7NWL: Human integrin alpha5beta1

Cryo-EM structure of human integrin alpha5beta1 (open form) in complex with fibronectin and TS2/16 Fv-clasp. Determined by electron microscopy at 3.1 Å resolution. Released 2 Jun 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 13,904
Mol. weight: 280.94 kDa
Ligands: MN
Released: 2 Jun 2021

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

Secondary structure: helices and β-sheets

7NWL contains 55 α-helices and 140 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: 13 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	22-26	5	3
β-strand	34-39	6	3
β-strand	54-59	6	3
β-strand	68-70	3	3
α-helix	76-78	3
β-strand	79	1	4
α-helix	80	1
α-helix	83-86	4
β-strand	92	1	4
β-strand	95	1	5
β-strand	104-108	5	6
β-strand	111-116	6	6
β-strand	120	1	5
β-strand	121-122	2	7
β-strand	129-130	2	7
β-strand	134-139	6	6
β-strand	144-148	5	6
β-strand	169-172	4	8
β-strand	178-182	5	8
α-helix	185-188	4
β-strand	190	1	9
β-strand	191-195	5	8
α-helix	197-203	7
β-strand	217-218	2	8
α-helix	219-221	3
α-helix	224-226	3
β-strand	231	1	9
β-strand	234-238	5	10
β-strand	247-252	6	10
α-helix	255-258	4
β-strand	261-265	5	10
β-strand	272-277	6	10
β-strand	288-292	5	11
β-strand	301-306	6	11
β-strand	310-312	3	12
β-strand	318-320	3	12
β-strand	323-327	5	11
α-helix	328	1
β-strand	329	1	13
α-helix	330	1
β-strand	334	1	13
β-strand	340-343	4	11
β-strand	354-357	4	14
β-strand	369-373	5	14
β-strand	383-387	5	14
β-strand	400-402	3	14
α-helix	407-408	2
β-strand	418-423	6	2
β-strand	432-437	6	2
β-strand	442-446	5	2
β-strand	448	1	1
α-helix	449-450	2
β-strand	451-460	10	15
β-strand	464-465	2	16
α-helix	466	1
β-strand	472	1	17
β-strand	479	1	17
β-strand	481-492	12	15
β-strand	498-507	10	18
β-strand	519-521	3	15
β-strand	528-536	9	18
β-strand	543-550	8	15
β-strand	563-571	9	18
β-strand	585-586	2	15
β-strand	593-598	6	18
β-strand	599-600	2	16

Chain B: 19 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	15-21	7
β-strand	26	1	19
β-strand	27-28	2	20
β-strand	45	1	19
α-helix	47-52	6
β-strand	60-61	2	20
β-strand	68	1	21
α-helix	74-76	3
α-helix	81-83	3
β-strand	98-102	5	21
β-strand	104	1	22
β-strand	107	1	22
β-strand	109-116	8	23
β-strand	123-130	8	24
α-helix	133-135	3
α-helix	139-156	18
β-strand	160-167	8	24
α-helix	180-184	5
α-helix	193	1
β-strand	194	1	25
α-helix	195-196	2
β-strand	199-206	8	24
α-helix	209-217	9
β-strand	222	1	25
β-strand	229	1	26
α-helix	231-240	10
α-helix	242-245	4
β-strand	251-258	8	24
β-strand	262	1	26
α-helix	275-277	3
β-strand	283	1	27
β-strand	287	1	24
β-strand	288	1	27
α-helix	295-298	4
α-helix	299-309	11
β-strand	311-317	7	24
α-helix	322-331	10
β-strand	335-339	5	24
α-helix	345-356	12
β-strand	360-362	3	28
β-strand	365	1	29
β-strand	373-379	7	23
α-helix	382-384	3
β-strand	395-398	4	28
β-strand	403-412	10	23
β-strand	421-425	5	21
β-strand	426	1	29
β-strand	434-439	6	21

Chain C: 16 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	1144-1146	3
β-strand	1150-1152	3	30
β-strand	1160-1163	4	30
α-helix	1165-1167	3
β-strand	1174-1181	8	31
α-helix	1182-1184	3
β-strand	1190-1195	6	31
β-strand	1200-1203	4	30
β-strand	1212-1220	9	31
β-strand	1223-1224	2	31
α-helix	1226-1227	2
β-strand	1228-1232	5	31
α-helix	1233-1239	7
β-strand	1240-1245	6	32
β-strand	1252-1257	6	32
α-helix	1258-1259	2
β-strand	1266-1273	8	33
β-strand	1281-1285	5	33
β-strand	1291-1294	4	32
α-helix	1297-1298	2
β-strand	1302-1311	10	33
β-strand	1314-1315	2	33
α-helix	1317-1318	2
β-strand	1319-1324	6	33
α-helix	1327-1330	4
β-strand	1331-1336	6	34
β-strand	1343-1348	6	34
β-strand	1356-1363	8	35
α-helix	1369-1371	3
β-strand	1372-1376	5	35
β-strand	1381-1384	4	34
α-helix	1387-1388	2
β-strand	1392-1401	10	35
β-strand	1404-1405	2	35
α-helix	1406-1408	3
β-strand	1409-1414	6	35
β-strand	1421-1428	8	36
β-strand	1433-1438	6	36
α-helix	1439-1440	2
β-strand	1446-1453	8	37
α-helix	1459-1460	2
β-strand	1461-1466	6	37
β-strand	1471-1474	4	36
α-helix	1477-1478	2
β-strand	1482-1490	9	37
β-strand	1499	1	37
α-helix	1500-1502	3
β-strand	1503-1508	6	37

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	38
β-strand	12	1	39
β-strand	17-25	9	38
β-strand	34-39	6	40
β-strand	45-51	7	40
β-strand	57-58	2	40
β-strand	67-72	6	38
β-strand	77-82A	7	38
α-helix	84-86	3
β-strand	88-97	10	40
β-strand	100B-103	5	40
β-strand	107-109	3	40
β-strand	111	1	39
α-helix	115-122	8
α-helix	125-163	39

Chain E: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	41
β-strand	10-13	4	40
β-strand	19-25	7	41
β-strand	33-38	6	40
β-strand	45-49	5	40
β-strand	53-54	2	40
α-helix	55	1
β-strand	63-67	5	41
β-strand	70-75	6	41
β-strand	84-90	7	40
β-strand	97-98	2	40
α-helix	99-101	3
β-strand	102-106	5	40
α-helix	112-115	4
α-helix	120-158	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-5	A	protein	1008	Homo sapiens	P08648 (AlphaFold model)
Integrin beta-1	B	protein	778	Homo sapiens	P05556 (AlphaFold model)
Isoform 1 of Fibronectin	C	protein	368	Homo sapiens	P02751 (AlphaFold model)
TS2/16 VH(S112C)-SARAH Chimera	D	protein	172	Mus musculus
TS2/16 VL-SARAH(S37C) Chimera	E	protein	164	Mus musculus

Sequence of entity 1 (A), FASTA

>7NWL_1 Integrin alpha-5 (chains A)
FNLDAEAPAVLSGPPGSFFGFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPW
GASPTQCTPIEFDSKGSRLLESSLSSSEGEEPVEYKSLQWFGATVRAHGSSILACAPLYS
WRTEKEPLSDPVGTCYLSTDNFTRILEYAPCRSDFSWAAGQGYCQGGFSAEFTKTGRVVL
GGPGSYFWQGQILSATQEQIAESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEF
SGDDTEDFVAGVPKGNLTYGYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLD
DLLVGAPLLMDRTPDGRPQEVGRVYVYLQHPAGIEPTPTLTLTGHDEFGRFGSSLTPLGD
LDQDGYNDVAIGAPFGGETQQGVVFVFPGGPGGLGSKPSQVLQPLWAASHTPDFFGSALR
GGRDLDGNGYPDLIVGSFGVDKAVVYRGRPIVSASASLTIFPAMFNPEERSCSLEGNPVA
CINLSFCLNASGKHVADSIGFTVELQLDWQKQKGGVRRALFLASRQATLTQTLLIQNGAR
EDCREMKIYLRNESEFRDKLSPIHIALNFSLDPQAPVDSHGLRPALHYQSKSRIEDKAQI
LLDCGEDNICVPDLQLEVFGEQNHVYLGDKNALNLTFHAQNVGEGGAYEAELRVTAPPEA
EYSGLVRHPGNFSSLSCDYFAVNQSRLLVCDLGNPMKAGASLWGGLRFTVPHLRDTKKTI
QFDFQILSKNLNNSQSDVVSFRLSVEAQAQVTLNGVSKPEAVLFPVSDWHPRDQPQKEED
LGPAVHHVYELINQGPSSISQGVLELSCPQALEGQQLLYVTRVTGLNCTTNHPINPKGLE
LDPEGSLHHQQKREAPSRSSASSGPQILKCPEAECFRLRCELGPLHQQESQSLQLHFRVW
AKTFLQREHQPFSLQCEAVYKALKMPYRILPRQLPQKERQVATAVQWTKAEGSYGVPLWI
IILAILFGLLLLGLLIYILYKLGFFKRSLPYGTAMEKAQLKPPATSDA

Sequence of entity 2 (B), FASTA

>7NWL_2 Integrin beta-1 (chains B)
QTDENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPTSARCDDLEALKKKGCPPDDI
ENPRGSKDIKKNKNVTNRSKGTAEKLKPEDIHQIQPQQLVLRLRSGEPQTFTLKFKRAED
YPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDFRIGFGSFVEKTVMPYISTTP
AKLRNPCTSEQNCTTPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAV
CGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIA
HLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSS
EVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDS
DSFKIRPLGFTEEVEVILQYICECECQSEGIPESPKCHEGNGTFECGACRCNEGRVGRHC
ECSTDEVNSEDMDAYCRKENSSEICSNNGECVCGQCVCRKRDNTNEIYSGKFCECDNFNC
DRSNGLICGGNGVCKCRVCECNPNYTGSACDCSLDTSTCEASNGQICNGRGICECGVCKC
TDPKFQGQTCEMCQTCLGVCAEHKECVQCRAFNKGEKKDTCTQECSYFNITKVESRDKLP
QPVQPDPVSHCKEKDVDDCWFYFTYSVNGNNEVMVHVVENPECPTGPDIIPIVAGVVAGI
VLIGLALLLIWKLLMIIHDRREFAKFEKEKMNAKWDTGENPIYKSAVTTVVNPKYEGK

Sequence of entity 3 (C), FASTA

>7NWL_3 Isoform 1 of Fibronectin (chains C)
PLSPPTNLHLEANPDTGVLTVSWERSTTPDITGYRITTTPTNGQQGNSLEEVVHADQSSC
TFDNLSPGLEYNVSVYTVKDDKESVPISDTIIPAVPPPTDLRFTNIGPDTMRVTWAPPPS
IDLTNFLVRYSPVKNEEDVAELSISPSDNAVVLTNLLPGTEYVVSVSSVYEQHESTPLRG
RQKTGLDSPTGIDFSDITANSFTVHWIAPRATITGYRIRHHPEHFSGRPREDRVPHSRNS
ITLTNLTPGTEYVVSIVALNGREESPLLIGQQSTVSDVPRDLEVVAATPTSLLISWDAPA
VTVRYYRITYGETGGNSPVQEFTVPGSKSTATISGLKPGVDYTITVYAVTGRGDSPASSK
PISINYRT

Sequence of entity 4 (D), FASTA

>7NWL_4 TS2/16 VH(S112C)-SARAH Chimera (chains D)
MDVKLVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVATISSGGSYTY
YPDSVKGRFTISRDKAKNTLYLQMGSLKSEDTAMYYCTRIGYDEDYAMDHWGQGTSVTVC
SGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQSKRQPILDAIEAK

Sequence of entity 5 (E), FASTA

>7NWL_5 TS2/16 VL-SARAH(S37C) Chimera (chains E)
GSHMQIVVTQRPTTMAASPGDKIIITCSVSSIISSNYLHWYSQKPGFSPKLLIYRTSNLA
SGVPPRFSGSGSGTSYSLTIGTMEAEDVATYYCQQGSDIPLTFGDGTKLDLKRGSDYEFL
KSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDAIEAK

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	7

Primary citation

Structural insights into integrin alpha 5 beta 1 opening by fibronectin ligand. Schumacher, S., Dedden, D., Nunez, R.V. et al. Sci Adv (2021) 7. DOI 10.1126/sciadv.abe9716 · PubMed

Other PDB entries of the same protein (UniProt P08648 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WK0 1.78 Å, Metal Ion and Ligand Binding of Integrin
4WJK 1.85 Å, Metal Ion and Ligand Binding of Integrin
9HMH 1.92 Å, Crystal structure of the Calf domains of Integrin Alpha5
4WK2 2.5 Å, Metal Ion and Ligand Binding of Integrin
4WK4 2.5 Å, Metal Ion and Ligand Binding of Integrin
9B9J 2.6 Å, Integrin alpha-5 beta-1 in complex with BIIG2 Fab
9P6S 2.61 Å, Cryo-EM structure of human integrin alpha5beta1 in complex with fibronectin (FN 7-10)
9B9K 2.7 Å, Integrin alpha-5 beta-1 in complex with MINT1526A Fab
9HMI 2.87 Å, Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2…
3VI3 2.9 Å, Crystal structure of alpha5beta1 integrin headpiece (ligand-free form)
3VI4 2.9 Å, Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide
9DIA 2.97 Å, Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin candidate 2

Browse structure collections

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