9XMM: Integrin alpha-V heavy chain

Cryo-EM structure of Integrin alpha V beta 6 complex with a bicyclic inhibitory peptide. Determined by electron microscopy at 2.88 Å resolution. Released 15 Apr 2026.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 5,447
Mol. weight: 120.35 kDa
Ligands: CA, NAG, MAN, MN
Released: 15 Apr 2026

Explore 9XMM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XMM contains 19 α-helices and 52 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: 6 helices, 41 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	35-40	6	3
β-strand	54	1	4
β-strand	55-60	6	3
β-strand	67-69	3	3
α-helix	77-78	2
β-strand	79-81	3	5
β-strand	84-85	2	5
β-strand	87-88	2	6
β-strand	94	1	4
β-strand	97-101	5	7
β-strand	104-109	6	7
β-strand	113-114	2	6
β-strand	123-124	2	6
β-strand	127-132	6	7
β-strand	135-139	5	7
β-strand	160-163	4	8
β-strand	168-173	6	8
β-strand	182-187	6	8
α-helix	188-193	6
β-strand	208-209	2	8
α-helix	215-217	3
β-strand	225-229	5	9
α-helix	237	1
β-strand	238-243	6	9
β-strand	252-256	5	9
β-strand	263-268	6	9
β-strand	280-283	4	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
α-helix	321	1
β-strand	326-332	7	10
β-strand	343-346	4	12
β-strand	358-362	5	12
α-helix	367-369	3
β-strand	372-376	5	12
β-strand	378	1	13
β-strand	383	1	13
β-strand	389-392	4	12
β-strand	408-413	6	2
β-strand	422-427	6	2
β-strand	432-436	5	2
β-strand	438	1	1

Chain B: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	116-123	8	14
α-helix	126-128	3
α-helix	132-149	18
β-strand	153-160	8	14
α-helix	173-176	4
α-helix	188-190	3
β-strand	193-200	8	14
α-helix	204-211	8
β-strand	223	1	15
α-helix	225-234	10
β-strand	246-253	8	14
β-strand	257	1	15
α-helix	260-266	7
α-helix	271-272	2
β-strand	278	1	16
β-strand	283	1	14
β-strand	284	1	16
α-helix	291-293	3
α-helix	295-304	10
β-strand	307-313	7	14
α-helix	315-317	3
α-helix	318-327	10
β-strand	332-335	4	14
α-helix	341-352	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V heavy chain	A	protein	595	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-6	B	protein	474	Homo sapiens	P18564 (AlphaFold model)
Ala-trp-arg-gly-asp-chg-cys-asn-pro	E	protein	9	synthetic construct

Sequence of entity 1 (A), FASTA

>9XMM_1 Integrin alpha-V heavy chain (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSGCPPSFGYSMKGATDIDKNGY
PDLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCL
KADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELI
AYLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILL

Sequence of entity 2 (B), FASTA

>9XMM_2 Integrin beta-6 (chains B)
HVQGGCALGGAETCEDCLLIGPQCAWCAQENFTHPSGVGERCDTPANLLAKGCQLNFIEN
PVSQVEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYY
LMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPC
SSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIG
WRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLID
KLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVEL
EVLGDTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKP
VGLGDALELLVSPECNCDCQKEVEVNSSKCHHGNGSFQCGVCACHPGHMGPRCE

Sequence of entity 3 (E), FASTA

>9XMM_3 ALA-TRP-ARG-GLY-ASP-CHG-CYS-ASN-PRO (chains E)
AWRGDXCNP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MAN	alpha-D-mannopyranose	C6 H12 O6	1
MN	Manganese (II) ion	Mn	3

Primary citation

Ansamer-Controlled Bicyclic Peptides as Integrin alpha v beta 6 Targeting Agents. Yang, H., Dong, W., An, Y. et al. Angew Chem Int Ed Engl (2026) 65:e1254428-e1254428. DOI 10.1002/anie.1254428 · 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

Browse structure collections

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