9P6S: Human integrin alpha5beta1

Cryo-EM structure of human integrin alpha5beta1 in complex with fibronectin (FN 7-10). Determined by electron microscopy at 2.61 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 2.61 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,778
Mol. weight: 139.28 kDa
Ligands: NAG, MN
Released: 25 Mar 2026

Explore 9P6S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9P6S contains 31 α-helices and 95 β-strands across 3 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: 10 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	23-26	4	3
β-strand	34-39	6	3
β-strand	54-59	6	3
β-strand	68-69	2	3
β-strand	79	1	4
α-helix	81-85	5
β-strand	92	1	4
β-strand	94-95	2	5
β-strand	104-108	5	6
β-strand	111-116	6	6
β-strand	120-122	3	5
β-strand	129-130	2	5
β-strand	134-139	6	6
β-strand	144-148	5	6
β-strand	169-172	4	7
β-strand	178-182	5	7
α-helix	185-188	4
β-strand	190	1	8
β-strand	191-195	5	7
α-helix	197-202	6
β-strand	217-218	2	7
α-helix	219-221	3
α-helix	224-226	3
β-strand	231	1	8
β-strand	235-238	4	9
β-strand	247-252	6	9
α-helix	255-258	4
β-strand	261-265	5	9
β-strand	272-277	6	9
β-strand	288-292	5	10
β-strand	301-306	6	10
β-strand	310-312	3	11
β-strand	318-320	3	11
β-strand	323-327	5	10
β-strand	329	1	12
β-strand	334	1	12
β-strand	340-343	4	10
β-strand	354-359	6	13
β-strand	368-373	6	13
β-strand	383-387	5	13
β-strand	389-390	2	14
β-strand	393-394	2	14
β-strand	400-402	3	13
β-strand	418-423	6	2
β-strand	432-437	6	2
β-strand	442-446	5	2
β-strand	448	1	1
β-strand	451-460	10	15
β-strand	472	1	16
β-strand	479	1	16
β-strand	481-492	12	15
β-strand	498-507	10	17
α-helix	509-512	4
β-strand	519-520	2	15
β-strand	528-536	9	17
β-strand	542-550	9	15
α-helix	551	1
α-helix	562	1
β-strand	563-568	6	17
β-strand	571	1	17
α-helix	576-577	2
β-strand	585-586	2	15
β-strand	593-598	6	17

Chain B: 17 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	18
α-helix	47-52	6
β-strand	60	1	18
β-strand	66-71	6	19
α-helix	73-76	4
β-strand	94	1	20
β-strand	98-103	6	19
β-strand	109-116	8	20
α-helix	120-122	3
β-strand	123-130	8	21
α-helix	133-138	6
α-helix	139-156	18
β-strand	160-167	8	21
α-helix	194-196	3
β-strand	199-206	8	21
α-helix	209-217	9
β-strand	229	1	22
α-helix	231-240	10
α-helix	242-245	4
β-strand	251-258	8	21
β-strand	262	1	22
α-helix	268-271	4
α-helix	276-277	2
β-strand	283-284	2	21
β-strand	287-288	2	21
α-helix	295-298	4
α-helix	299-309	11
β-strand	311-317	7	21
α-helix	319-321	3
α-helix	322-331	10
β-strand	335-339	5	21
α-helix	345-357	13
β-strand	360-365	6	23
β-strand	374-381	8	20
β-strand	385-388	4	20
α-helix	391-393	3
β-strand	394-398	5	23
β-strand	403-411	9	20
β-strand	421-425	5	19
β-strand	426-428	3	23
β-strand	434-440	7	19

Chain C: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	1333-1336	4	24
β-strand	1343-1347	5	24
β-strand	1356-1363	8	25
α-helix	1369-1370	2
β-strand	1371-1376	6	25
β-strand	1381-1384	4	24
α-helix	1387-1388	2
β-strand	1392-1401	10	25
β-strand	1404-1405	2	25
β-strand	1409-1414	6	25
α-helix	1415-1417	3
β-strand	1421-1428	8	26
β-strand	1433-1438	6	26
β-strand	1446-1453	8	27
α-helix	1458-1460	3
β-strand	1461-1466	6	27
β-strand	1471-1474	4	26
β-strand	1482-1490	9	27
β-strand	1499	1	27
β-strand	1503-1508	6	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-5	A	protein	601	Homo sapiens	P08648 (AlphaFold model)
Integrin beta-1	B	protein	440	Homo sapiens	P05556 (AlphaFold model)
Fibronectin	C	protein	183	Homo sapiens	P02751 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9P6S_1 Integrin alpha-5 (chains A)
FNLDAEAPAVLSGPPGSFFGFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPW
GASPTQCTPIEFDSKGSRLLESSLSSSEGEEPVEYKSLQWFGATVRAHGSSILACAPLYS
WRTEKEPLSDPVGTCYLSTDNFTRILEYAPCRSDFSWAAGQGYCQGGFSAEFTKTGRVVL
GGPGSYFWQGQILSATQEQIAESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEF
SGDDTEDFVAGVPKGNLTYGYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLD
DLLVGAPLLMDRTPDGRPQEVGRVYVYLQHPAGIEPTPTLTLTGHDEFGRFGSSLTPLGD
LDQDGYNDVAIGAPFGGETQQGVVFVFPGGPGGLGSKPSQVLQPLWAASHTPDFFGSALR
GGRDLDGNGYPDLIVGSFGVDKAVVYRGRPIVSASASLTIFPAMFNPEERSCSLEGNPVA
CINLSFCLNASGKHVADSIGFTVELQLDWQKQKGGVRRALFLASRQATLTQTLLIQNGAR
EDCREMKIYLRNESEFRDKLSPIHIALNFSLDPQAPVDSHGLRPALHYQSKSRIEDKAQI
L

Sequence of entity 2 (B), FASTA

>9P6S_2 Integrin beta-1 (chains B)
RCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPTSARCDDLEALKKKGCPPDDIENPRG
SKDIKKNKNVTNRSKGTAEKLKPEDIHQIQPQQLVLRLRSGEPQTFTLKFKRAEDYPIDL
YYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDFRIGFGSFVEKTVMPYISTTPAKLRN
PCTSEQNCTTPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAVCGSLI
GWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIAHLVQK
LSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSSEVILE
NGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKI
RPLGFTEEVEVILQYICECE

Sequence of entity 3 (C), FASTA

>9P6S_3 Fibronectin (chains C)
LDSPTGIDFSDITANSFTVHWIAPRATITGYRIRHHPEHFSGRPREDRVPHSRNSITLTN
LTPGTEYVVSIVALNGREESPLLIGQQSTVSDVPRDLEVVAATPTSLLISWDAPAVTVRY
YRITYGETGGNSPVQEFTVPGSKSTATISGLKPGVDYTITVYAVTGRGDSPASSKPISIN
YRT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
MN	Manganese (II) ion	Mn	7

Primary citation

Allosteric regulation of fibronectin binding by the anti-beta 1 integrin antibody TS2/16. Ding, J., Fantini, D.A., Dedden, D. et al. PNAS Nexus (2026) 5:pgag044-pgag044. DOI 10.1093/pnasnexus/pgag044 · 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
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
7NWL 3.1 Å, Cryo-EM structure of human integrin alpha5beta1 (open form) in complex with fibronectin…

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