4G1M: Re-refinement of alpha V beta 3 structure

Re-refinement of alpha V beta 3 structure. Determined by X-ray diffraction at 2.9 Å resolution. Released 12 Dec 2012.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 13,132
Mol. weight: 190.31 kDa
Ligands: CA, NAG
Released: 12 Dec 2012

Explore 4G1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4G1M contains 45 α-helices and 137 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: 12 helices, 85 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	35-40	6	3
β-strand	55-59	5	3
β-strand	67-69	3	3
β-strand	79-81	3	4
β-strand	84-85	2	4
β-strand	87-88	2	5
β-strand	97-101	5	6
β-strand	104-109	6	6
β-strand	113-114	2	5
β-strand	123	1	5
β-strand	127-132	6	6
β-strand	135-139	5	6
β-strand	160-163	4	7
β-strand	168-173	6	7
α-helix	176-179	4
β-strand	181	1	8
β-strand	182-187	6	7
α-helix	188-193	6
β-strand	208-209	2	7
α-helix	215-217	3
β-strand	222	1	8
β-strand	225-229	5	9
β-strand	238-243	6	9
α-helix	246-249	4
β-strand	252-256	5	9
β-strand	263-268	6	9
β-strand	279-283	5	10
β-strand	292-297	6	10
β-strand	301-303	3	11
β-strand	309-311	3	11
β-strand	314-320	7	10
β-strand	326-332	7	10
β-strand	343-348	6	12
β-strand	357-362	6	12
α-helix	367-369	3
β-strand	372-377	6	12
β-strand	378-379	2	13
β-strand	382-383	2	13
β-strand	389-392	4	12
β-strand	407-412	6	2
β-strand	421-426	6	2
α-helix	427-429	3
β-strand	431-435	5	2
α-helix	436	1
β-strand	437	1	1
α-helix	438-439	2
β-strand	440-441	2	14
β-strand	442-450	9	15
β-strand	453-454	2	16
β-strand	461-462	2	17
α-helix	463	1
β-strand	469-470	2	17
β-strand	473-482	10	15
β-strand	490-499	10	18
β-strand	511-513	3	15
β-strand	520-528	9	18
β-strand	534-542	9	15
β-strand	555-561	7	18
β-strand	577-578	2	14
β-strand	585-590	6	18
β-strand	591-592	2	16
β-strand	606-610	5	19
β-strand	617-618	2	20
β-strand	622-633	12	19
β-strand	638	1	21
β-strand	641-646	6	22
β-strand	651-656	6	19
β-strand	664	1	19
β-strand	667-671	5	22
β-strand	678-684	7	22
β-strand	687	1	21
β-strand	692-702	11	19
β-strand	710-718	9	22
β-strand	726	1	22
β-strand	730-735	6	22
β-strand	736-737	2	20
β-strand	742-749	8	23
β-strand	752-755	4	24
α-helix	757	1
α-helix	769-772	4
β-strand	775-784	10	23
β-strand	790	1	25
β-strand	792-802	11	24
β-strand	809-817	9	23
β-strand	820-824	5	24
β-strand	869-872	4	24
β-strand	878-886	9	24
β-strand	889	1	25
β-strand	893-903	11	23
α-helix	905-909	5
β-strand	911	1	26
β-strand	913	1	26
β-strand	917-930	14	24
β-strand	941-953	13	24

Chain B: 33 helices, 52 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	13-19	7
β-strand	23-26	4	27
β-strand	33	1	28
β-strand	35	1	28
β-strand	38-40	3	27
α-helix	41-46	6
α-helix	51-53	3
β-strand	54-55	2	27
β-strand	60-65	6	29
α-helix	67-70	4
α-helix	79-80	2
β-strand	83-84	2	30
β-strand	87-92	6	29
β-strand	97-105	9	30
β-strand	112-119	8	31
α-helix	122-124	3
α-helix	125-130	6
α-helix	134-143	10
β-strand	149-156	8	31
α-helix	170-174	5
α-helix	185-187	3
β-strand	190-197	8	31
α-helix	201-209	9
β-strand	220	1	32
α-helix	222-231	10
α-helix	233-236	4
β-strand	243-250	8	31
β-strand	254	1	32
α-helix	259-263	5
α-helix	267-269	3
β-strand	275	1	33
β-strand	280	1	31
β-strand	281	1	33
α-helix	282-285	4
α-helix	288-291	4
α-helix	292-301	10
β-strand	304-311	8	31
α-helix	312-314	3
α-helix	315-322	8
β-strand	329-333	5	31
α-helix	334	1
α-helix	340-351	12
β-strand	355-356	2	34
β-strand	357-360	4	29
β-strand	366-375	10	30
β-strand	378-381	4	30
β-strand	385-386	2	34
β-strand	394-403	10	30
β-strand	412-418	7	29
β-strand	425-431	7	29
α-helix	436-438	3
β-strand	442	1	35
β-strand	455-456	2	35
β-strand	459-460	2	35
α-helix	493	1
α-helix	494-497	4
β-strand	499-501	3	36
β-strand	506-508	3	36
α-helix	509-510	2
β-strand	516-517	2	37
β-strand	523-524	2	37
β-strand	530	1	38
β-strand	535	1	38
α-helix	536-538	3
β-strand	540-542	3	39
β-strand	547-549	3	39
β-strand	553-554	2	40
β-strand	560-561	2	40
α-helix	565-567	3
β-strand	568	1	41
β-strand	574	1	41
β-strand	579-582	4	42
β-strand	585-588	4	42
β-strand	594	1	43
β-strand	600	1	43
α-helix	605-606	2
α-helix	608-620	13
α-helix	624-627	4
α-helix	631-634	4
β-strand	638-642	5	44
β-strand	653-658	6	44
β-strand	664-669	6	44
β-strand	678-682	5	44
β-strand	686	1	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V	A	protein	959	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-3	B	protein	692	Homo sapiens	P05106 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4G1M_1 Integrin alpha-V (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDCGEDN
VCKPKLEVSVDSDQKKIYIGDDNPLTLIVKAQNQGEGAYEAELIVSIPLQADFIGVVRNN
EALARLSCAFKTENQTRQVVCDLGNPMKAGTQLLAGLRFSVHQQSEMDTSVKFDLQIQSS
NLFDKVSPVVSHKVDLAVLAAVEIRGVSSPDHVFLPIPNWEHKENPETEEDVGPVVQHIY
ELRNNGPSSFSKAMLHLQWPYKYNNNTLLYILHYDIDGPMNCTSDMEINPLRIKISSLQT
TEKNDTVAGQGERDHLITKRDLALSEGDIHTLGCGVAQCLKIVCQVGRLDRGKSAILYVK
SLLWTETFMNKENQNHSYSLKSSASFNVIEFPYKNLPIEDITNSTLVTTNVTWGIQPAP

Sequence of entity 2 (B), FASTA

>4G1M_2 Integrin beta-3 (chains B)
GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSE
ARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDL
SYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDM
KTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRN
DASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLS
QKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVR
DLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVG
FKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCECSEEDYRP
SQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHG
QCSCGDCLCDSDWTGYYCNCTTRTDTCMSSNGLLCSGRGKCECGSCVCIQPGSYGDTCEK
CPTCPDACTFKKECVECKKFDRGALHDENTCNRYCRDEIESVKELKDTGKDAVNCTYKNE
DDCVVRFQYYEDSSGKSILYVVEEPECPKGPD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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

Primary citation

Alpha V Beta 3 Integrin Crystal Structures and their Functional Implications. Dong, X., Mi, L.Z., Zhu, J. et al. Biochemistry (2012) 51:8814-8828. DOI 10.1021/bi300734n · PubMed

Other PDB entries of the same protein (UniProt P06756 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CZD 2.23 Å, Crystal structure of integrin avb6 headpiece in complex with compound 30
5FFG 2.25 Å, Crystal structure of integrin alpha V beta 6 head
8W30 2.45 Å, Crystal structure of alpha-V beta-1 integrin headpiece in complex with TR01225179
9CZA 2.49 Å, Crystal structure of integrin avb6 headpiece in complex with compound 18
4UM9 2.5 Å, Crystal structure of alpha V beta 6 with peptide
9CZF 2.53 Å, Crystal structure of integrin avb6 headpiece in complex with compound MORF-627
9CZ7 2.57 Å, Crystal structure of integrin avb6 headpiece in complex with compound 12
6OM1 2.66 Å, Crystal structure of an atypical integrin
8VS6 2.73 Å, L-TGF-b3/avb8
6OM2 2.77 Å, Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide
9IUJ 2.78 Å, Integrin alpha-v beta-3 in complex with rhodostomin
9LT3 2.79 Å, Integrin alpha-v beta-3 in complex with Trimucrin

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