3V4V: A4b7 headpiece

crystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376. Determined by X-ray diffraction at 3.1 Å resolution. Released 11 Jan 2012.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 21,791
Mol. weight: 342.63 kDa
Ligands: MG, NAG, CA, 0DU
Released: 11 Jan 2012

Explore 3V4V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V4V contains 76 α-helices and 268 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, 57 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	69-71	3	3
β-strand	87-88	2	4
β-strand	94-100	7	5
β-strand	108-112	5	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	1	7
β-strand	204	1	7
β-strand	205	1	9
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	305-309	5	10
β-strand	310-311	2	11
α-helix	312	1
β-strand	318-319	2	11
β-strand	325	1	10
β-strand	339-340	2	12
β-strand	353-357	5	12
α-helix	360-363	4
β-strand	365	1	2
β-strand	366-370	5	12
β-strand	372-373	2	13
β-strand	376-377	2	13
β-strand	383-386	4	12
α-helix	387-389	3
β-strand	397-405	9	2
β-strand	414-419	6	2
α-helix	420-422	3
β-strand	424-428	5	2
β-strand	430	1	1
α-helix	431-432	2
β-strand	433-434	2	14
β-strand	435-441	7	15
β-strand	445	1	16
β-strand	455	1	17
β-strand	458	1	17
β-strand	462-472	11	15
β-strand	479-487	9	18
α-helix	496-498	3
β-strand	500-501	2	15
β-strand	510-518	9	18
β-strand	523-531	9	15
α-helix	532	1
β-strand	542-550	9	18
α-helix	551-552	2
β-strand	569-570	2	14
β-strand	578-583	6	18
β-strand	584	1	16

Chains B and D: 18 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	83-86	4	19
α-helix	90-92	3
β-strand	93	1	20
β-strand	102	1	20
β-strand	104-105	2	21
β-strand	108-112	5	19
β-strand	114	1	22
β-strand	117	1	22
β-strand	119-126	8	21
β-strand	133-140	8	23
α-helix	143-145	3
α-helix	146-154	9
α-helix	157-163	7
β-strand	170-177	8	23
α-helix	190-194	5
α-helix	205-207	3
β-strand	210-217	8	23
α-helix	221-227	7
β-strand	240	1	24
α-helix	242-251	10
α-helix	253-256	4
β-strand	262-269	8	23
β-strand	273	1	24
α-helix	274-275	2
α-helix	278-280	3
α-helix	287-289	3
β-strand	294	1	25
β-strand	299	1	23
β-strand	300	1	25
α-helix	301-305	5
α-helix	307-310	4
α-helix	311-321	11
β-strand	323-329	7	23
α-helix	334-341	8
β-strand	348-351	4	23
α-helix	359-371	13
β-strand	374-377	4	19
α-helix	380-382	3
β-strand	385-388	4	21
β-strand	389	1	26
β-strand	391-392	2	21
β-strand	404	1	26
β-strand	407-409	3	19
β-strand	417-426	10	21
β-strand	435-441	7	19
β-strand	446-450	5	19

Chain C: 12 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	38
β-strand	9-12	4	39
β-strand	22-28	7	40
β-strand	31-38	8	40
α-helix	41-43	3
β-strand	54-59	6	40
β-strand	69-71	3	40
β-strand	87-88	2	41
β-strand	94-100	7	42
β-strand	108-112	5	42
β-strand	116-117	2	41
β-strand	130	1	43
β-strand	132-135	4	42
α-helix	141-143	3
β-strand	145-147	3	42
β-strand	167	1	43
β-strand	171-173	3	44
β-strand	177-182	6	44
α-helix	185-188	4
β-strand	190	1	45
β-strand	191-196	6	44
β-strand	201	1	44
β-strand	204	1	44
β-strand	205	1	46
β-strand	218	1	45
β-strand	221-225	5	46
β-strand	234-239	6	46
α-helix	242-244	3
β-strand	247-253	7	46
β-strand	258-265	8	46
β-strand	276-280	5	47
β-strand	289-294	6	47
β-strand	305-309	5	47
β-strand	310-311	2	48
α-helix	312	1
β-strand	318-319	2	48
β-strand	325	1	47
β-strand	338-340	3	49
β-strand	353-357	5	49
α-helix	360-363	4
β-strand	365	1	39
β-strand	366-370	5	49
β-strand	372-373	2	50
β-strand	376-377	2	50
β-strand	383-386	4	49
α-helix	387-389	3
β-strand	397-405	9	39
β-strand	414-419	6	39
α-helix	420-422	3
β-strand	424-428	5	39
β-strand	430	1	38
β-strand	433-434	2	51
β-strand	436-441	6	52
β-strand	445-446	2	53
β-strand	455	1	54
β-strand	458	1	54
β-strand	462-471	10	52
β-strand	479-487	9	55
α-helix	496-498	3
β-strand	500-501	2	52
β-strand	510-518	9	55
β-strand	523-531	9	52
α-helix	532	1
β-strand	542-550	9	55
α-helix	551-552	2
β-strand	569-570	2	51
α-helix	571-574	4
β-strand	579-583	5	55
β-strand	584-585	2	53

Chains H and M: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	27
β-strand	9-12	4	28
β-strand	18-25	8	27
α-helix	29-31	3
β-strand	33-39	7	28
β-strand	46-52	7	28
β-strand	57-60	4	28
β-strand	65	1	27
β-strand	68-73	6	27
β-strand	78-83	6	27
α-helix	88-90	3
β-strand	92-102	11	28
β-strand	105-111	7	28
β-strand	112	1	27
β-strand	115-119	5	28
β-strand	125	1	29
β-strand	128-132	5	30
β-strand	143-153	11	30
β-strand	154	1	29
β-strand	159-161	3	31
β-strand	171-173	3	30
α-helix	174-176	3
β-strand	177-179	3	30
β-strand	182-192	11	30
β-strand	203-207	5	31
β-strand	212-216	5	31

Chains L and N: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	32
β-strand	10-13	4	28
β-strand	19-25	7	32
β-strand	30	1	33
β-strand	36	1	33
β-strand	38-43	6	28
β-strand	50-54	5	28
β-strand	58-59	2	28
α-helix	60	1
β-strand	67-72	6	32
β-strand	75-80	6	32
β-strand	90-95	6	28
α-helix	101	1
β-strand	102-103	2	28
β-strand	107-111	5	28
β-strand	116	1	34
β-strand	119-123	5	35
α-helix	127-130	4
β-strand	136-144	9	35
β-strand	145	1	34
β-strand	151-155	5	36
β-strand	158-159	2	36
β-strand	164-168	5	35
β-strand	178-185	8	35
α-helix	188-192	5
β-strand	196-201	6	36
β-strand	204	1	37
β-strand	206	1	37
α-helix	209	1
β-strand	210-211	2	36
β-strand	214-215	2	36

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

>3V4V_1 Integrin alpha-4 (chains A, C)
YNVDTESALLYQGPHNTLFGYSVVLHSHGANRWLLVGAPTANWLANASVINPGAIYRCRI
GKNPGQTCEQLQLGSPNGEPCGKTCLEERDNQWLGVTLSRQPGENGSIVTCGHRWKNIFY
IKNENKLPTGGCYGVPPDLRTELSKRIAPCYQDYVKKFGENFASCQAGISSFYTKDLIVM
GAPGSSYWTGSLFVYNITTNKYKAFLDKQNQVKFGSYLGYSVGAGHFRSQHTTEVVGGAP
QHEQIGKAYIFSIDEKELNILHEMKGKKLGSYFGASVCAVDLNADGFSDLLVGAPMQSTI
REEGRVFVYINSGSGAVMNAMETNLVGSDKYAARFGESIVNLGDIDNDGFEDVAIGAPQE
DDLQGAIYIYNGRADGISSTFSQRIEGLQISKSLSMFGQSISGQIDADNNGYVDVAVGAF
RSDSAVLLRTRPVVIVDASLSHPESVNRTKFDCVENGWPSVCIDLTLCFSYKGKEVPGYI
VLFYNMSLDVNRKAESPPRFYFSSNGTSDVITGSIQVSSREANCRTHQAFMRKDVRDILT
PIQIEAAYHLGPHVISKASTEEFPPLQPILQQKKEKDIMKKTINFARTGGLENLYFQ

Sequence of entity 2 (B, D), FASTA

>3V4V_2 Integrin beta-7 (chains B, D)
ELDAKIPSTGDATEWRNPHLSMLGSCQPAPSCQKCILSHPSCAWCKQLNFTASGEAEARR
CARREELLARGCPLEELEEPRGQQEVLQDQPLSQGARGEGATQLAPQRVRVTLRPGEPQQ
LQVRFLRAEGYPVDLYYLMDLSYSMKDDLERVRQLGHALLVRLQEVTHSVRIGFGSFVDK
TVLPFVSTVPSKLRHPCPTRLERCQSPFSFHHVLSLTGDAQAFEREVGRQSVSGNLDSPE
GGFDAILQAALCQEQIGWRNVSRLLVFTSDDTFHTAGDGKLGGIFMPSDGHCHLDSNGLY
SRSTEFDYPSVGQVAQALSAANIQPIFAVTSAALPVYQELSKLIPKSAVGELSEDSSNVV
QLIMDAYNSLSSTVTLEHSSLPPGVHISYESQCEGPEKREGKAEDRGQCNHVRINQTVTF
WVSLQATHCLPEPHLLRLRALGFSEELIVELHTLCDCNCSDTQPQAPHCSDGQGHLQCGV
CSCAPGRLGRLCESRGLENLYFQ

Sequence of entity 3 (H, M), FASTA

>3V4V_3 MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN (chains H, M)
QVQLQQPGAELVKPGTSVKLSCKGYGYTFTSYWMHWVKQRPGQGLEWIGEIDPSESNTNY
NQKFKGKATLTVDISSSTAYMQLSSLTSEDSAVYYCARGGYDGWDYAIDYWGQGTSVTVS
SAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLES
DLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIV

Sequence of entity 4 (L, N), FASTA

>3V4V_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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11
CA	Calcium ion	Ca	10
0DU	N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropy…	C24 H19 Cl2 F3 N2 O4	2

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
9P96 3.1 Å, CryoEM structure of the apo integrin alpha4beta7
3V4P 3.15 Å, crystal structure of a4b7 headpiece complexed with Fab ACT-1

Browse structure collections

About this viewer

MolViewer shows 3V4V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.