3V4P: A4b7 headpiece

crystal structure of a4b7 headpiece complexed with Fab ACT-1. Determined by X-ray diffraction at 3.15 Å resolution. Released 11 Jan 2012.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 21,722
Mol. weight: 342.67 kDa
Ligands: MG, 15P, NAG, CA
Released: 11 Jan 2012

Explore 3V4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V4P contains 78 α-helices and 252 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: 12 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	22-28	7	3
β-strand	31-38	8	3
α-helix	41-43	3
β-strand	54-59	6	3
β-strand	68-71	4	3
β-strand	87-88	2	4
β-strand	97-100	4	5
β-strand	108-111	4	5
β-strand	116-117	2	4
β-strand	130	1	6
β-strand	132-135	4	5
α-helix	141-143	3
β-strand	145-147	3	5
β-strand	167	1	6
β-strand	171-173	3	7
β-strand	177-182	6	7
α-helix	185-188	4
β-strand	190	1	8
β-strand	191-196	6	7
β-strand	201-204	4	7
β-strand	218	1	8
β-strand	222-225	4	9
β-strand	234-239	6	9
α-helix	242-244	3
β-strand	247-253	7	9
β-strand	258-265	8	9
β-strand	276-280	5	10
β-strand	289-294	6	10
β-strand	305-311	7	10
α-helix	312	1
β-strand	318-320	3	10
β-strand	325	1	10
β-strand	338-340	3	11
β-strand	353-357	5	11
α-helix	360-363	4
β-strand	366-370	5	11
β-strand	372-373	2	12
β-strand	376-377	2	12
β-strand	383-386	4	11
α-helix	387-389	3
β-strand	397-405	9	2
β-strand	414-419	6	2
β-strand	424-428	5	2
α-helix	429	1
β-strand	430	1	1
α-helix	431-432	2
β-strand	433-434	2	13
β-strand	435-441	7	14
β-strand	445	1	15
β-strand	455	1	16
β-strand	458	1	16
β-strand	462-472	11	14
β-strand	479-487	9	17
α-helix	496-498	3
β-strand	500-501	2	14
β-strand	510-518	9	17
β-strand	523-531	9	14
α-helix	532	1
β-strand	542-550	9	17
α-helix	564-567	4
β-strand	569-570	2	13
β-strand	578-583	6	17
β-strand	584	1	15

Chain B: 17 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	83-86	4	18
α-helix	90-92	3
β-strand	104-105	2	19
β-strand	108-112	5	18
β-strand	119-126	8	19
β-strand	133-140	8	20
α-helix	143-145	3
α-helix	146-152	7
α-helix	155-163	9
β-strand	170-177	8	20
α-helix	190-194	5
α-helix	205-207	3
β-strand	210-217	8	20
α-helix	221-227	7
β-strand	240	1	21
α-helix	242-251	10
α-helix	253-256	4
β-strand	262-269	8	20
β-strand	273	1	21
α-helix	278-282	5
β-strand	286	1	22
α-helix	287-289	3
β-strand	294	1	23
β-strand	299	1	20
β-strand	300	1	23
α-helix	301-305	5
β-strand	306	1	22
α-helix	307-310	4
α-helix	311-321	11
β-strand	323-329	7	20
α-helix	334-341	8
β-strand	348-351	4	20
α-helix	359-370	12
β-strand	373-377	5	18
α-helix	380-382	3
β-strand	385-388	4	19
β-strand	389	1	24
β-strand	391-392	2	19
β-strand	404	1	24
β-strand	407-410	4	18
β-strand	417-426	10	19
β-strand	435-441	7	18
β-strand	446-450	5	18

Chain C: 12 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	25
β-strand	9-12	4	26
β-strand	22-28	7	27
β-strand	31-38	8	27
α-helix	41-43	3
β-strand	54-59	6	27
β-strand	68-71	4	27
β-strand	87-88	2	28
β-strand	97-100	4	29
β-strand	108-111	4	29
β-strand	116-117	2	28
β-strand	130	1	30
β-strand	132-135	4	29
α-helix	141-143	3
β-strand	145-147	3	29
β-strand	167	1	30
β-strand	171-173	3	31
β-strand	177-182	6	31
α-helix	185-188	4
β-strand	190	1	32
β-strand	191-196	6	31
β-strand	201-204	4	31
β-strand	218	1	32
β-strand	222-225	4	33
β-strand	234-239	6	33
α-helix	242-244	3
β-strand	247-253	7	33
β-strand	258-265	8	33
β-strand	276-280	5	34
β-strand	289-294	6	34
β-strand	305-311	7	34
α-helix	312	1
β-strand	318-320	3	34
β-strand	325	1	34
β-strand	338-340	3	35
β-strand	353-357	5	35
α-helix	360-363	4
β-strand	366-370	5	35
β-strand	372-373	2	36
β-strand	376-377	2	36
β-strand	383-386	4	35
α-helix	387-389	3
β-strand	397-405	9	26
β-strand	414-419	6	26
β-strand	424-428	5	26
α-helix	429	1
β-strand	430	1	25
α-helix	431-432	2
β-strand	433-434	2	37
β-strand	435-441	7	38
β-strand	445	1	39
β-strand	455	1	40
β-strand	458	1	40
β-strand	462-472	11	38
β-strand	479-487	9	41
β-strand	500-501	2	38
β-strand	510-518	9	41
β-strand	523-531	9	38
α-helix	532	1
α-helix	541	1
β-strand	542-550	9	41
α-helix	551-552	2
β-strand	569-570	2	37
β-strand	578-583	6	41
β-strand	584	1	39

Chain D: 17 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	83-86	4	42
α-helix	90-92	3
β-strand	104-105	2	43
β-strand	108-112	5	42
β-strand	119-126	8	43
β-strand	133-140	8	44
α-helix	143-145	3
α-helix	146-152	7
α-helix	155-163	9
β-strand	170-177	8	44
α-helix	190-194	5
α-helix	205-207	3
β-strand	210-217	8	44
α-helix	221-227	7
β-strand	240	1	45
α-helix	242-251	10
α-helix	253-256	4
β-strand	262-269	8	44
β-strand	273	1	45
α-helix	278-282	5
β-strand	286	1	46
α-helix	287-289	3
β-strand	294	1	47
β-strand	299	1	44
β-strand	300	1	47
α-helix	301-305	5
β-strand	306	1	46
α-helix	307-310	4
α-helix	311-321	11
β-strand	323-329	7	44
α-helix	334-341	8
β-strand	348-351	4	44
α-helix	359-370	12
β-strand	374-377	4	42
α-helix	380-382	3
β-strand	385-388	4	43
β-strand	389	1	48
β-strand	391-392	2	43
β-strand	404	1	48
β-strand	407-409	3	42
β-strand	417-426	10	43
β-strand	435-441	7	42
β-strand	446-450	5	42

Chains H and M: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	49
β-strand	9-12	4	50
β-strand	18-20	3	49
β-strand	23-25	3	49
α-helix	29-31	3
β-strand	33-39	7	50
β-strand	46-52	7	50
β-strand	57-60	4	50
β-strand	65	1	49
β-strand	68-73	6	49
β-strand	78-83	6	49
β-strand	92-102	11	50
β-strand	105-111	7	50
β-strand	112	1	49
β-strand	115-119	5	50
α-helix	122-124	3
β-strand	125	1	51
β-strand	128-132	5	52
β-strand	144-153	10	52
β-strand	154	1	51
β-strand	159-161	3	53
β-strand	171-173	3	52
α-helix	174-176	3
β-strand	177-179	3	52
β-strand	182-191	10	52
β-strand	203-207	5	53
β-strand	212-216	5	53

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	54
β-strand	10-13	4	50
β-strand	19-25	7	54
β-strand	30	1	55
β-strand	36	1	55
β-strand	38-43	6	50
β-strand	50-54	5	50
β-strand	58-59	2	50
α-helix	60	1
β-strand	67-72	6	54
β-strand	75-80	6	54
α-helix	85-87	3
β-strand	90-95	6	50
α-helix	101	1
β-strand	102-103	2	50
β-strand	107-111	5	50
β-strand	116	1	56
β-strand	119-123	5	57
α-helix	124-126	3
α-helix	127-130	4
β-strand	136-144	9	57
β-strand	145	1	56
β-strand	150-155	6	58
β-strand	158-159	2	58
β-strand	164-168	5	57
β-strand	178-185	8	57
α-helix	188-192	5
β-strand	196-202	7	58
α-helix	209	1
β-strand	210-215	6	58

Chain N: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	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	50-54	5	65
β-strand	58-59	2	65
α-helix	60	1
β-strand	67-72	6	64
β-strand	75-80	6	64
α-helix	85-87	3
β-strand	90-95	6	65
α-helix	101	1
β-strand	103	1	65
β-strand	107-111	5	65
β-strand	116	1	67
β-strand	119-123	5	68
α-helix	124-126	3
α-helix	127-130	4
β-strand	136-144	9	68
β-strand	145	1	67
β-strand	150-155	6	69
β-strand	158-159	2	69
β-strand	164-168	5	68
β-strand	178-185	8	68
α-helix	188-192	5
β-strand	196-202	7	69
α-helix	209	1
β-strand	210-215	6	69

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-4	A, C	protein	597	Homo sapiens	P13612 (AlphaFold model)
Integrin beta-7	B, D	protein	503	Homo sapiens	P26010 (AlphaFold model)
Monoclonal antibody act-1 heavy chain	H, M	protein	219	Mus musculus
Monoclonal antibody act-1 light chain	L, N	protein	217	Mus musculus

Sequence of entity 1 (A, C), FASTA

>3V4P_1 Integrin alpha-4 (chains A, C)
YNVDTESALLYQGPHNTLFGYSVVLHSHGANRWLLVGAPTANWLANASVINPGAIYRCRI
GKNPGQTCEQLQLGSPNGEPCGKTCLEERDNQWLGVTLSRQPGENGSIVTCGHRWKNIFY
IKNENKLPTGGCYGVPPDLRTELSKRIAPCYQDYVKKFGENFASCQAGISSFYTKDLIVM
GAPGSSYWTGSLFVYNITTNKYKAFLDKQNQVKFGSYLGYSVGAGHFRSQHTTEVVGGAP
QHEQIGKAYIFSIDEKELNILHEMKGKKLGSYFGASVCAVDLNADGFSDLLVGAPMQSTI
REEGRVFVYINSGSGAVMNAMETNLVGSDKYAARFGESIVNLGDIDNDGFEDVAIGAPQE
DDLQGAIYIYNGRADGISSTFSQRIEGLQISKSLSMFGQSISGQIDADNNGYVDVAVGAF
RSDSAVLLRTRPVVIVDASLSHPESVNRTKFDCVENGWPSVCIDLTLCFSYKGKEVPGYI
VLFYNMSLDVNRKAESPPRFYFSSNGTSDVITGSIQVSSREANCRTHQAFMRKDVRDILT
PIQIEAAYHLGPHVISKASTEEFPPLQPILQQKKEKDIMKKTINFARTGGLENLYFQ

Sequence of entity 2 (B, D), FASTA

>3V4P_2 Integrin beta-7 (chains B, D)
ELDAKIPSTGDATEWRNPHLSMLGSCQPAPSCQKCILSHPSCAWCKQLNFTASGEAEARR
CARREELLARGCPLEELEEPRGQQEVLQDQPLSQGARGEGATQLAPQRVRVTLRPGEPQQ
LQVRFLRAEGYPVDLYYLMDLSYSMKDDLERVRQLGHALLVRLQEVTHSVRIGFGSFVDK
TVLPFVSTVPSKLRHPCPTRLERCQSPFSFHHVLSLTGDAQAFEREVGRQSVSGNLDSPE
GGFDAILQAALCQEQIGWRNVSRLLVFTSDDTFHTAGDGKLGGIFMPSDGHCHLDSNGLY
SRSTEFDYPSVGQVAQALSAANIQPIFAVTSAALPVYQELSKLIPKSAVGELSEDSSNVV
QLIMDAYNSLSSTVTLEHSSLPPGVHISYESQCEGPEKREGKAEDRGQCNHVRINQTVTF
WVSLQATHCLPEPHLLRLRALGFSEELIVELHTLCDCNCSDTQPQAPHCSDGQGHLQCGV
CSCAPGRLGRLCESRGLENLYFQ

Sequence of entity 3 (H, M), FASTA

>3V4P_3 MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN (chains H, M)
QVQLQQPGAELVKPGTSVKLSCKGYGYTFTSYWMHWVKQRPGQGLEWIGEIDPSESNTNY
NQKFKGKATLTVDISSSTAYMQLSSLTSEDSAVYYCARGGYDGWDYAIDYWGQGTSVTVS
SAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLES
DLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIV

Sequence of entity 4 (L, N), FASTA

>3V4P_4 MONOCLONAL ANTIBODY Act-1 LIGHT CHAIN (chains L, N)
DVVVTQTPLSLPVSFGDQVSISCRSSQSLAKSYGNTYLSWYLHKPGQSPQLLIYGISNRF
SGVPDRFSGSGSGTDFTLKISTIKPEDLGMYYCLQGTHQPYTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWNIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
15P	Polyethylene glycol (N=34)	C69 H140 O35	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9
CA	Calcium ion	Ca	10

Water and common crystallization additives (TRS) are not listed.

Primary citation

Structural specializations of a4b7, an Integrin that Mediates Rolling Adhesion. Yu, Y., Zhu, J., Mi, L.Z. et al. J Cell Biol (2012) 196:131-146. DOI 10.1083/jcb.201110023 · PubMed

Other PDB entries of the same protein (UniProt P13612 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HKC 2.2 Å, 14-3-3-zeta in complex with S1011 phosphorylated integrin alpha-4 peptide
5C7Z 2.77 Å, AP2 Mu2 adaptin C-terminal domain complexed with integrin alpha-4 peptide
5FPI 2.77 Å, Mu2 adaptin subunit of the AP2 adaptor (C-terminal domain) complexed with Integrin…
9P95 3.05 Å, CryoEM structure of integrin alpha4beta7 bound to MAdCAM-1
3V4V 3.1 Å, crystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376
9P96 3.1 Å, CryoEM structure of the apo integrin alpha4beta7

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