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9xmm

Cryo-EM structure of Integrin alpha V beta 6 complex with a bicyclic inhibitory peptide

Method: ELECTRON MICROSCOPY D_max: 85.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xmm
deposition_date	2025-11-11
title	Cryo-EM structure of Integrin alpha V beta 6 complex with a bicyclic inhibitory peptide
keywords	Integrin, Complex, Bicyclic peptide, CELL ADHESION; CELL ADHESION
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	26.94 Å
rg_electron	25.86 Å
i0	98282200.00
molecular_weight	77537.0 kDa
excluded_volume	96691 Å³
envelope_volume	114510 Å³
shell_volume	35741 Å³
envelope_diameter	88.5 Å
shell_rg	34.12 Å
envelope_rg	26.25 Å
shape_rg	25.84 Å
total_rg	26.77 Å
total_atoms	10651
n_residues	689
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	85.6 Å
rg_real	26.85 Å
rg_real_error	0.42 Å
i0_real	9.8280e+07
i0_real_error	1.3460e+06
rg_reciprocal	26.88 Å
i0_reciprocal	98280000.0000
total_estimate	0.8962
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	31.9 Å
skewness	0.284
kurtosis	-0.358
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	22850000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.976

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Integrin alpha-V heavy chain
formula_weight	65410.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10651

FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSGCPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLKADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Integrin beta-6
formula_weight	51981.1 kDa
mutation	I270C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

HVQGGCALGGAETCEDCLLIGPQCAWCAQENFTHPSGVGERCDTPANLLAKGCQLNFIENPVSQVEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYYLMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPCSSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIGWRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLIDKLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVELEVLGDTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKPVGLGDALELLVSPECNCDCQKEVEVNSSKCHHGNGSFQCGVCACHPGHMGPRCE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	ALA-TRP-ARG-GLY-ASP-CHG-CYS-ASN-PRO
formula_weight	1058.2 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

AWRGDXCNP

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	syn
entity_count	1

Entity 5 branched

description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	1

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	man
entity_count	4

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	alpha-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	3

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6. Citations (1)

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resolution	2.88 Å
resolution_method	—
num_particles	273385

fit	/app/data/saxs_computation/xm/9xmm/9xmm.fit
pddf	/app/data/pr_computation/xm/9xmm/9xmm.pr.out
profile	/app/data/saxs_computation/xm/9xmm/9xmm.dat

Cryo-EM structure of Integrin alpha V beta 6 complex with a bicyclic inhibitory peptide

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 branched

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)