9HLL | pdb_00009hll

murine aM I-domain in complex with nanobody aCR3

PDB DOI: https://doi.org/10.2210/pdb9HLL/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Lama glama
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-05 Released: 2025-12-17
Deposition Author(s): Fruergaard, M.U., Andersen, G.R.
Funding Organization(s): Other private, Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9HLL

Ligand Structure Quality Assessment

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

Literature

murine aM I-domain in complex with nanobody aCR3

Fruergaard, M.U., Andersen, G.R.

To be published.

Macromolecule Content

Total Structure Weight: 65.98 kDa
Atom Count: 4,407
Modeled Residue Count: 550
Deposited Residue Count: 588
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-M	A	198	Mus musculus	Mutation(s): 0 Gene Names: Itgam
UniProt & NIH Common Fund Data Resources
Find proteins for P05555 (Mus musculus) Explore P05555 Go to UniProtKB: P05555
IMPC: MGI:96607
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05555
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
aCR3 nanobody	B, C, D	130	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth D] SDF format, chain E [auth D] MOL2 format, chain G [auth D] MOL2 format, chain F [auth D] MOL2 format, chain E [auth D] mmCIF format, chain G [auth D] mmCIF format, chain F [auth D] mmCIF format, chain E [auth D]	E [auth D], F [auth D], G [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Interactions & Density Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.402	α = 90
b = 127.444	β = 90
c = 125.855	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Fruergaard, M.U.

Funding Organization	Location	Grant Number
Other private		Leo LF-OC-22-001076
Other private	Denmark	Alexion Discovery RN7049
Other government	Denmark	FNU 3103-00009B

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.