9B9J: Integrin alpha-5 beta-1

Integrin alpha-5 beta-1 in complex with BIIG2 Fab. Determined by electron microscopy at 2.6 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 4
Atoms: 8,517
Mol. weight: 242.7 kDa
Ligands: CA, NAG
Released: 5 Feb 2025

Explore 9B9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B9J contains 32 α-helices and 88 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: 10 helices, 42 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
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	120-121	2	5
β-strand	130	1	5
β-strand	134-139	6	6
β-strand	144-148	5	6
β-strand	155	1	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	197-203	7
α-helix	212-213	2
β-strand	217-218	2	8
α-helix	219-221	3
α-helix	224-226	3
β-strand	231	1	9
β-strand	235-238	4	10
α-helix	246	1
β-strand	247-256	10	10
β-strand	259-265	7	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
β-strand	329-330	2	13
β-strand	333-334	2	13
β-strand	340-343	4	11
α-helix	351-353	3
β-strand	354-359	6	14
β-strand	368-373	6	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	432-436	5	2
α-helix	438-440	3
β-strand	442-446	5	2
β-strand	448	1	1

Chain B: 18 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	66-71	6	15
α-helix	73-75	3
β-strand	94	1	16
β-strand	98-104	7	15
β-strand	109-116	8	16
β-strand	123-130	8	17
α-helix	133-135	3
α-helix	136-142	7
α-helix	145-153	9
β-strand	160-167	8	17
α-helix	180-184	5
β-strand	199-206	8	17
α-helix	209-217	9
β-strand	229	1	18
α-helix	231-240	10
α-helix	242-244	3
β-strand	251-258	8	17
β-strand	262	1	18
α-helix	268-271	4
α-helix	276-277	2
β-strand	283-284	2	17
β-strand	287-288	2	17
α-helix	290-292	3
α-helix	295-298	4
α-helix	299-308	10
β-strand	311-317	7	17
α-helix	319-321	3
α-helix	322-331	10
β-strand	335-339	5	17
α-helix	347-359	13
β-strand	361-363	3	19
β-strand	364-366	3	15
β-strand	373-380	8	16
α-helix	382-384	3
β-strand	386-388	3	16
α-helix	389-393	5
β-strand	394-396	3	19
β-strand	403-412	10	16
β-strand	421-427	7	15
β-strand	434-441	8	15

Chain H: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	11-12	2	21
β-strand	17-25	9	20
β-strand	33-39	7	22
β-strand	46-51	6	22
β-strand	57-59	3	22
β-strand	68-72	5	20
β-strand	77-82A	7	20
α-helix	83-85	3
β-strand	88-95	8	22
β-strand	100	1	7
β-strand	102-103	2	22
β-strand	107-109	3	22
β-strand	110-111	2	21

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	23
β-strand	10-13	4	24
β-strand	19-25	7	23
β-strand	33-38	6	24
β-strand	45-49	5	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	85-90	6	24
α-helix	96	1
β-strand	97-98	2	24
β-strand	102-106	5	24

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)
BIIG2 Fab Heavy Chain	H	protein	217	Rattus norvegicus
BIIG2 Fab Light Chain	L	protein	214	Rattus norvegicus

Sequence of entity 1 (A), FASTA

>9B9J_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

>9B9J_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

>9B9J_3 BIIG2 Fab Heavy Chain (chains H)
DVQLMESGPGLVQPSETLSLTCTVSGFSLTSYNVHWVRQPPGKGLEWMGVMWSGGSTDYN
STLKSRLSISRDTSQNQVFLKMNSLQSEDTTTYYCARDRTMGMTTPFDYWGQGVMVTVSS
AQTTAPSVYPLAPGCGDTTSSTVTLGCLVKGYFPEPVTVTWNSGALSSDVHTFPAVLQSG
LYTLTSSVTSSTWPSQTVTCNVAHPASSTKVDKKVER

Sequence of entity 4 (L), FASTA

>9B9J_4 BIIG2 Fab Light Chain (chains L)
DVQMTQSPSNLAASPGESVSINCKASKRISKYLAWYQQKPGKANKLLIYSGSTLQSGTPS
RFSGSGSGTDFTLTIRNLEPEDFGLYYCQQHKEYPPTFGAGTKLELKRADAAPTVSIFPP
STEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLS
LTKADYESHNLYTCEVVHXTSSSPVVKSFNRNEC

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
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
7NWL 3.1 Å, Cryo-EM structure of human integrin alpha5beta1 (open form) in complex with fibronectin…

Browse structure collections

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