9B9K: Integrin alpha-5 beta-1

Integrin alpha-5 beta-1 in complex with MINT1526A Fab. Determined by electron microscopy at 2.7 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Homo sapiens, unidentified
Chains: 4
Atoms: 9,153
Mol. weight: 221.25 kDa
Ligands: CA, NAG
Released: 5 Feb 2025

Explore 9B9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B9K contains 39 α-helices and 99 β-strands across 4 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, 52 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	53	1	4
β-strand	54-59	6	3
β-strand	68-69	2	3
β-strand	79	1	5
α-helix	81-84	4
β-strand	92	1	5
β-strand	94-95	2	6
β-strand	101	1	4
β-strand	104-108	5	7
β-strand	111-115	5	7
β-strand	120-121	2	6
β-strand	130	1	6
β-strand	135-139	5	7
β-strand	144-148	5	7
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	197-202	6
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
β-strand	261-265	5	10
β-strand	272-277	6	10
β-strand	288-292	5	11
α-helix	300	1
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	329-330	2	13
β-strand	333-334	2	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
α-helix	438-440	3
β-strand	442-447	6	2
β-strand	448	1	1
α-helix	449-450	2
β-strand	451-452	2	15
β-strand	453-458	6	16
β-strand	486-491	6	16
β-strand	498-505	8	17
β-strand	529-536	8	17
β-strand	542-544	3	16
β-strand	566-571	6	17
α-helix	576-578	3
α-helix	584	1
β-strand	585-586	2	15
α-helix	587	1
β-strand	593-595	3	17

Chain B: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	66-69	4	18
α-helix	73-79	7
α-helix	82-84	3
α-helix	85-87	3
β-strand	94	1	19
β-strand	98-103	6	18
β-strand	109-116	8	19
β-strand	123-130	8	20
α-helix	133-135	3
α-helix	136-142	7
α-helix	145-153	9
β-strand	160-167	8	20
α-helix	180-184	5
α-helix	193-196	4
β-strand	199-206	8	20
α-helix	209-216	8
β-strand	229	1	21
α-helix	232-240	9
β-strand	251-258	8	20
β-strand	262	1	21
α-helix	267-271	5
β-strand	275	1	22
α-helix	276-277	2
β-strand	283-284	2	20
β-strand	287-288	2	20
β-strand	294	1	22
α-helix	295-298	4
α-helix	299-308	10
β-strand	311-318	8	20
α-helix	322-331	10
β-strand	335-340	6	20
α-helix	347-359	13
β-strand	362-363	2	23
β-strand	364-366	3	18
α-helix	367-370	4
β-strand	374-380	7	19
α-helix	382-384	3
β-strand	386-388	3	19
α-helix	389-393	5
β-strand	394-395	2	23
β-strand	403-411	9	19
β-strand	420-427	8	18
β-strand	434-440	7	18

Chain H: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	11-12	2	25
β-strand	18-24	7	24
α-helix	29-31	3
β-strand	33-39	7	26
β-strand	45-51	7	26
α-helix	52B-53	3
β-strand	57-59	3	26
β-strand	67-72	6	24
β-strand	77-82	6	24
α-helix	84-86	3
β-strand	88-95	8	26
β-strand	100A-103	4	26
α-helix	106	1
β-strand	107-109	3	26
β-strand	110-111	2	25

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	27
β-strand	9-13	4	28
β-strand	19-25	7	27
α-helix	27-28	3
β-strand	33-37	5	28
α-helix	42-44	3
β-strand	45-50	6	28
β-strand	52D-54	3	28
β-strand	62-67	6	27
β-strand	70-75	6	27
α-helix	80-82	3
β-strand	85-92	8	28
β-strand	95-98	4	28
β-strand	102-106	5	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-5 light chain	A	protein	995	Homo sapiens	P08648 (AlphaFold model)
Integrin beta-1	B	protein	728	Homo sapiens	P05556 (AlphaFold model)
MINT1526A Fab Heavy Chain	H	protein	120	unidentified
MINT1526A Fab Light Chain	L	protein	112	unidentified

Sequence of entity 1 (A), FASTA

>9B9K_1 Integrin alpha-5 light chain (chains A)
MGSRTPESPLHAVQLRWGPRRRPPLLPLLLLLLPPPPRVGGFNLDAEAPAVLSGPPGSFF
GFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPWGASPTQCTPIEFDSKGSRL
LESSLSSSEGEEPVEYKSLQWFGATVRAHGSSILACAPLYSWRTEKEPLSDPVGTCYLST
DNFTRILEYAPCRSDFSWAAGQGYCQGGFSAEFTKTGRVVLGGPGSYFWQGQILSATQEQ
IAESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEFSGDDTEDFVAGVPKGNLTY
GYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLDDLLVGAPLLMDRTPDGRPQ
EVGRVYVYLQHPAGIEPTPTLTLTGHDEFGRFGSSLTPLGDLDQDGYNDVAIGAPFGGET
QQGVVFVFPGGPGGLGSKPSQVLQPLWAASHTPDFFGSALRGGRDLDGNGYPDLIVGSFG
VDKAVVYRGRPIVSASASLTIFPAMFNPEERSCSLEGNPVACINLSFCLNASGKHVADSI
GFTVELQLDWQKQKGGVRRALFLASRQATLTQTLLIQNGAREDCREMKIYLRNESEFRDK
LSPIHIALNFSLDPQAPVDSHGLRPALHYQSKSRIEDKAQILLDCGEDNICVPDLQLEVF
GEQNHVYLGDKNALNLTFHAQNVGEGGAYEAELRVTAPPEAEYSGLVRHPGNFSSLSCDY
FAVNQSRLLVCDLGNPMKAGASLWGGLRFTVPHLRDTKKTIQFDFQILSKNLNNSQSDVV
SFRLSVEAQAQVTLNGVSKPEAVLFPVSDWHPRDQPQKEEDLGPAVHHVYELINQGPSSI
SQGVLELSCPQALEGQQLLYVTRVTGLNCTTNHPINPKGLELDPEGSLHHQQKREAPSRS
SASSGPQILKCPEAECFRLRCELGPLHQQESQSLQLHFRVWAKTFLQREHQPFSLQCEAV
YKALKMPYRILPRQLPQKERQVATAVQWTKAEGSY

Sequence of entity 2 (B), FASTA

>9B9K_2 Integrin beta-1 (chains B)
MNLQPIFWIGLISSVCCVFAQTDENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPT
SARCDDLEALKKKGCPPDDIENPRGSKDIKKNKNVTNRSKGTAEKLKPEDITQIQPQQLV
LRLRSGEPQTFTLKFKRAEDYPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDF
RIGFGSFVEKTVMPYISTTPAKLRNPCTSEQNCTSPFSYKNVLSLTNKGEVFNELVGKQR
ISGNLDSPEGGFDAIMQVAVCGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQ
CHLENNMYTMSHYYDYPSIAHLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTL
SANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISI
GDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYICECECQSEGIPESPKCHEG
NGTFECGACRCNEGRVGRHCECSTDEVNSEDMDAYCRKENSSEICSNNGECVCGQCVCRK
RDNTNEIYSGKFCECDNFNCDRSNGLICGGNGVCKCRVCECNPNYTGSACDCSLDTSTCE
ASNGQICNGRGICECGVCKCTDPKFQGQTCEMCQTCLGVCAEHKECVQCRAFNKGEKKDT
CTQECSYFNITKVESRDKLPQPVQPDPVSHCKEKDVDDCWFYFTYSVNGNNEVMVHVVEN
PECPTGPD

Sequence of entity 3 (H), FASTA

>9B9K_3 MINT1526A Fab Heavy Chain (chains H)
EVHLVESGGDLVQPGSSLKLSCAASGFTFSNRWLYWVKQAPGKGLEWVGGLKTKPNLYAT
EYADSVKGRFTISRDDSKNSLYLQMNTLRVDDTALYYCTSLTGMRYFDYWGQGTMVTVSS

Sequence of entity 4 (L), FASTA

>9B9K_4 MINT1526A Fab Light Chain (chains L)
LDVLTQSPSASASLGNSVKLTCTLSSQHSTYTIGWYQAGHPDKAPKYVMYLNSDGSHNKG
DGLPDRFSGSSSGAHRYLSISNIQPEDEADYFCGSSYSSGYVFGSGTKVELK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Shared ligand-blocking mechanism but distinct conformational modulation by alpha 5-targeting antibodies BIIG2 and MINT1526A. Nguyen, A., Heim, J.B., Cordara, G. et al. bioRxiv (2025). DOI 10.1101/2025.01.08.631572 · 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)
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…

Browse structure collections

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