertussis
Chains: 5
Atoms: 19,065
Mol. weight: 362.3 kDa
Ligands: NAG, CA
Released: 17 Aug 2022

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

Secondary structure: helices and β-sheets

7USL contains 59 α-helices and 240 β-strands across 5 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: 17 helices, 83 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	21-25	5	3
β-strand	29-34	6	3
β-strand	45	1	4
β-strand	46-51	6	3
β-strand	57-59	3	3
α-helix	60-61	2
β-strand	73	1	4
β-strand	76-80	5	5
β-strand	85-96	12	5
β-strand	101-110	10	5
β-strand	119	1	5
β-strand	341-343	3	6
β-strand	348-351	4	6
α-helix	355-358	4
β-strand	360	1	7
β-strand	362-365	4	6
β-strand	371-374	4	6
α-helix	381-383	3
β-strand	388	1	7
β-strand	391-397	7	8
β-strand	400-407	8	8
α-helix	410-412	3
β-strand	414	1	9
β-strand	415-422	8	8
β-strand	425-433	9	8
β-strand	441	1	9
β-strand	444-448	5	10
β-strand	458-467	10	10
β-strand	471-473	3	11
β-strand	474-479	6	10
α-helix	480-481	2
α-helix	485-487	3
β-strand	491-493	3	10
β-strand	499-504	6	11
β-strand	508-512	5	12
β-strand	521-526	6	12
α-helix	529-532	4
β-strand	534	1	13
β-strand	535-539	5	12
β-strand	541-542	2	14
β-strand	546-547	2	14
β-strand	553-556	4	12
α-helix	557-559	3
β-strand	567	1	13
β-strand	570-575	6	2
β-strand	584-589	6	2
β-strand	592-597	6	2
β-strand	598	1	1
β-strand	601-610	10	15
β-strand	615	1	16
α-helix	617-620	4
β-strand	634-643	10	15
α-helix	649-650	2
β-strand	656-664	9	17
β-strand	674-675	2	18
β-strand	682-689	8	17
β-strand	694-699	6	15
β-strand	700-701	2	18
β-strand	713-723	11	17
α-helix	724-725	2
β-strand	726	1	19
α-helix	727-729	3
β-strand	732	1	19
β-strand	735-736	2	15
β-strand	743-748	6	17
α-helix	749	1
β-strand	750	1	16
α-helix	751-752	2
β-strand	764-769	6	20
β-strand	776-778	3	21
β-strand	783-784	2	20
β-strand	787-792	6	20
β-strand	797-798	2	22
β-strand	801-806	6	23
β-strand	810-816	7	20
β-strand	829-832	4	23
β-strand	844-850	7	23
β-strand	854-855	2	22
β-strand	859-869	11	20
β-strand	878-886	9	23
β-strand	898-904	7	23
β-strand	905-908	4	21
β-strand	912-915	4	24
β-strand	922-924	3	25
β-strand	933-942	10	24
β-strand	949-960	12	25
β-strand	965	1	25
β-strand	967-974	8	24
β-strand	981-987	7	25
α-helix	994-1000	7
β-strand	1003-1004	2	25
β-strand	1010-1021	12	25
β-strand	1026-1035	10	24
β-strand	1048-1057	10	25
β-strand	1063-1064	2	21
α-helix	1065-1066	2
α-helix	1070-1072	3
β-strand	1074-1082	9	25

Chain B: 31 helices, 54 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
β-strand	21-23	3	26
β-strand	24	1	27
α-helix	36-39	4
β-strand	40-42	3	26
α-helix	43-48	6
β-strand	56	1	27
β-strand	62-66	5	28
β-strand	76-77	2	29
β-strand	80-85	6	28
α-helix	86	1
β-strand	91-97	7	29
β-strand	99	1	30
β-strand	105-112	8	31
α-helix	115-117	3
α-helix	118-124	7
α-helix	128-136	9
β-strand	142-149	8	31
α-helix	162-166	5
α-helix	177-179	3
β-strand	183-189	7	31
α-helix	192-199	8
β-strand	212	1	32
α-helix	214-223	10
α-helix	225-228	4
β-strand	234-240	7	31
β-strand	245	1	32
α-helix	250-254	5
α-helix	258-260	3
β-strand	267	1	31
β-strand	270	1	31
α-helix	278-281	4
α-helix	282-292	11
β-strand	294-300	7	31
α-helix	302-304	3
α-helix	305-309	5
α-helix	311-314	4
β-strand	319-322	4	31
α-helix	330-343	14
β-strand	345-349	5	28
β-strand	356-363	8	29
β-strand	370-373	4	29
β-strand	376-378	3	28
β-strand	383	1	30
β-strand	387-395	9	29
β-strand	402-408	7	28
β-strand	414-421	8	28
α-helix	435-437	3
β-strand	441-444	4	33
β-strand	447-450	4	33
β-strand	454-455	2	34
β-strand	461-462	2	34
α-helix	466-468	3
α-helix	470-475	6
α-helix	482	1
α-helix	483-486	4
β-strand	488-491	4	35
β-strand	494-497	4	35
β-strand	508	1	36
β-strand	514	1	36
β-strand	521-522	2	37
β-strand	525-526	2	37
β-strand	533-536	4	38
β-strand	539-542	4	38
α-helix	543	1
β-strand	547	1	39
β-strand	553	1	39
β-strand	561	1	40
β-strand	567	1	40
α-helix	568-570	3
β-strand	572-575	4	41
β-strand	578-581	4	41
α-helix	585-586	2
α-helix	596-598	3
α-helix	599-601	3
α-helix	604-610	7
β-strand	617	1	42
β-strand	619	1	42
β-strand	628-630	3	43
β-strand	638-639	2	43
β-strand	642-643	2	44
β-strand	649-650	2	44
β-strand	652-656	5	43
β-strand	663-667	5	43
β-strand	672	1	44

Chain C: 5 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	756-766	11
β-strand	772	1	45
β-strand	775	1	46
β-strand	776-779	4	47
α-helix	780-781	2
α-helix	782-791	10
β-strand	800-803	4	47
β-strand	807	1	45
β-strand	808	1	48
β-strand	811	1	48
β-strand	819-821	3	49
β-strand	826-828	3	49
β-strand	838-839	2	45
β-strand	841	1	46
β-strand	845	1	50
β-strand	851-853	3	51
β-strand	862	1	52
β-strand	867-869	3	51
β-strand	875-879	5	49
β-strand	886-888	3	45
β-strand	892	1	50
β-strand	895-897	3	53
β-strand	903-905	3	53
β-strand	908-912	5	49
β-strand	919-921	3	45
β-strand	927-930	4	49
β-strand	937-939	3	45
β-strand	948-953	6	49
β-strand	957-964	8	49
β-strand	968-975	8	53
β-strand	978-979	2	52
β-strand	986-987	2	52
β-strand	990-997	8	53
β-strand	1001-1008	8	49
β-strand	1012-1014	3	45
β-strand	1021-1023	3	49
β-strand	1030-1032	3	45
β-strand	1039-1041	3	49
β-strand	1048-1050	3	45
β-strand	1057-1059	3	49
β-strand	1066-1068	3	45
β-strand	1076-1079	4	49
β-strand	1086-1088	3	45
α-helix	1093-1095	3
α-helix	1096-1102	7
β-strand	1105-1110	6	49
β-strand	1115-1117	3	49
β-strand	1127-1131	5	49
β-strand	1135-1137	3	45
β-strand	1142-1146	5	49
β-strand	1153-1155	3	45
β-strand	1161-1164	4	49
β-strand	1171-1173	3	45
β-strand	1180-1182	3	49
β-strand	1189-1191	3	45
β-strand	1200-1202	3	49
β-strand	1209-1211	3	45
β-strand	1225	1	49
β-strand	1232-1234	3	49
β-strand	1239-1244	6	49
β-strand	1249-1255	7	49
β-strand	1259-1261	3	45
β-strand	1268-1270	3	49
β-strand	1277-1279	3	45
β-strand	1286-1288	3	49
β-strand	1295-1297	3	45
β-strand	1304-1306	3	49
β-strand	1313-1315	3	45
β-strand	1322-1324	3	49
β-strand	1331-1333	3	45
β-strand	1341-1344	4	49
β-strand	1351-1353	3	45
β-strand	1373-1375	3	49
β-strand	1380-1382	3	49
β-strand	1392-1396	5	49
β-strand	1400-1402	3	45
β-strand	1409-1411	3	49
β-strand	1418-1420	3	45
β-strand	1427-1429	3	49
β-strand	1436-1438	3	45
β-strand	1445-1446	2	49
β-strand	1454-1456	3	45
β-strand	1463-1465	3	49
β-strand	1474-1476	3	45
β-strand	1483-1485	3	49

Chain H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	54
β-strand	10-12	3	55
β-strand	18-23	6	54
α-helix	26-31	6
β-strand	34-39	6	56
β-strand	46-51	6	56
β-strand	57-59	3	56
α-helix	61-63	3
β-strand	67-72	6	54
β-strand	77-82	6	54
α-helix	84-86	3
β-strand	89-94	6	56
β-strand	102-103	2	56
β-strand	107-108	2	56
β-strand	109-111	3	55

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	57
β-strand	10-13	4	58
β-strand	19-25	7	57
β-strand	33-38	6	58
β-strand	44-48	5	58
α-helix	53	1
β-strand	54	1	58
α-helix	55	1
β-strand	62-67	6	57
β-strand	70-75	6	57
β-strand	85-90	6	58
α-helix	96	1
β-strand	98	1	58
β-strand	102-106	5	58

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-M	A	protein	1162	Homo sapiens	P11215 (AlphaFold model)
Integrin beta	B	protein	730	Homo sapiens	P05107 (AlphaFold model)
Bifunctional hemolysin-adenylate cyclase	C	protein	960	Bordetella pertussis	P0DKX7 (AlphaFold model)
M1F5 fab heavy chain	H	protein	228	Homo sapiens
M1F5 fab light chain	L	protein	213	Homo sapiens

Sequence of entity 1 (A), FASTA

>7USL_1 Integrin alpha-M (chains A)
FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPI
RLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQK
FPEALRGCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEF
RIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVI
TDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVN
NFEALKTIQNQLREKIFAIEGTQTGSSSSFEHEMSQEGFSAAITSNGPLLSTVGSYDWAG
GVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFR
QNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPL
PRGRARWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLFH
GTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQP
VLRVKAIMEFNPREVARNVFECNDQVVKGKEAGEVRVCLHVQKSTRDRLREGQIQSVVTY
DLALDSGRPHSRAVFNETKNSTRRQTQVLGLTQTCETLKLQLPNCIEDPVSPIVLRLNFS
LVGTPLSAFGNLRPVLAEDAQRLFTALFPFEKNCGNDNICQDDLSITFSFMSLDCLVVGG
PREFNVTVTVRNDGEDSYRTQVTFFFPLDLSYRKVSTLQNQRSQRSWRLACESASSTEVS
GALKSTSCSINHPIFPENSEVTFNITFDVDSKASLGNKLLLKANVTSENNMPRTNKTEFQ
LELPVKYAVYMVVTSHGVSTKYLNFTASENTSRVMQHQYQVSNLGQRSLPISLVFLVPVR
LNQTVIWDRPQVTFSENLSSTCHTKERLPSHSDFLAELRKAPVVNCSIAVCQRIQCDIPF
FGIQEEFNATLKGNLSFDWYIKTSHNHLLIVSTAEILFNDSVFTLLPGQGAFVRSQTETK
VEPFEVPNGCGGLEVLFQGPGENAQCEKELQALEKENAQLEWELQALEKELAQWSHPQFE
KGGGSGGGGSGGSAWSHPQFEK

Sequence of entity 2 (B), FASTA

>7USL_2 Integrin beta (chains B)
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPT
SLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDD
LRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPF
AFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFA
TDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAV
TSRMVKTYEKLTEIIPKSAVGELSEDSSNVVHLIKNAYNKLSSRVFLDHNALPDTLKVTY
DSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVL
PQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNN
SIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKC
RCHPGFEGSACQCERTTEGCLNPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPC
GKYISCAECLKFEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQDGM
DRYLIYVDESRECVAGPDGCGLEVLFQGPGKNAQCKKKLQALKKKNAQLKWKLQALKKKL
AQGGHHHHHH

Sequence of entity 3 (C), FASTA

>7USL_3 Bifunctional hemolysin-adenylate cyclase (chains C)
GPGSANSDGLRKMLADLQAGWNASSVIGVQTTEISKSALELAAITGNADNLKSVDVFVDR
FVQGERVAGQPVVLDVAAGGIDIASRKGERPALTFITPLAAPGEEQRRRTKTGKSEFTTF
VEIVGKQDRWRIRDGAADTTIDLAKVVSQLVDANGVLKHSIKLDVIGGDGDDVVLANASR
IHYDGGAGTNTVSYAALGRQDSITVSADGERFNVRKQLNNANVYREGVATQTTAYGKRTE
NVQYRHVELARVGQLVEVDTLEHVQHIIGGAGNDSITGNAHDNFLAGGSGDDRLDGGAGN
DTLVGGEGQNTVIGGAGDDVFLQDLGVWSNQLDGGAGVDTVKYNVHQPSEERLERMGDTG
IHADLQKGTVEKWPALNLFSVDHVKNIENLHGSRLNDRIAGDDQDNELWGHDGNDTIRGR
GGDDILRGGLGLDTLYGEDGNDIFLQDDETVSDDIDGGAGLDTVDYSAMIHPGRIVAPHE
YGFGIEADLSREWVRKASALGVDYYDNVRNVENVIGTSMKDVLIGDAQANTLMGQGGDDT
VRGGDGDDLLFGGDGNDMLYGDAGNDTLYGGLGDDTLEGGAGNDWFGQTQAREHDVLRGG
DGVDTVDYSQTGAHAGIAAGRIGLGILADLGAGRVDKLGEAGSSAYDTVSGIENVVGTEL
ADRITGDAQANVLRGAGGADVLAGGEGDDVLLGGDGDDQLSGDAGRDRLYGEAGDDWFFQ
DAANAGNLLDGGDGRDTVDFSGPGRGLDAGAKGVFLSLGKGFASLMDEPETSNVLRNIEN
AVGSARDDVLIGDAGANVLNGLAGNDVLSGGAGDDVLLGDEGSDLLSGDAGNDDLFGGQG
DDTYLFGVGYGHDTIYESGGGHDTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWY
RDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPDPGAAAAAPPAARVPDTLMQSLAVNWR

Sequence of entity 4 (H), FASTA

>7USL_4 M1F5 fab heavy chain (chains H)
QVQLKQSGPELVKPGASVRMSCKGSGYSFTFHNIHWVKQRPGQGLEWIGWIYPGDGNTKY
NEKFKGKTTLTVDKSSNTAYMLLSSLTSEDSAIYFCAYGNYYFDQWGQGTTLTVSSRSTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 5 (L), FASTA

>7USL_5 M1F5 fab light chain (chains L)
IQMMQSTSSLSASLGDRVTISCSASQGITNYLNWYQQKPDGTVKLLIYYTSSLHSGVPSR
FSGSGSGTDYSLTISNLEPEDIATYYCQQYSNLPWTFGGGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11
CA	Calcium ion	Ca	33

Primary citation

Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin. Goldsmith, J.A., DiVenere, A.M., Maynard, J.A. et al. Cell Rep (2022) 40:111196-111196. DOI 10.1016/j.celrep.2022.111196 · PubMed

Other PDB entries of the same protein (UniProt P11215 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MF7 1.25 Å, Integrin alpha M I domain
1NA5 1.5 Å, Integrin alpha M I domain
8CE6 1.58 Å, Crystal structure of human Cd11b I domain in P212121 space group
1IDO 1.7 Å, I-domain from integrin CR3, MG2+ bound
1JLM 2.0 Å, I-domain from integrin CR3, MN2+ bound
4XW2 2.0 Å, Structural basis for simvastatin competitive antagonism of complement receptor 3
8CE9 2.11 Å, Crystal structure of human Cd11b I domain in C121 space group
1M1U 2.3 Å, An isoleucine-based allosteric switch controls affinity and shape shifting in integrin…
1N9Z 2.5 Å, Integrin alpha M I domain mutant
9RM9 2.6 Å, Cryo-EM structure of alphaM/beta2 headpiece complex without alphaM I-domain - the…
1BHO 2.7 Å, Mac-1 I domain magnesium complex
1BHQ 2.7 Å, Mac-1 I domain cadmium complex

Browse structure collections

About this viewer

MolViewer shows 7USL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.