9T5V | pdb_00009t5v

Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO1 3D class reconstruction)

PDB DOI: https://doi.org/10.2210/pdb9T5V/pdb
EM Map EMD-55596: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-11-06 Released: 2026-03-25
Deposition Author(s): Andersen, G.R., Fruergaard, M.U.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9T5V

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

Literature

Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO1 3D class reconstruction)

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

To be published.

Macromolecule Content

Total Structure Weight: 189.67 kDa
Atom Count: 12,937
Modeled Residue Count: 1,632
Deposited Residue Count: 1,680
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Integrin alpha-M	A	763	Homo sapiens	Mutation(s): 2 Gene Names: ITGAM, CD11B, CR3A
UniProt & NIH Common Fund Data Resources
Find proteins for P11215 (Homo sapiens) Explore P11215 Go to UniProtKB: P11215
PHAROS: P11215 GTEx: ENSG00000169896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11215
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A	Go to GlyGen: P11215-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-2	B	469	Homo sapiens	Mutation(s): 3 Gene Names: ITGB2, CD18, MFI7
UniProt & NIH Common Fund Data Resources
Find proteins for P05107 (Homo sapiens) Explore P05107 Go to UniProtKB: P05107
PHAROS: P05107 GTEx: ENSG00000160255
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05107
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B	Go to GlyGen: P05107-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C3d-anti-CR3-Nb fusion ligand	C	448	Lama glama	Mutation(s): 0 Gene Names: C3, CPAMD1

Oligosaccharides

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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, F	5		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Fruergaard, M.U.

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2026-03-25
Type: Initial release

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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.