9P97 | pdb_00009p97

CryoEM structure of the closed integrin alphaEbeta7 bound to fab LF61

PDB DOI: https://doi.org/10.2210/pdb9P97/pdb
EM Map EMD-71401: EMDB EMDataResource

Classification: CELL ADHESION
Organism(s): Homo sapiens, Mus musculus
Expression System: Cricetulus griseus, Mus musculus
Mutation(s): No

Deposited: 2025-06-24 Released: 2025-09-24
Deposition Author(s): Hollis, J.A., Campbell, M.G.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Molecular exaptation by the integrin alpha I domain.

Hollis, J.A., Chan, M.C., Malik, H.S., Campbell, M.G.

(2025) Sci Adv 11: eadx9567-eadx9567

PubMed: 40929264 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adx9567
Primary Citation of Related Structures:
9P95, 9P96, 9P97, 9P98, 9P99

PubMed Abstract:
Integrins bind ligands between their alpha (α) and beta (β) subunits and transmit signals through conformational changes. Early in chordate evolution, some α subunits acquired an "inserted" (I) domain that expanded integrin's ligand-binding repertoire but obstructed the ancestral ligand pocket, seemingly blocking conventional integrin activation. Here, we compare cryo-electron microscopy structures of apo and ligand-bound states of the I domain-containing αEβ ₇ integrin and the I domain-lacking α ₄β ₇ integrin to illuminate how the I domain intrinsically mimics an extrinsic ligand to preserve integrin function. We trace the I domain's evolutionary origin to an ancestral collagen-collagen interaction domain, identifying an ancient molecular exaptation that facilitated integrin activation immediately upon I domain insertion. Our analyses reveal the evolutionary and biochemical basis of expanded cellular communication in vertebrates.

Organizational Affiliation

Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.

Macromolecule Content

Total Structure Weight: 264.81 kDa
Atom Count: 12,243
Modeled Residue Count: 1,570
Deposited Residue Count: 2,387
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-E	A	1,176	Homo sapiens	Mutation(s): 0 Gene Names: ITGAE
UniProt & NIH Common Fund Data Resources
Find proteins for P38570 (Homo sapiens) Explore P38570 Go to UniProtKB: P38570
PHAROS: P38570 GTEx: ENSG00000083457
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38570
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A	Go to GlyGen: P38570-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-7	B	776	Homo sapiens	Mutation(s): 0 Gene Names: ITGB7
UniProt & NIH Common Fund Data Resources
Find proteins for P26010 (Homo sapiens) Explore P26010 Go to UniProtKB: P26010
PHAROS: P26010 GTEx: ENSG00000139626
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26010
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B	Go to GlyGen: P26010-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab LF61 Heavy Chain	C [auth H]	220	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab LF61 Light Chain	D [auth L]	215	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	5		N-Glycosylation	Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D], H [auth F]	2		N-Glycosylation	Interactions Focus chain F [auth D] Focus chain H [auth F] Interactions & Density Focus chain F [auth D] Focus chain H [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth E]	3		N-Glycosylation	Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B]	I [auth A], J [auth A], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth B]	K [auth A] L [auth A] M [auth A] N [auth B] O [auth B] K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Hollis, J.A.

Campbell, M.G.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM147414
National Science Foundation (NSF, United States)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008268