3VI4: Alpha5beta1 integrin headpiece

Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide. Determined by X-ray diffraction at 2.9 Å resolution. Released 22 Feb 2012.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 10
Atoms: 22,882
Mol. weight: 339.88 kDa
Ligands: NAG, CA, MG
Released: 22 Feb 2012

Explore 3VI4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VI4 contains 97 α-helices and 254 β-strands across 8 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: 11 helices, 59 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
β-strand	79	1	4
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	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	197-203	7
α-helix	212-213	2
β-strand	217-218	2	7
α-helix	219-223	5
α-helix	224-226	3
β-strand	231	1	8
β-strand	235-238	4	9
α-helix	246	1
β-strand	247-256	10	9
β-strand	259-265	7	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	329-330	2	12
β-strand	333-334	2	12
β-strand	340-343	4	10
α-helix	351-353	3
β-strand	354-357	4	13
β-strand	369-373	5	13
β-strand	382	1	14
β-strand	383-387	5	13
β-strand	389-390	2	15
β-strand	393-394	2	15
β-strand	400-402	3	13
α-helix	407-408	2
β-strand	415	1	14
β-strand	418-423	6	2
β-strand	432-437	6	2
α-helix	438-440	3
β-strand	442-446	5	2
β-strand	448	1	1
α-helix	449-450	2
β-strand	451-452	2	16
β-strand	453-460	8	17
β-strand	464-465	2	18
β-strand	472-473	2	19
β-strand	478-479	2	19
β-strand	481-491	11	17
β-strand	498-507	10	20
α-helix	509-511	3
β-strand	519-521	3	17
β-strand	528-536	9	20
β-strand	544-550	7	17
β-strand	563-571	9	20
β-strand	585-586	2	16
β-strand	593-598	6	20
β-strand	599-600	2	18

Chain B: 21 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
β-strand	67-68	2	21
α-helix	73-77	5
β-strand	94-95	2	22
β-strand	100-103	4	21
β-strand	104	1	23
β-strand	107	1	23
β-strand	111-116	6	22
β-strand	123-130	8	24
α-helix	133-135	3
α-helix	136-141	6
α-helix	142-144	3
α-helix	145-154	10
β-strand	160-167	8	24
α-helix	194-196	3
β-strand	199-206	8	24
α-helix	209-216	8
α-helix	219-221	3
β-strand	229	1	25
α-helix	231-240	10
α-helix	242-245	4
β-strand	251-258	8	24
β-strand	262	1	25
α-helix	268-271	4
α-helix	276-277	2
β-strand	283-284	2	24
β-strand	287-288	2	24
α-helix	295-298	4
α-helix	299-308	10
β-strand	311-318	8	24
α-helix	319-321	3
α-helix	322-331	10
β-strand	335-340	6	24
α-helix	341	1
α-helix	347-360	14
β-strand	362-363	2	26
β-strand	364-366	3	21
β-strand	373-380	8	22
α-helix	382-384	3
β-strand	386-388	3	22
α-helix	391-393	3
β-strand	394-395	2	26
β-strand	403-412	10	22
β-strand	422-427	6	21
β-strand	434-440	7	21

Chain C: 11 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	27
β-strand	9-11	3	28
β-strand	22-26	5	29
β-strand	34-39	6	29
β-strand	54-59	6	29
β-strand	68-69	2	29
α-helix	77-78	2
β-strand	79	1	30
α-helix	80	1
α-helix	81-83	3
β-strand	92	1	30
β-strand	94-95	2	31
β-strand	104-108	5	32
β-strand	111-116	6	32
β-strand	120-121	2	31
β-strand	130	1	31
β-strand	134-139	6	32
β-strand	144-148	5	32
β-strand	169-172	4	33
β-strand	178-182	5	33
α-helix	185-188	4
β-strand	190	1	34
β-strand	191-195	5	33
α-helix	197-201	5
β-strand	217-218	2	33
α-helix	219-221	3
α-helix	224-226	3
β-strand	231	1	34
β-strand	235-238	4	35
α-helix	246	1
β-strand	247-252	6	35
β-strand	261-265	5	35
β-strand	272-277	6	35
β-strand	289-292	4	36
β-strand	301-306	6	36
β-strand	310-312	3	37
β-strand	318-320	3	37
β-strand	323-327	5	36
β-strand	329-330	2	38
β-strand	333-334	2	38
β-strand	340-343	4	36
α-helix	351-353	3
β-strand	354-359	6	39
β-strand	368-373	6	39
β-strand	383-387	5	39
β-strand	400-402	3	39
β-strand	419-423	5	28
β-strand	432-437	6	28
α-helix	438-440	3
β-strand	442-446	5	28
β-strand	448	1	27
β-strand	451-452	2	40
β-strand	455-460	6	41
β-strand	472-473	2	42
β-strand	478-479	2	42
β-strand	481-489	9	41
β-strand	499-506	8	43
β-strand	519-521	3	41
β-strand	528-535	8	43
β-strand	542-550	9	41
α-helix	551-552	2
β-strand	566-571	6	43
β-strand	585-586	2	40
β-strand	593-594	2	43

Chain D: 20 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	15-21	7
α-helix	47-50	4
β-strand	66-71	6	44
α-helix	73-77	5
β-strand	94-95	2	45
β-strand	98-103	6	44
β-strand	109-116	8	45
β-strand	123-130	8	46
α-helix	133-135	3
α-helix	137-139	3
α-helix	148-153	6
β-strand	160-167	8	46
α-helix	180-184	5
β-strand	194	1	47
α-helix	195-196	2
β-strand	199-206	8	46
α-helix	209-216	8
α-helix	219-221	3
β-strand	222	1	47
β-strand	229	1	48
α-helix	231-240	10
α-helix	242-245	4
β-strand	251-258	8	46
β-strand	262	1	48
α-helix	267-271	5
β-strand	275	1	49
α-helix	276-277	2
β-strand	283	1	50
β-strand	287	1	46
β-strand	288	1	50
β-strand	294	1	49
α-helix	299-308	10
β-strand	311-318	8	46
α-helix	319-321	3
α-helix	322-330	9
β-strand	335-340	6	46
α-helix	347-359	13
β-strand	362-363	2	51
β-strand	364-365	2	52
β-strand	374-380	7	45
α-helix	382-384	3
β-strand	386-387	2	45
α-helix	389-393	5
β-strand	394-395	2	51
β-strand	403-411	9	45
β-strand	420-425	6	44
β-strand	426-427	2	52
β-strand	434-440	7	44

Chain E: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	64
β-strand	10-13	4	65
β-strand	19-25	7	64
β-strand	30	1	66
β-strand	36	1	66
β-strand	38-43	6	65
β-strand	50-53	4	65
α-helix	58	1
β-strand	59	1	65
α-helix	60	1
β-strand	67-71	5	64
β-strand	75-80	6	64
α-helix	85-87	3
β-strand	89-95	7	65
α-helix	101	1
β-strand	102-103	2	65
α-helix	104-105	2
β-strand	107-111	5	65
β-strand	116	1	67
β-strand	120-123	4	68
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	68
β-strand	145	1	67
β-strand	151-155	5	69
β-strand	158-160	3	69
β-strand	164-168	5	68
α-helix	169-172	4
β-strand	178-187	10	68
α-helix	188-191	4
β-strand	196-201	6	69
β-strand	210-215	6	69

Chain F: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	70
β-strand	10-12	3	71
β-strand	17-25	9	70
α-helix	29-31	3
β-strand	33-40	8	71
β-strand	44-52	9	71
β-strand	57-60	4	71
α-helix	62-64	3
β-strand	65	1	70
β-strand	68-73	6	70
α-helix	74-76	3
β-strand	78-84	7	70
β-strand	92-99	8	71
β-strand	104-108	5	71
β-strand	112-116	5	71
α-helix	119-121	3
β-strand	122	1	72
α-helix	123-124	2
β-strand	125-129	5	73
β-strand	140-150	11	73
β-strand	151	1	72
β-strand	156-159	4	74
α-helix	160-162	3
β-strand	164	1	74
β-strand	168-170	3	73
α-helix	171-173	3
β-strand	174-175	2	73
β-strand	180-189	10	73
α-helix	190-192	3
β-strand	199-204	6	74
α-helix	205-207	3
β-strand	209-214	6	74

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	59
α-helix	7	1
β-strand	10-12	3	60
β-strand	18-25	8	59
β-strand	33-39	7	60
β-strand	46-51	6	60
β-strand	58-60	3	60
α-helix	62-64	3
β-strand	68-73	6	59
α-helix	74-76	3
β-strand	78-83	6	59
α-helix	88-90	3
β-strand	92-100	9	60
β-strand	103-104	2	60
β-strand	112-116	5	60
β-strand	122	1	61
α-helix	123-124	2
β-strand	125-129	5	62
β-strand	140-150	11	62
β-strand	151	1	61
β-strand	156-159	4	63
α-helix	160-162	3
β-strand	168-170	3	62
α-helix	171-173	3
β-strand	174-175	2	62
β-strand	180-189	10	62
α-helix	190-192	3
β-strand	199-204	6	63
α-helix	205-207	3
β-strand	209-214	6	63

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	53
β-strand	10-13	4	54
β-strand	19-25	7	53
β-strand	30	1	55
β-strand	36	1	55
β-strand	38-43	6	54
β-strand	50-54	5	54
β-strand	58-59	2	54
α-helix	60	1
β-strand	68-71	4	53
β-strand	75-80	6	53
α-helix	85-87	3
β-strand	89-95	7	54
α-helix	101	1
β-strand	102-103	2	54
β-strand	107-111	5	54
β-strand	116	1	56
β-strand	119-123	5	57
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	57
β-strand	145	1	56
β-strand	150-155	6	58
β-strand	158-159	2	58
β-strand	164-168	5	57
α-helix	169-172	4
β-strand	178-187	10	57
α-helix	188-191	4
β-strand	196-202	7	58
β-strand	210-215	6	58

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-5	A, C	protein	632	Homo sapiens	P08648 (AlphaFold model)
Integrin beta-1	B, D	protein	454	Homo sapiens	P05556 (AlphaFold model)
SG/19 Fab fragment (Light chain)	E, L	protein	219	Mus musculus
SG/19 Fab fragment (Heavy chain)	F, H	protein	218	Mus musculus
RGD peptide	G, I	protein	5

Sequence of entity 1 (A, C), FASTA

>3VI4_1 Integrin alpha-5 (chains A, C)
FNLDAEAPAVLSGPPGSFFGFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPW
GASPTQCTPIEFDSKGSRLLESSLSSSEGEEPVEYKSLQWFGATVRAHGSSILACAPLYS
WRTEKEPLSDPVGTCYLSTDNFTRILEYAPCRSDFSWAAGQGYCQGGFSAEFTKTGRVVL
GGPGSYFWQGQILSATQEQIAESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEF
SGDDTEDFVAGVPKGNLTYGYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLD
DLLVGAPLLMDRTPDGRPQEVGRVYVYLQHPAGIEPTPTLTLTGHDEFGRFGSSLTPLGD
LDQDGYNDVAIGAPFGGETQQGVVFVFPGGPGGLGSKPSQVLQPLWAASHTPDFFGSALR
GGRDLDGNGYPDLIVGSFGVDKAVVYRGRPIVSASASLTIFPAMFNPEERSCSLEGNPVA
CINLSFCLNASGKHVADSIGFTVELQLDWQKQKGGVRRALFLASRQATLTQTLLIQNGAR
EDCREMKIYLRNESEFRDKLSPIHIALNFSLDPQAPVDSHGLRPALHYQSKSRIEDKAQI
LLDCGEDNICVPDLQLEVFGEQNGGLENLYFQ

Sequence of entity 2 (B, D), FASTA

>3VI4_2 Integrin beta-1 (chains B, D)
QTDENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPTSARCDDLEALKKKGCPPDDI
ENPRGSKDIKKNKNVTNRSKGTAEKLKPEDIHQIQPQQLVLRLRSGEPQTFTLKFKRAED
YPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDFRIGFGSFVEKTVMPYISTTP
AKLRNPCTSEQNCTTPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAV
CGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIA
HLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSS
EVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDS
DSFKIRPLGFTEEVEVILQYICECEGGLENLYFQ

Sequence of entity 3 (E, L), FASTA

>3VI4_3 SG/19 Fab fragment (Light chain) (chains E, L)
DIVMTQATPSIPVTPGESVSISCRSNKSLLHSNGNTYLYWFLQRPGQSPRLLIFRMSNLA
SGVPDRFSGSGSGTAFTLRISRVEAADVGIYFCLQHLEYPFTFGAGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 4 (F, H), FASTA

>3VI4_4 SG/19 Fab fragment (Heavy chain) (chains F, H)
QVHLQQSGAELMKPGASVKISCKATGYTFTSYWIEWVKQRPGHGLEWLGEILPGSGYIHY
NEKFKGKATFTTDTSSNTAYMQLSSLTSEDSAVYYCSRALALYAMDYWGQGTSVTVSSAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 5 (G, I), FASTA

>3VI4_5 RGD peptide (chains G, I)
RGDNP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11
CA	Calcium ion	Ca	10
MG	Magnesium ion	Mg	2

Primary citation

Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor. Nagae, M., Re, S., Mihara, E. et al. J Cell Biol (2012) 197:131-140. DOI 10.1083/jcb.201111077 · 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)
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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