7NXD: Integrin alpha-5

Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation. Determined by electron microscopy at 4.6 Å resolution. Released 25 Aug 2021.

Method: Electron microscopy
Resolution: 4.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 12,805
Mol. weight: 204.74 kDa
Ligands: CA, NAG, MG
Released: 25 Aug 2021

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

Secondary structure: helices and β-sheets

7NXD contains 48 α-helices and 124 β-strands across 2 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: 19 helices, 77 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	68-70	3	3
α-helix	76-78	3
α-helix	81-86	6
β-strand	94-95	2	4
β-strand	104-108	5	5
β-strand	111-115	5	5
β-strand	120-121	2	4
β-strand	136-139	4	5
β-strand	144-146	3	5
β-strand	169-172	4	6
β-strand	178-182	5	6
α-helix	185-188	4
β-strand	190	1	7
β-strand	191-195	5	6
α-helix	197-203	7
β-strand	217-218	2	6
α-helix	219-221	3
α-helix	224-226	3
β-strand	231	1	7
β-strand	234-238	5	8
α-helix	246	1
β-strand	247-251	5	8
α-helix	255-258	4
β-strand	261-266	6	8
β-strand	271-277	7	8
β-strand	288-292	5	9
β-strand	301-306	6	9
β-strand	311-312	2	10
β-strand	318-319	2	10
β-strand	323-327	5	9
β-strand	340-343	4	9
β-strand	354-357	4	11
β-strand	369-373	5	11
β-strand	382	1	12
β-strand	383-387	5	11
α-helix	388-389	2
β-strand	400-402	3	11
α-helix	407-408	2
β-strand	415	1	12
β-strand	418-421	4	2
β-strand	433-437	5	2
β-strand	442-446	5	2
β-strand	448	1	1
β-strand	451-452	2	13
β-strand	453-459	7	14
β-strand	465	1	15
β-strand	473	1	16
β-strand	478	1	16
β-strand	481-491	11	14
β-strand	498-499	2	17
β-strand	501-507	7	18
α-helix	509-511	3
β-strand	519-521	3	14
β-strand	526	1	14
β-strand	529-532	4	18
β-strand	535-536	2	17
α-helix	540-541	2
β-strand	542-550	9	14
α-helix	562	1
β-strand	563-568	6	18
β-strand	570-571	2	18
α-helix	575-577	3
β-strand	585-586	2	13
β-strand	593-598	6	18
β-strand	600	1	15
β-strand	614-621	8	19
β-strand	625	1	20
β-strand	632-641	10	19
α-helix	644	1
β-strand	650-655	6	21
β-strand	661-667	7	19
β-strand	677-680	4	21
β-strand	687-693	7	21
β-strand	701-709	9	19
β-strand	720-727	8	21
α-helix	736-738	3
β-strand	739-743	5	21
β-strand	745	1	20
β-strand	751-757	7	22
β-strand	787-793	7	22
β-strand	800-807	8	23
β-strand	818-824	7	22
β-strand	828-830	3	23
β-strand	866-868	3	23
α-helix	870-872	3
β-strand	878-882	5	23
β-strand	890-899	10	22
α-helix	901-906	6
β-strand	912-924	13	23
α-helix	933-935	3
β-strand	937-945	9	23

Chain B: 29 helices, 47 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	15-21	7
β-strand	25-27	3	24
α-helix	40-42	3
β-strand	44-46	3	24
α-helix	47-53	7
β-strand	61	1	24
β-strand	67-68	2	25
β-strand	98-101	4	25
β-strand	109-111	3	26
β-strand	114-116	3	27
β-strand	123-130	8	28
α-helix	133-135	3
α-helix	136-156	21
β-strand	160-167	8	28
α-helix	180-184	5
α-helix	194-196	3
β-strand	199-201	3	28
β-strand	206	1	28
α-helix	209-218	10
β-strand	229	1	29
α-helix	231-241	11
β-strand	251-258	8	28
β-strand	262	1	29
α-helix	268-270	3
α-helix	275-277	3
β-strand	287	1	28
α-helix	295-298	4
α-helix	299-308	10
β-strand	311-317	7	28
α-helix	322-331	10
β-strand	335-339	5	28
α-helix	347-360	14
β-strand	362-363	2	30
β-strand	365	1	31
α-helix	366-368	3
β-strand	373-379	7	26
β-strand	388	1	26
α-helix	390-393	4
β-strand	394-395	2	30
α-helix	398-399	2
β-strand	403-405	3	27
β-strand	406-412	7	26
β-strand	421-425	5	25
β-strand	426	1	31
β-strand	434-438	5	25
α-helix	445-449	5
α-helix	451	1
β-strand	462-463	2	32
β-strand	470-471	2	32
α-helix	503	1
α-helix	504-507	4
β-strand	509-512	4	33
β-strand	515-518	4	33
α-helix	519-520	2
α-helix	528	1
β-strand	542	1	34
β-strand	547	1	34
α-helix	548-550	3
β-strand	553-555	3	35
β-strand	558-560	3	35
α-helix	561-562	2
β-strand	565	1	36
β-strand	573	1	36
β-strand	592-594	3	37
β-strand	597-599	3	37
β-strand	606	1	38
β-strand	612	1	38
α-helix	619-622	4
α-helix	647-648	2
β-strand	649	1	39
β-strand	671-674	4	40
β-strand	680-683	4	40
β-strand	685	1	39
β-strand	695	1	39
β-strand	702	1	40

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)

Sequence of entity 1 (A), FASTA

>7NXD_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

>7NXD_2 Integrin beta-1 (chains B)
QTDENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPTSARCDDLEALKKKGCPPDDI
ENPRGSKDIKKNKNVTNRSKGTAEKLKPEDIHQIQPQQLVLRLRSGEPQTFTLKFKRAED
YPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDFRIGFGSFVEKTVMPYISTTP
AKLRNPCTSEQNCTTPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAV
CGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIA
HLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSS
EVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDS
DSFKIRPLGFTEEVEVILQYICECECQSEGIPESPKCHEGNGTFECGACRCNEGRVGRHC
ECSTDEVNSEDMDAYCRKENSSEICSNNGECVCGQCVCRKRDNTNEIYSGKFCECDNFNC
DRSNGLICGGNGVCKCRVCECNPNYTGSACDCSLDTSTCEASNGQICNGRGICECGVCKC
TDPKFQGQTCEMCQTCLGVCAEHKECVQCRAFNKGEKKDTCTQECSYFNITKVESRDKLP
QPVQPDPVSHCKEKDVDDCWFYFTYSVNGNNEVMVHVVENPECPTGPDIIPIVAGVVAGI
VLIGLALLLIWKLLMIIHDRREFAKFEKEKMNAKWDTGENPIYKSAVTTVVNPKYEGK

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
MG	Magnesium ion	Mg	1

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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